Evolution of prokaryotic respiratory molybdoenzymes and the frequency of their genomic co-occurrence.
Molybdoenzymes are an ancient protein family found in phylogenetically and ecologically diverse prokaryotes. Under anaerobic conditions, respiratory molybdoenzymes catalyze redox reactions that transfer electrons to a variety of substrates that act as terminal electron acceptors for energy generation. Here, we used probe sequences to conduct an extensive genomic survey and phylogenetic inference for NarG, DmsA, TorA and nine other respiratory molybdoenzyme subfamilies. Our analysis demonstrates their abundance in 60% of prokaryotic phyla. In contrast to many other autonomic genetic units in prokaryotes, the major route of evolution of their predominant subfamilies is vertical gene transfer, gene duplication and divergence. Our results show the robustness of genomic co-occurrence of respiratory molybdoenzymes genes, found in the majority of studied species, for most of the enzyme subfamilies. Genomes which encode for multiple respiratory molybdoenzymes are also enriched in genes regulating replication, recombination and mobility of genetic elements. Respiratory molybdoenzymes were found in prokaryotes associated with diverse environments occupying terrestrial, aquatic, food and host-related habitats, emphasizing their essential role in adaptation of prokaryotes to changing environments. Interestingly, host-associated prokaryotes such as human pathogens more frequently carry multiple respiratory molybdoenzyme genes compared with non-host-associated prokaryotes, highlighting the importance of metabolic flexibility in host-microbiome environments.
Department of Vegetable Research, Institute of Plant Sciences, Volcani Center, ARO, 68 HaMaccabim Road, Rishon LeZion 7505101, ISRAEL Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Science, Rutgers the State University of New Jersey, 71 Dudley Road, New Brunswick, NJ 08901, USA aryeharel@volcani.agri.gov.il.
Arye
A
Harel
Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, 76 Lipman Drive, New Brunswick, NJ 08901, USA.
Max M
MM
Häggblom
Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Science, Rutgers the State University of New Jersey, 71 Dudley Road, New Brunswick, NJ 08901, USA.
Paul G
PG
Falkowski
Department of Environmental Sciences, Rutgers, The State University of New Jersey, 14 College Farm Road, New Brunswick, NJ 08901, USA.
Nathan
N
Yee
D001105:Archaea / Q000201:enzymology* / Q000235:genetics / Q000378:metabolism; D001419:Bacteria / Q000201:enzymology* / Q000235:genetics / Q000378:metabolism; D005075:Biological Evolution; D020745:Genome, Archaeal / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics; D006801:Humans; D064307:Microbiota / Q000235:genetics; D008982:Molybdenum / Q000737:chemistry; D050901:Nitrate Reductase / Q000235:genetics*; D010084:Oxidation-Reduction; D010089:Oxidoreductases, N-Demethylating / Q000235:genetics*; D010802:Phylogeny
D008982:Molybdenum; D010089:Oxidoreductases, N-Demethylating; C023186:trimethylamine dehydrogenase; D050901:Nitrate Reductase
DMSO reductases; genomic co-occurrence; host microbiome; molybdoenzymes; plasticity; respiratory flexibility