title: Deciphering primordial cyanobacterial genome functions from protein network analysis.
abstract: The Great Oxidation Event (GOE) ∼2.4 billion years ago resulted from the accumulation of oxygen by the ancestors of cyanobacteria [1-3]. Cyanobacteria continue to play a significant role in primary production [4] and in regulating the global marine and limnic nitrogen cycles [5, 6]. Relatively little is known, however, about the evolutionary history and gene content of primordial cyanobacteria [7, 8]. To address these issues, we used protein similarity networks [9], containing proteomes from 48 cyanobacteria as the test group, and reference proteomes from 84 microbes representing four distinct metabolic groups from most reducing to most oxidizing: methanogens, obligate anaerobes (nonmethanogenic), facultative aerobes, and obligate aerobes. These four metabolic groups represent extant bioinformatic proxies for ancient redox chemistries, extending from an anoxic origin through the GOE and ultimately to obligate aerobes [10-13]. Analysis of the network metric degree showed a strong relationship between cyanobacteria and obligate anaerobes, from which cyanobacteria presumably arose, for core functions that include translation, photosynthesis, energy conservation, and environmental interactions. These data were used to reconstruct primordial functions in cyanobacteria that included nine gene families involved in photosynthesis, hydrogenases, and proteins involved in defense from environmental stress. The presence of 60% of these genes in both reaction center I (RC-I) and RC-II-type bacteria may be explained by selective loss of either RC in the evolutionary history of some photosynthetic lineages. Finally, the network reveals that cyanobacteria occupy a unique position among prokaryotes as a hub between anaerobes and obligate aerobes.
authors: Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, 71 Dudley Road, New Brunswick, NJ, 08901, USA; Department of Ecology, Evolution, and Natural Resources, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, USA. Electronic address: harelarik@gmail.com.
authors: Arye
authors: A
authors: Harel
authors: Department of Ecology, Evolution, and Natural Resources, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, USA.
authors: Slim
authors: S
authors: Karkar
authors: Department of Ecology, Evolution, and Natural Resources, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, USA.
authors: Shu
authors: S
authors: Cheng
authors: Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, 71 Dudley Road, New Brunswick, NJ, 08901, USA; Department of Earth and Planetary Sciences, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
authors: Paul G
authors: PG
authors: Falkowski
authors: Department of Ecology, Evolution, and Natural Resources, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, USA. Electronic address: debash.bhattacharya@gmail.com.
authors: Debashish
authors: D
authors: Bhattacharya
mesh_terms: D001421:Bacteria, Anaerobic / Q000235:genetics*; D019295:Computational Biology; D000458:Cyanobacteria / Q000235:genetics*; D019143:Evolution, Molecular; D016680:Genome, Bacterial / Q000235:genetics*; D006864:Hydrogenase / Q000235:genetics; D005810:Multigene Family / Q000235:genetics*; D010084:Oxidation-Reduction; D010788:Photosynthesis / Q000235:genetics; D060066:Protein Interaction Maps / Q000235:genetics*; D040901:Proteomics / Q000379:methods; D013045:Species Specificity
chemical_list: D006864:Hydrogenase