title: A phylogenomic study of DNA repair genes, proteins, and processes.
abstract: The ability to recognize and repair abnormal DNA structures is common to all forms of life. Studies in a variety of species have identified an incredible diversity of DNA repair pathways. Documenting and characterizing the similarities and differences in repair between species has important value for understanding the origin and evolution of repair pathways as well as for improving our understanding of phenotypes affected by repair (e.g., mutation rates, lifespan, tumorigenesis, survival in extreme environments). Unfortunately, while repair processes have been studied in quite a few species, the ecological and evolutionary diversity of such studies has been limited. Complete genome sequences can provide potential sources of new information about repair in different species. In this paper, we present a global comparative analysis of DNA repair proteins and processes based upon the analysis of available complete genome sequences. We use a new form of analysis that combines genome sequence information and phylogenetic studies into a composite analysis we refer to as phylogenomics. We use this phylogenomic analysis to study the evolution of repair proteins and processes and to predict the repair phenotypes of those species for which we now know the complete genome sequence.
authors.affiliation: Department of Biological Sciences, Stanford University, Stanford, CA 94305-5020, USA. jeisen@tigr.org
authors.forename: J A
authors.initials: JA
authors.lastname: Eisen
authors.forename: P C
authors.initials: PC
authors.lastname: Hanawalt
mesh_terms: D000251:Adenosine Triphosphatases / Q000235:genetics; D000478:Alkylation; D001426:Bacterial Proteins / Q000096:biosynthesis / Q000235:genetics; D020137:Base Pair Mismatch; D004249:DNA Damage; D045647:DNA Glycosylases; D004265:DNA Helicases; D011088:DNA Ligases / Q000235:genetics*; D004254:DNA Nucleotidyltransferases / Q000235:genetics; D004260:DNA Repair / Q000235:genetics*; D004261:DNA Replication / Q000235:genetics; D004269:DNA, Bacterial / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics; D043382:DNA-Formamidopyrimidine Glycosylase; D043224:Deoxyribonuclease (Pyrimidine Dimer); D003851:Deoxyribonucleases / Q000235:genetics; D004706:Endodeoxyribonucleases / Q000235:genetics; D029968:Escherichia coli Proteins; D005057:Eukaryotic Cells / Q000378:metabolism; D043211:Exodeoxyribonuclease V; D005090:Exodeoxyribonucleases / Q000235:genetics; D005092:Exonucleases / Q000235:genetics; D005798:Genes, Bacterial; D016158:Genes, p53; D016678:Genome; D020745:Genome, Archaeal; D019426:Integrases; D005810:Multigene Family; D009699:N-Glycosyl Hydrolases / Q000235:genetics; D010802:Phylogeny; D051721:Rad52 DNA Repair and Recombination Protein; D045522:Recombinases; D011995:Recombination, Genetic; D013014:SOS Response, Genetics / Q000235:genetics; D012697:Serine Endopeptidases / Q000096:biosynthesis / Q000235:genetics; D051981:Uracil-DNA Glycosidase; D000099160:LexA Repressor Protein
chemical_list: D000251:Adenosine Triphosphatases; D001426:Bacterial Proteins; D045647:DNA Glycosylases; D004265:DNA Helicases; D011088:DNA Ligases; D004254:DNA Nucleotidyltransferases; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D043382:DNA-Formamidopyrimidine Glycosylase; D043224:Deoxyribonuclease (Pyrimidine Dimer); D003851:Deoxyribonucleases; D004706:Endodeoxyribonucleases; D029968:Escherichia coli Proteins; D043211:Exodeoxyribonuclease V; D005090:Exodeoxyribonucleases; D005092:Exonucleases; D019426:Integrases; D009699:N-Glycosyl Hydrolases; D051721:Rad52 DNA Repair and Recombination Protein; D045522:Recombinases; D012697:Serine Endopeptidases; D051981:Uracil-DNA Glycosidase; D000099160:LexA Repressor Protein; C061563:SbcC protein, Bacteria; C489229:SbcC protein, E coli; C058093:UvrB protein, E coli; C489340:recF protein, E coli; C066218:recF protein, Bacteria; C115006:integron integrase IntI1; C081229:sbcD protein, E coli; C038225:recE protein, E coli; C028450:exodeoxyribonuclease I; C066567:UvrC protein, E coli; C106403:NTH protein, E coli; C061738:mutY adenine glycosylase; C068631:UvrA protein, E coli