Biology subjects

Letarov, A. V.

Publications and source records attributed to Letarov, A. V..

9 recordsLinked to original sources

bioRxiv2026

Bacteriophage infection reveals pre-emptive cooperative dormancy in stationary phase Escherichia coli

Bacterial cultures entering stationary phase (SP) undergo complex physiological alterations, helping the cells to survive when medium resources are exhausted. The onset of various stress responses underlying SP physiology is generally believed to be due to reactions of individual cells to the environmental cues such as starvation, toxic metabolites, etc. The SP physiological state makes bacteria unsuitable for the replication of most bacteriophages; however, some phages are able to infect and multiply in them. We investigated Escherichia coli phage DH23 growth in SP cultures of E. coli MG1655 infected at different hours post inoculation (ages). Under our conditions the cells enter SP at about 6 h, but the phage replication was possible till 11h and then dropped abruptly by 13h of culture aging, indicating an abrupt physiological change to deeper dormancy during SP. The onset of this phage-inhibiting middle-SP dormancy (MSPD) turned out to be mediated by intercellular communication mediated by the middle-SP signal particles (MSP) which are larger than 100 kDa and contain both RNA and DNA. These MSP are inactivated by RNAse or by DNAse, enabling phage growth in 14h-old cultures and lifts the tolerance of such cultures to kanamycin. Moreover, the RNAse or DNAse treatment makes 24h culture spent media suitable for additional cell growth, and cultures initiated in fresh LB supplemented with RNAse reach an OD600 about 1.5 times higher compared to the untreated control. This indicates that MSP signaling influences cell physiology well before the MSPD onset and helps the population cease growth pre-emptively to save about 1/3 of medium resources to support the viability during SP.

microbiology↗

bioRxiv2026

Structural features of E. coli Stx bacteriophage phi24B revealed with cryo-electron microscopy

Shiga toxin-converting bacteriophages play a critical role in the emergence and virulence of pathogenic Escherichia coli strains. Despite their significance, detailed structural information on these phages remains scarce. Here we present a high-resolution cryo-electron microscopy and proteomic analysis of the phi24B bacteriophage, revealing an icosahedral capsid with T=9 symmetry, decorated by a processed esterase protein (gp84) and stabilized by cementing proteins. The tail assembly comprises a dodecameric portal, two rings of adapter proteins sharing a common fold, a hexameric nozzle, six lateral tail fibers, and a flexible central needle fiber. The binding sites of the fibers are described. Comparative analysis indicates conservation of the tail structure with related podoviruses but very different peripheral features.

biophysics↗

bioRxiv2022

Seasonal dynamics of a complex cheilostome bryozoan symbiosis - vertical transfer challenged

Symbiotic associations are dynamic systems influenced by both intrinsic and extrinsic factors. Here we describe for the first time the developmental and seasonal changes of the funicular bodies in the bryozoan Dendrobeania fruticosa, which are unique temporary organs of cheilostome bryozoans containing prokaryotic symbionts. Histological and ultrastructural studies showed that these organs undergo strong seasonal modification in the White Sea during the ice-free period. Initially (in June) they play a trophic function and support the development of a large population of bacteria. From June to September, both funicular bodies and bacteria show signs of degradation accompanied by development of presumed virus-like particles (VLPs); these self-organize to hollow spheres inside bacteria and are also detected outside of them. Although the destruction of bacteria coincides with the development of VLPs and spheres, the general picture differs considerably from the known instances of bacteriophagy in bryozoans. We broadly discuss potential routes of bacterial infection in Bryozoa and question the hypothesis of vertical transfer, which, although popular in the literature, is contradicted by molecular, morphological and ecological evidence.

zoology↗

bioRxiv2022

Diversity-generating retroelements in prokaryotic immunity

Adaptive immunity systems found in different organisms fall into two major types. Prokaryotes possess CRISPR-Cas systems, recognizing former invaders using the memorized (captured) pieces of their DNA as the pathogen signatures. Mammals possess a vast repertory of antibodies and T-cell receptors variants generated in advance. In this second type of adaptive immunity, a pathogen presentation to the immune system specifically activates the cells expressing matching antibodies or receptors. These cells proliferate to fight the infection and to form the immune memory. The principle of preemptive production of diverse defense proteins for future use can hypothetically take place in microbes too. In this study we test the hypothesis that prokaryotes employ diversity-generating retroelements to prepare defense proteins against yet-unknown invaders. We identified several candidate defense systems and characterised them.

bioinformatics↗

bioRxiv2021

Equine intestinal O-seroconverting temperate coliphage Hf4s: genomic and biological characterization

Tailed bacteriophages constitute the bulk of the intestinal viromes of the vertebrate animals. However, the relationships between lytic and lysogenic lifestyles of the phages in these ecosystems are not always clear and may vary between the species or even between the individuals. The human intestinal (fecal) viromes are believed to be dominated by temperate phages, while in the horse feces the virulent phages are more prevalent. Almost all the isolates of horse fecal coliphages are virulent. Phage Hf4s is the first temperate equine intestinal coliphage characterized. It was isolated from the horse feces on the indigenous equine E. coli 4s strain. It is a podovirus, related to Lederbergvirus genus (including the well-characterized Salmonella phage P22). Hf4s recognizes the host O antigen as its primary receptor and possesses a functional O-antigen seroconversion cluster that renders the lysogens protected from the superinfection by the same phage and also abolishes the adsorption of some indigenous equine virulent coliphages, such as DT57C, while the other phages, such as G7C or phiKT retain the ability to infect E. coli 4s (Hf4s) lysogens. ImportanceThe relationships between virulent and temperate bacteriophages and their impact on high-density symbiotic microbial ecosystems of the animal are not always clear and may vary between the species or even between the individuals. The horse intestinal virome is dominated by the virulent phages, and Hf4s is the first temperate equine intestinal coliphage characterized. It recognizes the host O antigen as its primary receptor and possesses a functional O-antigen seroconversion cluster that renders the lysogens protected from the superinfection by some indigenous equine virulent coliphages, such as DT57C, while the other phages, such as G7C or phiKT retain the ability to infect E. coli 4s (Hf4s) lysogens. microbial viruses in the mammal intestinal ecosystems.

microbiology↗

bioRxiv2020

The ecogenomics of dsDNA bacteriophages in feces of stabled and feral horses

The viromes of the mammalian lower gut were shown to be heavily dominated by bacteriophages; however, only for humans were the composition and intervariability of the bacteriophage communities studied in depth. Here we present an ecogenomics survey of dsDNA bacteriophage diversity in the feces of horses (Equus caballus), comparing two groups of stabled horses, and a further group of feral horses that were isolated on an island. Our results indicate that the dsDNA viromes of the horse feces feature higher richness than in human viromes, with more even distribution of genotypes. No over-represented phage genotypes, such as CrAssphage-related viruses found in humans, were identified. Additionally, many bacteriophage genus-level clusters were found to be present in all three geographically isolated populations. The diversity of the horse intestinal bacteriophages is severely undersampled, and so consequently only a minor fraction of the phage contigs could be linked with the bacteriophage genomes. Our study indicates that bacteriophage ecological parameters in the intestinal ecosystems in horses and humans differ significantly, leading them to shape their corresponding viromes in different ways. Therefore, the diversity and structure of the intestinal virome in different animal species needs to be experimentally studied. Short abstract (needed in some journals as eLife)The viromes of the mammalian gut were shown to be heavily dominated by bacteriophages; however, only for humans were the composition and intervariability of the bacteriophage communities studied in depth. Here we present an ecogenomics survey of dsDNA bacteriophage diversity in the feces of horses (Equus caballus), comparing stabled horses, and feral horses that were isolated on an island. The viromes equine fecal viromes feature higher richness than in human viromes, with more even distribution of genotypes. No over-represented phage genotypes were identified. Additionally, many bacteriophage genus-level clusters were found to be present in geographically isolated populations. Only a minor fraction of the phage contigs could be linked with the bacteriophage genomes. Our study indicates that bacteriophage ecological parameters in the intestinal ecosystems in horses and humans differ significantly, leading them to shape their corresponding viromes in different ways. Importance. (needed for mBio)The study presents the first in depth analysis of the composition and variability of the gut dsDNA bacteriophage community in the mammalian species, other than humans. The study demonstrates that the bacteriophage ecology in the gut is substantially different in different animal species. The results also indicate that the genetic diversity of the equine intestinal bacteriophages is immense and almost totally unexplored by the moment.

genomics↗

bioRxiv2020

First evidence of virus-like particles in the bacterial symbionts of Bryozoa

Bacteriophage communities associated with humans and vertebrate animals have been extensively studied, but the data on phages living in invertebrates remain scarce. In fact, they have never been reported for most animal phyla. Our ultrastructural study showed for the first time a variety of virus-like particles (VLPs) and supposed virus-related structures inside symbiotic bacteria in two marine species from the phylum Bryozoa, the cheilostomes Bugula neritina and Paralicornia sinuosa. We also documented the effect of VLPs on bacterial hosts: we explain different bacterial ultrastructural types detected in bryozoan tissues as stages in the gradual destruction of prokaryotic cells caused by viral multiplication during the lytic cycle. We speculate that viruses destroying bacteria regulate symbiont numbers in the bryozoan hosts, a phenomenon known in some insects. We develop two hypotheses explaining exo- and endogenous circulation of the viruses during the life-cycle of B. neritina. Finally, we compare unusual sea-urchin-like structures found in the collapsed bacteria in P. sinuosa with so-called metamorphosis associated complexes (MACs) known to trigger larval metamorphosis in a polychaete worm. ImportanceComplex symbiotic systems, including metazoan hosts, their bacterial symbionts and bacteriophages are widely studied using vertebrate models whereas much less is known about invertebrates. Our ultrastructural research revealed replication of the viruses and/or activation of virus related elements in the bacterial symbionts inhabiting tissues of the marine colonial invertebrates (phylum Bryozoa). The virus activity in the bacterial cells that are believed to be transmitted exclusively vertically is of a special importance. In addition, in the bacterial symbionts of one of the bryozoan hosts we observed the massive replication of the structures seemingly related to the Metamorphosis associated complexes (MAC). To our knowledge, MACs were never reported in the animal prokaryotic symbionts. Our findings indicate that Bryozoa may be new suitable model to study the role of bacteriophages and phage-related structures in the complex symbiotic systems hosted by marine invertebrates.

microbiology↗

bioRxiv2019

The lysogenization of the non-O157 Escherichia coli strains by stx-converting bacteriophage phi24B is associated with the O antigen loss and reduced fitness

The ability of the Shiga-toxigenic E. coli (STEC) to produce the toxin depends on the lysogenic conversion by stx-bacteriophages. The canonical stx-phage phi24B can lysogenize a wide variety of E. coli strains. In vivo the secondary lysogenization of symbiotic E. coli strains by the phages released by infecting STEC populations may contribute to the overall patient toxic load and to lead to the emergence of new pathogenic STEC strains. However, in our experiment all the phi24B lysogens obtained from the environmental E. coli isolates had compromised O-antigen (Oag) biosynthesis. These lysogenic strains gained the sensitivity to the T5-like bacteriophages and featured increased sensitivity to the bactericidal activity of the horse serum. We conclude that in most of E. coli strains the Oag effectively restricts phi24B infection. The lysogenic clones predominantly rise from the Oag deficient mutants and therefore they have reduced fitness compared to the parental strain.

microbiology↗

bioRxiv2019

Phages associated with horses provide new insights into the dominance of lateral gene transfer in virulent bacteriophages evolution in natural systems

Tailed bacteriophages (Caudovirales order) are omnipresent on our planet. Their impressive ecological and evolutionary success largely relies on the bacteriophage potential to adapt to great variety of the environmental conditions found in the Biosphere. It is believed that the adaptation of bacteriophages, including short time scale adaptation, is achieved almost exclusively via the (micro)evolution processes. In order to analyze the major mechanisms driving adaptation of phage genomes in a natural habitat we used comparative genomics of G7C-like coliphage isolates obtained during 7 years period from the feces of the horses belonging to a local population. The data suggest that even at this relatively short time scale the impact of various recombination events overwhelms the impact of the accumulation of point mutations. The access to the large pool of the genes of a complex microbial and viral community of the animal gut had major effect on the evolutionary trajectories of these phages. Thus the "real world" bacteriophage evolution mechanisms may differ significantly from those observed in the simplified laboratory model systems.

evolutionary biology↗