A compendium of viruses from methanogenic archaea reveals their diversity and adaptations to the gut environment

Nature Microbiology, Год журнала: 2023, Номер 8(11), С. 2170 - 2182

Опубликована: Сен. 25, 2023

Язык: Английский

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Structural RNA components supervise the sequential DNA cleavage in R2 retrotransposon

Cell, Год журнала: 2023, Номер 186(13), С. 2865 - 2879.e20

Опубликована: Июнь 1, 2023

Язык: Английский

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Ubiquitous purine sensor modulates diverse signal transduction pathways in bacteria

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Июль 12, 2024

Abstract Purines and their derivatives control intracellular energy homeostasis nucleotide synthesis, act as signaling molecules. Here, we combine structural sequence information to define a purine-binding motif that is present in sensor domains of thousands bacterial receptors modulate motility, gene expression, metabolism, second-messenger turnover. Microcalorimetric titrations selected validate ability specifically bind purine derivatives, evolutionary analyses indicate sensors share common ancestor with amino-acid receptors. Furthermore, provide experimental evidence physiological relevance sensing system modulates c-di-GMP levels.

Язык: Английский

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Targeted hypermutation of putative antigen sensors in multicellular bacteria

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(9)

Опубликована: Фев. 14, 2024

Diversity-generating retroelements (DGRs) are used by bacteria, archaea, and viruses as a targeted mutagenesis tool. Through error-prone reverse transcription, DGRs introduce random mutations at specific genomic loci, enabling rapid evolution of these genes. However, the function benefits DGR-diversified proteins in cellular hosts remain elusive. We find that 82% from one major monophyletic lineages DGR transcriptases encoded multicellular which often have two or more loci their genomes. Using purple sulfur bacterium Thiohalocapsa sp. PB-PSB1 an example, we characterized nine distinct capable generating 10 282 different combinations target proteins. With environmental metagenomes individual aggregates, show most PB-PSB1’s genes diversified across its biogeographic range, with spatial heterogeneity diversity each locus. In other bacteria hosting this lineage DGRs, associated NACHT-domain anti-phage defenses putative ternary conflict systems previously shown to be enriched bacteria. propose targets act antigen sensors confer form adaptive immunity consortia, though remains experimentally tested. These findings could implications for understanding multicellularity, share both domain homology conceptual similarities innate immune programmed cell death pathways plants metazoans.

Язык: Английский

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Emergence of an Auxin Sensing Domain in Plant-Associated Bacteria

mBio, Год журнала: 2023, Номер 14(1)

Опубликована: Янв. 5, 2023

Bacteria have evolved a sophisticated array of signal transduction systems that allow them to adapt their physiology and metabolism changing environmental conditions. Typically, these recognize signals through dedicated ligand binding domains (LBDs) ultimately trigger diversity physiological responses. Nonetheless, an increasing number reports reveal receptors also bind antagonists inhibit responses mediated by agonists. The mechanisms which block the downstream signaling cascade remain largely unknown. To advance our knowledge in this field, we used LysR-type transcriptional regulator AdmX as model. activates expression antibiotic biosynthetic cluster rhizobacterium Serratia plymuthica. specifically recognizes auxin phytohormone indole-3-acetic acid (IAA) its intermediate indole-3-pyruvic (IPA) signals. However, only IAA, but not IPA, was shown regulate production S. Here, report high-resolution structures LBD complex with IAA IPA. We found IPA compete for AdmX. Although does alter oligomeric state AdmX, causes higher degree compactness protein structure. Molecular dynamics simulations revealed significant differences modes inspection three-dimensional evidenced differential agonist- antagonist-mediated structural changes. Key residues were identified recognition motif defined. Phylogenetic clustering supports recent evolutionary emergence plant-associated enterobacteria. IMPORTANCE different bacterial receptors, are still at early stages understanding molecular details molecules exert inhibitory effects. provide insight into changes resulting from agonist antagonist sensor protein. Our data indicate is characterized small conformational LBDs can be efficiently transmitted output domain modulate final response. subject strong selective pressures rapidly evolving domains. An support idea factors drive evolution Given history homologs, well narrow phyletic distribution within bacteria, results accordance plant-mediated process resulted receptor proteins sense phytohormones.

Язык: Английский

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Evolution of genome fragility enables microbial division of labor

Molecular Systems Biology, Год журнала: 2023, Номер 19(3)

Опубликована: Фев. 2, 2023

Abstract Division of labor can evolve when social groups benefit from the functional specialization its members. Recently, a novel means coordinating division was found in antibiotic‐producing bacterium Streptomyces coelicolor , where specialized cells are generated through large‐scale genomic re‐organization. We investigate how evolution genome architecture enables such mutation‐driven labor, using multiscale computational model bacterial evolution. In this model, behavior—antibiotic production or replication—is determined by structure and composition their genome, which encodes antibiotics, growth‐promoting genes, fragile loci that induce chromosomal deletions. find organization evolves, partitions genes antibiotic‐coding into distinct parts separated loci. Mutations caused these sites mostly delete generating sterile, mutants weakly‐producing progenitors, agreement with experimental observations. This enhances competition between colonies promoting antibiotic diversity. These results show co‐evolve instabilities to enable reproductive labor.

Язык: Английский

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Systematic annotation of hyper-variability hotspots in phage genomes and plasmids

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Окт. 16, 2024

Abstract Bacterial and bacteriophage genomes contain genomic regions of hyper-variability (diversity hotspots) caused by insertions mobile genetic elements (MGEs), non-homologous recombination events non-horizontal hypermutation. Accessory genes encoded in the diversity hotspots are involved anti-MGE defence counter-defence, virulence antimicrobial resistance (AMR), thus playing key roles interactions amongst phages, MGEs, bacteria eukaryotic hosts. To date majority research has been focused on either individual or relatively limited sets a small set genomes, typically from single species. A global understanding hotspot dynamics still lacking. address this gap, we developed iLund4u, an algorithm for systematic annotation across millions sequences. Using proteome composition approach, iLund4u detects communities, annotates accessory proteins identifies hotspots. By analysing 873K phage 696K plasmid sequences identified 13.7K 171K diverse protein families there as cargo. Furthermore, allows search functions versus precomputed database. In mode all that encode homologues query protein. searching communities similar proteomes. Detailed documentation, user guide source code available at home page: art-egorov.github.io/ilund4u.

Язык: Английский

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DNA very fun facts

Elsevier eBooks, Год журнала: 2025, Номер unknown, С. 177 - 254

Опубликована: Янв. 1, 2025

Язык: Английский

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A global virome of methanogenic archaea highlights novel diversity and adaptations to the gut environment

Research Square (Research Square), Год журнала: 2023, Номер unknown

Опубликована: Фев. 9, 2023

Abstract Mobile genetic elements (MGEs), especially viruses, have a major impact on microbial communities. Methanogenic archaea play key environmental and economical roles, being the main producers of methane -a potent greenhouse gas an energy source. They are widespread in diverse anoxic artificial natural environments, including animal gut microbiomes. However, their viruses remain vastly unknown. Here, we carried out global investigation MGEs 3436 genomes metagenome-assembled covering all known diversity methanogens using newly assembled CRISPR database consisting 60,000 spacers methanogens, most extensive collection to date. We obtained 248 high-quality (pro)viral 63 plasmid sequences assigned hosts belonging nine orders methanogenic archaea, first Methanonatronarchaeales, Methanocellales Methanoliparales archaea. found novel arrays ‘ Ca. Methanomassiliicoccus intestinalis’ Methanomethylophilus’ with targeting small ssDNA Smacoviridae, supporting extending hypothesis interaction between smacoviruses associated Methanomassiliicoccales. Gene network analysis shows that encompass unique interconnected MGE repertoire, viral families head-tailed Caudoviricetes , but also icosahedral archaeal-specific pleomorphic, spherical, spindle (pro)viruses. reveal well-delineated modules for virus-host interaction, genome replication virion assembly, rich repertoire defense counter-defense systems suggesting highly dynamic complex interactions MGEs. identify potential conjugation composed VirB4, VirB5 VirB6 proteins encoded plasmids (pro)viruses Methanosarcinales, report Euryarchaeota. identified 15 new infecting Methanobacteriales, prominent microbiome. These encode large protein domains recognizing cleaving pseudomurein entry egress, convergent adaptation bacterial archaeal presence cell wall. Finally, highlight enrichment glycan-binding (immunoglobulin-like (Ig-like)/Flg_new) diversity-generating retroelements (DGRs) from gut-associated role host environments remarkable convergence phages bacteria. Our work represents important step toward characterization vast better understanding regulating communities globally development much-needed tools.

Язык: Английский

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Sensing the environment by bacterial plant pathogens: What do their numerous chemoreceptors recognize?

Microbial Biotechnology, Год журнала: 2023, Номер 17(1)

Опубликована: Ноя. 6, 2023

Abstract Bacteria have evolved multiple sensing strategies to efficiently adapt their natural hosts and environments. In the context of plant pathology, chemotaxis allows phytopathogenic bacteria direct movement towards through detection a landscape plant‐derived molecules, facilitating initiation infective process. The importance for lifestyle phytopathogens is also reflected in fact that they have, on average, twice as many chemoreceptors do not interact with plants. Paradoxically, knowledge about function pathogen scarce. Notably, these receptors seem be specific plant‐interacting bacteria, suggesting may recognize plant‐specific compounds. Here, we highlight need advance our phytopathogen chemoreceptor function, which serve base development anti‐infective therapies control phytopathogens.

Язык: Английский

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