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: The gene for 4‐hydroxybutyryl‐CoA dehydratase was found in GOS metagenome and ALOHA fosmids, whereas no matches were observed in KM3 metagenome. Since the distance between this gene and rRNA operon in N. maritimus SCM1 is about 716.5 kb, it was not expected to find it among SSU rRNA‐containing fosmids from KM3. Two almost identical (95–100% nucleotide sequence identity) ALOHA fosmids HF4000_APKG7F11 and HF4000_APKG3H9 contained a stretch of open reading frames highly syntenic at the amino acid level to a 40‐kb‐long genomic fragment downstream of dehydratase gene identified in N. maritimus SCM1 (Fig. 5A). Based on this conservation, paired‐end analysis of individual reads assembled in HF4000_APKG7F11 contig revealed some assembly errors (Fig. 5B). Further analysis of the genomic context around the gene encoding 4‐hydroxybutyryl‐CoA dehydratase in C. symbiosum A and Sargasso Sea scaffold AACY020562346 revealed little conservation of genes adjacent to this locus (Fig. 5A). As a consequence, all analysed sequences possess only a 7.4‐kb‐long common genomic fragment containing nine predicted open reading frames (Fig. 5C). Three genes within this fragment code for conserved hypothetical and are therefore of potential interest in the context of 3‐HP/4‐HB pathway.
Affiliation: Institute for Coastal Marine Environment (IAMC), CNR, Spianata S. Raineri 86, 98122 Messina, Italy.