Interesting article on Abiogenesis
Source:
The physiology and habitat of the last universal common ancestor : Nature Microbiology
The physiology and habitat of the last universal common ancestor
Madeline C. Weiss, Filipa L. Sousa, Natalia Mrnjavac, Sinje Neukirchen, Mayo Roettger, Shijulal Nelson-Sathi & William F. Martin
The concept of a last universal common ancestor of all cells (LUCA, or the progenote) is central to the study of early evolution and life's origin, yet information about how and where LUCA lived is lacking. We 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, we identified 355 protein families (∼0.1%) that trace to LUCA by phylogenetic criteria. Because these proteins are not universally distributed, they can shed light on LUCA's physiology. Their functions, properties and prosthetic groups depict LUCA as anaerobic, CO2-fixing, H2-dependent with a Wood–Ljungdahl pathway, N2-fixing and thermophilic. LUCA's biochemistry was replete with FeS clusters and radical reaction mechanisms. Its cofactors reveal dependence upon transition metals, flavins, S-adenosyl methionine, coenzyme A, ferredoxin, molybdopterin, corrins and selenium. Its genetic code required nucleoside modifications and S-adenosyl methionine-dependent methylations. The 355 phylogenies identify clostridia and methanogens, whose modern lifestyles resemble that of LUCA, as basal among their respective domains. LUCA inhabited a geochemically active environment rich in H2, CO2 and iron. The data support the theory of an autotrophic origin of life involving the Wood–Ljungdahl pathway in a hydrothermal setting.
The last universal common ancestor (LUCA) is an inferred evolutionary intermediate1 that links the abiotic phase of Earth's history with the first traces of microbial life in rocks that are 3.8–3.5 billion years of age2. Although LUCA was long considered the common ancestor of bacteria, archaea and eukaryotes3,4, newer two-domain trees of life have eukaryotes arising from prokaryotes5,6, making LUCA the common ancestor of bacteria and archaea. Previous genomic investigations of LUCA's gene content have focused on genes that are universally present across genomes4,7,8, revealing that LUCA had 30–100 proteins for ribosomes and translation. In principle, genes present in one archaeon and one bacterium might trace to LUCA, although their phylogenetic distribution could also be the result of post-LUCA gene origin and interdomain lateral gene transfer (LGT)8, given that thousands of such gene transfers between prokaryotic domains have been detected9.
To identify genes that can illuminate the biology of LUCA, we took a phylogenetic approach. Among proteins encoded in sequenced prokaryotic genomes, we 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, 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, we can identify genes involved in LUCA's physiology—the ways that cells access carbon, energy and nutrients from the environment for growth.
