Biology subjects

Li, T.

Publications and source records attributed to Li, T..

At least 199 records · Page 11Linked to original sources

bioRxiv2025

Molecular Basis of PAC1R Allosteric Modulation with Lipids in Membranes

The pituitary adenylate cyclase-activating polypeptide receptor I (PAC1R) represents a highly sought-after therapeutic target for chronic pain, migraine, and post-traumatic stress. As a class B G protein-coupled receptor (GPCR), the PAC1R is highly expressed throughout the neuronal and central nervous system membranes, with the receptor subject to hormone activation and subsequent signal transduction. Despite its desirable indication, small molecule agonists for PAC1R have been notoriously difficult to develop due to competition with PACAP. For this reason, allosteric activation of the receptor has emerged as a promising pathway. To probe potential allosteric sites, herein, we present a study of the receptor in biomimetic concentrations of lipid membranes. Our results reveal that cholesterol recognizes two canonical and two non-canonical binding sites at PAC1R, which may influence critical residues in the transmembrane domain and PAC1R activation. Also, our simulations suggest the glycolipid GM3 interacts with PAC1R in both the extracellular and transmembrane domains. These lipid binding hotspots may hold high potential for advancing our understanding of class B GPCR signaling and the discovery of new molecules targeting PAC1R. Statement of SignificanceThe PAC1R is a highly sought after therapeutic target in the GPCR family. Understanding its natural process signaling is highly interesting in identifying new modes of control and is currently not well established. This work uses coarse-grained molecular dynamics simulations to examine diverse PAC1R models interactions with their endogenous lipid bilayer in compositions that match the regions in the brain where the receptor is expressed. Two lipids, cholesterol and GM3, have been previously identified in similar receptors as allosteric modulators and were specifically examined in this study. This work also showcases multiple new lipid binding sites at transmembrane and extracellular sites highly implicated in PAC1R signaling.

biophysics↗

bioRxiv2025

Functional impact of rare variants and sex across the X-chromosome and autosomes

The human X-chromosome contains hundreds of genes and has well-established impacts on sex differences and traits. However, the X-chromosome is often excluded from many genetic analyses, limiting broader understanding of variant effects. In particular, the functional impact of rare variants on the X-chromosome is understudied. To investigate functional rare variants on the X-chromosome, we use observations of outlier gene expression from GTEx consortium data. We show outlier genes are enriched for having nearby rare variants on the X-chromosome, and this enrichment is stronger for males. Using the RIVER model, we identified 753 rare variants in 449 genes predicted to have functional differences between males and females. We examined the pharmacogenetic implications of these variants and observed that 25% of drugs with a known sex difference in adverse drug reactions were connected to genes that contained a sex-biased rare variant. We further identify that sex-biased rare variants preferentially impact transcription factors with predicted sex-differential binding, such as the XIST-modulated SIX1. Combined, our study investigates functional rare variants on the X-chromosome, and further details how sex-stratification of variant effect prediction improves identification of rare variants with predicted sex-biased effects, transcription factor biology, and pharmacogenomic impacts.

genomics↗

bioRxiv2025

Inhibition of Glutamine Metabolism Suppresses Tumor Progression through Remodeling of the Macrophage Immune Microenvironment

BackgroundTargeting glutamine metabolism has emerged as a promising strategy in cancer therapy. However, several barriers, such as in vivo anti-tumor efficacy, drug toxicity, and safety, remain to be overcome to achieve clinical utility. Prior preclinical in vivo studies had generated encouraging data showing promises of cancer metabolism targeting drugs, although most were performed on immune-deficient murine models. It is being recognized that aside from tumor cells, normal cells such as immune cells in the tumor microenvironment may also utilize glutamine for maintaining physiological functions. To provide an in-depth view of glutamine antagonist (GLNi) treatment on the tumor immune microenvironment, the current study made several unique approaches. MethodFirst, to evaluate GLNi treatment modality that potentially involves immune cells, the study was performed on immunocompetent murine models of gynecological cancers. Second, to enhance safety and reduce potential off-target effects, we developed a GLNi prodrug, JHU083, which is bio-activated restrictively in cancer tissues. Third, to unbiasedly decode the response of single cells in the tumor microenvironment to GLNi treatment, single-cell RNA sequencing (scRNA-seq) was performed on cells prepared from tumors of the JHU083 or vehicle control-treated mice. ResultsIn both immunocompetent murine tumor models, we observed a significant anti-tumor efficacy, resulting in reduced tumor burden and impeded tumor progression. Similarly, in both tumor models, scRNA-seq revealed significantly impeded immunosuppressive M2-like macrophages by JHU083, while the treatment spared pro-inflammatory M1-like tumor macrophages. In many tumor microenvironment (TME) cells, JHU083 downregulated genes regulated by Myc and hypoxia. M2 macrophages greater sensitivity to glutamine antagonism when compared to M1 macrophages or monocytes was further validated on ex vivo cultures of bone marrow-derived macrophages. ConclusionOur findings support a converged mechanism of glutamine metabolism antagonists. JHU083 exerted its anti-tumor efficacy through not only direct targeting of glutamine-addicted cancer cells but also by suppressing glutamine-dependent M2 macrophages, leading to a shift in the M1/M2 macrophage landscape in favor of an immune-stimulatory microenvironment.

cancer biology↗

bioRxiv2025

A Novel XACT lncRNA Transcript with Functions Transcending X-Chromosome Inactivation.

X-chromosome inactivation (XCI) is initiated during early mammalian embryogenesis by a long non-coding RNA (lncRNA) XIST, which coats one of the two X-chromosomes and facilitates epigenetic transcriptional silencing. A second, evolutionarily recent primate-specific lncRNA XACT was proposed to antagonize XISTs ability to induce XCI. XACT expression is restricted to pluripotent states and early embryonic stages and coats the active X-chromosome in both females and males. Here, we report a novel XACT transcript expressed in normal and cancerous somatic cells from both the inactive (Xi) and active (Xa) X chromosomes. It coexists with XIST on the Xi without affecting XIST expression or (re)activating X-linked genes inactivated by XCI. During hematopoietic stem cell (HSC) differentiation, XACT is primarily expressed in myeloid progenitors in both sexes. XACT expression is activated in HSCs and peaks in megakaryocyte-erythrocyte progenitor cells (MEPs) before rapidly declining as the MEPs differentiate into megakaryocytes or erythrocytes. By combining CRISPR-based XACT perturbation with epigenomic and transcriptional studies, we revealed the key role of XACT in the self-renewal and differentiation of erythroid progenitors into erythrocytes, by recruiting cis-regulatory proteins and regulating transcription through ETS and AP-1 transcription factors. Furthermore, XACT is expressed in a subset of acute myeloid leukemia (AML) patients, with high levels found in erythroid-megakaryocytic blast cells; suggesting XACTs potential as a marker for AML subtypes. Thus, we identified a novel XACT transcript with a unique expression profile and important roles in normal and cancer cells, revealing XACT lncRNA functions beyond its previously proposed role in XCI during embryogenesis.

genetics↗

bioRxiv2024

Identification of SMARCA1 as a key regulator for Colorectal Cancer

Emerging evidence indicates that aberrations in the writing, reading, or erasure of chromatin modification codes are pivotal events in various human cancers. In this study, we conducted a systematic investigation of histone modification recognition proteins in a pair of colorectal cancer cell lines, SW480 and SW620. Using chromatin fractionation combined with data-independent acquisition mass spectrometry (DIA-MS), we developed a robust method to identify changes in histone modification recognition proteins during cancer progression. Our analysis revealed 22 proteins that were significantly upregulated and 22 proteins that were significantly downregulated in SW620 cells compared to SW480 cells. Notably, SMARCA1, a member of the ISWI family belonging to ATP-dependent chromatin remodeling complexes, was downregulated in SW620 cells compared to SW480 cells. Its high expression was strongly correlated with poor patient prognosis, aligning with the proposed role of SMARCA1 in promoting colorectal cancer (CRC) metastasis. Furthermore, reduced SMARCA1 expression altered the levels of metastasis-related matrix metalloproteinases (MMPs) in these cells. In conclusion, by systematically profiling histone modification recognition proteins in a matched pair of primary and metastatic CRC cell lines, we identified SMARCA1 as a potential driver of CRC metastasis and a promising therapeutic target for CRC patients.

cancer biology↗

bioRxiv2024

An endogenous cluster of target-directed microRNA degradation sites induces decay of distinct microRNA families

While much is known about miRNA biogenesis and canonical miRNA targeting, relatively less is understood about miRNA decay. The major miRNA decay pathway in metazoans is mediated through target-directed miRNA degradation (TDMD), in which certain RNAs can "trigger" miRNA decay. All known triggers for TDMD base pair with the miRNA seed, and extensively base pair on the miRNA 3' end, a pattern that supposedly induces a TDMD-competent conformational change of Argonaute (Ago), allowing for miRNA turnover. Here, we utilized Ago1-CLASH to find that the Drosophila transcript Kah contains at least two triggers, a "trigger cluster", against miR-9b and the miR-279 family. One of these triggers contains minimal/non-canonical 3' end base pairing but is still sufficient to induce TDMD of the entire miR-279 family. We found that these clustered triggers likely lack cooperativity, the minimal 3' pairing is required for miR-279 family turnover, and probed the in-cell RNA structure of the Kah trigger cluster. Overall, this study expands the list of endogenous triggers and the unexpectedly complex regulatory network governing miRNA degradation.

molecular biology↗

bioRxiv2024

A novel membrane stress-response that blocks chromosomal replication by targeting the DnaA initiator via the ClpP protease

In Escherichia coli, membrane-stress due to interrupted lipoprotein (Lpp) maturation impairs DNA replication and arrests cell growth. How the two disparate processes of Lpp maturation and DNA replication are connected remains unclear. We demonstrate that upon membrane-stress the Rcs stress-response pathway is activated and the replication initiator DnaA is lost, which explains the replication block. However, the Lon protease, a key regulator of the Rcs pathway, is not required for the DnaA loss. We further ruled out the involvement of (p)ppGpp, one of the major mediators of stress-response in bacteria. However, upon deletion of the ClpP protease gene, DnaA was stable, replication initiated, and there was no cell-growth arrest. In wildtype cells, overexpression of DnaA was lethal even without the membrane-stress apparently from hyper-initiation. The hyper-initiation was restrained in {Delta}crp cells, and overexpression of DnaA was able to overcome the growth-arrest. {Delta}fis cells, which were earlier found resistant to the membrane-stress, showed DnaA stability and normal replication upon induction of the membrane-stress. We conclude that DnaA loss suffices to explain the growth-arrest upon the membrane-stress. The stress-response pathway described here appears novel because of its independence from Lon and (p)ppGpp, which have been implicated in other stress-responses that block DNA replication. SignificanceThe seminal observation that DNA replication-stress can block cell division in E. coli (SOS response), introduced the concept of checkpoint control in the cell cycle. Here, we describe a novel checkpoint control that functions in the opposite direction: membrane-stress causing replication block. We show how two apparently unrelated outcomes of reducing a membrane phospholipid, accumulation of a precursor lipoprotein (pLpp) and block of replication initiation, could be linked. The pLpp accumulation stresses the membrane that causes a response culminating in activating the ClpP protease that blocks replication by targeting the initiator DnaA. DnaA being vital and highly conserved, the detail understanding of the response pathway is likely to open new avenues to treat bacterial infection.

microbiology↗

bioRxiv2024

NJGPT: A Large Language Model-Driven, User-Friendly Solution for Phylogenetic Tree Construction

MotivationPhylogenetic reconstruction plays an integral part in much of the research in evolutionary biology. Currently, a newly minted phylogeneticist must choose amongst a relatively large array of phylogenetic software, each often with its own analytical routines, inputs and outputs. Our overarching aim is to construct a user-friendly pipeline with the most recent generative AI tool, ChatGPT-4 (at the time of writing) released by OpenAI, that is able to understand queries written in natural language, to build a phylogenetic tree using sequence data. By doing this, we demonstrate how generative AI may be used in phylogenetics, as a proof-of-concept. We also demonstrate the steps needed, presently, to ensure that ChatGPT can build phylogenetic trees accurately. ResultsWe present NJGPT, a phylogenetic tool built using ChatGPT, a Large Language Model (LLM) Generative Pre-trained Transformer (GPT),which employs the Neighbor-Joining method to construct phylogenetic trees. NJGPT simplifies phylogenetic tree construction by allowing users to generate and visualize trees using natural language queries. It supports multiple sequence file formats, matrix calculation models, and gap-deletion methods. To evaluate the performance of NJGPT, we compared output and runtimes with the widely-used phylogenetic software, MEGA. Our results show that NJGPT produces identical trees over a range of sequence lengths and simple models of evolution. However, NJGPT faces visualization issues with datasets over 50 taxa and operational failures with larger datasets due to token limits. NJGPT runtimes were also substantially slower than MEGA; however, NJGPTs user-friendly interface makes it ideal for beginners. AvailabilityThis plugin is available for free at https://chatgpt.com/g/g-1OzP3Qviw-njgpt, the source code is available on GitHub (https://github.com/ZWan622/NJGPT1.0.git) and is implemented using Python Contactzwan622@aucklanduni.ac.nz Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2024

Sequence Composition Dictates Condensate Miscibility

Numerous biomolecular condensates coexist within cells, yet the mechanisms governing their mixing and demixing remain elusive. To investigate how the amino acid composition of intrinsically disordered regions (IDRs) affects condensate coexistence, we paired and tested 28 IDRs in 378 different combinations. Our results reveal that IDRs enriched in serine or aromatic amino acids tend to form miscible condensates. Conversely, IDRs with high charge levels form immiscible condensates, even when the serine levels are artificially boosted. Additionally, phosphorylation acts as a switch, modulating condensate miscibility. We also observed that the miscibility between transcription factor condensates and Pol II condensates profoundly influences transcription. We engineered transcription factors by increasing serine content, enhancing both their miscibility with Pol II and their transcriptional activity. However, introducing high levels of charge had the opposite effect. These findings shed light on the fundamental mechanisms controlling condensate miscibility and offer insights for designing specific functional condensates.

molecular biology↗

bioRxiv2024

Combining Glycosidases and Nanopore Technology for Glycan Sequencing

The efficient characterization of glycan structures remains a critical challenge. Direct glycan sequencing technologies with improved sensitivity and throughput are still needed. Here, we propose a glycan sequencing strategy based on glycosidase -assisted nanopore sensing. We used engineered nanopore -hemolysin (M113R/T115A), which provided high-resolution discrimination of monosaccharide volume differences and sensitivity to variations in glycan chain length. By utilizing the specificity of glycosidases, we sequentially hydrolyzed the terminal residues of the glycan chains and detected the characteristic shifts in electrical signals generated by the translocation of hydrolysis products. The accuracy of recognition of hydrolysis fragments achieved over 90 % using machine learning. This allowed us to efficiently and conveniently determine the sequence of consecutive monosaccharide units in the glycan chains. Based on this principle, we conducted a proof-of-concept demonstration on actual samples and verified the accuracy via HPLC-MS. We achieved the sequencing of consecutive units in glycan chains, confirming the theoretical feasibility of glycosidase -assisted nanopore glycan sequencing. With future optimization, the development of arrayed nanopore glycan sequencing technology based on hydrolysis strategy will provide an innovative approach for rapid decoding of glycans, which could promote the progress of glycomics research and glycobiology.

biochemistry↗

bioRxiv2024

Structure-Based Design of Covalent Nanobody Binders for a Thermostable Green Fluorescence Protein

Green fluorescence protein (GFP) lights up almost every aspects of life sciences. An ultra thermostable GFP (TGP), engineered from a coral GFP, offers potential advantages over traditional jellyfish-derived GFP due to its high stability. However, owing to its later discovery, TGP lacks the extensive toolsets available for GFP, such as heavy chain-only antibody binders known as nanobodies. In this study, we have structurally characterized TGP in complex with Sb92, a synthetic nanobody identified from a previous in vitro screening, revealing its precise three-dimensional epitope. This structural insight, alongside the previously characterized Sb44-TGP complex, have allowed us to rationally design disulfide bonds between antigen and antibody for tighter interactions. Using biochemical analyses, we identify two bridged complexes (TGP A18C-Sb44 V100C, TGP E118C-Sb92 S57C), with the TGP-Sb92 disulfide pair showing high resistance to reducing agents. Our study expands the toolkit available for TGP and should encourage its wider applications.

biochemistry↗

bioRxiv2024

Distinct Binding Modes of Inter-Spike Cross-Linking Suggest a Supplementary Mechanism for SARS-CoV-2 Antibody Neutralization

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its Omicron subvariants drastically amplifies transmissibility, infectivity, and immune escape, mainly due to their resistance to most neutralizing antibodies. Thus, exploring the mechanisms underlying antibody evasion is crucial. Although the full-length native form of antibody, immunoglobulin G (IgG), offers valuable insights into the neutralization, structural investigations primarily focus on the fragment of antigen-binding (Fab). Here, we employ single-particle cryo-electron microscopy (cryo-EM) to characterize a W328-6H2 antibody, in its native IgG form complexed with severe acute respiratory syndrome (SARS), severe acute respiratory syndrome coronavirus 2 wild-type (WT) and Omicron variant BA.1 spike protein (S). Three high-resolution structures reveal that the full-length IgG forms a centered head-to-head dimer of trimer when bound fully stoichiometrically with both SARS and WT S, while adopting a distinct offset configuration with Omicron BA.1 S. Combined with functional assays, our results suggest that, beyond the binding affinity between the RBD epitope and Fab, the higher-order architectures of S trimer and full-length IgG play an additional role in neutralization, elucidate a potential molecular basis of Omicron immune escape, and expand our understanding on antibody evasion mechanisms.

immunology↗

bioRxiv2024

A post-translational cysteine-to-serine conversion in human and mouse insulin generates a diabetogenic neoepitope

The evolving antigenic landscape of autoimmune diabetes reflects a dynamic failure to preserve self-tolerance. Yet, how novel neoantigens emerge in humans remains incompletely understood. Here, we designed an immunopeptidomics-based approach to probe HLA-II-bound, islet-derived neoepitopes in patients with type 1 diabetes (T1D). We uncovered a microenvironment-driven Cys[->]Ser transformation, conserved between mice and humans, that reshapes autoreactivity to insulin, the core {beta}-cell antigen, at the single-residue level. This transformation, which we call "C19S," arises from oxidative remodeling of insulin in stressed pancreatic islets and can also occur in inflammatory antigen-presenting cells, contributing to a feed-forward loop of neoepitope formation and presentation as diabetes progresses. Despite involving just one amino acid, C19S is specifically recognized by HLA-DQ8-restricted, register-specific CD4+ T cells that expand in individuals with T1D. These C19S-specific CD4+ T cells lack regulatory potential but acquire a poised central memory phenotype that persists at different disease stages. These findings reveal a distinct, microenvironment-driven route of neoantigen formation that fuels sustained autoreactivity in diabetes.

immunology↗

bioRxiv2024

Single-cell profiling of trabecular meshwork identifies mitochondrial dysfunction in a glaucoma model that is protected by vitamin B3 treatment

Since the trabecular meshwork (TM) is central to intraocular pressure (IOP) regulation and glaucoma, a deeper understanding of its genomic landscape is needed. We present a multimodal, single-cell resolution analysis of mouse limbal cells (includes TM). In total, we sequenced 9,394 wild-type TM cell transcriptomes. We discovered three TM cell subtypes with characteristic signature genes validated by immunofluorescence on tissue sections and whole-mounts. The subtypes are robust, being detected in datasets for two diverse mouse strains and in independent data from two institutions. Results show compartmentalized enrichment of critical pathways in specific TM cell subtypes. Distinctive signatures include increased expression of genes responsible for 1) extracellular matrix structure and metabolism (TM1 subtype), 2) secreted ligand signaling to support Schlemms canal cells (TM2), and 3) contractile and mitochondrial/metabolic activity (TM3). ATAC-sequencing data identified active transcription factors in TM cells, including LMX1B. Mutations in LMX1B cause high IOP and glaucoma. LMX1B is emerging as a key transcription factor for normal mitochondrial function and its expression is much higher in TM3 cells than other limbal cells. To understand the role of LMX1B in TM function and glaucoma, we single-cell sequenced limbal cells from Lmx1bV265D/+mutant mice (2,491 TM cells). In V265D/+ mice, TM3 cells were uniquely affected by pronounced mitochondrial pathway changes. Mitochondria in TM cells of V265D/+ mice are swollen with a reduced cristae area, further supporting a role for mitochondrial dysfunction in the initiation of IOP elevation in these mice. Importantly, treatment with vitamin B3 (nicotinamide), to enhance mitochondrial function and metabolic resilience, significantly protected Lmx1b mutant mice from IOP elevation.

molecular biology↗

bioRxiv2024

Spatiotemporal map of the developing human reproductive tract at single-cell resolution

The human reproductive tract plays an essential role in species perpetuation. Its development involves complex processes of sex specification, tissue patterning and morphogenesis, which, if disrupted, can cause lifelong health issues, including infertility. Here, we generated an extensive single-cell and spatial multi-omic atlas of the human reproductive tract during prenatal development, which allowed us to answer questions that smaller-scale, organ-focused experiments could not address before. We identified potential regulators of sexual dimorphism in reproductive organs, pinpointing novel genes involved in urethral canalisation of the penis, with relevance to hypospadias. By combining histological features with gene expression data, we defined the transcription factors and cell signalling events required for the regionalisation of the Mullerian and Wolffian ducts. This led to a refinement of how the HOX code is established in the distinct reproductive organs, including increased expression of thoracic HOX genes in the rostral mesenchyme of the fallopian tube and epididymis. Our study further revealed that the epithelial regionalisation of the fallopian tube and epididymis required for sperm maturation in adulthood is established early in development. In contrast, later events in gestation or postnatally are necessary for the regionalisation of the uterocervical canal epithelium. By mapping sex-specific reproductive tract regionalisation and differentiation at the cellular level, our study offers valuable insights into the causes and potential treatments of reproductive disorders.

developmental biology↗

bioRxiv2024

TaxonGPT: Taxonomic Classification Using Generative Artificial Intelligence

To address the challenges of consistency and quality in taxonomic classifications, we have developed a Python program called TaxonGPT, that utilizes the natural language processing capabilities of generative artificial intelligence (gAI, specifically, ChatGPT-4o) to generate taxonomic descriptions and taxonomic keys. To counter the propensity for large language model gAIs to "hallucinate", we use knowledge graph semantic representation and an error-checking module to ensure that accurate taxonomic descriptions and keys are obtained. In this paper, we describe how TaxonGPT embeds ChatGPT-4os responses as outputs. We also report on benchmark tests for accuracy, efficiency and reproducibility. These tests demonstrate that TaxonGPT excels in generating taxonomic keys and descriptions.

bioinformatics↗

bioRxiv2024

Aerobic capacity and exercise mediate protection against hepatic steatosis via enhanced bile acid metabolism.

High cardiorespiratory fitness and exercise show evidence of altering bile acid (BA) metabolism and are known to protect or treat diet-induced hepatic steatosis, respectively. Here, we tested the hypothesis that high intrinsic aerobic capacity and exercise both increase hepatic BA synthesis measured by the incorporation of 2H2O. We also leveraged mice with inducible liver-specific deletion of Cyp7a1 (LCyp7a1KO), which encodes the rate-limiting enzyme for BA synthesis, to test if exercise-induced BA synthesis is critical for exercise to reduce hepatic steatosis. The synthesis of hepatic BA, cholesterol, and de novo lipogenesis was measured in rats bred for either high (HCR) vs. low (LCR) aerobic capacity consuming acute and chronic high-fat diets. HCR rats had increased synthesis of cholesterol and certain BA species in the liver compared to LCR rats. We also found that chronic exercise with voluntary wheel running (VWR) (4 weeks) increased newly synthesized BAs of specific species in male C57BL/6J mice compared to sedentary mice. Loss of Cyp7a1 resulted in fewer new BAs and increased liver triglycerides compared to controls after a 10-week high-fat diet. Additionally, exercise via VWR for 4 weeks effectively reduced hepatic triglycerides in the high-fat diet-fed control male and female mice as expected; however, exercise in LCyp7a1KO mice did not lower liver triglycerides in either sex. These results show that aerobic capacity and exercise increase hepatic BA metabolism, which may be critical for combatting hepatic steatosis. HighlightsO_LIRats with intrinsic high aerobic capacity have more significant reductions in de novo lipogenesis and increased cholesterol and bile acid synthesis on a high-fat diet compared to rats with low aerobic capacity. C_LIO_LIChronic exercise increases hepatic bile acid synthesis in mice. C_LIO_LILoss of Cyp7a1 blunts the capacity for exercise to increase bile acid synthesis and treat hepatic steatosis in male and female mice fed a high-fat diet. C_LI

physiology↗

bioRxiv2024

Comparative genomic analysis reveals reduced pathogenicity of Ralstonia spp. in water

Ralstonia spp., known for their adaptability across various habitats, are known to cause infections. The adaptive metabolic diversity of those inhabiting aquatic ecosystems remains poorly understood. We report four new Ralstonia pickettii genomes enriched in the cyanobacterial culture derived from bloom-forming cyanobacteria, Dolichospermum. A total of 228 complete genomes from the Ralstonia genus were utilized for phylogenetic inference, categorizing them based on isolation environment and host: water, soil, plant, and human groups. Meanwhile, the abundance of carbohydrate-active enzymes and secondary metabolites in water and human groups differed from the plant-host associate habitat. CeoB and two {beta}-lactamases types of OXA were identified in the water habitat, showing similarities to certain strains in the human-host but differences from other habitats. The infectivity within water habitats seems to diminish, as evidenced by the decreased abundance of T3SS virulence proteins. Moreover, a distinctive pyrimidine degradation pathway in water degrades exogenous pyrimidines to supply nitrogen and other compounds for energy metabolism to provide a potential for broader habitat adaptability. Fluorescence in situ hybridization results confirmed that R. pickettii rarely attached to cyanobacterial cells, indicating that they are not parasitic relationships. We postulate that the absence of T3SS and the unique metabolic profile represent adaptations of Ralstonia to an aquatic free-living lifestyle.

microbiology↗