We are analyzing https://link.springer.com/article/10.1007/s00239-021-10044-y.

Title:
The Ancient Origins of Death Domains Support the ‘Original Sin’ Hypothesis for the Evolution of Programmed Cell Death | Journal of Molecular Evolution
Description:
The discovery of caspase homologs in bacteria highlighted the relationship between programmed cell death (PCD) evolution and eukaryogenesis. However, the origin of PCD genes in prokaryotes themselves (bacteria and archaea) is poorly understood and a source of controversy. Whether archaea also contain C14 peptidase enzymes and other death domains is largely unknown because of a historical dearth of genomic data. Archaeal genomic databases have grown significantly in the last decade, which allowed us to perform a detailed comparative study of the evolutionary histories of PCD-related death domains in major archaeal phyla, including the deepest branching phyla of Candidatus Aenigmarchaeota, Candidatus Woesearchaeota, and Euryarchaeota. We identified death domains associated with executioners of PCD, like the caspase homologs of the C14 peptidase family, in 321 archaea sequences. Of these, 15.58% were metacaspase type I orthologues and 84.42% were orthocaspases. Maximum likelihood phylogenetic analyses revealed a scattered distribution of orthocaspases and metacaspases in deep-branching bacteria and archaea. The tree topology was incongruent with the prokaryote 16S phylogeny suggesting a common ancestry of PCD genes in prokaryotes and subsequent massive horizontal gene transfer coinciding with the divergence of archaea and bacteria. Previous arguments for the origin of PCD were philosophical in nature with two popular propositions being the “addiction” and ‘original sin’ hypotheses. Our data support the ‘original sin’ hypothesis, which argues for a pleiotropic origin of the PCD toolkit with pro-life and pro-death functions tracing back to the emergence of cellular life—the Last Universal Common Ancestor State.
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Keywords {🔍}

article, pubmed, google, scholar, cas, cell, death, central, biol, programmed, mol, evolution, origin, archaea, microbiol, archaeal, gene, nature, koonin, durand, supplementary, protein, sci, bacteria, metacaspase, metacaspases, nat, httpsdoiorg, data, evolutionary, bacterial, httpsdoiorgs, apoptosis, origins, domains, hypothesis, caspase, differ, aravind, rev, content, original, pcd, transfer, genomics, role, caspases, structure, microbial, evol,

Topics {✒️}

month download article/chapter estimating maximum-likelihood phylogenies �original sin’ hypothesis phage lysis-lysogeny switches virus-host arms race programmed cell death—ii �original sin’ hypotheses prokaryotic caspase homologs bacterial pseudo-orthocaspases underline full article pdf pcd-related death domains proto wr archaeal “tack” superphylum programmed cell death author information authors major archaeal phyla privacy choices/manage cookies palgrave macmillan asplund-samuelsson durand pm cell death pathway massive gene exchange horizontal gene transfer programmed cell suicide caspase homologs ancestral state reconstruction caspase-hemoglobinase fold cell death programme hidden markov model cell cycle progression archaeal genomic databases predicting transmembrane helices lateral gene transfer cell death proteases cell fate regulation check access instant access article la related subjects universal protein knowledgebase view prokaryote–eukaryote interface death domains support horizontal gene flow groisman ea identified death domains leishmania major metacaspase wd-repeat proteins european economic area scope submit manuscript

Questions {❓}

Blackstone NW (2013) Why did eukaryotes evolve only once?
Frade JM, Michaelidis TM (1997) Origin of eukaryotic programmed cell death: a consequence of aerobic metabolism?
Galperin MY, Koonin EV (2000) Who’s your neighbor?
Proto WR, Coombs GH, Mottram JC (2013) Cell death in parasitic protozoa: regulated or incidental?
Ramisetty BCM, Natarajan B, Santhosh RS (2015) MazEF-mediated programmed cell death in bacteria: “What is this?
Ratel D, Boisseau S, Nasser V et al (2001) Programmed cell death or cell death programme?
Vercammen D, Declercq W, Vandenabeele P, Van Breusegem F (2007) Are metacaspases caspases?

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         description:The discovery of caspase homologs in bacteria highlighted the relationship between programmed cell death (PCD) evolution and eukaryogenesis. However, the origin of PCD genes in prokaryotes themselves (bacteria and archaea) is poorly understood and a source of controversy. Whether archaea also contain C14 peptidase enzymes and other death domains is largely unknown because of a historical dearth of genomic data. Archaeal genomic databases have grown significantly in the last decade, which allowed us to perform a detailed comparative study of the evolutionary histories of PCD-related death domains in major archaeal phyla, including the deepest branching phyla of Candidatus Aenigmarchaeota, Candidatus Woesearchaeota, and Euryarchaeota. We identified death domains associated with executioners of PCD, like the caspase homologs of the C14 peptidase family, in 321 archaea sequences. Of these, 15.58% were metacaspase type I orthologues and 84.42% were orthocaspases. Maximum likelihood phylogenetic analyses revealed a scattered distribution of orthocaspases and metacaspases in deep-branching bacteria and archaea. The tree topology was incongruent with the prokaryote 16S phylogeny suggesting a common ancestry of PCD genes in prokaryotes and subsequent massive horizontal gene transfer coinciding with the divergence of archaea and bacteria. Previous arguments for the origin of PCD were philosophical in nature with two popular propositions being the “addiction” and ‘original sin’ hypotheses. Our data support the ‘original sin’ hypothesis, which argues for a pleiotropic origin of the PCD toolkit with pro-life and pro-death functions tracing back to the emergence of cellular life—the Last Universal Common Ancestor State.
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