Asgard archaea defense systems and their roles in the origin of eukaryotic immunity

Leão, Pedro; Little, Mary E.; Appler, Kathryn E.; Sahaya, Daphne; Aguilar-Pine, Emily; Currie, Kathryn; Finkelstein, Ilya J.; De Anda, Valerie; Baker, Brett J.

doi:10.1038/s41467-024-50195-2

Cited by 4 publications

References 48 publications

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Genomic landscape of antiviral defense systems in prokaryotes and phages

Li,

Gu,

Xia

et al. 2024

Preprint

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Prokaryotes and their viruses have co-evolved for billions of years, resulting in emergence of numerous antiviral defense systems. With the development of bioinformatic technologies and experimental studies, more and more novel defense systems have been discovered in the near decades. However, the origin and mechanism of these systems are still largely unknown. This study provides a systematic analysis of 132 defense systems within 212,599 prokaryotic genomes, which should be the largest analyzed data so far, revealing the diversity and distribution of these systems across different taxonomic units. Our findings also reveal that not only well-studied bacteria, but also archaea and virus encode diverse antiviral defense systems with specific features. In summary, this work classify 132 known defense systems, provides a comprehensive view of prokaryotic defense systems and insights into the evolution of immune responses.

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Genomic landscape of antiviral defense systems in prokaryotes and phages

Li,

Gu,

Xia

et al. 2024

Preprint

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Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements

Valentin-Alvarado,

Shi,

Appler

et al. 2024

Genome Res.

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Asgard archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, a wetland Asgard archaea lineage represented by two complete genomes. We used soil depth–resolved population metagenomic data sets to track 18 MGEs for which genome structures were defined and precise chromosome integration sites could be identified for confident host linkage. Additionally, we identified a complete 20.67 kbp circular plasmid and two family-level groups of viruses linked to Atabeyarchaeia, via CRISPR spacer targeting. Closely related 40 kbp viruses possess a hypervariable genomic region encoding combinations of specific genes for small cysteine-rich proteins structurally similar to restriction-homing endonucleases. One 10.9 kbp integrative conjugative element (ICE) integrates genomically into theAtabeyarchaeum deiterrae-1chromosome and has a 2.5 kbp circularizable element integrated within it. The 10.9 kbp ICE encodes an expressed Type IIG restriction-modification system with a sequence specificity matching an active methylation motif identified by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing. Restriction-modification of Atabeyarchaeia differs from that of another coexisting Asgard archaea, Freyarchaeia, which has few identified MGEs but possesses diverse defense mechanisms, including DISARM and Hachiman, not found in Atabeyarchaeia. Overall, defense systems and methylation mechanisms of Asgard archaea likely modulate their interactions with MGEs, and integration/excision and copy number variation of MGEs in turn enable host genetic versatility.

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Nature should be the model for microbial sciences

Baker,

Hyde,

Leão

2024

J Bacteriol

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Until recently, microbiologists have relied on cultures to understand the microbial world. As a result, model organisms have been the focus of research into understanding Bacteria and Archaea at a molecular level. Diversity surveys and metagenomic sequencing have revealed that these model species are often present in low abundance in the environment; instead, there are microbial taxa that are cosmopolitan in nature. Due to the numerical dominance of these microorganisms and the size of their habitats, these lineages comprise mind-boggling population sizes upward of 10 28 cells on the planet. Many of these dominant groups have cultured representatives and have been shown to be involved in mediating key processes in nature. Given their importance and the increasing need to understand changes due to climate change, we propose that members of Nitrosophaerota ( Nitrosopumilus maritimus ), SAR11 ( Pelagibacter ubique ), Hadesarchaeia, Bathyarchaeia, and others become models in the future. Abundance should not be the only measure of a good model system; there are other organisms that are well suited to advance our understanding of ecology and evolution. For example, the most well-studied symbiotic bacteria, like Buchnera , Aliivibrio , and Rhizobium , should be models for understanding host-associations. Also, there are organisms that hold new insights into major transitions in the evolution of life on the planet like the Asgard Archaea (Heimdallarchaeia). Innovations in a variety of in situ techniques have enabled us to circumvent culturing when studying everything from genetics to physiology. Our deepest understanding of microbiology and its impact on the planet will come from studying these microbes in nature. Laboratory-based studies must be grounded in nature, not the other way around.

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Asgard archaea defense systems and their roles in the origin of eukaryotic immunity

Cited by 4 publications

References 48 publications

Genomic landscape of antiviral defense systems in prokaryotes and phages

Genomic landscape of antiviral defense systems in prokaryotes and phages

Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements

Nature should be the model for microbial sciences

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