1052 Citations
Described herein are methods for stratifying and evaluating melanoma treatment response in a subject using single-cell RNA sequencing scRNA-seq and a two-step deconvolution analysis and optionally administering a treatment depending on the results Embodiment described herein are methods for stratifying and evaluating melanoma treatment response in a subject based on single cell or bulk RNA sequencing bulk transcriptome profiling and or transcript counting and a two-step deconvolution analysis and optionally administering a treatment depending on the results
Transporters of the Nramp Natural resistance-associated macrophage protein family import divalent transition metal ions into cells of most organisms By supporting metal homeostasis Nramps prevent diseases and disorders related to metal insufficiency or overload Previous studies revealed that Nramps take on a LeuT fold and identified the metal-binding site We present high-resolution structures of Deinococcus radiodurans Dra Nramp in three stable conformations of the transport cycle revealing that global conformational changes are supported by distinct coordination geometries of its physiological substrate Mn across conformations and by conserved networks of polar residues lining the inner and outer gates In addition a ... More
Transporters of the Nramp (Natural resistance-associated macrophage protein) family import divalent transition metal ions into cells of most organisms. By supporting metal homeostasis, Nramps prevent diseases and disorders related to metal insufficiency or overload. Previous studies revealed that Nramps take on a LeuT fold and identified the metal-binding site. We present high-resolution structures of Deinococcus radiodurans (Dra)Nramp in three stable conformations of the transport cycle revealing that global conformational changes are supported by distinct coordination geometries of its physiological substrate, Mn2+, across conformations, and by conserved networks of polar residues lining the inner and outer gates. In addition, a high-resolution Cd2+-bound structure highlights differences in how Cd2+ and Mn2+ are coordinated by DraNramp. Complementary metal binding studies using isothermal titration calorimetry with a series of mutated DraNramp proteins indicate that the thermodynamic landscape for binding and transporting physiological metals like Mn2+ is different and more robust to perturbation than for transporting the toxic Cd2+ metal. Overall, the affinity measurements and high-resolution structural information on metal substrate binding provide a foundation for understanding the substrate selectivity of essential metal ion transporters like Nramps. Less
Hydromedusan photoproteins responsible for the bioluminescence of a variety of marine jellyfish and hydroids are a unique biochemical system recognized as a stable enzyme-substrate complex consisting of apoprotein and preoxygenated coelenterazine which is tightly bound in the protein inner cavity The binding of calcium ions to the photoprotein molecule is only required to initiate the light emission reaction Although numerous experimental and theoretical studies on the bioluminescence of these photoproteins were performed many features of their functioning are yet unclear In particular which ionic state of dioxetanone intermediate decomposes to yield a coelenteramide in an excited state and the role ... More
Hydromedusan photoproteins responsible for the bioluminescence of a variety of marine jellyfish and hydroids are a unique biochemical system recognized as a stable enzyme-substrate complex consisting of apoprotein and preoxygenated coelenterazine, which is tightly bound in the protein inner cavity. The binding of calcium ions to the photoprotein molecule is only required to initiate the light emission reaction. Although numerous experimental and theoretical studies on the bioluminescence of these photoproteins were performed, many features of their functioning are yet unclear. In particular, which ionic state of dioxetanone intermediate decomposes to yield a coelenteramide in an excited state and the role of the water molecule residing in a proximity to the N1 atom of 2-hydroperoxycoelenterazine in the bioluminescence reaction are still under discussion. With the aim to elucidate the function of this water molecule as well as to pinpoint the amino acid residues presumably involved in the protonation of the primarily formed dioxetanone anion, we constructed a set of single and double obelin and aequorin mutants with substitutions of His, Trp, Tyr, and Ser to residues with different properties of side chains and investigated their bioluminescence properties (specific activity, bioluminescence spectra, stopped-flow kinetics, and fluorescence spectra of Ca2+-discharged photoproteins). Moreover, we determined the spatial structure of the obelin mutant with a substitution of His64, the key residue of the presumable proton transfer, to Phe. On the ground of the bioluminescence properties of the obelin and aequorin mutants as well as the spatial structures of the obelin mutants with the replacements of His64 and Tyr138, the conclusion was made that, in fact, His residue of the Tyr-His-Trp triad and the water molecule perform the “catalytic function” by transferring the proton from solvent to the dioxetanone anion to generate its neutral ionic state in complex with water, as only the decomposition of this form of dioxetanone can provide the highest light output in the light-emitting reaction of the hydromedusan photoproteins. Less
An oxalate-degrading bacterium in the gut microbiota absorbs food-derived oxalate to use this as a carbon and energy source thereby reducing the risk of kidney stone formation in host animals The bacterial oxalate transporter OxlT selectively uptakes oxalate from the gut to bacterial cells with a strict discrimination from other nutrient carboxylates Here we present crystal structures of oxalate-bound and ligand-free OxlT in two distinct conformations occluded and outward-facing states The ligand-binding pocket contains basic residues that form salt bridges with oxalate while preventing the conformational switch to the occluded state without an acidic substrate The occluded pocket can accommodate ... More
An oxalate-degrading bacterium in the gut microbiota absorbs food-derived oxalate to use this as a carbon and energy source, thereby reducing the risk of kidney stone formation in host animals. The bacterial oxalate transporter OxlT selectively uptakes oxalate from the gut to bacterial cells with a strict discrimination from other nutrient carboxylates. Here, we present crystal structures of oxalate-bound and ligand-free OxlT in two distinct conformations, occluded and outward-facing states. The ligand-binding pocket contains basic residues that form salt bridges with oxalate while preventing the conformational switch to the occluded state without an acidic substrate. The occluded pocket can accommodate oxalate but not larger dicarboxylates, such as metabolic intermediates. The permeation pathways from the pocket are completely blocked by extensive interdomain interactions, which can be opened solely by a flip of a single side chain neighbouring the substrate. This study shows the structural basis underlying metabolic interactions enabling favourable symbiosis. Less
Pseudomonas aeruginosa is a multi-drug resistant human opportunistic pathogen If left untreated P aeruginosa can cause severe to life-threatening infections in people with burns cystic fibrosis and in immunocompromised patients During chronic infections P aeruginosa primarily co-ordinates virulence in the host through a cell-to-cell communication mechanism called quorum sensing QS There are three key QS systems in P aeruginosa responsible for driving global changes in virulence gene expression the las rhl and pqs systems Each of the las rhl and pqs systems rely on a receptor-autoinducer relationship these receptor-autoinducer complexes are LasR-OdDHL RhlR-BHL and PqsR-PQS respectively When the receptors LasR ... More
Pseudomonas aeruginosa is a multi-drug resistant, human opportunistic pathogen. If left untreated, P. aeruginosa can cause severe to life-threatening infections in people with burns, cystic fibrosis, and in immunocompromised patients. During chronic infections, P. aeruginosa primarily co-ordinates virulence in the host through a cell-to-cell communication mechanism called quorum sensing (QS). There are three key QS systems in P. aeruginosa responsible for driving global changes in virulence gene expression: the las, rhl, and pqs systems. Each of the las, rhl, and pqs systems rely on a receptor-autoinducer relationship: these receptor-autoinducer complexes are LasR-OdDHL, RhlR-BHL, and PqsR-PQS, respectively. When the receptors (LasR, RhlR, PqsR) bind with their cognate autoinducer (OdDHL, BHL, PQS, respectively), they act as transcription factors that ultimately stimulate the expression of hundreds of virulence-associated genes. The influence these QS systems have on the expression of virulence determinants has led to decades of scientific research focusing on the characterisation of these regulators. Although LasR and PqsR have been structurally elucidated, the RhlR crystal structure has long eluded characterisation and has been highly sought after due to its obvious potential as a therapeutic target.
In a collaborative research effort, I helped to identify ten additional proteins as putative binding partners of the pqs autoinducer, PQS. Four of the ten proteins identified were the cyanide synthase (HcnC), a putative protease (PfpI), a phenazine biosynthetic protein (PhzD1), and the QS regulator RhlR. For this PhD project, I aimed to structurally and biochemically characterise these four proteins to, in part, confirm their proposed interaction with PQS. A novel ligand (benzoic acid) was discovered bound in the active site of PhzD1 (crystal structure solved to 1.1 Å). Additionally, the crystal structure for PfpI was resolved at 1.4 Å resolution. The PfpI tertiary and quaternary structures obtained in this study suggested a possible role in electrophile detoxification, a hypothesis which I confirmed in vitro using 1D NMR. To complement the novel PfpI structural and biochemical data, I generated and confirmed “clean” pfpI deletion mutants for phenotypic and ‘omic analyses. I observed discrepancies in phenotypes between the pfpI deletion mutant and the pfpI transposon mutants previously reported in the published literature, which I sought to reconcile through subsequent whole genome sequencing (WGS) of these previously published strains. WGS of the pfpI transposon mutants revealed a plethora of unexpected mutations elsewhere in the genome, which likely contribute to many of the reported phenotypes. The “clean” deletion mutant that I generated harboured no significant additional mutations. Proteomic profiling of the pfpI deletion mutant exhibited altered protein expression in systems involved in Type VI secretion, motility, and metabolism.
Overall, the work presented in this dissertation further illustrates the intractability of purifying the QS transcriptional regulator, RhlR. I report benzoic acid to be a novel binding partner for the phenazine biosynthetic protein, PhzD1. Phenotypic analyses of pfpI mutants and consequent WGS highlight the need for rigorous strain validation when using transposon mutant libraries. Using the PfpI structural data I obtained during this study, I hypothesised and confirmed a novel detoxification role for PfpI in P. aeruginosa. Lastly, proteomic analysis of a pfpI deficient mutant revealed global dysregulation of key biological processes. Less
In a collaborative research effort, I helped to identify ten additional proteins as putative binding partners of the pqs autoinducer, PQS. Four of the ten proteins identified were the cyanide synthase (HcnC), a putative protease (PfpI), a phenazine biosynthetic protein (PhzD1), and the QS regulator RhlR. For this PhD project, I aimed to structurally and biochemically characterise these four proteins to, in part, confirm their proposed interaction with PQS. A novel ligand (benzoic acid) was discovered bound in the active site of PhzD1 (crystal structure solved to 1.1 Å). Additionally, the crystal structure for PfpI was resolved at 1.4 Å resolution. The PfpI tertiary and quaternary structures obtained in this study suggested a possible role in electrophile detoxification, a hypothesis which I confirmed in vitro using 1D NMR. To complement the novel PfpI structural and biochemical data, I generated and confirmed “clean” pfpI deletion mutants for phenotypic and ‘omic analyses. I observed discrepancies in phenotypes between the pfpI deletion mutant and the pfpI transposon mutants previously reported in the published literature, which I sought to reconcile through subsequent whole genome sequencing (WGS) of these previously published strains. WGS of the pfpI transposon mutants revealed a plethora of unexpected mutations elsewhere in the genome, which likely contribute to many of the reported phenotypes. The “clean” deletion mutant that I generated harboured no significant additional mutations. Proteomic profiling of the pfpI deletion mutant exhibited altered protein expression in systems involved in Type VI secretion, motility, and metabolism.
Overall, the work presented in this dissertation further illustrates the intractability of purifying the QS transcriptional regulator, RhlR. I report benzoic acid to be a novel binding partner for the phenazine biosynthetic protein, PhzD1. Phenotypic analyses of pfpI mutants and consequent WGS highlight the need for rigorous strain validation when using transposon mutant libraries. Using the PfpI structural data I obtained during this study, I hypothesised and confirmed a novel detoxification role for PfpI in P. aeruginosa. Lastly, proteomic analysis of a pfpI deficient mutant revealed global dysregulation of key biological processes. Less
Background Lower limb peripheral artery disease PAD is the main risk of diabetes mellitus which result to high mortality rate Approximately of patients who receive several treatments have passed away or lost limbs at a year s follow-up Secretome of hypoxia mesenchymal stem cells S-MSCs contains several active soluble molecules from hypoxia MSCs H-MSCs that capable inducing anti-inflammatory and vascular regeneration in PAD Objective In this study we investigated the therapeutic potential of S-MSCs in improving dynamic function and angiogenesis of PAD diabetic rats Methods The PAD was established by the incision from the groin to the inner thigh and ... More
Background:
Lower limb peripheral artery disease (PAD) is the main risk of diabetes mellitus which result to high mortality rate. Approximately, 50% of patients who receive several treatments have passed away or lost limbs at a year’s follow-up. Secretome of hypoxia mesenchymal stem cells (S-MSCs) contains several active soluble molecules from hypoxia MSCs (H-MSCs) that capable inducing anti-inflammatory and vascular regeneration in PAD.
Objective:
In this study, we investigated the therapeutic potential of S-MSCs in improving dynamic function and angiogenesis of PAD diabetic rats.
Methods:
The PAD was established by the incision from the groin to the inner thigh and distal ligation of femoral arteries in rats with diabetes. Rats were administered with 200 µL and 400 µL S-MSCs that successfully filtrated using tangential flow filtration (TFF) system based on various molecular weight cut-off categories intravenously. ELISA assay was used to analyze the cytokines and growth factors contained in S-MSCs. Tarlov score were examined at day 1, 3, 5, 7, 10 and 14. The rats were sacrificed at day 14 and muscle tissues were collected for immunohistochemistry (IHC) and gene expression analysis.
Results:
ELISA assay showed that S-MSCs provides abundant level of VEGF, PDGF, bFGF, IL-10 and TGFβ. In vivo administration of S-MSCs remarkably enhanced the Tarlov score. S-MSCs improved angiogenesis through enhancing VEGF gene expression and significantly increasing CD31 positive area in muscle tissue of PAD diabetic rats.
Conclusion:
Our findings suggest that S-MSCs could improves dynamic function and angiogenesis in PAD diabetic rats. Less
Lower limb peripheral artery disease (PAD) is the main risk of diabetes mellitus which result to high mortality rate. Approximately, 50% of patients who receive several treatments have passed away or lost limbs at a year’s follow-up. Secretome of hypoxia mesenchymal stem cells (S-MSCs) contains several active soluble molecules from hypoxia MSCs (H-MSCs) that capable inducing anti-inflammatory and vascular regeneration in PAD.
Objective:
In this study, we investigated the therapeutic potential of S-MSCs in improving dynamic function and angiogenesis of PAD diabetic rats.
Methods:
The PAD was established by the incision from the groin to the inner thigh and distal ligation of femoral arteries in rats with diabetes. Rats were administered with 200 µL and 400 µL S-MSCs that successfully filtrated using tangential flow filtration (TFF) system based on various molecular weight cut-off categories intravenously. ELISA assay was used to analyze the cytokines and growth factors contained in S-MSCs. Tarlov score were examined at day 1, 3, 5, 7, 10 and 14. The rats were sacrificed at day 14 and muscle tissues were collected for immunohistochemistry (IHC) and gene expression analysis.
Results:
ELISA assay showed that S-MSCs provides abundant level of VEGF, PDGF, bFGF, IL-10 and TGFβ. In vivo administration of S-MSCs remarkably enhanced the Tarlov score. S-MSCs improved angiogenesis through enhancing VEGF gene expression and significantly increasing CD31 positive area in muscle tissue of PAD diabetic rats.
Conclusion:
Our findings suggest that S-MSCs could improves dynamic function and angiogenesis in PAD diabetic rats. Less
Clostridioides difficile is a Gram-positive opportunistic human pathogen that causes deaths annually in the United States prompting a need for vaccine development In addition to the important toxins TcdA and TcdB binary toxin CDT plays a significant role in the pathogenesis of certain C difficile ribotypes by catalyzing the ADP-ribosylation of actin in host cells However the mechanisms of CDT neutralization by antibodies have not been studied limiting our understanding of key epitopes for CDT antigen design Therefore we isolated neutralizing monoclonal antibodies against CDT and characterized their mechanisms of neutralization structurally and biochemically Here - and - resolution X-ray ... More
Clostridioides difficile is a Gram-positive opportunistic human pathogen that causes 15,000 deaths annually in the United States, prompting a need for vaccine development. In addition to the important toxins TcdA and TcdB, binary toxin (CDT) plays a significant role in the pathogenesis of certain C. difficile ribotypes by catalyzing the ADP-ribosylation of actin in host cells. However, the mechanisms of CDT neutralization by antibodies have not been studied, limiting our understanding of key epitopes for CDT antigen design. Therefore, we isolated neutralizing monoclonal antibodies against CDT and characterized their mechanisms of neutralization structurally and biochemically. Here, 2.5-Å and 2.6-Å resolution X-ray crystal structures of the antibodies BINTOXB/22 and BINTOXB/9, respectively, in complex with CDTb—the CDT subunit that forms a heptameric pore for the delivery of toxic CDTa enzyme into the host cytosol—showed that both antibodies sterically clash with adjacent protomers in the assembled heptamer. Assessment of trypsin-induced oligomerization of the purified CDTb protoxin in vitro showed that BINTOXB/22 and BINTOXB/9 prevented the assembly of di-heptamers upon prodomain cleavage. This work suggests that the CDT oligomerization process can be effectively targeted by antibodies, which will aid in the development of C. difficile vaccines and therapeutics. Less
Background With an increasing interest in the manipulation of methane produced from livestock cultivation the microbiome of Australian marsupials provides a unique ecological and evolutionary comparison with low-methane emitters Previously marsupial species were shown to be enriched for novel lineages of Methanocorpusculum as well as Methanobrevibacter Methanosphaera and Methanomassiliicoccales Despite sporadic reports of Methanocorpusculum from stool samples of various animal species there remains little information on the impacts of these methanogens on their hosts Results Here we characterise novel host-associated species of Methanocorpusculum to explore unique host-specific genetic factors and their associated metabolic potential We performed comparative analyses on Methanocorpusculum ... More
Background
With an increasing interest in the manipulation of methane produced from livestock cultivation, the microbiome of Australian marsupials provides a unique ecological and evolutionary comparison with ‘low-methane’ emitters. Previously, marsupial species were shown to be enriched for novel lineages of Methanocorpusculum, as well as Methanobrevibacter, Methanosphaera, and Methanomassiliicoccales. Despite sporadic reports of Methanocorpusculum from stool samples of various animal species, there remains little information on the impacts of these methanogens on their hosts.
Results
Here, we characterise novel host-associated species of Methanocorpusculum, to explore unique host-specific genetic factors and their associated metabolic potential. We performed comparative analyses on 176 Methanocorpusculum genomes comprising 130 metagenome-assembled genomes (MAGs) recovered from 20 public animal metagenome datasets and 35 other publicly available Methanocorpusculum MAGs and isolate genomes of host-associated and environmental origin. Nine MAGs were also produced from faecal metagenomes of the common wombat (Vombatus ursinus) and mahogany glider (Petaurus gracilis), along with the cultivation of one axenic isolate from each respective animal; M. vombati (sp. nov.) and M. petauri (sp. nov.).
Conclusions
Through our analyses, we substantially expand the available genetic information for this genus by describing the phenotypic and genetic characteristics of 23 host-associated species of Methanocorpusculum. These lineages display differential enrichment of genes associated with methanogenesis, amino acid biosynthesis, transport system proteins, phosphonate metabolism, and carbohydrate-active enzymes. These results provide insights into the differential genetic and functional adaptations of these novel host-associated species of Methanocorpusculum and suggest that this genus is ancestrally host-associated. Less
With an increasing interest in the manipulation of methane produced from livestock cultivation, the microbiome of Australian marsupials provides a unique ecological and evolutionary comparison with ‘low-methane’ emitters. Previously, marsupial species were shown to be enriched for novel lineages of Methanocorpusculum, as well as Methanobrevibacter, Methanosphaera, and Methanomassiliicoccales. Despite sporadic reports of Methanocorpusculum from stool samples of various animal species, there remains little information on the impacts of these methanogens on their hosts.
Results
Here, we characterise novel host-associated species of Methanocorpusculum, to explore unique host-specific genetic factors and their associated metabolic potential. We performed comparative analyses on 176 Methanocorpusculum genomes comprising 130 metagenome-assembled genomes (MAGs) recovered from 20 public animal metagenome datasets and 35 other publicly available Methanocorpusculum MAGs and isolate genomes of host-associated and environmental origin. Nine MAGs were also produced from faecal metagenomes of the common wombat (Vombatus ursinus) and mahogany glider (Petaurus gracilis), along with the cultivation of one axenic isolate from each respective animal; M. vombati (sp. nov.) and M. petauri (sp. nov.).
Conclusions
Through our analyses, we substantially expand the available genetic information for this genus by describing the phenotypic and genetic characteristics of 23 host-associated species of Methanocorpusculum. These lineages display differential enrichment of genes associated with methanogenesis, amino acid biosynthesis, transport system proteins, phosphonate metabolism, and carbohydrate-active enzymes. These results provide insights into the differential genetic and functional adaptations of these novel host-associated species of Methanocorpusculum and suggest that this genus is ancestrally host-associated. Less
Vision is initiated by the rhodopsin family of light-sensitive G protein-coupled receptors GPCRs A photon is absorbed by the -cis retinal chromophore of rhodopsin which isomerizes within femtoseconds to the all-trans conformation thereby initiating the cellular signal transduction processes that ultimately lead to vision However the intramolecular mechanism by which the photoactivated retinal induces the activation events inside rhodopsin remains experimentally unclear Here we use ultrafast time-resolved crystallography at room temperature to determine how an isomerized twisted all-trans retinal stores the photon energy that is required to initiate the protein conformational changes associated with the formation of the G protein-binding ... More
Vision is initiated by the rhodopsin family of light-sensitive G protein-coupled receptors (GPCRs)1. A photon is absorbed by the 11-cis retinal chromophore of rhodopsin, which isomerizes within 200 femtoseconds to the all-trans conformation2, thereby initiating the cellular signal transduction processes that ultimately lead to vision. However, the intramolecular mechanism by which the photoactivated retinal induces the activation events inside rhodopsin remains experimentally unclear. Here we use ultrafast time-resolved crystallography at room temperature3 to determine how an isomerized twisted all-trans retinal stores the photon energy that is required to initiate the protein conformational changes associated with the formation of the G protein-binding signalling state. The distorted retinal at a 1-ps time delay after photoactivation has pulled away from half of its numerous interactions with its binding pocket, and the excess of the photon energy is released through an anisotropic protein breathing motion in the direction of the extracellular space. Notably, the very early structural motions in the protein side chains of rhodopsin appear in regions that are involved in later stages of the conserved class A GPCR activation mechanism. Our study sheds light on the earliest stages of vision in vertebrates and points to fundamental aspects of the molecular mechanisms of agonist-mediated GPCR activation. Less
Background In aquatic ecosystems the health and performance of fish depend greatly on the dynamics of microbial community structure in the background environment Nonetheless finding microbes with profound impacts on fish s performance out of thousands of candidate species remains a major challenge Methods We examined whether time-series analyses of microbial population dynamics could illuminate core components and structure of fish-associated microbiomes in the background environmental water By targeting eel-aquaculture-tank microbiomes as model systems we reconstructed the population dynamics of the bacterial and archaeal species strains across days Results Due to the remarkable increase decrease of constituent microbial population densities ... More
Background
In aquatic ecosystems, the health and performance of fish depend greatly on the dynamics of microbial community structure in the background environment. Nonetheless, finding microbes with profound impacts on fish’s performance out of thousands of candidate species remains a major challenge.
Methods
We examined whether time-series analyses of microbial population dynamics could illuminate core components and structure of fish-associated microbiomes in the background (environmental) water. By targeting eel-aquaculture-tank microbiomes as model systems, we reconstructed the population dynamics of the 9605 bacterial and 303 archaeal species/strains across 128 days.
Results
Due to the remarkable increase/decrease of constituent microbial population densities, the taxonomic compositions of the microbiome changed drastically through time. We then found that some specific microbial taxa showed a positive relationship with eels’ activity levels even after excluding confounding effects of environmental parameters (pH and dissolved oxygen level) on population dynamics. In particular, a vitamin-B12-producing bacteria, Cetobacterium somerae, consistently showed strong positive associations with eels’ activity levels across the replicate time series of the five aquaculture tanks analyzed. Network theoretical and metabolic modeling analyses further suggested that the highlighted bacterium and some other closely-associated bacteria formed “core microbiomes” with potentially positive impacts on eels.
Conclusions
Overall, these results suggest that the integration of microbiology, ecological theory, and network science allows us to explore core species and interactions embedded within complex dynamics of fish-associated microbiomes. Less
In aquatic ecosystems, the health and performance of fish depend greatly on the dynamics of microbial community structure in the background environment. Nonetheless, finding microbes with profound impacts on fish’s performance out of thousands of candidate species remains a major challenge.
Methods
We examined whether time-series analyses of microbial population dynamics could illuminate core components and structure of fish-associated microbiomes in the background (environmental) water. By targeting eel-aquaculture-tank microbiomes as model systems, we reconstructed the population dynamics of the 9605 bacterial and 303 archaeal species/strains across 128 days.
Results
Due to the remarkable increase/decrease of constituent microbial population densities, the taxonomic compositions of the microbiome changed drastically through time. We then found that some specific microbial taxa showed a positive relationship with eels’ activity levels even after excluding confounding effects of environmental parameters (pH and dissolved oxygen level) on population dynamics. In particular, a vitamin-B12-producing bacteria, Cetobacterium somerae, consistently showed strong positive associations with eels’ activity levels across the replicate time series of the five aquaculture tanks analyzed. Network theoretical and metabolic modeling analyses further suggested that the highlighted bacterium and some other closely-associated bacteria formed “core microbiomes” with potentially positive impacts on eels.
Conclusions
Overall, these results suggest that the integration of microbiology, ecological theory, and network science allows us to explore core species and interactions embedded within complex dynamics of fish-associated microbiomes. Less
The modified nucleosides -deoxy- -cyano- and -deoxy- -amido- -deazaguanosine dPreQ and dADG respectively recently discovered in DNA are the products of the bacterial queuosine tRNA modification pathway and the dpd gene cluster the latter of which encodes proteins that comprise the elaborate Dpd restriction modification system present in diverse bacteria Recent genetic studies implicated the dpdA dpdB and dpdC genes as encoding proteins necessary for DNA modification with dpdD dpdK contributing to the restriction phenotype Here we report the in vitro reconstitution of the Dpd modification machinery from Salmonella enterica serovar Montevideo the elucidation of the roles of each protein ... More
The modified nucleosides 2′-deoxy-7-cyano- and 2′-deoxy-7-amido-7-deazaguanosine (dPreQ0 and dADG, respectively) recently discovered in DNA are the products of the bacterial queuosine tRNA modification pathway and the dpd gene cluster, the latter of which encodes proteins that comprise the elaborate Dpd restriction–modification system present in diverse bacteria. Recent genetic studies implicated the dpdA, dpdB and dpdC genes as encoding proteins necessary for DNA modification, with dpdD–dpdK contributing to the restriction phenotype. Here we report the in vitro reconstitution of the Dpd modification machinery from Salmonella enterica serovar Montevideo, the elucidation of the roles of each protein and the X-ray crystal structure of DpdA supported by small-angle X-ray scattering analysis of DpdA and DpdB, the former bound to DNA. While the homology of DpdA with the tRNA-dependent tRNA-guanine transglycosylase enzymes (TGT) in the queuosine pathway suggested a similar transglycosylase activity responsible for the exchange of a guanine base in the DNA for 7-cyano-7-deazaguanine (preQ0), we demonstrate an unexpected ATPase activity in DpdB necessary for insertion of preQ0 into DNA, and identify several catalytically essential active site residues in DpdA involved in the transglycosylation reaction. Further, we identify a modification site for DpdA activity and demonstrate that DpdC functions independently of DpdA/B in converting preQ0-modified DNA to ADG-modified DNA. Less
A rare coding variant in PLC P R expressed in microglia induces a mild activation of enzymatic activity when compared to wild-type This mutation is reported to be protective against the cognitive decline associated with late-onset Alzheimer's disease LOAD and therefore activation of wild-type PLC has been suggested as a potential therapeutic target for the prevention and treatment of LOAD Additionally PLC has been associated with other diseases such as cancer and some autoimmune disorders where mutations with much greater increases in PLC activity have been identified Here pharmacological inhibition may provide a therapeutic effect In order to facilitate our ... More
A rare coding variant in PLCγ2 (P522R) expressed in microglia induces a mild activation of enzymatic activity when compared to wild-type. This mutation is reported to be protective against the cognitive decline associated with late-onset Alzheimer's disease (LOAD) and therefore, activation of wild-type PLCγ2 has been suggested as a potential therapeutic target for the prevention and treatment of LOAD. Additionally, PLCγ2 has been associated with other diseases such as cancer and some autoimmune disorders where mutations with much greater increases in PLCγ2 activity have been identified. Here, pharmacological inhibition may provide a therapeutic effect. In order to facilitate our investigation of the activity of PLCγ2, we developed an optimized fluorogenic substrate to monitor enzymatic activity in aqueous solution. This was accomplished by first exploring the spectral properties of various “turn-on” fluorophores. The most promising turn-on fluorophore was incorporated into a water-soluble PLCγ2 reporter substrate, which we named C8CF3-coumarin. The ability of PLCγ2 to enzymatically process C8CF3-coumarin was confirmed, and the kinetics of the reaction were determined. Reaction conditions were optimized to identify small molecule activators, and a pilot screen of the Library of Pharmacologically Active Compounds 1280 (LOPAC1280) was performed with the goal of identifying small molecule activators of PLCγ2. The optimized screening conditions allowed identification of potential PLCγ2 activators and inhibitors, thus demonstrating the feasibility of this approach for high-throughput screening. Less
The human brain undergoes rapid development at mid-gestation from a pool of neural stem and progenitor cells NSPCs that give rise to the neurons oligodendrocytes and astrocytes of the mature brain Functional study of these cell types has been hampered by a lack of precise purification methods We describe a method for prospectively isolating ten distinct NSPC types from the developing human brain using cell-surface markers CD THY lo cells were enriched for radial glia which robustly engrafted and differentiated into all three neural lineages in the mouse brain THY hi cells marked unipotent oligodendrocyte precursors committed to an oligodendroglial ... More
The human brain undergoes rapid development at mid-gestation from a pool of neural stem and progenitor cells (NSPCs) that give rise to the neurons, oligodendrocytes, and astrocytes of the mature brain. Functional study of these cell types has been hampered by a lack of precise purification methods. We describe a method for prospectively isolating ten distinct NSPC types from the developing human brain using cell-surface markers. CD24−THY1−/lo cells were enriched for radial glia, which robustly engrafted and differentiated into all three neural lineages in the mouse brain. THY1hi cells marked unipotent oligodendrocyte precursors committed to an oligodendroglial fate, and CD24+THY1−/lo cells marked committed excitatory and inhibitory neuronal lineages. Notably, we identify and functionally characterize a transcriptomically distinct THY1hiEGFRhiPDGFRA− bipotent glial progenitor cell (GPC), which is lineage-restricted to astrocytes and oligodendrocytes, but not to neurons. Our study provides a framework for the functional study of distinct cell types in human neurodevelopment. Less
Ubiquitination is a complex and reversible protein post-translational modification in which the subsequent action of enzymes belonging to three different families broadly referred to as E E and E results in the covalent linking of ubiquitin to a target protein While this linkage is canonically an isopeptide bond between the C-terminus of ubiquitin and the lysine residue of the target protein Ser Thr and Tyr can also be susceptible to ubiquitination through an oxyester bond Once ubiquitinated multiple units of ubiquitin can be attached to the initial ubiquitin thus extending it to a chain of ubiquitins Ubiquitination regulates multiple cellular ... More
Ubiquitination is a complex and reversible protein post-translational modification in which the subsequent action of enzymes belonging to three different families, broadly referred to as E1, E2 and E3, results in the covalent linking of ubiquitin to a target protein. While this linkage is canonically an isopeptide bond between the C-terminus of ubiquitin and the lysine residue of the target protein, Ser, Thr, and Tyr can also be susceptible to ubiquitination through an oxyester bond. Once ubiquitinated, multiple units of ubiquitin can be attached to the initial ubiquitin thus extending it to a chain of ubiquitins. Ubiquitination regulates multiple cellular processes, but it is best known as a modification that targets proteins for proteasomal degradation following the formation poly-ubiquitin chains linked through lysine 48 or 63 of ubiquitin. Dysregulation of ubiquitination has been associated with multiple types of cancer and efforts have been carried out to develop technologies that lead to the identification of inhibitors of the enzymes involved in the ubiquitination cascade. Herein, we present the development of a FRET-based assay that allows us to monitor auto-ubiquitination of DTX3L, a RING-type E3 ubiquitin ligase. Our method shows a robust signal window with a robust average Z’ factor of 0.76. From a validatory screening experiment we have identified the first molecules that inhibit DTX3L with potencies in the low micromolar range. Additionally, we have expanded the system to study deubiquitinases such as USP28 that lead to reduction of FRET due to hydrolysis of fluorescent poly-Ub chains. Less
Analyzing proteins from single cells by tandem mass spectrometry MS has recently become technically feasible While such analysis has the potential to accurately quantify thousands of proteins across thousands of single cells the accuracy and reproducibility of the results may be undermined by numerous factors affecting experimental design sample preparation data acquisition and data analysis We expect that broadly accepted community guidelines and standardized metrics will enhance rigor data quality and alignment between laboratories Here we propose best practices quality controls and data-reporting recommendations to assist in the broad adoption of reliable quantitative workflows for single-cell proteomics
We report the structural biochemical and functional characterization of the product of gene PA from Pseudomonas aeruginosa PAO The protein termed Pa Dps adopts the Dps subunit fold and oligomerizes into a nearly spherical -mer quaternary structure at pH or in the presence of divalent cations at neutral pH and above The -Mer Pa Dps contains two di-iron centers at the interface of each subunit dimer coordinated by conserved His Glu and Asp residues In vitro the di-iron centers catalyze the oxidation of Fe utilizing H O not O as an oxidant suggesting Pa Dps functions to aid P aeruginosa ... More
We report the structural, biochemical, and functional characterization of the product of gene PA0962 from Pseudomonas aeruginosa PAO1. The protein, termed Pa Dps, adopts the Dps subunit fold and oligomerizes into a nearly spherical 12-mer quaternary structure at pH 6.0 or in the presence of divalent cations at neutral pH and above. The 12-Mer Pa Dps contains two di-iron centers at the interface of each subunit dimer, coordinated by conserved His, Glu, and Asp residues. In vitro, the di-iron centers catalyze the oxidation of Fe2+ utilizing H2O2 (not O2) as an oxidant, suggesting Pa Dps functions to aid P. aeruginosa to survive H2O2-mediated oxidative stress. In agreement, a P. aeruginosa Δdps mutant is significantly more susceptible to H2O2 than the parent strain. The Pa Dps structure harbors a novel network of Tyr residues at the interface of each subunit dimer between the two di-iron centers, which captures radicals generated during Fe2+ oxidation at the ferroxidase centers and forms di-tyrosine linkages, thus effectively trapping the radicals within the Dps shell. Surprisingly, incubating Pa Dps and DNA revealed unprecedented DNA cleaving activity that is independent of H2O2 or O2 but requires divalent cations and 12-mer Pa Dps. Less
Tyrosine kinases TKs play essential roles in signaling processes that regulate cell survival migration and proliferation Dysregulation of tyrosine kinases underlies many disorders including cancer cardiovascular and developmental diseases as well as pathologies of the immune system Ack and Brk are nonreceptor tyrosine kinases NRTKs best known for their roles in cancer Here we have biochemically characterized novel Ack and Brk mutations identified in patients with systemic lupus erythematosus SLE These mutations are the first SLE-linked polymorphisms found among NRTKs We show that two of the mutants are catalytically inactive while the other three have reduced activity To understand the ... More
Tyrosine kinases (TKs) play essential roles in signaling processes that regulate cell survival, migration, and proliferation. Dysregulation of tyrosine kinases underlies many disorders, including cancer, cardiovascular and developmental diseases, as well as pathologies of the immune system. Ack1 and Brk are nonreceptor tyrosine kinases (NRTKs) best known for their roles in cancer. Here, we have biochemically characterized novel Ack1 and Brk mutations identified in patients with systemic lupus erythematosus (SLE). These mutations are the first SLE-linked polymorphisms found among NRTKs. We show that two of the mutants are catalytically inactive, while the other three have reduced activity. To understand the structural changes associated with the loss-of-function phenotype, we solved the crystal structure of one of the Ack1 kinase mutants, K161Q. Furthermore, two of the mutated residues (Ack1 A156 and K161) critical for catalytic activity are highly conserved among other TKs, and their substitution in other members of the kinase family could have implications in cancer. In contrast to canonical gain-of-function mutations in TKs observed in many cancers, we report loss-of-function mutations in Ack1 and Brk, highlighting the complexity of TK involvement in human diseases. Less
Since the discovery of penicillin over a century ago secondary metabolites from all kingdoms of life have proven to be of high medical value One class of proteins prevalent in the production of secondary metabolites are polyketide synthases PKSs Their polyketide products are complex organic compounds based on carbon chains assembled from carboxylic acid precursors Many polyketides are produced by their hosts with the primary purpose of gaining an advantage in their ecological niche To contribute to such an advantage a significant proportion of polyketides are active against pro- and eukaryotic microorganisms Type I PKSs are giant multienzyme proteins employing ... More
Since the discovery of penicillin over a century ago, secondary metabolites from all kingdoms of life have proven to be of high medical value. One class of proteins prevalent in the production of secondary metabolites are polyketide synthases (PKSs). Their polyketide products are complex organic compounds based on carbon chains assembled from carboxylic acid precursors. Many polyketides are produced by their hosts with the primary purpose of gaining an advantage in their ecological niche. To contribute to such an advantage, a significant proportion of polyketides are active against pro- and eukaryotic microorganisms. Type I PKSs are giant multienzyme proteins employing an assembly line logic for the synthesis of the most complex polyketides. They are composed of one or more functional and structural modules, each capable of carrying out one step of precursor elongation during the formation of an extended polyketide product.
In this thesis, I address two fundamental and open questions in the biosynthesis of polyketides: First, what is the unique architecture underlying the assembly line logic of multimodular PKS assembly lines; and second, how is atomic accuracy achieved in cyclization and aromatic ring formation in the final step of PKS action.
The first aim is addressed in chapter two, which provides for the first time detailed structural insights into the organization of type I PKS multimodules. This is achieved by cryo-electron microscopic analysis of filamentous and non-filamentous forms of K3DAK4, a bimodular trans-acyltransferase (AT) PKS fragment from Brevibacillus brevis. Overall reconstructions are provided at an intermediate resolution of 7 Å, with detailed insights into individual domains at sub-3Å resolution from cryo-electron microscopy and X-ray crystallography. The bimodule core displays a vertical stacking of its two modules along the central dimer axis of all three enzymatic domains involved. Additionally, K3DAK4 oligomerizes into filaments horizontally via small scaffolding domains in a trans-AT PKS-specific manner.
In chapter three the second aim is tackled, as I visualize an intermediate of the enigmatic targeted cyclization and aromatic ring formation in the product template domain (PT) of the aflatoxin-producing PksA at 2.7 Å resolution using X-ray crystallography. To this end a substrate-analogue mimicking the transient intermediate after the first of two cyclization steps facilitated by the enzyme is covalently crosslinked to the active site. The positioning of the ligand relative to previously known ligands representing the pre-and post-cyclization states indicate an outward movement of the substrate throughout the process and a substantial effect of progressing cyclization on the meticulous positioning of the intermediates.
The work provides detailed insights into core aspects of PKS biology from the atomistic picture of guided product modification to the giant overall assembly line architecture. In chapter four, both of these levels are put into context with current advances in the analysis of modular structure and dynamics of PKSs, such as recent structural models of cis-AT PKS modules and iterative PKSs. Furthermore, it addresses currently open questions, such as the interaction of trans-AT PKS with their cognate trans-acting enzymes. Altogether, the current progress in mechanistic understanding of PKS systems makes systematic and structure-guided efforts to unleash the full potential of PKS bioengineering ever more achievable. Less
In this thesis, I address two fundamental and open questions in the biosynthesis of polyketides: First, what is the unique architecture underlying the assembly line logic of multimodular PKS assembly lines; and second, how is atomic accuracy achieved in cyclization and aromatic ring formation in the final step of PKS action.
The first aim is addressed in chapter two, which provides for the first time detailed structural insights into the organization of type I PKS multimodules. This is achieved by cryo-electron microscopic analysis of filamentous and non-filamentous forms of K3DAK4, a bimodular trans-acyltransferase (AT) PKS fragment from Brevibacillus brevis. Overall reconstructions are provided at an intermediate resolution of 7 Å, with detailed insights into individual domains at sub-3Å resolution from cryo-electron microscopy and X-ray crystallography. The bimodule core displays a vertical stacking of its two modules along the central dimer axis of all three enzymatic domains involved. Additionally, K3DAK4 oligomerizes into filaments horizontally via small scaffolding domains in a trans-AT PKS-specific manner.
In chapter three the second aim is tackled, as I visualize an intermediate of the enigmatic targeted cyclization and aromatic ring formation in the product template domain (PT) of the aflatoxin-producing PksA at 2.7 Å resolution using X-ray crystallography. To this end a substrate-analogue mimicking the transient intermediate after the first of two cyclization steps facilitated by the enzyme is covalently crosslinked to the active site. The positioning of the ligand relative to previously known ligands representing the pre-and post-cyclization states indicate an outward movement of the substrate throughout the process and a substantial effect of progressing cyclization on the meticulous positioning of the intermediates.
The work provides detailed insights into core aspects of PKS biology from the atomistic picture of guided product modification to the giant overall assembly line architecture. In chapter four, both of these levels are put into context with current advances in the analysis of modular structure and dynamics of PKSs, such as recent structural models of cis-AT PKS modules and iterative PKSs. Furthermore, it addresses currently open questions, such as the interaction of trans-AT PKS with their cognate trans-acting enzymes. Altogether, the current progress in mechanistic understanding of PKS systems makes systematic and structure-guided efforts to unleash the full potential of PKS bioengineering ever more achievable. Less
Exonucleases are essential enzymes that remove nucleotides from free DNA ends during DNA replication DNA repair and telomere maintenance Due to their essential role they are potential targets for novel anticancer and antimicrobial drugs but have so far been little exploited Here we present a simple and versatile real-time exonuclease assay based on -aminopurine an intrinsically fluorescent nucleotide that is quenched by neighboring bases when embedded in DNA We show that our assay is applicable to different eukaryotic and bacterial exonucleases acting on both and DNA ends over a wide range of protein activities and suitable for a high-throughput inhibitor ... More
Exonucleases are essential enzymes that remove nucleotides from free DNA ends during DNA replication, DNA repair, and telomere maintenance. Due to their essential role, they are potential targets for novel anticancer and antimicrobial drugs but have so far been little exploited. Here, we present a simple and versatile real-time exonuclease assay based on 2-aminopurine, an intrinsically fluorescent nucleotide that is quenched by neighboring bases when embedded in DNA. We show that our assay is applicable to different eukaryotic and bacterial exonucleases acting on both 3′ and 5′ DNA ends over a wide range of protein activities and suitable for a high-throughput inhibitor screening campaign. Using our assay, we discover a novel inhibitor of the Mycobacterium tuberculosis PHP-exonuclease that is part of the replicative DNA polymerase DnaE1. Hence, our novel assay will be a useful tool for high-throughput screening for novel exonuclease inhibitors that may interfere with DNA replication or DNA maintenance. Less
Pure bacterial cultures remain essential for detailed experimental and mechanistic studies in microbiome research and traditional methods to isolate individual bacteria from complex microbial ecosystems are labor-intensive difficult-to-scale and lack phenotype genotype integration Here we describe an open-source high-throughput robotic strain isolation platform for the rapid generation of isolates on demand We develop a machine learning approach that leverages colony morphology and genomic data to maximize the diversity of microbes isolated and enable targeted picking of specific genera Application of this platform on fecal samples from humans yields personalized gut microbiome biobanks totaling isolates that represented of all abundant taxa ... More
Pure bacterial cultures remain essential for detailed experimental and mechanistic studies in microbiome research, and traditional methods to isolate individual bacteria from complex microbial ecosystems are labor-intensive, difficult-to-scale and lack phenotype–genotype integration. Here we describe an open-source high-throughput robotic strain isolation platform for the rapid generation of isolates on demand. We develop a machine learning approach that leverages colony morphology and genomic data to maximize the diversity of microbes isolated and enable targeted picking of specific genera. Application of this platform on fecal samples from 20 humans yields personalized gut microbiome biobanks totaling 26,997 isolates that represented >80% of all abundant taxa. Spatial analysis on >100,000 visually captured colonies reveals cogrowth patterns between Ruminococcaceae, Bacteroidaceae, Coriobacteriaceae and Bifidobacteriaceae families that suggest important microbial interactions. Comparative analysis of 1,197 high-quality genomes from these biobanks shows interesting intra- and interpersonal strain evolution, selection and horizontal gene transfer. This culturomics framework should empower new research efforts to systematize the collection and quantitative analysis of imaging-based phenotypes with high-resolution genomics data for many emerging microbiome studies. Less
Diffraction-based structural methods contribute a large fraction of the biomolecular structural models available providing a critical understanding of macromolecular architecture These methods require crystallization of the target molecule which remains a primary bottleneck in crystal-based structure determination The National High-Throughput Crystallization Center at Hauptman Woodward Medical Research Institute has focused on overcoming obstacles to crystallization through a combination of robotics-enabled high-throughput screening and advanced imaging to increase the success of finding crystallization conditions This paper will describe the lessons learned from over years of operation of our high-throughput crystallization services The current experimental pipelines instrumentation imaging capabilities and software for ... More
Diffraction-based structural methods contribute a large fraction of the biomolecular structural models available, providing a critical understanding of macromolecular architecture. These methods require crystallization of the target molecule, which remains a primary bottleneck in crystal-based structure determination. The National High-Throughput Crystallization Center at Hauptman–Woodward Medical Research Institute has focused on overcoming obstacles to crystallization through a combination of robotics-enabled high-throughput screening and advanced imaging to increase the success of finding crystallization conditions. This paper will describe the lessons learned from over 20 years of operation of our high-throughput crystallization services. The current experimental pipelines, instrumentation, imaging capabilities and software for image viewing and crystal scoring are detailed. New developments in the field and opportunities for further improvements in biomolecular crystallization are reflected on. Less
Subcutaneous SC administration is a desired route for monoclonal antibodies mAbs However formulating mAbs for small injection volumes at high concentrations with suitable stability and injectability is a significant challenge Here this work presents a platform technology that combines the stability of crystalline antibodies with injectability and tunability of soft hydrogel particles Composite alginate hydrogel particles are generated via a gentle centrifugal encapsulation process which avoids use of chemical reactions or an external organic phase Crystalline suspension of anti-programmed cell death protein PD- antibody pembrolizumab is utilized as a model therapeutic antibody Crystalline forms of the mAb encapsuled in the ... More
Subcutaneous (SC) administration is a desired route for monoclonal antibodies (mAbs). However, formulating mAbs for small injection volumes at high concentrations with suitable stability and injectability is a significant challenge. Here, this work presents a platform technology that combines the stability of crystalline antibodies with injectability and tunability of soft hydrogel particles. Composite alginate hydrogel particles are generated via a gentle centrifugal encapsulation process which avoids use of chemical reactions or an external organic phase. Crystalline suspension of anti-programmed cell death protein 1 (PD-1) antibody (pembrolizumab) is utilized as a model therapeutic antibody. Crystalline forms of the mAb encapsuled in the hydrogel particles lead to stable, high concentration, and injectable formulations. Formulation concentrations as high as 315 mg mL−1 antibody are achieved with encapsulation efficiencies in the range of 89–97%, with no perceivable increase in the number of antibody aggregates. Bioanalytical studies confirm superior maintained quality of the antibody in comparison with formulation approaches involving organic phases and chemical reactions. This work illustrates tuning the alginate particles’ disintegration by using partially oxide alginates. Crystalline mAb-laden particles are evaluated for their biocompatibility using cell-based in vitro assays. Furthermore, the pharmacokinetics (PK) of the subcutaneously delivered human anti-PD-1 mAb in crystalline antibody-laden alginate hydrogel particles in Wistar rats is evaluated. Less
Breastmilk is thought to influence the infant gut by supplying prebiotics in the form of human milk oligosaccharides and potentially seeding the gut with breastmilk microbes However the presence of a breastmilk microbiota and origins of these microbes are still debated As a pilot study we assessed the microbes present in expressed breastmilk at six-weeks postpartum using shotgun metagenomic sequencing in a heterogenous cohort of women who delivered by vaginal n and caesarean delivery n In addition we estimated the microbial load of breastmilk at six-weeks post-partum with quantitative PCR targeting the S rRNA gene Breastmilk at six-weeks postpartum had ... More
Breastmilk is thought to influence the infant gut by supplying prebiotics in the form of human milk oligosaccharides and potentially seeding the gut with breastmilk microbes. However, the presence of a breastmilk microbiota and origins of these microbes are still debated. As a pilot study, we assessed the microbes present in expressed breastmilk at six-weeks postpartum using shotgun metagenomic sequencing in a heterogenous cohort of women who delivered by vaginal (n = 8) and caesarean delivery (n = 8). In addition, we estimated the microbial load of breastmilk at six-weeks post-partum with quantitative PCR targeting the 16S rRNA gene. Breastmilk at six-weeks postpartum had a low microbial mass, comparable with PCR no-template and extraction controls. Microbes identified through metagenomic sequencing were largely consistent with skin and oral microbes, with four samples returning no identifiable bacterial sequences. Our results do not provide convincing evidence for the existence of a breastmilk microbiota at six-weeks postpartum. It is more likely that microbes present in breastmilk are sourced by ejection from the infant’s mouth and from surrounding skin, as well as contamination during sampling and processing. Less
PT Formulatrix is one of the industries that produce automation tools or robots therefore companies are required to produce automation products that meet the needs of the world market PT Formulatrix has production divisions LH Liquid Handling and RI Rock Imager Examples of the production of automation equipment include NT Formulator for liquid handling and RI RI RI for rock imagers The difference lies in the shape and function of each product The problem focuses on the rock imager production process where production is made with a make to order system and the assembly process is parallel making the assembly ... More
PT. Formulatrix is one of the industries that produce automation tools or robots, therefore companies are required to produce automation products that meet the needs of the world market. PT. Formulatrix has 2 production divisions LH (Liquid Handling) and RI (Rock Imager). Examples of the production of automation equipment include, NT8, Formulator for liquid handling and RI 1000, RI 182, RI 54 for rock imagers. The difference lies in the shape and function of each product. The problem focuses on the rock imager production process, where production is made with a make to order system and the assembly process is parallel, making the assembly not smooth because you have to choose components, waiting for replacement components because they are damaged or missing to assemble. To improve the effective and efficient production process, replace the better production process. While production in liquid handling is said to be smooth because the production is small and the product is small compared to the rock imager. Assembling in parallel makes assemblers a hassle when assembling robots, because they have to sort out robot components in one container. Making assembly inefficient and ineffective. After collecting 5S data to support the kitting process in the rock imager assembling division, the process of assembling a one-table robot with components. As for the application of the 5S method applied at PT. Formulatrix Indonesia. The seiri method is applied to every division without exception, because in each division many mechanical equipment is found scattered on tables or on the floor. Seiton is a continuation of seiri, where the sorting results that have been carried out will be followed by the process of arranging the sorted equipment. Seiso at this stage, what is being done is the cleaning process. The cleaning that is done is cleaning the work area, such as the floor of the equipment used for the production process. At this stage it is more directed at the process of monitoring the 5S method that has been implemented. This stage is the last part of the 5S method. This section focuses more on how to get used to the application of this method. With the kitting process and the 5S method, it is hoped that assembling robots will be more efficient and effective, because waiting, sorting out parts, and looking for tools to assemble will be more optimal than the old process. With the kitting process, the efficiency value is better than the old process, from the previous 83% to 92%, which the researchers got from a trial at PT. Formulatrix Indonesia. Keywords: Rock Imager production process, 5S, Kitting. Less
The use of periodically structured illumination coupled with spatial Fourier-transform fluorescence recovery after photobleaching FT-FRAP was shown to support diffusivity mapping within segmented domains of arbitrary shape Periodic comb-bleach patterning of the excitation beam during photobleaching encoded spatial maps of diffusion onto harmonic peaks in the spatial Fourier transform Diffusion manifests as a simple exponential decay of a given harmonic improving the signal to noise ratio and simplifying mathematical analysis Image segmentation prior to Fourier transformation was shown to support pooling for signal to noise enhancement for regions of arbitrary shape expected to exhibit similar diffusivity within a domain Following ... More
The use of periodically structured illumination coupled with spatial Fourier-transform fluorescence recovery after photobleaching (FT-FRAP) was shown to support diffusivity mapping within segmented domains of arbitrary shape. Periodic “comb-bleach” patterning of the excitation beam during photobleaching encoded spatial maps of diffusion onto harmonic peaks in the spatial Fourier transform. Diffusion manifests as a simple exponential decay of a given harmonic, improving the signal to noise ratio and simplifying mathematical analysis. Image segmentation prior to Fourier transformation was shown to support pooling for signal to noise enhancement for regions of arbitrary shape expected to exhibit similar diffusivity within a domain. Following proof-of-concept analyses based on simulations with known ground-truth maps, diffusion imaging by FT-FRAP was used to map spatially-resolved diffusion differences within phase-separated domains of model amorphous solid dispersion spin-cast thin films. Notably, multi-harmonic analysis by FT-FRAP was able to definitively discriminate and quantify the roles of internal diffusion and exchange to higher mobility interfacial layers in modeling the recovery kinetics within thin amorphous/amorphous phase-separated domains, with interfacial diffusion playing a critical role in recovery. These results have direct implications for the design of amorphous systems for stable storage and efficacious delivery of therapeutic molecules. Less
The adult spinal cord stem cell potential resides within the ependymal cell population and declines with age Ependymal cells are however heterogeneous and the biological diversity this represents and how it changes with age remain unknown Here we present a single-cell transcriptomic census of spinal cord ependymal cells from adult and aged mice identifying not only all known ependymal cell subtypes but also immature as well as mature cell states By comparing transcriptomes of spinal cord and brain ependymal cells which lack stem cell abilities we identify immature cells as potential spinal cord stem cells Following spinal cord injury these ... More
The adult spinal cord stem cell potential resides within the ependymal cell population and declines with age. Ependymal cells are, however, heterogeneous, and the biological diversity this represents and how it changes with age remain unknown. Here, we present a single-cell transcriptomic census of spinal cord ependymal cells from adult and aged mice, identifying not only all known ependymal cell subtypes but also immature as well as mature cell states. By comparing transcriptomes of spinal cord and brain ependymal cells, which lack stem cell abilities, we identify immature cells as potential spinal cord stem cells. Following spinal cord injury, these cells re-enter the cell cycle, which is accompanied by a short-lived reversal of ependymal cell maturation. We further analyze ependymal cells in the human spinal cord and identify widespread cell maturation and altered cell identities. This in-depth characterization of spinal cord ependymal cells provides insight into their biology and informs strategies for spinal cord repair. Less
This high-throughput protocol details the steps to extract protein from Gram-negative bacteria Gram-positive bacteria or non-filamentous fungi in -well plate format for quantitative proteomic workflows This protocol uses a bench-top automated liquid dispenser but the volumes and times also apply to manual and multi-channel pipetter use This protocol is designed for lab-based culture conditions and synthetic community experiments where complex sample matrices are minimized Additional sample preservation and or protein extraction methods may be required for environmental samples e g feces soil to minimize protein degradation and maintain sample integrity
Enzymatic pockets such as those of histone deacetylases HDACs are among the most favored targets for drug development However enzymatic inhibitors often exhibit low selectivity and high toxicity due to targeting multiple enzyme paralogs which are often involved in distinct multisubunit complexes Here we report the discovery and characterization of a non-enzymatic small molecule inhibitor of HDAC transcriptional repression functions with comparable anti-tumor activity to the enzymatic HDAC inhibitor Vorinostat and anti-psychedelic activity of an HDAC knockout in vivo We highlight that these phenotypes are achieved while modulating the expression of - and -fold fewer genes than enzymatic and genetic ... More
Enzymatic pockets such as those of histone deacetylases (HDACs) are among the most favored targets for drug development. However, enzymatic inhibitors often exhibit low selectivity and high toxicity due to targeting multiple enzyme paralogs, which are often involved in distinct multisubunit complexes. Here, we report the discovery and characterization of a non-enzymatic small molecule inhibitor of HDAC transcriptional repression functions with comparable anti-tumor activity to the enzymatic HDAC inhibitor Vorinostat, and anti-psychedelic activity of an HDAC2 knockout in vivo. We highlight that these phenotypes are achieved while modulating the expression of 20- and 80-fold fewer genes than enzymatic and genetic inhibition in the respective models. Thus, by achieving the same biological outcomes as established therapeutics while impacting a dramatically smaller number of genes, inhibitors of protein-protein interactions can offer important advantages in improving the selectivity of epigenetic modulators. Less
Background Xylem the most abundant tissue on Earth is responsible for lateral growth in plants Typical xylem has a radial system composed of ray parenchyma cells and an axial system of fusiform cells In most angiosperms fusiform cells comprise vessel elements for water transportation and libriform fibers for mechanical support while both functions are performed by tracheids in other vascular plants such as gymnosperms Little is known about the developmental programs and evolutionary relationships of these xylem cell types Results Through both single-cell and laser capture microdissection transcriptomic profiling we determine the developmental lineages of ray and fusiform cells in ... More
Background
Xylem, the most abundant tissue on Earth, is responsible for lateral growth in plants. Typical xylem has a radial system composed of ray parenchyma cells and an axial system of fusiform cells. In most angiosperms, fusiform cells comprise vessel elements for water transportation and libriform fibers for mechanical support, while both functions are performed by tracheids in other vascular plants such as gymnosperms. Little is known about the developmental programs and evolutionary relationships of these xylem cell types.
Results
Through both single-cell and laser capture microdissection transcriptomic profiling, we determine the developmental lineages of ray and fusiform cells in stem-differentiating xylem across four divergent woody angiosperms. Based on cross-species analyses of single-cell clusters and overlapping trajectories, we reveal highly conserved ray, yet variable fusiform, lineages across angiosperms. Core eudicots Populus trichocarpa and Eucalyptus grandis share nearly identical fusiform lineages, whereas the more basal angiosperm Liriodendron chinense has a fusiform lineage distinct from that in core eudicots. The tracheids in the basal eudicot Trochodendron aralioides, an evolutionarily reversed trait, exhibit strong transcriptomic similarity to vessel elements rather than libriform fibers.
Conclusions
This evo-devo framework provides a comprehensive understanding of the formation of xylem cell lineages across multiple plant species spanning over a hundred million years of evolutionary history. Less
Xylem, the most abundant tissue on Earth, is responsible for lateral growth in plants. Typical xylem has a radial system composed of ray parenchyma cells and an axial system of fusiform cells. In most angiosperms, fusiform cells comprise vessel elements for water transportation and libriform fibers for mechanical support, while both functions are performed by tracheids in other vascular plants such as gymnosperms. Little is known about the developmental programs and evolutionary relationships of these xylem cell types.
Results
Through both single-cell and laser capture microdissection transcriptomic profiling, we determine the developmental lineages of ray and fusiform cells in stem-differentiating xylem across four divergent woody angiosperms. Based on cross-species analyses of single-cell clusters and overlapping trajectories, we reveal highly conserved ray, yet variable fusiform, lineages across angiosperms. Core eudicots Populus trichocarpa and Eucalyptus grandis share nearly identical fusiform lineages, whereas the more basal angiosperm Liriodendron chinense has a fusiform lineage distinct from that in core eudicots. The tracheids in the basal eudicot Trochodendron aralioides, an evolutionarily reversed trait, exhibit strong transcriptomic similarity to vessel elements rather than libriform fibers.
Conclusions
This evo-devo framework provides a comprehensive understanding of the formation of xylem cell lineages across multiple plant species spanning over a hundred million years of evolutionary history. Less
Opioid-related fatal overdoses have reached epidemic proportions Because existing treatments for opioid use disorders offer limited long-term protection accelerating the development of newer approaches is critical Monoclonal antibodies mAbs are an emerging treatment strategy that targets and sequesters selected opioids in the bloodstream reducing drug distribution across the blood-brain barrier thus preventing or reversing opioid toxicity We previously identified a series of murine mAbs with high affinity and selectivity for oxycodone morphine fentanyl and nicotine To determine their binding mechanism we used X-ray crystallography to solve the structures of mAbs bound to their respective targets to resolution or higher Structural ... More
Opioid-related fatal overdoses have reached epidemic proportions. Because existing treatments for opioid use disorders offer limited long-term protection, accelerating the development of newer approaches is critical. Monoclonal antibodies (mAbs) are an emerging treatment strategy that targets and sequesters selected opioids in the bloodstream, reducing drug distribution across the blood-brain barrier, thus preventing or reversing opioid toxicity. We previously identified a series of murine mAbs with high affinity and selectivity for oxycodone, morphine, fentanyl, and nicotine. To determine their binding mechanism, we used X-ray crystallography to solve the structures of mAbs bound to their respective targets, to 2.2 Å resolution or higher. Structural analysis showed a critical convergent hydrogen bonding mode that is dependent on a glutamic acid residue in the mAbs’ heavy chain and a tertiary amine of the ligand. Characterizing drug-mAb complexes represents a significant step toward rational antibody engineering and future manufacturing activities to support clinical evaluation. Less
Chemical modifications of RNA have key roles in many biological processes N -methylguanosine m G is required for integrity and stability of a large subset of tRNAs The methyltransferase WD repeat-containing protein METTL WDR complex is the methyltransferase that modifies G in the variable loop of certain tRNAs and its dysregulation drives tumorigenesis in numerous cancer types Mutations in WDR cause human developmental phenotypes including microcephaly How METTL WDR modifies tRNA substrates and is regulated remains elusive Here we show through structural biochemical and cellular studies of human METTL WDR that WDR serves as a scaffold for METTL and the ... More
Chemical modifications of RNA have key roles in many biological processes1,2,3. N7-methylguanosine (m7G) is required for integrity and stability of a large subset of tRNAs4,5,6,7. The methyltransferase 1–WD repeat-containing protein 4 (METTL1–WDR4) complex is the methyltransferase that modifies G46 in the variable loop of certain tRNAs, and its dysregulation drives tumorigenesis in numerous cancer types8,9,10,11,12,13,14. Mutations in WDR4 cause human developmental phenotypes including microcephaly15,16,17. How METTL1–WDR4 modifies tRNA substrates and is regulated remains elusive18. Here we show, through structural, biochemical and cellular studies of human METTL1–WDR4, that WDR4 serves as a scaffold for METTL1 and the tRNA T-arm. Upon tRNA binding, the αC region of METTL1 transforms into a helix, which together with the α6 helix secures both ends of the tRNA variable loop. Unexpectedly, we find that the predicted disordered N-terminal region of METTL1 is part of the catalytic pocket and essential for methyltransferase activity. Furthermore, we reveal that S27 phosphorylation in the METTL1 N-terminal region inhibits methyltransferase activity by locally disrupting the catalytic centre. Our results provide a molecular understanding of tRNA substrate recognition and phosphorylation-mediated regulation of METTL1–WDR4, and reveal the presumed disordered N-terminal region of METTL1 as a nexus of methyltransferase activity. Less
Single-cell multi-omics can provide a unique perspective on tumor cellular heterogeneity Most previous single-cell whole-genome RNA sequencing scWGS-RNA-seq methods demonstrate utility with intact cells from fresh samples Among them many are not applicable to frozen samples that cannot produce intact single-cell suspensions We have developed scONE-seq a versatile scWGS-RNA-seq method that amplifies single-cell DNA and RNA without separating them from each other and hence is compatible with frozen biobanked samples We benchmarked scONE-seq against existing methods using fresh and frozen samples to demonstrate its performance in various aspects We identified a unique transcriptionally normal-like tumor clone by analyzing a -year ... More
Single-cell multi-omics can provide a unique perspective on tumor cellular heterogeneity. Most previous single-cell whole-genome RNA sequencing (scWGS-RNA-seq) methods demonstrate utility with intact cells from fresh samples. Among them, many are not applicable to frozen samples that cannot produce intact single-cell suspensions. We have developed scONE-seq, a versatile scWGS-RNA-seq method that amplifies single-cell DNA and RNA without separating them from each other and hence is compatible with frozen biobanked samples. We benchmarked scONE-seq against existing methods using fresh and frozen samples to demonstrate its performance in various aspects. We identified a unique transcriptionally normal-like tumor clone by analyzing a 2-year frozen astrocytoma sample, demonstrating that performing single-cell multi-omics interrogation on biobanked tissue by scONE-seq could enable previously unidentified discoveries in tumor biology. Less
Linear IgE epitopes play essential roles in persistent allergies including peanut and tree nut allergies Using chemically synthesized peptides attached to membranes and microarray experiments is one approach for determining predominant epitopes that has seen success However the overall expense of this approach and the inherent challenges in scaling up the production and purification of synthetic peptides precludes the general application of this approach To overcome this problem we have constructed a plasmid vector for expressing peptides sandwiched between an N-terminal His-tag and a trimeric protein The vector was used to make overlapping peptides derived from peanut allergens Ara h ... More
Linear IgE epitopes play essential roles in persistent allergies, including peanut and tree nut allergies. Using chemically synthesized peptides attached to membranes and microarray experiments is one approach for determining predominant epitopes that has seen success. However, the overall expense of this approach and the inherent challenges in scaling up the production and purification of synthetic peptides precludes the general application of this approach. To overcome this problem, we have constructed a plasmid vector for expressing peptides sandwiched between an N-terminal His-tag and a trimeric protein. The vector was used to make overlapping peptides derived from peanut allergens Ara h 2. All the peptides were successfully expressed and purified. The resulting peptides were applied to identify IgE binding epitopes of Ara h 2 using four sera samples from individuals with known peanut allergies. New and previously defined dominant IgE binding epitopes of Ara h 2 were identified. This system may be readily applied to produce agents for component- and epitope-resolved food allergy diagnosis. Less
X-ray crystallography has long been a key method in solving the three-dimensional structure of proteins Structural information is essential for unraveling the molecular function of proteins and structure-based drug design However there are several obstacles associated with the structural determination of proteins using X-ray crystallography such as the generation of a large amount of protein samples instability of purified proteins and difficulty in obtaining large and well-diffracting crystals all of which can prolong the process of determining the crystal structure from months to years Over the past decade new techniques and strategies have been developed to assist X-ray crystallographers in ... More
X-ray crystallography has long been a key method in solving the three-dimensional structure of proteins. Structural information is essential for unraveling the molecular function of proteins and structure-based drug design. However, there are several obstacles associated with the structural determination of proteins using X-ray crystallography, such as the generation of a large amount of protein samples, instability of purified proteins, and difficulty in obtaining large and well-diffracting crystals, all of which can prolong the process of determining the crystal structure, from months to years. Over the past decade, new techniques and strategies have been developed to assist X-ray crystallographers in overcoming some of these obstacles. In this chapter, we discuss some of these technological advances. Familiarity with these new developments would benefit researchers in both academic and industrial environments who study macromolecular structural dynamics using X-ray crystallography. Less
The advent of SARS-CoV- the causative agent of COVID- and its worldwide impact on global health have provided the impetus for the development of effective countermeasures that can be deployed against the virus including vaccines monoclonal antibodies and direct-acting antivirals DAAs Despite these efforts the current paucity of DAAs has created an urgent need for the creation of an enhanced and diversified portfolio of broadly acting agents with different mechanisms of action that can effectively abrogate viral infection SARS-CoV- C-like protease CLpro an enzyme essential for viral replication is a validated target for the discovery of SARS-CoV- therapeutics In this ... More
The advent of SARS-CoV-2, the causative agent of COVID-19, and its worldwide impact on global health, have provided the impetus for the development of effective countermeasures that can be deployed against the virus, including vaccines, monoclonal antibodies, and direct-acting antivirals (DAAs). Despite these efforts, the current paucity of DAAs has created an urgent need for the creation of an enhanced and diversified portfolio of broadly acting agents with different mechanisms of action that can effectively abrogate viral infection. SARS-CoV-2 3C-like protease (3CLpro), an enzyme essential for viral replication, is a validated target for the discovery of SARS-CoV-2 therapeutics. In this report, we describe the structure-guided utilization of the cyclopropane moiety in the design of highly potent inhibitors of SARS-CoV-2 3CLpro, SARS-CoV-1 3CLpro, and MERS-CoV 3CLpro. High-resolution cocrystal structures were used to identify the structural determinants associated with the binding of the inhibitors to the active site of the enzyme and unravel the mechanism of action. Aldehydes 5c and 11c inhibited SARS-CoV-2 replication with EC50 values of 12 and 11 nM, respectively. Furthermore, the corresponding aldehyde bisulfite adducts 5d and 11d were equipotent with EC50 values of 13 and 12 nM, respectively. The safety index (SI) values for compounds 5c/11c and 5d/11d ranged between 7692 and 9090. Importantly, aldehydes 5c/11c and bisulfite adducts 5d/11d potently inhibited MERS-CoV 3CLpro with IC50 values of 80 and 120 nM, and 70 and 70 nM, respectively. Likewise, compounds 5c/11c and 5d/11d inhibited SARS-CoV-1 with IC50 values of 960 and 350 nM and 790 and 240 nM, respectively. Taken together, these studies suggest that the inhibitors described herein have low cytotoxicity and high potency and are promising candidates for further development as broad-spectrum direct-acting antivirals against highly pathogenic coronaviruses. Less
Enzymatic late-stage diversification of small molecules has the potential to rapidly generate diversity in compound libraries dedicated to drug discovery In this context freestanding Fe II -ketoglutarate-dependent halogenases have raised particular interest as this enzyme family allows the otherwise difficult regio- and stereoselective halogenation of unactivated C sp H bonds Here we report the development of two engineered variants of the halogenase WelO for the racemic resolution of a mixture of stereoisomers generated in the synthesis of a bioactive martinelline-derived fragment By screening a -site combinatorial variant library we could identify two variants exhibiting exquisite substrate selectivity towards the desired ... More
Enzymatic late-stage diversification of small molecules has the potential to rapidly generate diversity in compound libraries dedicated to drug discovery. In this context, freestanding Fe(II)/α-ketoglutarate-dependent halogenases have raised particular interest as this enzyme family allows the otherwise difficult regio- and stereoselective halogenation of unactivated C(sp3)−H bonds. Here, we report the development of two engineered variants of the halogenase WelO5* for the racemic resolution of a mixture of stereoisomers generated in the synthesis of a bioactive martinelline-derived fragment. By screening a 3-site combinatorial variant library, we could identify two variants exhibiting exquisite substrate selectivity towards the desired enantiomers. Strikingly, the inversion of substrate stereopreference between the halogenase variants was achieved by varying only three residues in the active site. Protein crystallization and subsequent structure elucidation of the wildtype enzyme and a WelO5* variant shed light on the factors governing substrate acceptance and selectivity. Less
Crystallization of proteins is a critical step in structural biology biopharmaceutical industry and materials science Microfluidic technology has emerged as a promising tool for screening the crystallization conditions with advantages of increased throughput reduced consumption of reagents and lower cost However current mirofluidic approches generally lack the module for high-speed data analysis ignore the time-resolved changes of protein crystalline states or morphologies in the crystallization process and suffer from inconsistency after scaling up due to the subnano- nano-liter-scaled volume To address the issues we propose a deep learning-aided programmable microliter-droplet system which allows the high-throughput screening of time-resolved protein crystallization ... More
Crystallization of proteins is a critical step in structural biology, biopharmaceutical industry and materials science. Microfluidic technology has emerged as a promising tool for screening the crystallization conditions with advantages of increased throughput, reduced consumption of reagents and lower cost. However, current mirofluidic approches generally lack the module for high-speed data analysis, ignore the time-resolved changes of protein crystalline states or morphologies in the crystallization process and suffer from inconsistency after scaling up due to the subnano-/nano-liter-scaled volume. To address the issues, we propose a deep learning-aided programmable microliter-droplet system, which allows the high-throughput screening of time-resolved protein crystallization in microliter scale. Based on the system, a series of temporal phase diagrams are acquired, which reveal the time-resolved crystallization of target proteins under different crystallization conditions. They provide precise guidance on the scale-up experiment (∼93 % in consistency), and help gain insight into the kinetic characteristics of protein crystallization. Less
Coproporphyrin ferrochelatases CpfCs are enzymes catalyzing the penultimate step in the coproporphyrin-dependent CPD heme biosynthesis pathway which is mainly utilized by monoderm bacteria Ferrochelatases insert ferrous iron into a porphyrin macrocycle and have been studied for many decades nevertheless many mechanistic questions remain unanswered to date Especially CpfCs which are found in the CPD pathway are currently in the spotlight of research This pathway was identified in and revealed that the correct substrate for these ferrochelatases is coproporphyrin III cpIII instead of protoporphyrin IX as believed prior the discovery of the CPD pathway The chemistry of cpIII which has four ... More
Coproporphyrin ferrochelatases (CpfCs) are enzymes catalyzing the penultimate step in the coproporphyrin-dependent (CPD) heme biosynthesis pathway, which is mainly utilized by monoderm bacteria. Ferrochelatases insert ferrous iron into a porphyrin macrocycle and have been studied for many decades, nevertheless many mechanistic questions remain unanswered to date. Especially CpfCs, which are found in the CPD pathway, are currently in the spotlight of research. This pathway was identified in 2015 and revealed that the correct substrate for these ferrochelatases is coproporphyrin III (cpIII) instead of protoporphyrin IX, as believed prior the discovery of the CPD pathway. The chemistry of cpIII, which has four propionates, differs significantly from protoporphyrin IX, which features two propionate and two vinyl groups. These findings let us to thoroughly describe the physiological cpIII-ferrochelatase complex in solution and in the crystal phase. Here, we present the first crystallographic structure of the CpfC from the representative monoderm pathogen Listeria monocytogenes bound to its physiological substrate, cpIII, together with the in-solution data obtained by resonance Raman and UV–vis spectroscopy, for wild-type ferrochelatase and variants, analyzing propionate interactions. The results allow us to evaluate the porphyrin distortion and provide an in-depth characterization of the catalytically-relevant binding mode of cpIII prior to iron insertion. Our findings are discussed in the light of the observed structural restraints and necessities for this porphyrin-enzyme complex to catalyze the iron insertion process. Knowledge about this initial situation is essential for understanding the preconditions for iron insertion in CpfCs and builds the basis for future studies. Less
Mitogen-activated protein kinase MAPK phosphatase MKP is responsible for regulating the activity of the stress-responsive MAPKs and has been put forth as a potential therapeutic target for a number of diseases including dystrophic muscle disease a fatal rare disease which has neither a treatment nor cure In previous work we identified Compound -dimethyl- - - methylthio - -dihydrothieno -h quinazolin- -yl thio butan- -one as the lead compound of a novel class of MKP inhibitors In this work we explore the structure-activity relationship for inhibition of MKP through modifications to the scaffold and functional groups present in A series of ... More
Mitogen-activated protein kinase (MAPK) phosphatase 5 (MKP5) is responsible for regulating the activity of the stress-responsive MAPKs and has been put forth as a potential therapeutic target for a number of diseases, including dystrophic muscle disease a fatal rare disease which has neither a treatment nor cure. In previous work, we identified Compound 1 (3,3-dimethyl-1-((9-(methylthio)-5,6-dihydrothieno[3,4-h]quinazolin-2-yl)thio)butan-2-one) as the lead compound of a novel class of MKP5 inhibitors. In this work, we explore the structure-activity relationship for inhibition of MKP5 through modifications to the scaffold and functional groups present in 1. A series of derivative compounds was designed, synthesized, and evaluated for inhibition of MKP5. In addition, the X-ray crystal structures of six enzyme-inhibitor complexes were solved, further elucidating the necessary requirements for MKP5 inhibition. We found that the parallel-displaced π-π interaction between the inhibitor three-ring core and Tyr435 is critical for modulating potency, and that modifications to the core and functionalization at the C-9 position are essential for ensuring proper positioning of the core for this interaction. These results lay the foundation from which more potent MKP5 allosteric inhibitors can be developed for potential therapeutics towards the treatment of dystrophic muscle disease. Less
Applying rational design we developed kDa cyanobacteriochrome-based near-infrared NIR-I fluorescent protein miRFP nano miRFP nano efficiently binds endogenous biliverdin chromophore and brightly fluoresces in mammalian cells and tissues miRFP nano has maximal emission at nm and an emission tail in the short-wave infrared SWIR region allowing deep-penetrating off-peak fluorescence imaging in vivo The miRFP nano structure reveals the molecular basis of its red shift We demonstrate superiority of miRFP nano-enabled SWIR imaging over NIR-I imaging of microbes in the mouse digestive tract mammalian cells injected into the mouse mammary gland and NF-kB activity in a mouse model of liver inflammation
Microfluidic paper-based analytical devices microPADs are an emerging platform for point-of-care assays with potential applications ranging from medical diagnostics to environmental monitoring A standard approach for signal generation and amplification on microPADs is the use of enzymes and chromogenic substrates which produce colored products and enable the qualitative and quantitative detection of analytes Horseradish peroxidase HRP is one of the most commonly used enzymes for this application While a wide variety of chromogenic substrates and substrate solutions are available for HRP these were all originally developed and optimized for other platforms and have not been systematically compared on microPADs In ... More
Microfluidic paper-based analytical devices (microPADs) are an emerging platform for point-of-care assays with potential applications ranging from medical diagnostics to environmental monitoring. A standard approach for signal generation and amplification on microPADs is the use of enzymes and chromogenic substrates, which produce colored products and enable the qualitative and quantitative detection of analytes. Horseradish peroxidase (HRP) is one of the most commonly used enzymes for this application. While a wide variety of chromogenic substrates and substrate solutions are available for HRP, these were all originally developed and optimized for other platforms and have not been systematically compared on microPADs. In this work, 33 chromogenic substrate solutions for HRP containing one of six different substrate molecules were evaluated in a standardized colorimetric assay and compared on the basis of limit of detection (LOD), lower limit of quantitation (LLOQ), upper limit of quantitation (ULOQ), sensitivity, dynamic range, stability, and cost. While the substrates tetramethylbenzidine (TMB) and o-phenylenediamine (OPD) were found to achieve the best overall analytical performance, each substrate had characteristics that may make them appealing for specific applications. The results of this work will facilitate the selection of substrate molecules and the formulation of substrate solutions for future colorimetric paper-based assays involving HRP. Less
Increasing rate of genetic gain for key agronomic traits through genomic selection requires the development of new molecular methods to run genome-wide single nucleotide polymorphisms SNPs The main limitation of current methods is the cost is too high to screen breeding populations Molecular inversion probes MIPs is a targeted genotyping-by-sequencing method that could be used for soybeans that is both cost effective high-throughput and provides high data quality to screen breeder s germplasm for genomic selection A K MIP SNP set was developed for soybean with uniformly distributed markers across the genome The SNPs were selected to maximize the number ... More
Increasing rate of genetic gain for key agronomic traits through genomic selection requires the development of new molecular methods to run genome-wide single nucleotide polymorphisms (SNPs). The main limitation of current methods is the cost is too high to screen breeding populations. Molecular inversion probes (MIPs) is a targeted genotyping-by-sequencing method that could be used for soybeans that is both cost effective, high-throughput, and provides high data quality to screen breeder’s germplasm for genomic selection. A 1K MIP SNP set was developed for soybean with uniformly distributed markers across the genome. The SNPs were selected to maximize the number of informative markers in germplasm being tested in soybean breeding programs located in the North Central and Mid-South regions of the United States. The 1K SNP MIP set was tested on diverse germplasm and a recombinant inbred line population. Targeted sequencing with MIPs obtained an 85% enrichment for the targeted SNPs. MIP’s genotyping accuracy was 93% overall while homozoygous call accuracy was 98% with less than 10% missing data. The accuracy of MIPs combined with its low per sample cost makes it a powerful tool to enable genomic selection within soybean breeding programs. Less
Coelenterazine-v CTZ-v a synthetic vinylene-bridged -extended derivative is able to significantly alter bioluminescence spectra of different CTZ-dependent luciferases and photoproteins by shifting them towards longer wavelengths However Ca -regulated photoproteins activated with CTZ-v display very low bioluminescence activities that hampers its usage as a substrate of photoprotein bioluminescence Here we report the crystal structure of semi-synthetic Ca -discharged obelin-v bound with the reaction product determined at resolution Comparison of the crystal structure of Ca -discharged obelin-v with those of other obelins before and after bioluminescence reaction reveals no considerable changes in the overall structure However the drastic changes in CTZ-binding ... More
Coelenterazine-v (CTZ-v), a synthetic vinylene-bridged π-extended derivative, is able to significantly alter bioluminescence spectra of different CTZ-dependent luciferases and photoproteins by shifting them towards longer wavelengths. However, Ca2+-regulated photoproteins activated with CTZ-v display very low bioluminescence activities that hampers its usage as a substrate of photoprotein bioluminescence. Here, we report the crystal structure of semi-synthetic Ca2+-discharged obelin-v bound with the reaction product determined at 2.1 Å resolution. Comparison of the crystal structure of Ca2+-discharged obelin-v with those of other obelins before and after bioluminescence reaction reveals no considerable changes in the overall structure. However, the drastic changes in CTZ-binding cavity are observed owing to the completely different reaction product, coelenteramine-v (CTM-v). Since CTM-v is certainly the main product of obelin-v bioluminescence and is considered to be a product of the “dark” pathway of dioxetanone intermediate decomposition, it explains the low bioluminescence activity of obelin and apparently of other photoproteins with CTZ-v. Less
The past fifty years have been marked by the surge of neurodegenerative diseases Unfortunately current treatments are only symptomatic Hence the search for new and innovative therapeutic targets for curative treatments becomes a major challenge Among these targets the adenosine A A receptor A AAR has been the subject of much research in recent years In this paper we report the design synthesis and pharmacological analysis of quinazoline derivatives as A AAR antagonists with high ligand efficiency This class of molecules has been discovered by a virtual screening and bears no structural semblance with reference antagonist ZM- More precisely we ... More
The past fifty years have been marked by the surge of neurodegenerative diseases. Unfortunately, current treatments are only symptomatic. Hence, the search for new and innovative therapeutic targets for curative treatments becomes a major challenge. Among these targets, the adenosine A2A receptor (A2AAR) has been the subject of much research in recent years. In this paper, we report the design, synthesis and pharmacological analysis of quinazoline derivatives as A2AAR antagonists with high ligand efficiency. This class of molecules has been discovered by a virtual screening and bears no structural semblance with reference antagonist ZM-241385. More precisely, we identified a series of 2-aminoquinazoline as promising A2AAR antagonists. Among them, one compound showed a high affinity towards A2AAR (21a, Ki = 20 nM). We crystallized this ligand in complex with A2AAR, confirming one of our predicted docking poses and opening up possibilities for further optimization to derive selective ligands for specific adenosine receptor subtypes. Less
Transmembrane ion transport is a key process in living cells Active transport of ions is carried out by various ion transporters including microbial rhodopsins MRs MRs perform diverse functions such as active and passive ion transport photo-sensing and others In particular MRs can pump various monovalent ions like Na K Cl I NO The only characterized MR proposed to pump sulfate in addition to halides belongs to the cyanobacterium Synechocystis sp PCC and is named Synechocystis halorhodopsin SyHR The structural study of SyHR may help to understand what makes an MR pump divalent ions Here we present the crystal structure ... More
Transmembrane ion transport is a key process in living cells. Active transport of ions is carried out by various ion transporters including microbial rhodopsins (MRs). MRs perform diverse functions such as active and passive ion transport, photo-sensing, and others. In particular, MRs can pump various monovalent ions like Na+, K+, Cl−, I−, NO3−. The only characterized MR proposed to pump sulfate in addition to halides belongs to the cyanobacterium Synechocystis sp. PCC 7509 and is named Synechocystis halorhodopsin (SyHR). The structural study of SyHR may help to understand what makes an MR pump divalent ions. Here we present the crystal structure of SyHR in the ground state, the structure of its sulfate-bound form as well as two photoreaction intermediates, the K and O states. These data reveal the molecular origin of the unique properties of the protein (exceptionally strong chloride binding and proposed pumping of divalent anions) and sheds light on the mechanism of anion release and uptake in cyanobacterial halorhodopsins. The unique properties of SyHR highlight its potential as an optogenetics tool and may help engineer different types of anion pumps with applications in optogenetics. Less
The transcription factor TEAD together with its coactivator YAP TAZ is a key transcriptional modulator of the Hippo pathway Activation of TEAD transcription by YAP has been implicated in a number of malignancies and this complex represents a promising target for drug discovery However both YAP and its extensive binding interfaces to TEAD have been difficult to address using small molecules mainly due to a lack of druggable pockets TEAD is post-translationally modified by palmitoylation that targets a conserved cysteine at a central pocket which provides an opportunity to develop cysteine-directed covalent small molecules for TEAD inhibition Here we employed ... More
The transcription factor TEAD, together with its coactivator YAP/TAZ, is a key transcriptional modulator of the Hippo pathway. Activation of TEAD transcription by YAP has been implicated in a number of malignancies, and this complex represents a promising target for drug discovery. However, both YAP and its extensive binding interfaces to TEAD have been difficult to address using small molecules, mainly due to a lack of druggable pockets. TEAD is post-translationally modified by palmitoylation that targets a conserved cysteine at a central pocket, which provides an opportunity to develop cysteine-directed covalent small molecules for TEAD inhibition. Here, we employed covalent fragment screening approach followed by structure-based design to develop an irreversible TEAD inhibitor MYF-03–69. Using a range of in vitro and cell-based assays we demonstrated that through a covalent binding with TEAD palmitate pocket, MYF-03–69 disrupts YAP-TEAD association, suppresses TEAD transcriptional activity and inhibits cell growth of Hippo signaling defective malignant pleural mesothelioma (MPM). Further, a cell viability screening with a panel of 903 cancer cell lines indicated a high correlation between TEAD-YAP dependency and the sensitivity to MYF-03–69. Transcription profiling identified the upregulation of proapoptotic BMF gene in cancer cells that are sensitive to TEAD inhibition. Further optimization of MYF-03–69 led to an in vivo compatible compound MYF-03–176, which shows strong antitumor efficacy in MPM mouse xenograft model via oral administration. Taken together, we disclosed a story of the development of covalent TEAD inhibitors and its high therapeutic potential for clinic treatment for the cancers that are driven by TEAD-YAP alteration. Less
Enzymatic late-stage diversification of small molecules has the potential to rapidly generate diversity in compound libraries dedicated to drug discovery In this context freestanding Fe II -ketoglutarate-dependent halogenases have raised particular interest as this enzyme family allows the otherwise difficult regio- and stereoselective halogenation of unactivated C sp H bonds Here we report the development of two engineered variants of the halogenase WelO for the racemic resolution of a mixture of stereoisomers generated in the synthesis of a bioactive martinelline-derived fragment By screening a -site combinatorial variant library we could identify two variants exhibiting exquisite substrate selectivity towards the desired ... More
Enzymatic late-stage diversification of small molecules has the potential to rapidly generate diversity in compound libraries dedicated to drug discovery. In this context, freestanding Fe(II)/α-ketoglutarate-dependent halogenases have raised particular interest as this enzyme family allows the otherwise difficult regio- and stereoselective halogenation of unactivated C(sp3)−H bonds. Here, we report the development of two engineered variants of the halogenase WelO5* for the racemic resolution of a mixture of stereoisomers generated in the synthesis of a bioactive martinelline-derived fragment. By screening a 3-site combinatorial variant library, we could identify two variants exhibiting exquisite substrate selectivity towards the desired enantiomers. Strikingly, the inversion of substrate stereopreference between the halogenase variants was achieved by varying only three residues in the active site. Protein crystallization and subsequent structure elucidation of the wildtype enzyme and a WelO5* variant shed light on the factors governing substrate acceptance and selectivity. Less
Histone deacetylase HDAC is an atypical lysine deacetylase with tandem catalytic domains and an ubiquitin-binding zinc finger domain HDAC is involved in various biological processes such as cell motility or stress responses and has been implicated in pathologies ranging from cancer to neurodegeneration Due to this broad range of functions there has been considerable interest in developing HDAC -specific small molecule inhibitors several of which are already available The crystal structure of the tandem catalytic domains of zebrafish HDAC has revealed an arrangement with twofold symmetry and extensive surface interaction between the catalytic domains Further dissection of the biochemical properties ... More
Histone deacetylase 6 (HDAC6) is an atypical lysine deacetylase with tandem catalytic domains and an ubiquitin-binding zinc finger domain. HDAC6 is involved in various biological processes, such as cell motility or stress responses, and has been implicated in pathologies ranging from cancer to neurodegeneration. Due to this broad range of functions, there has been considerable interest in developing HDAC6-specific small molecule inhibitors, several of which are already available. The crystal structure of the tandem catalytic domains of zebrafish HDAC6 has revealed an arrangement with twofold symmetry and extensive surface interaction between the catalytic domains. Further dissection of the biochemical properties of HDAC6 and the development of novel inhibitors will benefit from being able to routinely express high-quality protein. We present here our optimized protocol for expression and crystallization of the zebrafish tandem catalytic domains. Less
Colibactin a DNA cross-linking agent produced by gut bacteria is implicated in colorectal cancer Its biosynthesis uses a prodrug resistance mechanism a non-toxic precursor assembled in the cytoplasm is activated after export to the periplasm This activation is mediated by ClbP an inner-membrane peptidase with an N-terminal periplasmic catalytic domain and a C-terminal three-helix transmembrane domain Although the transmembrane domain is required for colibactin activation its role in catalysis is unclear Our structure of full-length ClbP bound to a product analog reveals an interdomain interface important for substrate binding and enzyme stability and interactions that explain the selectivity of ClbP ... More
Colibactin, a DNA cross-linking agent produced by gut bacteria, is implicated in colorectal cancer. Its biosynthesis uses a prodrug resistance mechanism: a non-toxic precursor assembled in the cytoplasm is activated after export to the periplasm. This activation is mediated by ClbP, an inner-membrane peptidase with an N-terminal periplasmic catalytic domain and a C-terminal three-helix transmembrane domain. Although the transmembrane domain is required for colibactin activation, its role in catalysis is unclear. Our structure of full-length ClbP bound to a product analog reveals an interdomain interface important for substrate binding and enzyme stability and interactions that explain the selectivity of ClbP for the N-acyl-d-asparagine prodrug motif. Based on structural and biochemical evidence, we propose that ClbP dimerizes to form an extended substrate-binding site that can accommodate a pseudodimeric precolibactin with its two terminal prodrug motifs in the two ClbP active sites, thus enabling the coordinated activation of both electrophilic warheads. Less
The human gut bacterial genotoxin colibactin is a possible key driver of colorectal cancer CRC development Understanding colibactin s biological effects remains difficult owing to the instability of the proposed active species and the complexity of the gut microbiota Here we report small molecule boronic acid inhibitors of colibactin biosynthesis Designed to mimic the biosynthetic precursor precolibactin these compounds potently inhibit the colibactin-activating peptidase ClbP Using biochemical assays and crystallography we show that they engage the ClbP binding pocket forming a covalent bond with the catalytic serine These inhibitors reproduce the phenotypes observed in a clbP deletion mutant and block ... More
The human gut bacterial genotoxin colibactin is a possible key driver of colorectal cancer (CRC) development. Understanding colibactin’s biological effects remains difficult owing to the instability of the proposed active species and the complexity of the gut microbiota. Here, we report small molecule boronic acid inhibitors of colibactin biosynthesis. Designed to mimic the biosynthetic precursor precolibactin, these compounds potently inhibit the colibactin-activating peptidase ClbP. Using biochemical assays and crystallography, we show that they engage the ClbP binding pocket, forming a covalent bond with the catalytic serine. These inhibitors reproduce the phenotypes observed in a clbP deletion mutant and block the genotoxic effects of colibactin on eukaryotic cells. The availability of ClbP inhibitors will allow precise, temporal control over colibactin production, enabling further study of its contributions to CRC. Finally, application of our inhibitors to related peptidase-encoding pathways highlights the power of chemical tools to probe natural product biosynthesis. Less