title: Macroevolutionary trends of atomic composition and related functional group proportion in eukaryotic and prokaryotic proteins.
abstract: To fully explore the trends of atomic composition during the macroevolution from prokaryote to eukaryote, five atoms (oxygen, sulfur, nitrogen, carbon, hydrogen) and related functional groups in prokaryotic and eukaryotic proteins were surveyed and compared. Genome-wide analysis showed that eukaryotic proteins have more oxygen, sulfur and nitrogen atoms than prokaryotes do. Clusters of Orthologous Groups (COG) analysis revealed that oxygen, sulfur, carbon and hydrogen frequencies are higher in eukaryotic proteins than in their prokaryotic orthologs. Furthermore, functional group analysis demonstrated that eukaryotic proteins tend to have higher proportions of sulfhydryl, hydroxyl and acylamino, but lower of sulfide and carboxyl. Taken together, an apparent trend of increase was observed for oxygen and sulfur atoms in the macroevolution; the variation of oxygen and sulfur compositions and their related functional groups in macroevolution made eukaryotic proteins carry more useful functional groups. These results will be helpful for better understanding the functional significances of atomic composition evolution.
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan Province 650223, PR China; Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing 401331, PR China.
authors.forename: Yu-Juan
authors.initials: YJ
authors.lastname: Zhang
authors.affiliation: Department of Biology, East Carolina University, Greenville, NC, USA.
authors.forename: Chun-Lin
authors.initials: CL
authors.lastname: Yang
authors.affiliation: Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing 401331, PR China.
authors.forename: You-Jin
authors.initials: YJ
authors.lastname: Hao
authors.affiliation: Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing 401331, PR China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Li
authors.affiliation: Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing 401331, PR China. Electronic address: c_bin@hotmail.com.
authors.forename: Bin
authors.initials: B
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan Province 650223, PR China. Electronic address: wenjf@mail.kiz.ac.cn.
authors.forename: Jian-Fan
authors.initials: JF
authors.lastname: Wen
mesh_terms: D005057:Eukaryotic Cells / Q000378:metabolism*; D019143:Evolution, Molecular; D016678:Genome; D055106:Genome-Wide Association Study; D011387:Prokaryotic Cells / Q000378:metabolism*; D011506:Proteins / Q000235:genetics* / Q000378:metabolism*
chemical_list: D011506:Proteins
keywords: 456 COGs from 44 mesophilic species; 604 COGs distributed in both prokaryotes and eukaryotes; AA; Amino acid; COG; COG1; COG2; COOH; Clusters of Orthologous Groups; Eukaryotes; H(2)NCO; H(3)CSH(3)C; K(e); K(p); Macroevolution; OH; Oxygen; Prokaryotes; SH; Sulfur; acylamino; amino acid; carboxyl; hydroxyl; sulfhydryl; sulfide; the proportion of Group to Atom on the side-chains of AA in eukaryotic proteins; the proportion of Group to Atom on the side-chains of AA in prokaryotic proteins