Biology subjects

Yakovleva, Y.

Publications and source records attributed to Yakovleva, Y..

3 recordsLinked to original sources

bioRxiv2025

Exogenous dsRNA made accessible to Dicer by two eukaryotic RNA-dependent RNA polymer-ases

Discrimination of self from non-self RNA is a critical requirement for any cell to respond to infections and to maintain cellular integrity. We report novel functions for two RNA-dependent RNA polymerases (RDRs) in Paramecium in the detection of exogenous RNA. In the RNA interference (RNAi) mechanism, RDRs are normally involved in the production of large amounts of secondary siRNAs in response to an initial primary siRNA. To characterize the function of RDRs in context of exogenous RNA recognition, we developed a novel dsRNA delivery system using dextran nanoparticles to deliver heteroduplex dsRNA to cells as food particles, mimicking the natural phagosomal entry pathway. Subsequent small RNA sequencing allows us to dissect siRNAs produced from exogenous RNA or RDR transcripts. Contrary to expectations of how dsRNA-induced silencing is triggered, our data show that Dicer is unable to directly cleave exogenous dsRNA while two RDRs are required for the initial steps of dsRNA-induced RNAi. Paradoxically, these two RDRs must replicate dsRNA to make it available for Dicer cleavage and primary siRNA accumulation. Our data also show that this system works efficiently also with exogenous ssRNA, although RDR2 is dispensable for ssRNA conversion. The function of RDRs in this protist is in contrast to that in animals, plants and fungi and extends the functional diversity of these polymerases. RDR-associated complexes appear to control the entry of food and symbiont-derived RNA into the RNAi machinery, enabling complex RNA interactions with the environment.

genetics↗

bioRxiv2021

PaReBrick: PArallel REarrangements and BReakpoints identification toolkit

MotivationHigh plasticity of bacterial genomes is provided by numerous mechanisms including horizontal gene transfer and recombination via numerous flanking repeats. Genome rearrangements such as inversions, deletions, insertions, and duplications may independently occur in different strains, providing parallel adaptation. Specifically, such rearrangements might be responsible for multi-virulence, antibiotic resistance, and antigenic variation. However, identification of such events requires laborious manual inspection and verification of phyletic pattern consistency. ResultsHere we define the term "parallel rearrangements" as events that occur independently in phylogenetically distant bacterial strains and present a formalization of the problem of parallel rearrangements calling. We implement an algorithmic solution for the identification of parallel rearrangements in bacterial population, as a tool PaReBrick. The tool takes synteny blocks and a phylogenetic tree as input and outputs rearrangement events. The tool tests each rearrangement for consistency with a tree, and sorts the events by their parallelism score and provides diagrams of the neighbors for each block of interest, allowing the detection of horizontally transferred blocks or their extra copies and the inversions in which copied blocks are involved. We proved PaReBricks efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity and adaptation in bacterial genomes. AvailabilityPaReBrick is written in Python and is available on GitHub

bioinformatics↗

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↗