Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes

Nature, Год журнала: 2023, Номер 618(7967), С. 992 - 999

Опубликована: Июнь 14, 2023

Abstract In the ongoing debates about eukaryogenesis—the series of evolutionary events leading to emergence eukaryotic cell from prokaryotic ancestors—members Asgard archaea play a key part as closest archaeal relatives eukaryotes 1 . However, nature and phylogenetic identity last common ancestor remain unresolved 2–4 Here we analyse distinct marker datasets an expanded genomic sampling evaluate competing scenarios using state-of-the-art phylogenomic approaches. We find that are placed, with high confidence, well-nested clade within sister lineage Hodarchaeales, newly proposed order Heimdallarchaeia. Using sophisticated gene tree species reconciliation approaches, show analogous evolution genomes, genome in involved significantly more duplication fewer loss compared other archaea. Finally, infer was probably thermophilic chemolithotroph which evolved adapted mesophilic conditions acquired genetic potential support heterotrophic lifestyle. Our work provides insights into prokaryote-to-eukaryote transition platform for better understanding cellular complexity cells.

Язык: Английский

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The nature of the last universal common ancestor and its impact on the early Earth system

Nature Ecology & Evolution, Год журнала: 2024, Номер 8(9), С. 1654 - 1666

Опубликована: Июль 12, 2024

Abstract The nature of the last universal common ancestor (LUCA), its age and impact on Earth system have been subject vigorous debate across diverse disciplines, often based disparate data methods. Age estimates for LUCA are usually fossil record, varying with every reinterpretation. LUCA’s metabolism has proven equally contentious, some attributing all core metabolisms to LUCA, whereas others reconstruct a simpler life form dependent geochemistry. Here we infer that lived ~4.2 Ga (4.09–4.33 Ga) through divergence time analysis pre-LUCA gene duplicates, calibrated using microbial fossils isotope records under new cross-bracing implementation. Phylogenetic reconciliation suggests had genome at least 2.5 Mb (2.49–2.99 Mb), encoding around 2,600 proteins, comparable modern prokaryotes. Our results suggest was prokaryote-grade anaerobic acetogen possessed an early immune system. Although is sometimes perceived as living in isolation, part established ecological would provided niche other community members hydrogen recycling by atmospheric photochemistry could supported modestly productive ecosystem.

Язык: Английский

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Genome organization and genomics in Chlamydia: whole genome sequencing increases understanding of chlamydial virulence, evolution, and phylogeny

Frontiers in Cellular and Infection Microbiology, Год журнала: 2023, Номер 13

Опубликована: Май 23, 2023

The genus Chlamydia contains important obligate intracellular bacterial pathogens to humans and animals, including C. trachomatis pneumoniae. Since 1998, when the first genome was published, our understanding of how these microbes interact, evolved adapted different host environments has been transformed due expansion chlamydial genomes. This review explores current state knowledge in genomics whole sequencing revolutionised virulence, evolution, phylogeny over past two a half decades. will also highlight developments multi-omics other approaches that have complemented advance pathogenesis future directions for genomics.

Язык: Английский

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Amoebae as training grounds for microbial pathogens

mBio, Год журнала: 2024, Номер 15(8)

Опубликована: Июль 8, 2024

Grazing of amoebae on microorganisms represents one the oldest predator-prey dynamic relationships in nature. It a genetic "melting pot" for an ancient and continuous multi-directional inter- intra-kingdom horizontal gene transfer between its preys, intracellular microbial residents, endosymbionts, giant viruses, which has shaped evolution, selection, adaptation microbes that evade degradation by predatory amoeba. Unicellular phagocytic are thought to be ancestors macrophages with highly conserved eukaryotic processes. Selection evolution within amoeba through their target processes have facilitated expansion host range mammals, causing various infectious diseases.

Язык: Английский

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Type III Secretion in Chlamydia

Microbiology and Molecular Biology Reviews, Год журнала: 2023, Номер 87(3)

Опубликована: Июнь 26, 2023

Type III secretion systems (T3SSs) are utilized by Gram-negative pathogens to enhance their pathogenesis. This system is associated with the delivery of effectors through a needle-like structure from bacterial cytosol directly into target eukaryotic cell.

Язык: Английский

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Genome reduction and horizontal gene transfer in the evolution of Endomicrobia—rise and fall of an intracellular symbiosis with termite gut flagellates

mBio, Год журнала: 2024, Номер 15(6)

Опубликована: Май 14, 2024

Bacterial endosymbionts of eukaryotic hosts typically experience massive genome reduction, but the underlying evolutionary processes are often obscured by lack free-living relatives. Endomicrobia, a family-level lineage host-associated bacteria in phylum Elusimicrobiota that comprises both representatives and termite gut flagellates, an excellent model to study evolution intracellular symbionts. We reconstructed 67 metagenome-assembled genomes (MAGs) Endomicrobiaceae among more than 1,700 MAGs from microbiota wide range termites. Phylogenomic analysis confirmed sister position termites ruminants, allowed propose eight new genera radiation Endomicrobiaceae. Comparative documented progressive erosion genus Endomicrobiellum, which all flagellate characterized date. Massive gene losses were accompanied acquisition functions horizontal transfer, led shift glucose-based energy metabolism one based on sugar phosphates. The breakdown glycolysis many anabolic pathways for amino acids cofactors several subgroups was compensated independent uptake systems, including ATP/ADP antiporter, other microbiota. putative donors mostly bacterial phyla, several, hitherto unknown lineages uncultured Alphaproteobacteria, documenting importance transfer convergent these symbioses. loss almost biosynthetic capacities some Endomicrobiellum suggests their originally mutualistic relationship with flagellates is its decline.IMPORTANCEUnicellular eukaryotes frequently colonized archaeal A prominent example cellulolytic termites, harbor diverse host-specific symbionts occur exclusively guts. One lineages, so-called endosymbiotic representatives, offers unique opportunity underpinning transition lifestyle. Our results revealed pathways, via bacteria, suggest eventual initially symbiosis. Evidence unrelated reflects adaptations environment flagellates.

Язык: Английский

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Description of Asgardarchaeum abyssi gen. nov. spec. nov., a novel species within the class Asgardarchaeia and phylum Asgardarchaeota in accordance with the SeqCode

Systematic and Applied Microbiology, Год журнала: 2024, Номер 47(4), С. 126525 - 126525

Опубликована: Июнь 15, 2024

Asgardarchaeota, commonly referred to as Asgard archaea, is a candidatus phylum-rank archaeal clade that includes the closest relatives of eukaryotes. Despite their prevalence in scientific literature, name Asgardarchaeota lacks nomenclatural validation. Here, we describe novel high-quality metagenome-assembled genome (MAG), AB3033_2

Язык: Английский

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Metagenome diversity illuminates the origins of pathogen effectors

mBio, Год журнала: 2024, Номер 15(5)

Опубликована: Апрель 2, 2024

Recent metagenome-assembled genome (MAG) analyses have profoundly impacted Rickettsiology systematics. The discovery of basal lineages (novel families Mitibacteraceae and Athabascaceae) with predicted extracellular lifestyles exposed an evolutionary timepoint for the transition to host dependency, which seemingly occurred independent mitochondrial evolution. Notably, these rickettsiae carry Rickettsiales vir homolog (rvh) type IV secretion system purportedly use rvh kill congener microbes rather than parasitize cells as described later-evolving rickettsial pathogens. MAG analysis also substantially increased diversity genus Rickettsia delineated a sister lineage (the novel Tisiphia) that stands inform on emergence human pathogens from protist invertebrate endosymbionts. Herein, we probed genomic distribution effectors ascertain their origins. A sparse most outside Rickettsiaceae illuminates unique evolution species other families. Remarkably, nearly every effector was found in multiple divergent forms variable architectures, indicating profound roles gene duplication recombination shaping repertoires Lateral transfer plays prominent role landscape, evinced by many plasmids conjugative transposons, well pervasive exchange between Legionella species. Our study exemplifies how MAGs can yield insight into pathogen origins, particularly architectures might become tailored discrete cell functions different eukaryotic hosts.IMPORTANCEWhile rickettsioses are deadly vector-borne diseases, factors distinguishing innumerable bevy environmental endosymbionts remain lacking. studies revealed timepoints transitions dependency. likely repurposed killing parasitizing over two dozen unearthed presence some non-pathogens. However, were recombination-fashioned shaped arsenals, exchanges origins processes tailoring biology.

Язык: Английский

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Chlamydia trachomatis : a model for intracellular bacterial parasitism

Journal of Bacteriology, Год журнала: 2025, Номер unknown

Опубликована: Фев. 20, 2025

ABSTRACT Chlamydia comprises a diverse group of obligate intracellular bacteria that cause infections in animals, including humans. These organisms share fascinating biology, distinct developmental stages, non-canonical cell surface structures, and adaptations to parasitism. trachomatis is particular interest due its significant clinical importance, causing both ocular sexually transmitted infections. The strain L2/434/Bu, responsible for lymphogranuloma venereum, the most common used study chlamydial molecular biology because it grows readily culture amenable genetic manipulation. Indeed, this has enabled researchers tackle fundamental questions about mechanisms underlying Chlamydia’s transitions biphasic lifecycle cellular parasitism, characterizing numerous conserved virulence genes defining immune responses. However, L2/434/Bu not representative C. strains urogenital humans, limiting utility addressing host tropism evasion reproductive organs. Recent research efforts are shifting toward understanding unique attributes more clinically relevant genovars.

Язык: Английский

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Origin and function of beneficial bacterial symbioses in insects

Nature Reviews Microbiology, Год журнала: 2025, Номер unknown

Опубликована: Март 27, 2025

Язык: Английский

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