| Value |
355
genes
|
| Organism |
Microbes |
| Reference |
Weiss MC et al., The physiology and habitat of the last universal common ancestor. Nat Microbiol. 2016 Jul 25 1(9):16116. doi: 10.1038/nmicrobiol.2016.116 abstract & p.3 left column top paragraphPubMed ID27562259
|
| Method |
P.1 left column 2nd paragraph: "To identify genes that can illuminate the biology of LUCA, [researchers] took a phylogenetic approach. Among proteins encoded in sequenced prokaryotic genomes, [they] sought those that fulfil two simple criteria: (1) the protein should be present in at least two higher taxa of bacteria and archaea, respectively, and (2) its tree should recover bacterial and archaeal monophyly (Fig. 1). Genes meeting both criteria are unlikely to have undergone transdomain LGT [lateral gene transfer], and thus were probably present in LUCA and inherited within domains since the time of LUCA. By focusing on phylogeny rather than universal gene presence, [they] can identify genes involved in LUCA’s physiology—the ways that cells access carbon, energy and nutrients from the environment for growth." |
| Comments |
Abstract: "[Researchers] investigated all clusters and phylogenetic trees for 6.1 million protein coding genes from sequenced prokaryotic genomes in order to reconstruct the microbial ecology of LUCA. Among 286,514 protein clusters, [they] identified 355 protein families (∼0.1%) that trace to LUCA by phylogenetic criteria...The 355 phylogenies identify clostridia and methanogens, whose modern lifestyles resemble that of LUCA, as basal among their respective domains." P.3 left column top paragraph: "The genes in LUCA’s list (Supplementary Table 2) and the basal lineages among the 355 reciprocally rooted trees (Supplementary Table 6) indicate that LUCA lived in an environment where the geochemical synthesis of methane from H2 and CO2 was taking place, hence where chemically accessible reduced C1
intermediates existed." |
| Entered by |
Uri M |
| ID |
113041 |