Biology subjects

Poudel, S.

Publications and source records attributed to Poudel, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Polyglutamine-expanded TBP rewires neuronal and muscle proteomes beyond transcription in a Drosophila model of SCA17

Spinocerebellar ataxia type 17 (SCA17) is an age-related neurodegenerative disorder caused by polyglutamine expansion in the TATA-binding protein (TBP). TBP is a core transcription factor, but pathogenic polyglutamine expansion likely rewires cellular programs beyond transcription. Here, we utilized Drosophila strains that express wild-type (WT) or pathogenic (SCA17) TBP in neurons or skeletal muscle, which we analyzed vs. controls via TMT mass spectrometry, profiling of eight post-translational modifications, and RNA-seq. Shared TBP-WT and TBP-SCA17 responses predominated, impacting ribosomes and mitochondria while repressing innate immunity. Disease-specific effects were narrower and tissue-dependent: SCA17 activated xenobiotic, retinoid, and glutathione-redox pathways in the CNS, but attenuated anabolism in muscle compared to TBP-WT. Many proteomic changes occurred independently of mRNA changes, implicating post-transcriptional mechanisms. Knockdown of select SCA17-regulated proteins reduced cytotoxicity, validating omics-identified modifiers of SCA17 pathology. These findings distinguish shared TBP dosage effects from disease-linked, tissue-specific polyglutamine responses and identify evolutionarily conserved targets for SCA17.

neuroscience↗

bioRxiv2026

MakeMyFigure: An Interactive Platform for Reproducible Quantitative Data Visualization, Analysis, and Scientific Figure Construction

Reproducible data analysis and visualization are essential for reliable biological and biomedical research, yet creating high-quality, publication-ready figures often requires moving data and results between multiple analysis, visualization, and graphics tools. This fragmented, multi-layered process can make it difficult to trace how individual figure panels were generated, preserve the underlying analytical decisions, and reproduce them later. Here, we introduce MakeMyFigure, a free and open-source platform for data visualization, analysis, and creation of multi-panel scientific figures. MakeMyFigure integrates data processing, statistical analysis, visualization, and figure assembly within a single workflow. It supports a range of quantitative data formats and structures, including feature-by-sample matrices and precomputed statistical results, and provides data-aware visualization recommendations to help users select appropriate plots from a library of 38 visualization types. These capabilities allow researchers to move directly from experimental measurements to commonly used statistical analyses and graphical representations without requiring programming expertise. Eighteen statistical procedures are implemented, and their results are drawn directly onto the plot families that support statistical annotation, keeping analytical results linked to the panels they generate. Importantly, MakeMyFigure uses machine-readable JSON specifications to record the identity and checksum of the source data, the processing steps, visualization settings, and statistical parameters used to generate each figure panel. It can also save a figure as a portable package, freezing the specifications together with the data. This allows figures to be regenerated from their recorded specifications and source data, or from the package alone on another computer, rather than relying on manually reconstructed workflows. Using published datasets from several biological fields, independent statistical validation in R, and a comparison with 15 representative analysis, visualization, and figure-generation tools, we show that MakeMyFigure combines accessible, code-free figure creation with panel-level computational reproducibility. Overall, MakeMyFigure provides a unified approach for creating, documenting, and reproducing scientific figures. Source code and documentation are available at https://github.com/surPoudel/make-my-figure, https://github.com/surPoudel/make-my-figure/releases/tag/v1.1.0.

bioinformatics↗

bioRxiv2026

High-resolution CRISPR/Cas9 screens identify PAK2 as a suppressor of macrophage proliferation

Macrophage abundance is regulated by pathways controlling survival and proliferation, yet the genetic determinants of macrophage fitness remain poorly understood. Here, we performed replicate genome-wide CRISPR/Cas9 screens in primary murine bone marrow-derived macrophages (BMDMs) to identify positive and negative regulators of macrophage fitness. Validity of the screens is supported by finding previously characterized core essential genes such as those encoding translation machinery, while disruption of established tumor suppressors increased BMDM representation in the culture. As expected, Csf1r encoding the macrophage growth factor emerged as a positive regulator of macrophage fitness. Unexpectedly, Pak2, encoding p21-activated kinase 2 (PAK2), emerged as a negative regulator of macrophage fitness. Targeted Pak2 disruption increased BMDM accumulation and was associated with elevated cyclin-D1 expression, identifying PAK2 as a suppressor of macrophage proliferation. PAK2 also localized to CSF1-induced actin-rich membrane ruffles, yet its depletion did not impair ruffle formation. Instead, PAK2-depleted macrophages exhibited persistent F-actin-rich ruffles, larger macropinosomes, and increased fluid-phase uptake. These changes were accompanied by altered LIMK/cofilin signaling and persistent cofilin localization at macropinocytic structures. Phosphoproteomic analysis further identified reduced phosphorylation of proteins associated with cytoskeletal regulation, phosphoinositide signaling, and endosomal trafficking. Together, these findings identify PAK2 as a context-dependent regulator that restrains macrophage proliferation and membrane-remodeling activity and demonstrate that PAK2 has markedly different fitness functions in primary macrophages than previously identified in several transformed cell types.

cell biology↗

bioRxiv2026

PI(3)P Signaling by VPS34 Complex II Orchestrates Macropinocytosis

Macrophage macropinocytosis contributes to wound healing, antigen presentation, and resolution of inflammation. Macropinocytosis also facilitates nutrient uptake and growth in macrophages, T cells, and cancer cells. Here, CRISPR/Cas9 whole-genome screens in murine bone-marrow derived macrophages (BMDM) identified genes regulating unstimulated, PMA-, and CSF1-stimulated uptake of the fluorescent pinocytosis solute tracer, Lucifer yellow. UVRAG and other members of VPS34 complex II (VPS34-II), which catalyze PI(3)P formation from phosphatidylinositol, were identified as positive regulators of macropinocytosis. Targeted gene disruption of Uvrag and Pik3r3 revealed that VPS34-II is required for efficient macropinocytosis with Uvrag-disrupted BMDM having fewer but larger macropinosomes. In contrast, depletion of ATG14, a unique component of VPS34 complex I, increased solute uptake and the number of macropinosomes. Live-cell imagining of macrophages expressing 2xFYVE-fluorescent protein fusions showed PI(3)P present on the plasma membrane, nascent macropinosomes, and endosomes. The presence of PI(3)P on the plasma membrane prior to macropinocytic cup closure, indicates a novel role on the plasma membrane. Quantitative imaging of fixed cells shows a decrease in concentration of PI(3)P in Uvrag-disrupted BMDMs while increase in concentration of PI(3)P in Atg14-disrupted BMDM compared to WT BMDMs. Treatment with the VPS34 inhibitor SAR-405 acutely decreased macropinocytosis but maintained AKT phosphorylation suggesting class I PI3K activity and PI(3,4,5)P3 production are independent of class III PI3K activity. These results suggest that PI(3)P is a key phosphoinositide governing macropinocytosis at the plasma membrane and that it is primarily formed via direct phosphorylation of PI rather than via the sequential dephosphorylation of PIP3.

cell biology↗

bioRxiv2026

A Single-Cell Framework for Classifying Human Th17 Pathogenicity Links Acylcarnitine Metabolism to Non-Pathogenic Inflammation in Type 2 Diabetes

Based on in vitro and animal studies, Th17 cells are classified as pathogenic (pTh17) or non-pathogenic (nTh17), but the inability to identify these subsets in primary human samples limits translation. We developed a single-cell ELISA to enrich human Th17s, enabling transcriptomic and flow-cytometric classification. nTh17 cells predominated in Type 2 diabetes and exhibited signatures of acylcarnitine synthesis, while knockdown of CPT1A demonstrated that acylcarnitine metabolism regulates Th17 pathogenicity.

immunology↗

bioRxiv2025

Suppression of non-canonical autophagy induces endothelial and cardiac dysfunction

BackgroundWhile roles for canonical autophagy in the pathophysiology of cardiovascular disease have been established, we have limited understanding of the non-canonical functions of autophagy proteins in this context. LC3-asssociated endocytosis (LANDO) is a novel non-canonical function of autophagy proteins, in which LC3 (microtubule-associated protein light chain 3) is conjugated to early endosome membranes using a portion of the canonical autophagy machinery, and functions in the endocytic recycling of several plasma membrane proteins. Here we ask whether perturbation of LANDO can promote cardiovascular pathogenesis. MethodsCardiac and endothelial functions were assessed by echocardiography and flow-mediated dilatation in mice lacking Rubicon (Rubcn-/-) or the WD domain of ATG16L1 (Atg16l1{Delta}WDki), two known effectors of LANDO. Mice with conditional depletion of Rubicon in the endothelial, myeloid and cardiomyocyte compartments were used as well. Three-dimensional murine cardiac vasculature leakiness was investigated by light sheet fluorescence microcopy. Endothelial activation induced by shear stress was characterized in vitro in primary endothelial cells isolated from murine lungs and human aortic endothelial cells. Associations between genetically predicted expression of candidate genes involved in LANDO and human cardiovascular parameters were studied in the Young Finns Study and the UK Biobank. ResultsCompared to littermate controls, young Rubcn-/- and Atg16l1{Delta}WDki mice showed a decrease in cardiac and endothelial functions, as did mice with endothelium-specific deficiency. VEGFR2 recycling to the plasma membrane and nitric oxide pathway during shear stress were disrupted in LANDO-deficient primary murine and human endothelial cells. Proteomic analysis in primary human aortic endothelial cells revealed an upregulation of intracellular hemoglobin subunit alpha (Hb-) upon shear stress, which was blunted when RUBCN was ablated. Genetic expression studies uncovered several candidate genes related to LANDO that correlated with cardiovascular parameters. These included the retromer complex subunit VPS29, disruption of which decreased Hb- expression levels in human endothelial cells. ConclusionsOur data support a pivotal role of non-canonical functions of autophagy proteins in recycling VEGFR2 upon shear stress activation in endothelial cells together with Hb- expression that may contribute to the etiology of cardiovascular diseases.

physiology↗

bioRxiv2025

Nitric Oxide-Releasing Thixotropic Hydrogels as Antibacterial and Hemocompatible Catheter Locks

Catheters are indispensable medical tools for accessing blood vessels, hollow organs, and body cavities to facilitate medication delivery and fluid drainage. However, they also serve as major entry points for bacterial contamination and trigger foreign body responses, necessitating locking strategies that are both bactericidal and biocompatible. This study introduces the first gel-based catheter lock, in contrast to conventional liquid locks. The gel is a poloxamer-based hydrogel formulated with 2-hydroxypropyl -cyclodextrin (HP-CD). HP-CD forms supramolecular complexes with the poloxamer to enhance gelation, and with the nitric oxide (NO) donor to modulate NO release kinetics. This thixotropic gel can be injected into the catheter lumen when the catheter is not in use and withdrawn when vascular access is needed. The gel matrix provides a physical barrier that slows bacterial migration and minimizes drug loss. Simultaneously, the released NO functions as a broad-spectrum antimicrobial agent, effectively preventing biofilm formation on both the internal and external surfaces of the catheter. The NO-releasing hydrogel also demonstrates excellent hemocompatibility and reduces clot adhesion. Together, the gel-based lock offers a promising strategy for more effective catheter maintenance and represents a new application of hydrogels.

bioengineering↗

bioRxiv2025

Harnessing the immune system to treat bone loss: The immunomodulatory and osteoprotective effects of the microalga Skeletonema costatum

The emerging field of osteoimmunology provides compelling evidence for the pivotal role of the immune system in the development of bone erosive pathologies such as osteoporosis. However, no immunomodulatory drug has yet been integrated into the therapeutic management of bone loss. Recently, driven by the demand for next-generation treatments for these conditions, natural compounds are gaining renewed attention as promising candidates for drug discovery. In this study, we explored the anti-osteoclastogenic effects of an emerging extract from the marine microalga Skeletonema costatum. Using a zebrafish model of bone regeneration, we demonstrated the extracts ability to inhibit the recruitment of osteoclast progenitors and block their differentiation into mature osteoclasts in vivo. Bulk RNA sequencing of early-stage fin blastemas revealed the downregulation of genes involved in inflammation, T-cell activation, and antigen presentation, suggesting that the extract exerts its effects primarily through immunomodulatory mechanisms. To further assess its therapeutic potential, we tested the extract in a medaka model of RANKL-induced osteoporosis and on a murine macrophage cell line. The extract effectively prevented bone loss in fish and inhibited osteoclastic differentiation in murine macrophages in vitro. Collectively, our findings provide mechanistic insights into a novel, therapeutically relevant natural extract, offering proof of concept for its osteoprotective potential through immune system modulation. SignificanceRecent findings in the field of osteoimmunology reveal the potential of targeting immune cells to regulate bone homeostasis. However, this approach has yet to be applied to therapies for bone erosive conditions. This study explores the potential of an immunomodulatory strategy using an emerging natural extract, which prevent osteoclast differentiation by modulating inflammation, T-cell activation, and macrophage fate determination in zebrafish and medaka models of bone regeneration and osteoporosis. The extract also inhibits osteoclastic differentiation in a murine macrophage line, suggesting its translatability to mammalian systems. By focusing on immune pathways, this research provides a proof of concept for developing immunomodulatory treatments for osteoporosis and similar conditions, addressing a critical need in bone health management.

immunology↗

bioRxiv2024

Human-mouse proteomics reveals the shared pathways in Alzheimer's disease and delayed protein turnover in the amyloidome

Murine models of Alzheimers disease (AD) are crucial for elucidating disease mechanisms but have limitations in fully representing AD molecular complexities. We comprehensively profiled age-dependent brain proteome and phosphoproteome (n > 10,000 for both) across multiple mouse models of amyloidosis. We identified shared pathways by integrating with human metadata, and prioritized novel components by multi-omics analysis. Collectively, two commonly used models (5xFAD and APP-KI) replicate 30% of the human protein alterations; additional genetic incorporation of tau and splicing pathologies increases this similarity to 42%. We dissected the proteome-transcriptome inconsistency in AD and 5xFAD mouse brains, revealing that inconsistent proteins are enriched within amyloid plaque microenvironment (amyloidome). Determining the 5xFAD proteome turnover demonstrates that amyloid formation delays the degradation of amyloidome components, including A{beta}-binding proteins and autophagy/lysosomal proteins. Our proteomic strategy defines shared AD pathways, identify potential new targets, and underscores that protein turnover contributes to proteome-transcriptome discrepancies during AD progression.

biochemistry↗

bioRxiv2024

Rapid metabolic regulation of a novel arginine methylation of KCa3.1 attenuates T cell exhaustion.

T cell receptor (TCR) engagement initiates the activation process, and this signaling event is regulated in multifaceted ways. Nutrient availability in the immediate niche is one such mode of regulation1-3. Here, we investigated how the availability of an essential amino acid methionine (Met) and TCR signaling might interplay in the earliest events of T cell activation to affect subsequent T cell fate and function. We found that limiting Met during only the initial 30 minutes of CD8+ T cell activation increased Ca2+ influx, Ca2+-mediated NFAT1 (Nfatc2) activation, NFAT1 promoter occupancy, and T cell exhaustion. We identified changes in the protein arginine methylome during the initial 30 min of TCR engagement and discovered a novel arginine methylation of a Ca2+-activated potassium transporter, KCa3.1, which regulates Ca2+-mediated NFAT1 signaling to ensure optimal activation. Ablation of arginine methylation in KCa3.1 led to increased NFAT1 activation, rendering T cells dysfunctional in murine tumour and infection models. Furthermore, acute Met supplementation at early stages reduced nuclear NFAT1 in tumour-infiltrating T cells and augmented their anti-tumour activity. Our findings identify a metabolic event occurring early after T cell activation that influences the subsequent fate of the cell.

immunology↗

bioRxiv2024

Nor-LAAM loaded PLGA Microparticles for Treating Opioid Use Disorder

The treatment landscape for opioid use disorder (OUD) faces challenges stemming from the limited efficacy of existing medications, poor adherence to prescribed regimens, and a heightened risk of fatal overdose post-treatment cessation. Therefore, there is a pressing need for innovative therapeutic strategies that enhance the effectiveness of interventions and the overall well-being of individuals with OUD. This study explored the therapeutic potential of nor-Levo--acetylmethadol (nor-LAAM) to treat OUD. We developed sustained release nor-LAAM-loaded poly (lactic-co-glycolic acid) (PLGA) microparticles (MP) using a hydrophobic ion pairing (HIP) approach. The nor-LAAM-MP prepared using HIP with pamoic acid had high drug loading and exhibited minimal initial burst release and sustained release. The nor-LAAM-MP was further optimized for desirable particle size, drug loading, and release kinetics. The lead nor-LAAM-MP (F4) had a relatively high drug loading (11 wt.%) and an average diameter (19 {micro}m) and maintained a sustained drug release for 4 weeks. A single subcutaneous injection of nor-LAAM-MP (F4) provided detectable nor-LAAM levels in rabbit plasma for at least 15 days. We further evaluated the therapeutic efficacy of nor-LAAM-MP (F4) in a well-established fentanyl-addiction rat model, and revealed a marked reduction in fentanyl choice and withdrawal symptoms in fentanyl-dependent rats. These findings provide insights into further developing long-acting nor-LAAM-MP for treating OUD. It has the potential to offer a new effective medication to the existing sparse armamentarium of products available to treat OUD.

bioengineering↗

bioRxiv2024

Human brain aging heterogeneity observed from multi-region omics data reveals a subtype closely related to Alzheimer's disease

INTRODUCTION: The interconnection between brain aging and Alzheimers disease (AD) remain to be elucidated. METHODS: We investigated multi-omics (transcriptomics and proteomics) data from multiple brain regions (i.e., the hippocampus (HIPP), prefrontal cortex (PFC), and cerebellum (CRBL)) in cognitively normal individuals. RESULTS: We found that brain samples could be divided into ADL (AD-like) and NL (normal) subtypes which were correlated across brain regions. The differentially expressed genes in the ADL samples highly overlapped with AD gene signatures and the changes were consistent across brain regions (PFC and HIPP) in the multi-omics data. Intriguingly, the ADL subtype in PFC showed more differentially expressed genes than other brain regions, which could be explained by the baseline gene expression differences in the PFC NL samples. DISCUSSION: We conclude that brain aging heterogeneity widely exists, and our findings corroborate with the hypothesis that AD-related changes occur decades before the clinical manifestation of cognitive impairment in a sub-population.

neuroscience↗

bioRxiv2024

Negative Synergistic Effects of Drought and Heat During Flowering and Seed Setting in Soybean

Rising temperatures and intense heatwaves combined with lower precipitations are the new norms of current global scenarios. These altered climatic conditions negatively impact soybean yield potential and quality. Ten soybean cultivars were subjected to four different growing conditions: control, drought, heat, and combined heat and drought to understand the physiological, yield, and molecular changes. Stomatal conductance was reduced by 62% and 10% under drought and heat, respectively. This reduction was further exacerbated to 93% when exposed to both stresses simultaneously. The highest canopy temperature was recorded at +8 {degrees}C with combinatorial treatments, whereas heat and drought exhibited +5.4 {degrees}C and +2 {degrees}C, respectively. Furthermore, combined stress displayed a more pronounced negative impact on greenness-associated vegetative index; the gene expression analysis further corroborated these findings. Particularly, each {degrees}C increase in temperature during flowering-seed filling reduced seed weight by [~]7% and [~]4% with and without drought, respectively. The seed protein increased under drought, whereas the oil showed a converse trend under drought and combined stresses. Most physiology and yield traits showed no significant correlations between control or individual and combined stress. This suggests that selection for combinatorial stress may not be appropriate based on nonstress or individual stress performance. Thus, incorporating stress-resilient traits into elite soybean cultivars could significantly boost soybean production under hot and dry climatic conditions.

plant biology↗

bioRxiv2023

Interpreting roles of mutations associated with the emergence of S. aureus USA300 strains using transcriptional regulatory network reconstruction

The Staphylococcus aureus clonal complex 8 (CC8) is made up of several subtypes with varying levels of clinical burden; from community-associated methicillin resistant S. aureus (CA-MRSA) USA300 strains to hospital-associated (HA-MRSA) USA500 strains and ancestral methicillin susceptible (MSSA) strains. This phenotypic distribution within a single clonal complex makes CC8 an ideal clade to study the emergence of mutations important for antibiotic resistance and community spread. Gene level analysis comparing USA300 against MSSA and HA-MRSA strains have revealed key horizontally acquired genes important for its rapid spread in the community. However, efforts to define the contributions of point mutations and indels have been confounded by strong linkage disequilibrium resulting from clonal propagation. To break down this confounding effect, we combined genetic association testing with a model of the transcriptional regulatory network (TRN) to find candidate mutations that may have led to changes in gene regulation. First, we used a De Bruijn graph genome-wide association study (DBGWAS) to enrich mutations unique to the USA300 lineages within CC8. Next, we reconstructed the TRN by using Independent Component Analysis on 670 RNA sequencing samples from USA300 and non-USA300 CC8 strains which predicted several genes with strain-specific altered expression patterns. Examination of the regulatory region of one of the genes enriched by both approaches, isdH, revealed a 38 base pair deletion containing a Fur binding site and a conserved Single Nucleotide Polymorphism (SNP) which likely led to the altered expression levels in USA300 strains. Taken together, our results demonstrate the utility of reconstructed TRNs to address the limits of genetic approaches when studying emerging pathogenic strains.

systems biology↗

bioRxiv2023

Printing double network tough hydrogels using Temperature-Controlled Projection Stereolithography (TOPS)

We report a new method to shape double-network (DN) hydrogels into customized microscale 3D structures that exhibit superior mechanical properties in both tension and compression. A one-pot prepolymer formulation containing photo-cross-linkable acrylamide and thermo-reversible sol-gel {kappa}-carrageenan with a suitable crosslinker, and photo-initiator/absorbers are optimized. A new TOPS system is utilized to photo-polymerize the primary acrylamide network into a 3D structure above the sol-gel transition of {kappa}-carrageenan (80{degrees}C), while cooling down generates the secondary physical {kappa}-carrageenan network to realize tough DN hydrogel structures. 3D structures, printed with high lateral (37m) and vertical (180m) resolutions and superior 3D design freedoms (internal voids), exhibit ultimate stress and strain of 200 kPa and 2400% respectively under tension, and simultaneously exhibit high compression stress of 15 MPa with a strain of 95%, both with high recovery rates. The roles of swelling, necking, self-healing, cyclic loading, dehydration, and rehydration on the mechanical properties of printed structures are also investigated. To demonstrate the potential of this technology to make mechanically reconfigurable flexible devices, we print an axicon lens and show that a Bessel beam can be dynamically tuned via user-defined tensile stretching of the device. This technique can be broadly applied to other hydrogels to make novel smart multifunctional devices for a range of applications.

bioengineering↗

bioRxiv2022

Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins

Streptococcus pyogenes can cause a wide variety of acute infections throughout the body of its human host. The underlying transcriptional regulatory network (TRN) is responsible for altering the physiological state of the bacterium to adapt to each host environment. Consequently, an in-depth understanding the comprehensive dynamics of its TRN could inform new therapeutic strategies. Here, we compiled 116 existing high-quality RNA-seq data sets of S. pyogenes serotype M1, and estimated the TRN structure in a top-down fashion by performing independent component analysis (ICA). The algorithm computed 42 independently modulated sets of genes (iModulons). Four iModulons contained nga-ifs-slo virulence-related operon, which allowed us to identify carbon sources that control its expression. In particular, dextrin utilization upregulated nga-ifs-slo operon by activation of two-component regulatory system CovRS-related iModulons, and changed bacterial hemolytic activity compared to glucose or maltose utilization. Finally, we show that the iModulon-based TRN structure can be used to simplify interpretation of noisy bacterial transcriptome at the infection site.

microbiology↗

bioRxiv2022

Coordination of CcpA and CodY regulators in Staphylococcus aureus USA300 strains

The complex crosstalk between metabolism and gene regulatory networks makes it difficult to untangle individual constituents and study their precise roles and interactions. To address this issue, we modularized the transcriptional regulatory network (TRN) of the Staphylococcus aureus USA300 strain by applying Independent Component Analysis (ICA) to 385 RNA sequencing samples. We then combined the modular TRN model with a metabolic model to study the regulation of carbon and amino acid metabolism. Our analysis showed that regulation of central carbon metabolism by CcpA and amino acid biosynthesis by CodY are closely coordinated. In general, S. aureus increases the expression of CodY-regulated genes in the presence of preferred carbons sources such as glucose. This transcriptional coordination was corroborated by metabolic model simulations that also showed increased amino acid biosynthesis in the presence of glucose. Further, we found that CodY and CcpA cooperatively regulate the expression of ribosome hibernation promoting factor, thus linking metabolic cues with translation. In line with this hypothesis, expression of CodY-regulated genes is tightly correlated with expression of genes encoding ribosomal proteins. Together, we propose a coarse-grained model where expression of S. aureus genes encoding enzymes that control carbon flux and nitrogen flux through the system is coregulated with expression of translation machinery to modularly control protein synthesis. While this work focuses on three key regulators, the full TRN model we present contains 76 total independently modulated sets of genes, each with the potential to uncover other complex regulatory structures and interactions. ImportanceStaphylococcus aureus is a versatile pathogen with an expanding antibiotic resistance profile. The biology underlying its clinical success emerges from an interplay of many systems such as metabolism and gene regulatory networks. This work brings together models for these two systems to establish fundamental principles governing the regulation of S. aureus central metabolism and protein synthesis. Studies of these fundamental biological principles are often confined to model organisms such as Escherichia coli. However, expanding these models to pathogens can provide a framework from which complex and clinically important phenotypes such as virulence and antibiotic resistance can be better understood. Additionally, the expanded gene regulatory network model presented herein can deconvolute the biology underlying other important phenotypes in this pathogen.

microbiology↗

bioRxiv2022

Design of a Minimal di-Nickel Hydrogenase Peptide

The most ancient processes for energy production in the evolution of life involve the reversible oxidation of molecular hydrogen by hydrogenase. Extant hydrogenase enzymes are complex, comprising hundreds of amino acids and multiple cofactors. We designed a 13 amino acid nickel-binding peptide capable of robustly producing molecular hydrogen from protons under a wide variety of conditions. The peptide forms a di-nickel cluster structurally analogous to a Ni-Fe cluster in [NiFe]-hydrogenase and the Ni-Ni cluster in acetyl-CoA synthase (ACS), two ancient, extant proteins central to metabolism. These experimental results clearly demonstrate that modern enzymes, despite their enormous complexity, likely evolved from simple peptide precursors on early Earth. One Sentence SummarySmall metal-binding peptides were the likely precursors of modern enzymes.

biochemistry↗