title: Comparative genomics of thiol oxidoreductases reveals widespread and essential functions of thiol-based redox control of cellular processes.
abstract: OBJECTIVE
  Redox regulation of cellular processes is an important mechanism that operates in organisms from bacteria to mammals. Much of the redox control is provided by thiol oxidoreductases: proteins that employ cysteine residues for redox catalysis. We wanted to identify thiol oxidoreductases on a genome-wide scale and use this information to obtain insights into the general principles of thiol-based redox control.
  
  
  RESULTS
  Thiol oxidoreductases were identified by three independent methods that took advantage of the occurrence of selenocysteine homologs of these proteins and functional linkages among thiol oxidoreductases revealed by comparative genomics. Based on these searches, we describe thioredoxomes, which are sets of thiol oxidoreductases in organisms. Their analyses revealed that these proteins are present in all living organisms, generally account for 0.5%-1% of the proteome and that their use correlates with proteome size, distinguishing these proteins from those involved in core metabolic functions. We further describe thioredoxomes of Saccharomyces cerevisiae and humans, including proteins which have not been characterized previously. Thiol oxidoreductases occur in various cellular compartments and are enriched in the endoplasmic reticulum and cytosol.
  
  
  METHODS
  We developed bioinformatics methods and used them to characterize thioredoxomes on a genome-wide scale, which in turn revealed properties of thioredoxomes.
  
  
  CONCLUSIONS
  These data provide information about organization and properties of thiol-based redox control, whose use is increased with the increase in complexity of organisms. Our data also show an essential combined function of a set of thiol oxidoreductases, and of thiol-based redox regulation in general, in all living organisms.
authors: Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, USA. dfomenko@genomics.unl.edu
authors: Dmitri E
authors: DE
authors: Fomenko
authors: Vadim N
authors: VN
authors: Gladyshev
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000201:enzymology / Q000235:genetics; D001419:Bacteria / Q000201:enzymology / Q000235:genetics; D001483:Base Sequence; D057225:Data Mining; D030541:Databases, Genetic; D023281:Genomics; D006801:Humans; D008660:Metabolism; D008969:Molecular Sequence Data; D046588:Nanoarchaeota / Q000201:enzymology / Q000235:genetics; D009876:Operon; D010084:Oxidation-Reduction; D050862:Oxidoreductases Acting on Sulfur Group Donors / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000235:genetics; D017385:Sequence Homology
chemical_list: D050862:Oxidoreductases Acting on Sulfur Group Donors