A phylogenomic profile of globins

BMC Evolutionary Biology

Volumn 6, Issue , 2006, Pages

  Vinogradov, Serge N ^a   Hoogewijs, David ^b   Bailly, Xavier ^c   Arredondo Peter, Raúl ^d   Gough, Julian ^e   Dewilde, Sylvia ^f   Moens, Luc ^f   Vanfleteren, Jacques R ^b  

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

^b GHENT UNIVERSITY   (Belgium)

^c STATION BIOLOGIQUE   (France)

^d UNIVERSIDAD AUTÓNOMA DEL ESTADO DE MORELOS   (Mexico)

^e RIKEN YOKOHAMA INSTITUTE   (Japan)

^f UNIVERSITY OF ANTWERP   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

GLOBIN; TRUNCATED HEMOGLOBIN;

ARCHAEBACTERIUM; ARTICLE; BACTERIAL GENOME; BACTEROIDETES; BIOSENSOR; CAENORHABDITIS; CHLAMYDIA; CHLOROBI; CILIATE; CONTROLLED STUDY; ENCEPHALITOZOON; ENTAMOEBA; EUKARYOTIC CELL; FLAGELLATE; FUNGUS; GENE SEQUENCE; GENOME SIZE; GREEN ALGA; LACTOBACILLALES; METAZOON; MOLECULAR EVOLUTION; MOLLICUTES; NEMATODE; NONHUMAN; NUCLEOTIDE SEQUENCE; PASTEURELLALES; PHYLOGENETIC TREE; PHYLOGENY; PLASMODIUM; PROTEIN DOMAIN; PROTEIN FUNCTION; RED ALGA; RICKETTSIALES; SPIROCHETE; SYMBIOSIS; TRYPANOSOMA; AMINO ACID SEQUENCE; ANIMAL; ARCHAEAL GENE; BACTERIAL GENE; CLASSIFICATION; COMPARATIVE STUDY; FUNGAL GENE; GENE; GENETICS; GENOME; HUMAN; MOLECULAR GENETICS; PLANT GENE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; VERTEBRATE;

ANIMALIA; ARCHAEA; BACTERIA (MICROORGANISMS); BACTEROIDETES; CAENORHABDITIS; CHLAMYDIA; CHLOROBI; CHLOROPHYTA; CILIOPHORA; DIPLOMONADIDA; ENCEPHALITOZOON; ENTAMOEBA; EUKARYOTA; FUNGI; LACTOBACILLALES; MASTIGOPHORA (FLAGELLATES); METAZOA; MOLLICUTES; MYCETOZOA; PASTEURELLALES; PLASMODIUM (APICOMPLEXA); PROTISTA; RHODOPHYTA; RICKETTSIALES; SPIROCHAETALES; SPIROCHAETES; TRYPANOSOMA;

AMINO ACID SEQUENCE; ANIMALS; EVOLUTION, MOLECULAR; GENES, ARCHAEAL; GENES, BACTERIAL; GENES, FUNGAL; GENES, HELMINTH; GENES, INSECT; GENES, PLANT; GENOME; GLOBINS; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SPECIES SPECIFICITY; TRUNCATED HEMOGLOBINS; VERTEBRATES;

EID: 33646370983     PISSN: 14712148     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-6-31     Document Type: Article

References (147)

1. Appleby C: Leghemoglobin and rhizobium respiration. Ann Rev Plant Physiol 1984, 345:443-478.
2. Vinogradov SN, Walz DA, Pohajdak B, Moens L, Kapp O, Suzuki T, Trotman C: Adventitious variability? The amino acid sequences of nonvertebrate globins. Comp Biochem Physiol 1993, B106:1-26.
3. Weber RE, Vinogradov SN: Nonvertebrate hemoglobins: functions and molecular adaptations. Physiol Rev 2001, 81:569-628.
4. Arredondo-Peter R, Hargrove MS, Moran J, Sarath G, Klucas RV: Plant hemoglobins. Plant Physiol 1998, 118:1121-1125.
5. Ross E, Lira-Ruan V, Arredondo-Peter R, Klucas R, Sarath G: Recent insights into plant hemoglobins. Rev Plant Biochem Biotechnol 2002, 1:173-189.
6. Dordas C, Rivoal J, Hill RD: Plant haemoglobins, nitric oxide and hypoxic stress. Ann Bot (Lond) 2003, 91:173-178.
7. Vasudevan S, Armarego W, Shaw D, Lilley P, Dixon N, Poole RK: Isolation and nucleotide sequence of the hmp gene that encodes a haemoglobin-like protein in Escherichia coli K-12. Mol Gen Genet 1991, 226:49-58.
8. Iwaasa H, Takagi T, Shikama K: Amino acid sequence of yeast hemoglobin. A twodomain structure. J Mol Biol 1992, 227:948-954.
9. Zhu H, Riggs A: Yeast flavohemoglobin is an ancient protein related to globins and a reductase family. Proc Natl Acad Sci USA 1992, 89:5015-5019.
10. Takagi T: Hemoglobins from single-celled organisms. Curr Opinion Struct Biol 1993, 3:413-418.
11. Potts M, Angeloni S, Ebel R, Bassam D: Myoglobin in a cyanobacterium. Science 1992, 256:1690-1692.
12. Kaneko T, Tabata S: Complete genome structure of the unicellular cyanobacterium Synechocystis sp. PCC6803. Plant Cell Physio 1997, 38:1171-1176.
13. Scott N, Falzone C, Vuletich D, Zhao J, Bryant V, Lecomte JT: Truncated hemoglobin from the cyanobacterium Synechococcus sp. PCC 7002: evidence for hexacoordination and covalent adduct formation in the ferric recombinant protein. Biochemistry 2002, 41:6902-6910.
14. Vandergon T, Riggs C, Gorr T, Colacino J, Riggs A: The mini-hemoglobins in neural and body wall tissue of the nemertean worm Cerebratulus lacteus. J Biol Chem 1998, 273:16998-17011.
15. Couture M, Yeh S, Wittenberg BA, Wittenberg JB, Ouellet Y, Rousseau D, Guertin M: A cooperative oxygen-binding hemoglobin from Mycobacterium tuberculosis. Proc Natl Acad Sci USA 1999, 96:1223-11228.
16. Wittenberg JB, Bolognesi M, Wittenberg BA, Guertin M: Truncated hemoglobins: a new family of hemoglobins widely distributed in bacteria, unicellular eukaryotes, and plants. J Biol Chem 2002, 277:871-874.
17. Couture M, Chamberland H, St-Pierre B, Lafontaine J, Guertin M: Nuclear genes encoding chloroplast hemoglobins in the unicellular green alga Chlamydomonas eugametos. Mol Gen Genet 1994, 243:185-197.
18. Couture M, Das T, Lee H, Peisach J, Rousseau D, Wittenberg BA, Wittenberg JB, Guertin M: Chlamydomonas chloroplast ferrous hemoglobin. Heme pocket structure and reactions with ligands. J Biol Chem 1999, 274:6898-6910.
19. Watts R, Hunt P, Hvitved A, Hargrove M, Peacock W, Dennis E: A hemoglobin from plants homologous to truncated hemoglobins of microorganisms. Proc Natl Acad Sci USA 2001, 98:10119-101124.
20. Pesce A, Couture M, Dewilde S, Guertin M, Yamauchi K, Ascenzi P, Moens L, Bolognesi M: A novel two-over-two alpha-helical sandwich fold is characteristic of the truncated hemoglobin family. EMBO J 2000, 19:2424-2434.
21. 2 diffusion to the haem. EMBO J 2001, 20:3902-3909.
22. Milani M, Savard P, Oullet H, Ascenzi P, Guertin M, Bolognesi M: A TyrCD1/TrpG8 hydrogen bond network and a TyrB10-TyrCD1 covalent link shape the heme distal site of Mycobacterium tuberculosis hemoglobin O. Proc Natl Acad Sci USA 2003, 100:5766-5771.
23. Blaxter ML: Nemoglobins: divergent nematode globins. Parasitology Today 1993, 9:353-360.
24. Kloek A, Sherman D, Goldberg DE: Novel gene structure and evolutionary context of Caenorhabditis elegans globin. Gene 1993, 129:215-221.
25. Kloek A, McCarter J, Setterquist R, Schedl T, Goldberg DE: Caenorhabditis globin genes: rapid intronic divergence contrasts with conservation of silent exonic sites. J Mol Evol 1996, 43:101-108.
26. Blaxter ML, Ingram L, Tweedie S: Sequence, expression and evolution of the globins of the parasitic nematode Nippostrongylus brasiliensis. Mol Biochem Parasitol 1994, 68:1-14.
27. Mansell J, Timms K, Tate W, Moens L, Trotman CN: Expression of a globin gene in Caenorhabditis elegans. Biochem Mol Biol Int 1993, 30:643-647.
28. Vanfleteren JR, Van de Peer Y, Blaxter M, Tweedie S, Trotman C, Lu L, Van Hauwaert M, Moens L: Molecular genealogy of some nematode taxa based on cytochrome c and globin amino acid sequences. Mol Phylogenet Evol 1994, 3:92-101.
29. Neuwald A, Liu J, Lipman D, Lawrence C: Extracting protein alignment models from the sequence database. Nucl Acids Re 1997, 25:1665-1677.
30. Hoogewijs D, Geuens E, Dewilde S, Moens L, Vierstraete A, Vinogradov SN, Vanfleteren JR: Genome-wide analysis of the globin gene family of C. elegans. IUBMB Life 2004, 56:697-702.
31. Burmester T, Hankeln T: A globin gene of Drosophila melanogaster. Mol Biol Evol 1999, 16:1809-1811.
32. Ebner B, Burmester T, Hankeln T: Globin genes are present in Ciona intestinalis. Mol Biol Evo 2003, 20:1521-1525.
33. Burmester T, Weich B, Reinhardt S, Hankeln T: A vertebrate globin expressed in the brain. Nature 2000, 407:520-523.
34. Trent J, Watts R, Hargrove M: Human neuroglobin, a hexacoordinate hemoglobin the reversibly binds oxygen. J Biol Chem 2001, 276:30106-30110.
35. Kawada N, Kristensen D, Asahina K, Nakatani K, Minamiyama Y, Seki S, Yoshizato K: Characterization of a stellate cell-activation associated protein (STAP) with peroxidase activity found in rat hepatic stellate cells. J Biol Chem 2001, 276:25318-25323.
36. Burmester T, Ebner B, Weich B, Hankeln T: Cytoglobin: a novel globin type ubiquitously expressed in vertebrate tissues. Mol Biol Evol 2002, 19:416-421.
37. Trent J, Hargrove MS: A ubiquitously expressed human hexacoordinate hemoglobin. J Biol Chem 2002, 277:19538-19545.
38. Hankeln T, Ebner B, Fuchs C, Gerlach F, Haberkamp M, Laufs TL, Roesner A, Schmidt M, Weich B, Wystub S, Saaler-Reinhardt S, Reuss S, Bolognesi M, De Sanctis D, Marden MC, Kiger L, Moens L, Dewilde S, Nevo E, Avivi A, Weber RE, Fago A, Burmester T: Neuroglobin and cytoglobin in search of their role in the vertebrate globin family. J Inorg Biochem 2005, 99:110-119.
39. Kugelstadt D, Haberkamp M, Hankeln T, Burmester T: Neuroglobin, cytoglobin, and a novel, eye-specific globin from chicken. Biochem Biophys Res Commun 2004, 325:719-225.
40. Roesner A, Fuchs C, Hankeln T, Burmester T: A globin gene of ancient evolutionary origin in lower vertebrates: evidence for two distinct globin families in animals. Mol Biol Evol 2005, 22:12-20.
41. Poole RK, Hughes MN: New functions for the ancient globin family: bacterial responses to nitric oxide and nitrosative stress. Mol Microbiol 2000, 36:775-783.
42. Frey AD, Kallio PT: Bacterial hemoglobins and flavohemoglobins: versatile proteins and their impact on microbiology and biotechnology. FEMS Microbiol Rev 2003, 27:525-545.
43. Wu G, Wainwright L, Poole RK: Microbial globins. Adv Microb Physiol 2003, 47:255-310.
44. Hou S, Larsen R, Boudko D, Riley C, Karatan E, Zimmer M, Ordal G, Alam M: Myoglobin-like aerotaxis transducers in Archaea and Bacteria. Nature 2000, 403:540-544.
45. Yu H, Saw J, Hou S, Larsen R, Watts K, Johnson M, Zimmer M, Ordal G, Taylor B, Alam M: Aerotactic responses in bacteria to photoreleased oxygen. FEMS Microbiol Lett 2002, 217:237-242.
46. Hou S, Freitas T, Larsen R, Piatibratov M, Sivozhelezev V, Yamamoto A, Meleshkevitch E, Zimmer M, Ordal G, Alam M: Globin-coupled sensors: a class of heme-containing sensors in Archaea and Bacteria. Proc Natl Acad Sci USA 2001, 98:9353-9358.
47. Freitas T, Hou S, Alam M: The diversity of globin-coupled sensors. FEBS Lett 2003, 552:99-104.
48. Freitas T, Hou S, Dioum E, Saito J, Newhouse J, Gonzalez G, Gilles-Gonzalez MA, Alam M: Ancestral hemoglobins in Archaea. Proc Natl Acad Sci USA 2004, 101:6675-6680.
49. Vinogradov SN, Hoogewijs D, Bailly X, Arredondo-Peter R, Guertin M, Gough J, Dewilde S, Moens L, Vanfleteren JR: Three globin lineages belonging to two structural classes in genomes from the three kingdoms of life. Proc Natl Acad Sc USA 2005, 102:11385-11389.
50. Baldauf SL, Bjattacharya D, Cockrill J, Hugenholtz D, Pawlowski J, Simpson A: The tree of life. An overview. In Assembling the Tree of Life Edited by: Cracraft J, Donaghue MJ. Oxford University Press, Oxford, UK; 2004:43-75.
51. Zhang W, Phillips GN Jr: Structure of the oxygen sensor in Bacillus subtilis. signal transduction of chemotaxis by control of symmetry. Structure 2003, 11:1097-1108.
52. Schleper C, Jurgens G, Jonuscheit M: Genomic studies of uncultivated Archaea. Nature Rev Microbiol 2005, 3:479-488.
53. Vuletich D, Lecomte JTJ: A phylogenetic and structural analysis of truncated hemoglobins. J Mol Evol 2006, 62:196-210.
54. Lira-Ruan V, Sarath G, Klucas RV, Arredondo-Peter R: In silico analysis of a flavohemoglobin from Sinorhizobium meliloti strain 1021. Microbiol Res 2003, 158:215-227.
55. Wakabayashi S, Matsubara H, Webster D: Primary sequence of a dimeric bacterial haemoglobin from Vitreoscilla. Nature 322:481-483.
56. Kim Y, Joachimiak A, Skarina T, Bochkarev A, Savchenko A, Edwards A: Crystal structure of Pa3967 from Pseudomonas aeruginosa Pao1, a hypothetical protein which is highly homologous to human hemoglobin in structure. 2004. unpublished
57. Tarricone C, Galizzi A, Coda A, Ascenzi P, Bolognesi M: Unusual structure of the oxygen-binding site in the dimeric bacterial hemoglobin from Vitreoscilla sp. Structure 1997, 5:497-507.
58. Ilari A, Bonamore A, Farina A, Johnson K, Boffi A: The X-ray structure of ferric Escherichia coli flavohemoglobin reveals an unexpected geometry of the distal heme pocket. J Biol Chem 2002, 277:23725-23732.
59. Ermler U, Siddiqui R, Cramm R, Friedrich B: Crystal structure of the flavohemoglobin from Alcaligenes eutrophus at 1.75 A resolution. EMBO J 1995, 14:6067-6077.
60. Vandamme P, Coenye T: Taxonomy of the genus Cupriavidus : a tale of lost and found. Int J Syst Evol Microbiol 2004, 54:2285-2289.
61. Freitas T, Saito J, Hou S, Alam M: Globin-coupled sensors, protoglobins, and the last universal common ancestor. J Inorg Biochem 2005, 99:23-33.
62. Zhang W, Phillips GN Jr: Structure of the oxygen sensor in Bacillus subtilis. signal transduction of chemotaxis by control of symmetry. Structure 2003, 11:1097-1108.
63. Moran NA: Tracing the evolution of gene loss in obligate bacterial symbionts. Curr Opinion Microbiol 2003, 6:512-518.
64. Goh S-H, Lee Y, Bhanu N, Cam M, Desper R, Martin B, Moharram R, Gherman R, Miller JL: A newly discovered human α-globin gene. Blood 2005, 106:1466-1472.
65. Brownlie A, Hersey C, Oates A, Paw B, Falick B, Witkowska H, Flint J, Higgs D, Jessen J, Bahary N, Zhu H, Lin S, Zon L: Characterization of embryonic globin genes of the zebrafish. Dev Biol 2003, 255:48-61.
66. Gillemans N, McMorrow T, Tewari R, Wai A, Burgtorf C, Drabek D, Ventress N, Langeveld A, Higgs D, Tan-Un K, Grosveld F, Philipsen S: Functional and comparative analysis of globin loci in pufferfish and humans. Blood 2003, 101:2842-2849.
67. Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM, Harafuji N, Hastings KE, Ho I, Hotta K, Huang W, Kawashima T, Lemaire P, Martinez D, Meinertzhagen IA, Necula S, Nonaka M, Putnam N, Rash S, Saiga H, Satake M, Terry A, Yamada L, Wang HG, Awazu S, Azumi K, Boore J, Branno M, Chin-Bow S, DeSantis R, Doyle S, Francino P, Keys DN, Haga S, Hayashi H, Hino K, Imai KS, Inaba K, Kano S, Kobayashi K, Kobayashi M, Lee BI, Makabe KW, Manohar C, Matassi G, Medina M, Mochizuki Y, Mount S, Morishita T, Miura S, Nakayama A, Nishizaka S, Nomoto H, Ohta F, Oishi K, Rigoutsos I, Sano M, Sasaki A, Sasakura Y, Shoguchi E, Shin-i T, Spagnuolo A, Stainier D, Suzuki MM, Tassy O, Takatori N, Tokuoka M, Yagi K, Yoshizaki F, Wada S, Zhang C, Hyatt PD, Larimer F, Detter C, Doggett N, Glavina T, Hawkins T, Richardson P, Lucas S, Kohara Y, Levine M, Satoh N, Rokhsar DS: The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 2002, 298:2157-2167.
68. Small D, Moylan T, Vayda M, Sidell BD: The myoglobin gene of the Antarctic icefish, Chaenocephalus aceratus, contains a duplicated TATAAAA sequence that interferes with transcription. J Exp Biol 206:131-139.
69. Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, Cherry JM, Henikoff S, Skupski MP, Misra S, Ashburner M, Birney E, Boguski MS, Brody T, Brokstein P, Celniker SE, Chervitz SA, Coates D, Cravchik A, Gabrielian A, Galle RF, Gelbart WM, George RA, Goldstein LS, Gong F, Guan P, Harris NL, Hay BA, Hoskins RA, Li J, Li Z, Hynes RO, Jones SJ, Kuehl PM, Lemaitre B, Littleton JT, Morrison DK, Mungall C, O'Farrell PH, Pickeral OK, Shue C, Vosshall LB, Zhang J, Zhao Q, Zheng XH, Lewis S: Comparative genomics of the eukaryotes. Science 287:2204-2215.
70. Hankeln T, Jaenicke V, Kiger L, Dewilde S, Ungerechts G, Schmidt M, Urban J, Marden M, Moens L, Burmester T: Characterization of Drosophila hemoglobin. Evidence for hemoglobin-mediated respiration in insects. J Biol Chem 2002, 277:29012-29017.
71. Richards S, Liu Y, Bettencourt B, Hradecky P, et al.: Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene and cis-element evolution. Genome Res 2005, 15:1-18.
72. Trevaskis B, Watts R, Andersson C, Llewellyn D, Hargrove MS, Olson JS, Dennis ES, Peacock WJ: Two hemoglobin genes in Arabidopsis thaliana : the evolutionary origins of leghemoglobins. Proc Natl Acad Sci USA 1997, 94:12230-12234.
73. Arredondo-Peter R, Hargrove M, Sarath G, Moran J, Lohrman J, Olson JS, Klucas RV: Rice haemoglobins. Gene cloning, analysis, and O-binding kinetics of a recombinant protein synthesized in Escherichia coli. Plant Physiol 1997, 115:1259-1266.
74. Lira-Ruan V, Ross E, Sarath G, Klucas RV, Arredondo-Peter R: Mapping and analysis of a hemoglobin gene family from Oryza sativa. Plant Physiol Biochem 2002, 40:199-202.
75. Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, et al.: Genome evolution in yeasts. Nature 2004, 430:35-44.
76. Sartori G, Aldegheri L, Mazzotta G, Lanfranchi G, Tournu H, Brown A, Carignani G: Characterization of a new hemoprotein in the yeast Saccharomyces cerevisiae. J Biol Chem 1999, 274:5032-5037.
77. Andersson J, Sjogren A, Davis L, Embley T, Roger RJ: Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes. Curr Biol 2003, 31:94-102.
78. Iijima M, Shimizu H, Tanaka Y, Urushihara H: Identification and characterization of two flavohemoglobin genes in Dictyostelium discoideum. Cell Struct Funct 2000, 25:47-55.
79. Hemmingsen EA: Respiratory and cardiovascular adaptation in hemoglobin-free fish: resolved and unresolved problems. In Biology of Antarctic Fish Edited by: di Prisco G, Maresca B, Tota B. Springer-Verlag, New York; 1991:191-203.
80. Vayda M, Small D, Yuan M, Costello L, Sidell B: Conservation of the myoglobin gene among Antarctic notothenioid fishes. Mol Mar Biol Biotechnol 1997, 6:207-216.
81. diPrisco G, Cocca E, Parker S, Detrich H: Tracking the evolutionary loss of hemoglobin expression by the white-blooded Antarctic icefishes. Gene 2002, 295:185-191.
82. Bargelloni L, Lecointre G: Four years of notothenioid systematics: a molecular perspective. In Fishes of Antarctica Edited by: di Prisco G, Pisano E, Clarke A. Springer-Verlag Italia, Milan, Italy; 1998:259-273.
83. Bishop J, Vandergon T, Green D, Doeller J, Kraus D: A high-affinity hemoglobin is expressed in the notochord of amphioxus, Branchiostoma californiense. Biol Bull 1998, 195:255-259.
84. Baker S, Terwilliger NB: Hemoglobin structure and function in the rat-tailed sea cucumber Paracaudina chilensis. Biol Bull 1993, 185:115-122.
85. Christensen A, Colacino J, Bonaventura C: Functional and biochemical properties of the hemoglobins of the burrowing brittle star Hemipholis elongata Say (Echinodermata, Ophiuroidea). Biol Bull 2003, 205:54-65.
86. Nielsen E, Mound L: Global diversity of insects: the problem of estimating numbers. In Nature and Human Society: The Quest for a Sustainable World Edited by: Raven PH. National Academy Press, Washington, DC; 1997:213-222.
87. Moreira D, Lopez-Garcia P: The molecular ecology of microbial eukaryotes unveils a hidden world. Trends Microbiol 2002, 10:31-38.
88. Falkowski P, Katz M, Knoll A, Quigg A, Raven J, Schofield O, Taylor F: The evolution of modern eukaryotic phytoplankton. Science 2004, 305:354-360.
89. Uma S, Matts R, Guo Y, White S, Chen JJ: The N-terminal region of the heme-regulated eIF2alpha kinase is an autonomous heme binding domain. Eur J Biochem 2000, 267:498-506.
90. Rafie-Kolpin M, Chefalo P, Hussain Z, Hahn J, Uma S, Matts R, Chen JJ: Two heme-binding domains of heme-regulated eukaryotic initiation factor-2alpha kinase. N terminus and kinase insertion. J Biol Chem 2000, 275:5171-5178.
91. Inuzuka T, Yun B, Ishikawa H, Takahashi S, Hori H, Matts R, Ishimori K, Morishima I: Identification of crucial histidines for heme binding in the N-terminal domain of the heme-regulated eIF2alpha kinase. J Biol Chem 2004, 279:6778-6782.
92. LaCount M, Zhang E, Chen Y, Han K, Whitton M, Lincoln D, Woodin S, Lebioda L: The crystal structure and amino acid sequence of dehaloperoxidase from Amphitrite ornat a indicate common ancestry with globins. J Biol Chem 2000, 27:18712-18716.
93. Hourdez S, Lallier F, De Cian M, Green B, Weber R, Toulmond A: Gas transfer system in Alvinella pompejana: functional properties of intracellular and extracellular hemoglobins. Physiol Biochem Zool 2000, 73:365-373.
94. Hardison RC: Organization, evolution and regulation of the globin genes. In Disorders of Hemoglobin Edited by: Steinberg MH, Forget BG, Higgs DR, Nagel RL. Cambridge University Press, Cambridgge, UK; 2001:95-116.
95. Goodman M, Pedwaydon J, Czelusniak J, Suzuki T, Gotoh T, Moens L, Shishikura F, Walz DA, Vinogradov SN: An evolutionary tree for invertebrate globin sequences. J Mol Evol 1988, 27:236-249.
96. Moens L, Vanfleteren J, Van de Peer Y, Peeters K, Kapp O, Czeluzniak J, Goodman M, Blaxter M, Vinogradov SN: Globins in nonvertebrate species: dispersal by horizontal gene transfer and evolution of the structure-function relationships. Mol Biol Evol 1996, 13:324-333.
97. Nakajima S, Álvarez-Salgado E, Kikuchi T, Arredondo-Peter R: Prediction of folding pathway and kinetics among plant hemoglobins using an average distance map method. Proteins Struct Funct Bioinfor 2005, 61:500-506.
98. Farres J, Rechsteiner M, Herold S, Frey AD, Kallio PT: Ligand binding properties of bacterial hemoglobins and flavohemoglobins. Biochemistry 2005, 44:4125-4134.
99. Gardner PM: Nitric oxide dioxygenase function and mechanism of flavohemoglobins, hemoglobins, myoglobins and their associated reductases. J Inorg Biochem 2005, 99:247-266.
100. Poole RK: Nitric oxide and nitrosative stress tolerance in bacteria. Biochem Soc Trans 2005, 33:176-180.
101. Bonamore A, Gentili P, Ilari A, Schinina M, Boffi A: Escherichia coli flavohemoglobin is an efficient alkylhydroperoxide reductase. J BiolChem 2003, 278:22272-22277.
102. Bonamore A, Farina A, Gattoni M, Schinina M, Bellelli A, Boffi A: Interaction with membrane lipids and heme ligand binding properties of Escherichia coli flavohemoglobin. Biochemistry 2003, 42:5792-5801.
103. D'Angelo P, Lucarelli D, della Longa S, Benfatto M, Hazemann J, Feis A, Smulevich G, Ilari A, Bonamore A, Boffi A: Unusual heme iron-lipid acyl chain coordination in Escherichia coli flavohemoglobin. Biophys J 2004, 86:3882-3892.
104. Frey AD, Kallio PT: Nitric oxide detoxification - a new era for bacterial globins in biotechnology? Trends Biotechnol 2005, 23:69-73.
105. Elvers K, Wu G, Gilberthorpe N, Poole RK, Park SF: Role of an inducible single-domain hemoglobin in mediating resistance to nitric oxide and nitrosative stress in Campylobacter jejuni and Campylobacter coli. J Bacteriol 2004, 186:5332-5341.
106. Wu G, Wainwright L, Membrillo-Hernández J, Poole RK: Bacterial hemoglobins: old proteins with "new" functions? Roles of respiratory and nitric oxide metabolism. In Respiration in Archea and Bacteria, Diversity of Prokaryotic Electron Transport Carriers Volume 1. Edited by: Zanoni D. Academic Press, London, UK; 2004:255-310.
107. Buisson N, Labbe-Bois R: Flavohemoglobin expression and function in Saccharomyces cerevisia e. No relationship with respiration and complex response to oxidative stress. J Biol Chem 1998, 273:9527-9533.
108. Elvers K, Turner S, Wainwright L, Marsden G, Hinds J, Cole J, Poole RK, Penn C, Park SF: NssR, a member of the Crp-Fnr superfamily from Campylobacter jejuni, regulates a nitrosative stress-responsive regulon that includes both a single-domain and a truncated haemoglobin. Mol Microbiol 2005, 57:735-750.
109. Liu L, Zeng M, Hausladen A, Heitman J, Stamler J: Protection from nitrosative stress by yeast flavohemoglobin. Proc Natl Acad Sci USA 2000, 97:4672-4676.
110. Shikama K, Matsuoka A: Structure-function relationships in unusual nonvertebrate globins. Crit Rev Biochem Mol Biol 2004, 39:217-259.
111. Stevanin T, Poole RK, Demoncheaux E, Read R: Flavohemoglobin Hmp protects Salmonella enterica serovar typhimurium from nitric oxide-related killing by human macrophages. Infect Immun 2000, 70:4399-4405.
112. Ullmann B, Myers H, Chiranand W, Lazzell A, Zhao Q, Vega L, Lopez-Ribot J, Gardner PR, Gustin M: Inducible defense mechanism against nitric oxide in Candida albicans. Eukaryote Cell 2004, 3:715-723.
113. de Jesus-Berrios M, Liu L, Nussbaum J, Cox G, Stamler J, Heitman J: Enzymes that counteract nitrosative stress promote fungal virulence. Curr Biol 2003, 13:1963-1968.
114. Idnurm A, Reedy J, Nussbaum J, Heitman J: Cryptococcus neoformans virulence gene discovery through insertional mutagenesis. Eukaryote Cell 2004, 3:420-429.
115. Ott T, van Dongen J, Gunther C, Krusell L, Desbrosses G, Vigeolas H, Bock V, Czechowski T, Geigenberger P, Udvardi MK: Symbiotic leghemoglobins are crucial for nitrogen fixation in legume root nodules but not for general plant growth and development. Curr Biol 2005, 15:531-5.
116. Kundu S, Trent J, Hargrove M: Plants, humans and hemoglobins. Trends Plant Sci 2003, 8:387-393.
117. Igamberdiev A, Baron K, Manac'h-Little N, Stoimenova M, Hill RD: The haemoglobin/nitric oxide cycle: involvement in floooding stress and effects of hormone signaling. Ann Bot 2005, 96:557-564.
118. Gilles-Gonzalez MA, Gonzalez G: Heme-based sensors: defining characteristics, recent developments, and regulatory hypotheses. J Inorg Biochem 2005, 99:1-22.
119. Bailly X, Jollivet D, Vanin S, Deutsch J, Zal F, Lallier F, Toulmond A: Evolution of the sulfide-binding function within the globin multigenic family of the deep-sea hydrothermal vent tube-worm Riftia pachyptila. Mol Biol Evol 2002, 19:1421-1433.
120. 2 S-binding function in annelids from sulfide-free habitats reveals molecular adaptation driven by Darwinian positive selection. Proc Natl Acad Sci USA 2003, 100:5885-5890.
121. Lecomte JTL, Vuletich D, Lesk AM: Structural divergence and distant relationships in proteins: evolution of the globins. Curr Opinion Struct Biol 2005, 15:290-301.
122. Ouellet H, Ouellet Y, Richard C, Labarre M, Wittenberg BA, Wittenberg JB, Guertin M: Truncated hemoglobin HbN protects Mycobacterium bovis from nitric oxide. Proc Natl Acad Sci USA 2002, 99:5902-5907.
123. Pathania R, Navani N, Rajamohan G, Dikshit KL: Mycobacterium tuberculosis hemoglobin HbO associates with membranes and stimulates cellular respiration of recombinant Escherichia coli. J Biol Chem 2002, 277:15293-15302.
124. Pathania R, Navani N, Gardner AM, Gardner PR, Dikshit KL: Nitric oxide scavenging and detoxification by the Mycobacterium tuberculosis haemoglobin. Mol Microbiol 2002, 45:1303-1314.
125. Milani M, Pesce A, Ouellet H, Guertin M, Bolognesi M: Truncated hemoglobins and nitric oxide action. IUBMB Life 2003, 55:623-627.
126. Mukai M, Savard P, Ouellet H, Guertin M, Yeh S: Unique ligand-protein interactions in a new truncated hemoglobin from Mycobacterium tuberculosis. Biochemistry 2002, 41:3897-3905.
127. Goldberg DE: Oxygen-avid hemoglobin of Ascaris. Chem Rev 1999, 99:3371-3378.
128. Minning D, Gow A, Bonaventura J, Braun R, Dewhirst M, Goldberg D, Stamler J: Ascaris haemoglobin is a nitric oxide-activated 'deoxygenase'. Nature 1999, 401:497-502.
129. Suzuki T, Imai K: Evolution of myoglobin. Cell Mol Life Sci 1998, 54:979-1004.
130. Immesberger A, Burmester T: Putative phenoloxidases in the tunicate Ciona intestinali s and the origin of the arthropod hemocyanin superfamily. J Comp Physiol 2004, B174:169-180.
131. Karlsen O, Ramsevik L, Bruseth L, Larsen Ø, Brenner A, Berven F, Jensen H, Lillhaug J: Characterization of a prokaryotic haemerythrin from the methanotrophic bacterium Methylococcus capsulatu s (Bath). FEBS J 2005, 272:2428-2440.
132. Gough J, Karplus K, Hughey R, 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 2001, 313:903-919.
133. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
134. Marchler-Bauer A, Bryant S: CD-Search: protein domain annotations on the fly. Nucleic Acids Res 2004, 32:W327-331.
135. Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy S, Griffiths-Jones S, Howe K, Marshall M, Sonnhammer E: The Pfam protein families database. Nucleic Acids Res 2002, 30:276-280.
136. Shi J, Blundell T, Mizuguchi K: FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol 2001, 310:243-257.
137. Kapp O, Moens L, Vanfleteren J, Trotman C, Suzuki T, Vinogradov SN: Alignment of 700 globin sequences: extent of amino acid substitution and its correlation in volume. Protein Sci 1995, 4:2179-2190.
138. Lesk AM, Chothia C: How different amino acid sequences determine similar protein structures. The structure and evolutionary dynamics of the globins. J Mol Biol 1980, 136:225-270.
139. Bashford D, Chothia C, Lesk AM: Determinants of a protein fold. Unique features of the globin amino acid sequences. J Mol Biol 1987, 196:199-216.
140. Gerstein M, Sonnhammer ELL, Chothia C: Volume changes in protein evolution. J Mol Biol 1994, 236:1067-1078.
141. Huelsenbeck JP, Ronquist F: MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17:754-755.
142. Swofford D: Phylogenetic Analysis Using Parsimony. In Ver.4.0b 10 Sinauer Associates; 2001.
143. Jones DT, Taylor WR, Thornton JM: The rapid generation of mutation data matrices from protein sequences. Cabios 1992, 8:275-282.
144. Singleton P, Sainsbury D: Dictionary of Microbiology and Molecular Biology. 3rd edition. J. Wiley & Sons, Chichester, UK; 2001.
145. Singleton P: Bacteria in Biology, Biotechnology and Medicine. 6th edition. J. Wiley & Sons, Chichester, UK; 2004.
146. Jaillon O, Aury J-M, Brune F, et al.: Genome duplication in the teleost fish Tetraodon nigroviridis reveal the early veertebrate proto-karyotype. Nature 2004, 431:946-975.
147. Kellis M, Patterson N, Endrizzi M, Birren B, Landers ES: Sequencing and comparison of yeast species to identify genes and regulatory element. Nature 2003, 423:241-254.