A model of globin evolution

Gene

Volumn 398, Issue 1-2 SPEC. ISS., 2007, Pages 132-142

  Vinogradov, Serge N ^a   Hoogewijs, David ^b   Bailly, Xavier ^c   Mizuguchi, Kenji ^d   Dewilde, Sylvia ^e   Moens, Luc ^e   Vanfleteren, Jacques R ^b  

^a WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b GHENT UNIVERSITY   (Belgium)

^c STATION BIOLOGIQUE   (France)

^d NATIONAL INSTITUTE OF BIOMEDICAL INNOVATION   (Japan)

^e UNIVERSITY OF ANTWERP   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

GLOBIN;

ARCHAEBACTERIUM; ARTICLE; BACTERIUM; BAYES THEOREM; CARBOXY TERMINAL SEQUENCE; EUKARYOTE; FUNGUS; GENE TRANSFER; GENOME; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL;

ANIMALS; ARCHAEA; BACTERIA; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; GLOBINS; MODELS, GENETIC; PHYLOGENY; TIME FACTORS;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; EURYARCHAEOTA; FUNGI; METAZOA;

EID: 34447526069     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2007.02.041     Document Type: Article

References (64)

1. Allwood A.C., Walter M., Kamber B., Marshall C., and Burch I. Stromatolite reef from the early Archaean era of Australia. Nature 441 (2006) 714-718
2. Altschul S.F., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
3. Bashford D., Chothia C., and Lesk A.M. Determinants of a protein fold. Unique features of the globin amino acid sequences. J. Mol. Biol. 196 (1987) 199-216
4. Bateman A., et al. The Pfam protein families database. Nucleic Acids Res. 30 (2002) 276-280
5. Battistuzzi F.U., Feijao A., and Hedges S.B. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol. Biol. 4 (2004) 44-54
6. Bekker A., et al. Dating the rise of atmospheric oxygen. Nature 427 (2006) 117-120
7. Bolognesi M., Bordo D., Rizzi M., Tarricone C., and Ascenzi P. Nonvertebrate hemoglobins: structural bases for reactivity. Prog. Biophys. Mol. Biol. 68 (1997) 29-68
8. Dagan T., and Martin W. The tree of one percent. Genome Biol. 7 (2006) 118-125
9. Doolittle W.F. The nature of the universal ancestor and the evolution of the proteome. Curr. Opin. Struct. Biol. 10 (2000) 355-358
10. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32 (2004) 1792-1797
11. Freitas T., et al. Ancestral hemoglobins in Archaea. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 6675-6680
12. Freitas T.A., Saito J., Hou S., and Alam M. Globin-coupled sensors, protoglobins, and the last universal common ancestor. J. Inorg. Biochem. 99 (2005) 23-33
13. Gerstein M., Sonnhammer E.L.L., and Chothia C. Volume changes in protein evolution. J. Mol. Biol. 236 (1994) 1067-1078
14. Gilles-Gonzalez M.A., and Gonzalez G. Heme-based sensors: defining characteristics, recent developments, and regulatory hypotheses. J. Inorg. Biochem. 99 (2005) 1-22
15. Goldblatt C., Lenton T.M., and Watson A.J. Bistability of atmospheric oxygen and the great oxidation. Nature 443 (2006) 683-686
16. Gough J., Karplus K., Hughey R., and Chothia C. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J. Mol. Biol. 313 (2001) 903-919
17. Hedges S.B. The origin and evolution of model organisms. Nature Rev. Genet. 3 (2002) 838-849
18. Hedges S.B., and Kumar S. Genomic clocks and evolutionary timescales. Trends Genet. 19 (2003) 200-206
19. Hedges S.B., Blair J., Venturi M., and Shoe J. A molecular timescale of eukaryote evolution and the rise of complex multicellular life. BMC Evol. Biol. 4 (2004) 2-18
20. Holland H.D. The oxygenation of the atmosphere and oceans. Phil. Trans. Roy. Soc. B 361 (2006) 903-916
21. Hou S., et al. Myoglobin-like aerotaxis transducers in Archaea and bacteria. Nature 403 (2000) 540-544
22. Hou S., et al. Globin-coupled sensors: a class of heme-containing sensors in Archaea and bacteria. Proc. Natl. Acad. Sci. U.S.A. 98 (2001) 9353-9358
23. Huang J., and Gogarten J.P. Ancient horizontal gene transfer can benefit phylogenetic reconstruction. Trends Genet. 22 (2006) 361-366
24. Huelsenbeck J.P., and Ronquist F. MRBAYES: bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
25. Jones D.T., Taylor W.R., and Thornton J.M. The rapid generation of mutation data matrices from protein sequences. Cabios 8 (1992) 275-282
26. Kapp O., Moens L., Vanfleteren J., Trotman C.N.A., Suzuki T., and Vinogradov S.N. Alignment of 700 globin sequences: extent of amino acid substitution and its correlation in volume. Protein Sci. 4 (1995) 2179-2190
27. Katoh K., Kuma K., Toh H., and Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33 (2005) 511-518
28. Koeberl C. The record of impact processes on the early Earth. In: Reimold W.U., and Gibson R.L. (Eds). Processes on the Early Earth, Geological Society of America Special Paper vol. 405 (2006) 1-22
29. Koonin E.V. Comparative genomics minimal gene-sets and the last universal common ancestor. Nature Rev. Microbiol. 1 (2003) 127-136
30. Kurland C.G., Collins L.J., and Penny D. Genomics and the irreducible nature of eukaryote cells. Science 312 (2006) 1011-1014
31. Lecomte J.T.L., Vuletich D., and Lesk A.M. Structural divergence and distant relationships in proteins: evolution of the globins. Curr. Opinion Struct. Biol. 15 (2005) 290-301
32. Lesk A.M., and Chothia C. How different amino acid sequences determine similar protein structures. The structure and evolutionary dynamics of the globins. J. Mol. Biol. 136 (1980) 225-270
33. Lester L., Meade A., and Pagel M. The slow road to the eukaryotic genome. Bioessays 28 (2006) 57-64
34. Marchler-Bauer A., and Bryant S. CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 32 (2004) W327-W331
35. Marsh L. Evolution of structural shape in bacterial globin-related proteins. J. Mol. Evol. 62 (2006) 575-587
36. Moens L., et al. Globins in nonvertebrate species: dispersal by horizontal gene transfer and evolution of the structure-function relationships. Mol. Biol. Evol. 13 (1996) 324-333
37. Moran N.A. Tracing the evolution of gene loss in obligate bacterial symbionts. Curr. Opin. Microbiol. 6 (2003) 512-518
38. Nuin P.A.S., Wang Z., and Tillier E.R.M. The accuracy of several multiple sequence alignment programs for proteins. BMC Bioinformatics 7 (2006) 471-479
39. Pastore A., and Lesk A.M. Comparison of the structures of globins and phycocyanins: evidence for evolutionary relationship. Prot. Struct. Func. Genet. 8 (1990) 133-155
40. Poole R.K., and Hughes M.N. New functions for the ancient globin family: bacterial responses to nitric oxide and nitrosative stress. Mol. Microbiol. 36 (2000) 775-783
41. Poole R.K. Nitric oxide and nitrosative stress tolerance in bacteria. Biochem. Soc. Trans. 33 (2005) 176-180
42. Ranea J.A., Sillero A., Thornton J.M., and Orengo C.A. Protein superfamily evolution and the Last Universal Common Ancestor (LUCA). J. Mol. Evol. 63 (2006) 13-25
43. Redei G.P., Koncz C., and Phillips J.D. Changing images of the gene. Adv. Genet. 56 (2006) 53-100
44. Richards T.A., and van der Giezen M. Evolution of the Isd11-IscS complex reveals a single-proteobacterial endosymbiosis for all eukaryotes. Mol. Biol. Evol. 23 (2006) 1341-1344
45. Rivera M.C., and Lake J.A. The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 431 (2004) 152-155
46. Rodriguez-Ezpeleta N., et al. Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes. Curr. Biol. 15 (2005) 1325-1330
47. Runnegar B. Derivation of the globins from type b cytochromes. J. Mol. Evol. 21 (1984) 33-41
48. Schaffer A.A., et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 29 (2001) 2994-3005
49. Shi J., Blundell T., and Mizuguchi K. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol. 310 (2001) 243-257
50. Simonson A.B., Servin J., Skophammer R., Herbold C., Rivera M., and Lake J.A. Decoding the genomic tree of life. Proc. Natl. Acad. Sci. U. S. A. 102 Suppl 1 (2005) 6608-6613
51. Sri Krishna S., Sadreyev R.I., and Grishin N.V. A tale of two ferredoxins: sequence similarity and structural differences. BMC Struct. Biol. 6 (2006) 8-19
52. Subbiah S., Laurents D.V., and Levitt M. Structural similarity of DNA-binding domains of bacteriophage repressors and the globin core. Curr. Biol. 3 (1993) 141-148
53. Ueno Y., Yamada K., Yoshida N., Maryama S., and Isozaki Y. Evidence from fluid inclusions for microbial methanogenesis in the early Archaean era. Nature 440 (2006) 516-519
54. Vinogradov S.N., et al. Three globin lineages belonging to two structural classes in genomes from the three kingdoms of life. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 11385-11389
55. Vinogradov S.N., et al. A phylogenomic profile of globins. BMC Evol. Biol. 6 (2006) 31-67
56. Vuletich D., and Lecomte J.T.J. A phylogenetic and structural analysis of truncated hemoglobins. J. Mol. Evol. 62 (2006) 196-210
57. Wang M., and Caetano-Anolles G. Global phylogeny determined by the combination of protein domains in proteomes. Mol. Biol. Evol. 23 (2006) 2444-2454
58. Westall F., et al. The 3.466 Ga "Kitty's Gap Chert", an early Archean microbial ecosystem. In: Reimold W.U., and Gibson R.L. (Eds). Processes on the Early Earth, Geological Society of America Special Paper vol. 405 (2006) 105-131
59. Wittenberg J.B., et al. Truncated hemoglobins: a new family of hemoglobins widely distributed in bacteria, unicellular eukaryotes, and plants. J. Biol. Chem. 277 (2002) 871-874
60. Woese C.R. The universal ancestor. Proc.Natl. Acad. Sci. U. S. A. 95 (1998) 6854-6859
61. Woese C.R. On the evolution of cells. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 8742-8747
62. Wu G., Wainwright L., and Poole R.K. Microbial globins. Adv. Microb. Physiol. 47 (2003) 255-310
63. Yu H., et al. Aerotactic responses in bacteria to photoreleased oxygen. FEMS Microbiol. Lett. 217 (2002) 237-242
64. Zhang W., and Phillips Jr. G.N. Structure of the oxygen sensor in Bacillus subtilis. signal transduction of chemotaxis by control of symmetry. Structure 11 (2003) 1097-1108