Evolution based on domain combinations: The case of glutaredoxins

BMC Evolutionary Biology

Volumn 9, Issue 1, 2009, Pages

  Alves, Rui ^a   Vilaprinyo, Ester ^b   Sorribas, Albert ^a   Herrero, Enrique ^a  

^a UNIVERSITY OF LLEIDA   (Spain)

^b BELLVITGE BIOMEDICAL RESEARCH INSTITUTE IDIBELL   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; DISULFIDE; GLUTAREDOXIN; HYBRID PROTEIN;

ACTINOBACTERIA; ARCHAEBACTERIUM; ARTICLE; CHLOROBI; CYANOBACTERIUM; EUKARYOTE; FLAVOBACTERIA; GENE DUPLICATION; GENETIC RECOMBINATION; HALOBACTERIUM; MOLECULAR EVOLUTION; NONHUMAN; OXIDATION REDUCTION REACTION; PROTEIN DOMAIN; REGULATORY MECHANISM; ALGORITHM; AMINO ACID SEQUENCE; ANIMAL; BACTERIUM; GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

EUKARYOTA;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; ARCHAEA; BACTERIA; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; GLUTAREDOXINS; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; RECOMBINATION, GENETIC; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 65549160983     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-9-66     Document Type: Article

References (51)

1. The relationship between domain duplication and recombination. C Vogel SA Teichmann J Pereira-Leal, J Mol Biol 2005 346 1 355 365 15663950 (Pubitemid 40128326)
2. Modules, multidomain proteins and organismic complexity. H Tordai A Nagy K Farkas L Banyai L Patthy, FEBS J 2005 272 19 5064 5078 16176277 (Pubitemid 41415127)
3. Supra-domains: evolutionary units larger than single protein domains. C Vogel C Berzuini M Bashton J Gough SA Teichmann, J Mol Biol 2004 336 3 809 823 15095989 (Pubitemid 38183030)
4. Domain tree-based analysis of protein architecture evolution. K Forslund A Henricson V Hollich EL Sonnhammer, Mol Biol Evol 2008 25 2 254 264 18025066
5. Convergent evolution of domain architectures (is rare). J Gough, Bioinformatics 2005 21 8 1464 1471 15585523 (Pubitemid 40552751)
6. Arrangements in the modular evolution of proteins. AD Moore AK Bjorklund D Ekman E Bornberg-Bauer A Elofsson, Trends Biochem Sci 2008 33 9 444 451 18656364
7. The Biological Big Bang model for the major transitions in evolution. EV Koonin, Biol Direct 2007 2 21 17708768 (Pubitemid 47399371)
8. Thioredoxin and glutaredoxin systems. A Holmgren, J Biol Chem 1989 264 24 13963 13966 2668278 (Pubitemid 19214215)
9. Thioredoxin - a fold for all reasons. JL Martin, Structure 1995 3 3 245 250 7788290
10. The plant thioredoxin system. E Gelhaye N Rouhier N Navrot JP Jacquot, Cell Mol Life Sci 2005 62 1 24 35 15619004 (Pubitemid 40933089)
11. Monothiol glutaredoxins: a common domain for multiple functions. E Herrero MA de la Torre-Ruiz, Cell Mol Life Sci 2007 64 12 1518 1530 17415523 (Pubitemid 46954154)
12. The glutaredoxin family in oxygenic photosynthetic organisms. SD Lemaire, Photosynth Res 2004 79 3 305 318 16328797 (Pubitemid 38370834)
13. Genome-wide analysis of plant glutaredoxin systems. N Rouhier J Couturier JP Jacquot, J Exp Bot 2006 57 8 1685 1696 16720602 (Pubitemid 43992218)
14. Two novel monothiol glutaredoxins from Saccharomyces cerevisiae provide further insight into iron-sulfur cluster binding, oligomerization, and enzymatic activity of glutaredoxins. N Mesecke S Mittler E Eckers JM Herrmann M Deponte, Biochemistry 2008 47 5 1452 1463 18171082
15. Saccharomyces cerevisiae Grx6 and Grx7 are monothiol glutaredoxins associated with the early secretory pathway. A Izquierdo C Casas U Muhlenhoff CH Lillig E Herrero, Eukaryot Cell 2008 7 8 1415 1426 18503006
16. A Novel Group of Glutaredoxins in the cis-Golgi Critical for Oxidative Stress Resistance. N Mesecke A Spang M Deponte JM Herrmann, Mol Biol Cell 2008 19 6 2673 2680 18400945
17. Glutaredoxin systems. CH Lillig C Berndt A Holmgren, Biochim Biophys Acta 2008 1780 11 1304 1317 18621099
18. Evolution and cellular function of monothiol glutaredoxins: involvement in iron-sulphur cluster assembly. F Vilella R Alves MT Rodriguez-Manzaneque G Belli S Swaminathan P Sunnerhagen E Herrero, Comp Funct Genomics 2004 5 4 328 341 18629168 (Pubitemid 38807673)
19. A glutaredoxin-fused thiol peroxidase acts as an important player in hydrogen peroxide detoxification in late-phased growth of Anabaena sp. PCC7120. SK Hong MK Cha IH Kim, Arch Biochem Biophys 2008 475 1 42 49 18440297
20. PICOT-HD: a highly conserved protein domain that is often associated with thioredoxin and glutaredoxin modules. N Isakov S Witte A Altman, Trends Biochem Sci 2000 25 11 537 539 11084362
21. Glutaredoxins: Glutathione-dependent redox enzymes with functions far beyond a simple thioredoxin backup system. AP Fernandes A Holmgren, Antioxidants & Redox Signaling 2004 6 1 63 74 14713336 (Pubitemid 38063976)
22. Maturation of iron-sulfur proteins in eukaryotes: mechanisms, connected processes, and diseases. R Lill U Muhlenhoff, Annu Rev Biochem 2008 77 669 700 18366324
23. Cytochromes c biogenesis in a photosynthetic bacterium requires a periplasmic thioredoxin-like protein. DL Beckman RG Kranz, Proc Natl Acad Sci USA 1993 90 6 2179 2183 8384715 (Pubitemid 23078589)
24. A thioreduction pathway tethered to the membrane for periplasmic cytochromes c biogenesis; in vitro and in vivo studies. EM Monika BS Goldman DL Beckman RG Kranz, J Mol Biol 1997 271 5 679 692 9299319 (Pubitemid 27376046)
25. Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. T Fukui H Atomi T Kanai R Matsumi S Fujiwara T Imanaka, Genome Res 2005 15 3 352 363 15710748 (Pubitemid 40467776)
26. Tree of life based on genome context networks. G Ding Z Yu J Zhao Z Wang Y Li X Xing C Wang L Liu, PLoS ONE 2008 3 10 e3357 18852873
27. A tree of life based on protein domain organizations. K Fukami-Kobayashi Y Minezaki Y Tateno K Nishikawa, Mol Biol Evol 2007 24 5 1181 1189 17331957 (Pubitemid 47343640)
28. Evidence, Content and Corroboration and the Tree of Life. E Kurt Lienau R Desalle, Acta Biotheor 2008 [DOI 10.1007/s10441-008-9066-5]. 19015816
29. Codon usage and genome evolution. PM Sharp G Matassi, Curr Opin Genet Dev 1994 4 6 851 860 7888755
30. Scoring residue conservation. WS Valdar, Proteins 2002 48 2 227 241 12112692 (Pubitemid 34743413)
31. Protein secondary structure: entropy, correlations and prediction. GE Crooks SE Brenner, Bioinformatics 2004 20 10 1603 1611 14988117 (Pubitemid 39023164)
32. Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions. GB Gloor LC Martin LM Wahl SD Dunn, Biochemistry 2005 44 19 7156 7165 15882054 (Pubitemid 40656660)
33. Estimation of evolutionary distances between homologous nucleotide sequences. M Kimura, Proc Natl Acad Sci USA 1981 78 1 454 458 6165991 (Pubitemid 11129426)
34. Evolutionary information for specifying a protein fold. M Socolich SW Lockless WP Russ H Lee KH Gardner R Ranganathan, Nature 2005 437 7058 512 518 16177782 (Pubitemid 41613543)
35. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. GM Suel SW Lockless MA Wall R Ranganathan, Nat Struct Biol 2003 10 1 59 69 12483203 (Pubitemid 36034178)
36. The Ka/Ks ratio: diagnosing the form of sequence evolution. LD Hurst, Trends Genet 2002 18 9 486 12175810
37. PlanTAPDB, a phylogeny-based resource of plant transcription-associated proteins. S Richardt D Lang R Reski W Frank SA Rensing, Plant Physiol 2007 143 4 1452 1466 17337525 (Pubitemid 46849460)
38. The structure and function of frataxin. KZ Bencze KC Kondapalli JD Cook S McMahon C Millan-Pacheco N Pastor TL Stemmler, Crit Rev Biochem Mol Biol 2006 41 5 269 291 16911956 (Pubitemid 44261883)
39. Common themes and variations in the rhodanese superfamily. R Cipollone P Ascenzi P Visca, IUBMB Life 2007 59 2 51 59 17454295 (Pubitemid 46535402)
40. The origin and evolution of Archaea: a state of the art. S Gribaldo C Brochier-Armanet, Philos Trans R Soc Lond B Biol Sci 2006 361 1470 1007 1022 16754611
41. Nuclear monothiol glutaredoxins of Saccharomyces cerevisiae can function as mitochondrial glutaredoxins. MM Molina G Belli MA de la Torre MT Rodriguez-Manzaneque E Herrero, J Biol Chem 2004 279 50 51923 51930 15456753 (Pubitemid 39656560)
42. The universal protein resource (UniProt). UNIPROT, Nucleic Acids Res 2008 36 Database D190 195 18045787
43. Rapid and sensitive sequence comparison with FASTP and FASTA. WR Pearson, Methods Enzymol 1990 183 63 98 2156132 (Pubitemid 20148813)
44. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. SF Altschul TL Madden AA Schaffer J Zhang Z Zhang W Miller DJ Lipman, Nucleic Acids Res 1997 25 17 3389 3402 9254694 (Pubitemid 27359211)
45. GenBank. DA Benson I Karsch-Mizrachi DJ Lipman J Ostell DL Wheeler, Nucleic Acids Res 2008 36 Database D25 30 18073190
46. "Decrease Redundancy" program at SWISSPROT. http://expasy.org/tools/redundancy/
47. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. K Tamura J Dudley M Nei S Kumar, Mol Biol Evol 2007 24 8 1596 1599 17488738 (Pubitemid 47236692)
48. Dendroscope: An interactive viewer for large phylogenetic trees. DH Huson DC Richter C Rausch T Dezulian M Franz R Rupp, BMC Bioinformatics 2007 8 460 18034891
49. Domain fishing: a first step in protein comparative modelling. B Contreras-Moreira PA Bates, Bioinformatics 2002 18 8 1141 1142 12176841
50. The PROSITE database. N Hulo A Bairoch V Bulliard L Cerutti E De Castro PS Langendijk-Genevaux M Pagni CJ Sigrist, Nucleic Acids Res 2006 34 Database D227 230 16381852
51. Characterization of Escherichia coli NrdH. A glutaredoxin-like protein with a thioredoxin-like activity profile. A Jordan F Aslund E Pontis P Reichard A Holmgren, J Biol Chem 1997 272 29 18044 18050 9218434 (Pubitemid 27306385)