Biology subjects

Bochkareva, O. O.

Publications and source records attributed to Bochkareva, O. O..

9 recordsLinked to original sources

bioRxiv2025

Rapid genetic diversification of Bacteroides thetaiotaomicron in mono-associated mice revealed through deep population-level sequencing

Bacteria often feature short generation times and large populations, thereby allowing them to quickly evolve and adapt to new environments. Although it is known that gut bacteria can evolve on relatively short time scales, the extent of genetic diversification of bacteria in the gut environment remains underexplored. Here, we characterize the genetic diversification of the gut commensal Bacteroides thetaiotaomicron during 28 days of colonization of germ-free mice using deep shotgun sequencing as well as genome analysis of evolved isolates. We detect thousands of genetic polymorphisms as early as three days post inoculation and observe highly dynamic genetic diversity in the distal gut. We identify multiple haplotypes of a phase-variable polysaccharide utilization locus (BT2260 - BT2268) and propose that phase variation may be an important mechanism for diversification and adaptation in the gut. In addition, we find evidence that hybrid two-component system (HTCS) regulators are mutational hotspots. We identify multiple persistent and parallelly evolved genetic polymorphisms in genes, including the TonB-dependent transporter BT0867 - a homolog of BF3581 from the commensal colonization factor (ccf) in B. fragilis. Lastly, we find that the small intestine accumulated approximately 20 times more polymorphisms compared to the large intestine, highlighting overall the importance of studying spatiotemporal distribution of genetic variants. These results underscore the prevalence of rapid genetic diversification of gut bacteria, which may have important implications for adaptation as well as interactions in the microbiome and with the host. ImportanceStudying the within-host evolution of gut commensals is an essential step for understanding the role of microbiome in health and disease. It can provide insights into the mechanisms underlying the development of various gastrointestinal disorders, metabolic conditions, autoimmune diseases, and other health disorders. Additionally, this kind of research can further drive the development of personalized therapies, such as strain-level or gene specific interventions for improving health outcomes. Here, we report extensive genetic variation within days upon colonization of mice with B. thetaiotaomicron and identify genes that accumulate persistent and highly prevalent genetic polymorphisms across a mouse population. We also detect several haplotypes in phase-variable loci. Altogether, our findings underscore the rapid pace of genetic diversification and phase variation upon colonization of the gut environment.

microbiology↗

bioRxiv2024

Pulsatile basal gene expression as a fitness determinant in bacteria

Active regulation of gene expression, orchestrated by complex interactions of activators and repressors at promoters, controls the fate of organisms. In contrast, basal expression at uninduced promoters is considered to be a dynamically inert mode of non-functional "promoter leakiness", merely a byproduct of transcriptional regulation. Here, we investigate the basal expression mode of the mar operon, the main regulator of intrinsic multiple antibiotic resistance in Escherichia coli, and link its dynamic properties to the non-canonical, yet highly conserved start codon of marR across Enterobacteriaceae. Real-time single-cell measurements across tens of generations, reveal that basal expression consists of rare stochastic gene expression pulses, which maximize variability in wildtype and, surprisingly, transiently accelerate cellular elongation rates. Competition experiments show that basal expression confers fitness advantages to wildtype across several transitions between exponential and stationary growth by shortening lag times. The dynamically rich basal expression of the mar operon, has likely been evolutionarily maintained for its role in growth homeostasis of Enterobacteria within the gut environment, thereby allowing other ancillary gene regulatory roles to evolve, e.g. control of costly-to-induce multi-drug efflux pumps. Understanding the complex selection forces governing genetic systems involved in intrinsic multi-drug resistance is crucial for effective public health measures.

systems biology↗

bioRxiv2023

Genome rearrangements drive evolution of ANK genes in Wolbachia

IntroductionGenus Wolbachia comprises endosymbionts infecting many arthropods and nematodes; it is a model for studying symbiosis as its members feature numerous, diverse mutualistic and parasitic adaptations to different hosts. In contrast to nematode-infecting Wolbachia, genomes of arthropod-infecting strains contain a high fraction of repetitive elements creating possibilities for multiple recombination events and causing genome rearrangements. The mechanisms and role of these features are still not fully understood. ResultsTransposons cover up to 18% of an arthropod-infecting Wolbachia genome and drive numerous genome rearrangements including inversions and segmental amplifications. ANK (ankyrin-repeat domain family) genes are also often found at the breakpoints of rearrangements, while less than 7% of them were found within locally collinear blocks (LCBs). We observed a strong correlation between the number of ANK genes and the genome size as well as significant overrepresentation of transposons adjacent to these genes. We also revealed numerous cases of integration of transposases to the ANK genes affecting the sequences and putative products of the latter. Our results uncover the role of mobile elements in the amplification and diversification of ANK genes. ConclusionsEvolution of arthropod-infecting Wolbachia was accompanied by diverse genome rearrangements driving the evolution of ANK genes important for bacteria-host interactions. This study demonstrates the effectiveness of our LCB-based approach to the Wolbachia genomics and provides a framework for understanding the impact of genome rearrangements on their rapid host adaptation.

evolutionary biology↗

bioRxiv2023

Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis

Antimicrobial resistance (AMR) poses a significant global health threat, and an accurate prediction of bacterial resistance patterns is critical for effective treatment and control strategies. In recent years, machine learning (ML) approaches have emerged as powerful tools for analyzing large-scale bacterial AMR data. However, ML methods often ignore evolutionary relationships among bacterial strains, which can greatly impact performance of the ML methods, especially if resistance-associated features are attempted to be detected. Genomewide association studies (GWAS) methods like linear mixed models accounts for the evolutionary relationships in bacteria, but they uncover only highly significant variants which have already been reported in literature. In this work, we introduce a novel phylogeny-related parallelism score (PRPS), which measures whether a certain feature is correlated with the population structure of a set of samples. We demonstrate that PRPS can be used, in combination with SVM- and random forest-based models, to reduce the number of features in the analysis, while simultaneously increasing models performance. We applied our pipeline to publicly available AMR data from PATRIC database for Mycobacterium tuberculosis against six common antibiotics. Using our pipeline, we re-discovered known resistance-associated mutations as well as new candidate mutations which can be related to resistance and not previously reported in the literature.

bioinformatics↗

bioRxiv2023

Evolutionary trajectories of secondary replicons in multipartite genomes

Most bacterial genomes have a single chromosome that may be supplemented by smaller, dispensable plasmids. However, approximately 10% of bacteria with completely sequenced genomes, mostly pathogens and plant symbionts, have more than one stable large replicon. Some secondary replicons are species-specific, carrying pathogenicity or symbiotic factors. Other replicons are common on at least the genus level, carry house-keeping genes, and may have a size of several million base pairs. We analyzed the abundance and sizes of large secondary replicons in different groups of bacteria and identified two patterns in the evolution of multipartite genomes. In nine genera of four families, Pseudoalteromonadaceae, Burkholderiaceae, Vibrionaceae, and Brucellaceae, we observed a positive correlation between the sizes of the chromosome and the secondary replicon with the slope in the range of 0.6-1.2. This indicates that in these genera the replicons evolve in a coordinated manner, with comparable rates of gene gain/loss, hence supporting classification of such secondary replicons as chromids. The second, more common pattern, features gene gains and losses mainly occurring in the primary replicon, yielding a stable size of the secondary replicon. Such secondary replicons are usually present in only a low fraction of the genus species. Hence, such replicons behave as megaplasmids. A mixed situation was observed in symbiotic genera from the Rhizobiaceae family where the large secondary replicons are of stable size, but present in all species. These results may provide a general framework for understanding the evolution of genome complexity in prokaryotes. SignificanceLarge secondary replicons are observed in representatives of many taxonomic groups of bacteria. Traditionally, they are referred to as second chromosomes, chromids, or megaplasmids, with little consistency, in particular because their evolution remains understudied. Here we demonstrate that the sizes of secondary replicons follow two main evolutionary trends: replicons whose size scales linearly with the size of the main chromosome (the suggested term chromids) typically contain numerous essential genes (rRNA, tRNA, ribosomal proteins), while large secondary replicons of stable size (termed megaplasmids) contain fewer or none such genes.

genomics↗

bioRxiv2021

Chromosome-encoded IpaH ubiquitin ligases indicate non-human pathogenic Escherichia

Until recently, Shigella and enteroinvasive Escherichia coli were thought to be primate-restricted pathogens. The base of their pathogenicity is the type 3 secretion system (T3SS) encoded by the pINV virulence plasmid, which facilitates host cell invasion and subsequent proliferation. A large family of T3SS effectors, E3 ubiquitin-ligases encoded by the ipaH genes, have a key role in the Shigella pathogenicity through the modulation of cellular ubiquitination that degrades host proteins. However, recent genomic studies identified ipaH genes in the genomes of Escherichia marmotae, a potential marmot pathogen, and an E. coli extracted from fecal samples of bovine calves, suggesting that non-human hosts may also be infected by these strains, potentially pathogenic to humans. We performed a comparative genomic study of the functional repertoires in the ipaH gene family in Shigella and enteroinvasive Escherichia from human and predicted non-human hosts. We found that fewer than half of Shigella genomes had a complete set of ipaH genes, with frequent gene losses and duplications that were not consistent with the species tree and nomenclature. Non-human host IpaH proteins had a diverse set of substrate-binding domains and, in contrast to the Shigella proteins, two different types of the NEL C-terminal domain. Only the ipaH9.8 gene was found in Escherichia derived from both human and non-human hosts. These results provide a framework for understanding of ipaH-mediated host-pathogens interactions and suggest a need for a genomic study of fecal samples from diseased animals.

microbiology↗

bioRxiv2020

Genome evolution and pathoadaptation of Shigella

Shigella are pathogens originating within the Escherichia lineage but frequently classified as a separate genus. Shigella genomes contain numerous insertion sequences (ISs) that lead to pseudogenization of affected genes and an increase of non-homologous recombination. Here, we study 414 genomes of E. coli and Shigella strains to assess the contribution of genomic rearrangements to Shigella evolution. We found that Shigella experienced exceptionally high rates of intragenomic rearrangements and had a decreased rate of homologous recombination compared to pathogenic and non-pathogenic E. coli. The high rearrangement rate resulted in independent disruption of syntenic regions and parallel rearrangements in different Shigella lineages. Specifically, we identified two types of chromosomally encoded E3 ubiquitin-protein ligases acquired independently by all Shigella strains that also showed a high level of sequence conservation in the promoter and further in the 5 intergenic region. In the only available enteroinvasive E. coli (EIEC) strain, which is a pathogenic E. coli with a phenotype intermediate between Shigella and non-pathogenic E. coli, we found a rate of genome rearrangements comparable to those in other E. coli and no functional copies of the two Shigella-specific E3 ubiquitin ligases. These data indicate that accumulation of ISs influenced many aspects of genome evolution and played an important role in the evolution of intracellular pathogens. Our research demonstrates the power of comparative genomics-based on synteny block composition and an important role of non-coding regions in the evolution of genomic islands. ImportancePathogenic Escherichia coli strains frequently cause infections in humans. Many E. coli exist in nature and their ability to cause disease is fueled by their ability to incorporate novel genetic information by extensive horizontal gene transfer of plasmids and pathogenicity islands. The emergence of antibiotic-resistant Shigella spp., which are pathogenic forms of E. coli, coupled with the absence of an effective vaccine against them, highlights the importance of the continuing study of these pathogenic bacteria. Our study contributes to the understanding of genomic properties associated with molecular mechanisms underpinning the pathogenic nature of Shigella. We characterize the contribution of insertion sequences to the genome evolution of these intracellular pathogens and suggest a role of upstream regions of chromosomal ipaH genes in the Shigella pathogenesis. The methods of rearrangement analysis developed here are broadly applicable to the analysis of genotype-phenotype correlation in historically recently emerging bacterial pathogens.

bioinformatics↗

bioRxiv2018

Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.

Chlamydia are ancient intracellular pathogens with reduced, though strikingly conserved genome. Despite their parasitic lifestyle and isolated intracellular environment, these bacteria managed to avoid accumulation of deleterious mutations leading to subsequent genome degradation characteristic for many parasitic bacteria.\n\nWe report pan-genomic analysis of eleven species from genus Chlamydia including identification and functional annotation of orthologous genes, and characterization of gene gains, losses, and rearrangements. We demonstrate the overall genome stability of these bacteria as indicated by a large fraction of common genes with conserved genomic locations. On the other hand, extreme evolvability is confined to several paralogous gene families such as polymorphic membrane proteins and phospholipase D and likely is caused by the pressure from the host immune system.\n\nThis combination of a large, conserved core genome and a small, evolvable periphery likely reflect the balance between the selective pressure towards genome reduction and the need to adapt to changing host environment.

genomics↗

bioRxiv2018

Genome evolution in Burkholderia spp

BackgroundThe genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization.\n\nResultsWe performed integrated genomic analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. Integrated reconstruction of chromosome rearrangements in the context of strains phylogeny reveals parallel rearrangements that may indicate inversion-based phase variation and integration of new genomic islands. In particular, we detected parallel inversions in the second chromosomes of B. pseudomallei with breakpoints formed by genes encoding membrane components of multidrug resistance complex, that may be linked to a phase variation mechanism. Two genomic islands, spreading horizontally between chromosomes, were detected in the B. cepacia group.\n\nConclusionsThis study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be a possible phase variation mechanism in B. pseudomallei.

genomics↗