Genomic signatures of fifth autotrophic carbon assimilation pathway in bathypelagic Crenarchaeota.
Bottom Line: Recent cultivation and genome sequencing of obligate chemoautotrophic Nitrosopumilus maritimus SCM1 were a major breakthrough towards understanding of their functioning and provide a valuable model for experimental validation of genomic data.These organisms are likely to use acetyl-CoA/propionyl-CoA carboxylase(s) as CO₂-fixing enzyme(s) to form succinyl-CoA, from which one molecule of acetyl-CoA is regenerated via 4-hydroxybutyrate cleavage and another acetyl-CoA to be the pathway product.The genetic distinctiveness and matching sympatric abundance imply that marine crenarchaeal genotypes from the three different geographic sites share similar ecophysiological properties, and therefore may represent fundamental units of marine ecosystem functioning.
Affiliation: Institute for Coastal Marine Environment (IAMC), CNR, Spianata S. Raineri 86, 98122 Messina, Italy.Show MeSH
Mentions: To identify homologues of the methylmalonyl‐CoA mutase subunits predicted in N. maritimus and C. symbiosum genomes, targeted searches were conducted against ALOHA, KM3 and GOS database and at least one contig from each of them was found (Fig. 4A). Comparison of genomic context around the mmm gene cluster in C. symbiosum A and GOS scaffold AACY020561430 revealed little conservation of genes adjacent to mmm locus, whereas the mmm‐containing genomic fragment greater than 19 kb in N. maritimus was identified to share a significant homology with fosmids recovered from bathypelagic zones of both Mediterranean Sea and Atlantic ocean (Fig. 4B). However, only 195 aa C‐terminal fragment of putative methylmalonyl‐CoA mutase large subunit is present at 5′‐terminus of ALOHA fosmid HF4000_APKG7F19. Besides methylmalonyl‐CoA mutase subunits, the highly syntenic block of 15 predicted open reading frames was found to contain genes encoding putative methylmalonyl‐CoA epimerase, phosphoenolpyruvate synthase and dihydroxyacetone 3‐phosphate isomerase. First enzyme converts (2R)‐methylmalonyl‐CoA to (2S)‐methylmalonyl‐CoA (substrate for methylmalonyl‐CoA mutase), while two remaining enzymes are involved in glyceraldehyde 3‐phosphate formation. As proposed elsewhere, this triosephosphate synthesis might be coupled with 3‐HP/4‐HB pathway following the equation (Berg et al., 2007; Fig. S1):
Affiliation: Institute for Coastal Marine Environment (IAMC), CNR, Spianata S. Raineri 86, 98122 Messina, Italy.