Molecular evolution and phylogeny of sipunculan hemerythrins

Journal of Molecular Evolution

Volumn 62, Issue 1, 2006, Pages 32-41

  Vanin, Stefano ^a   Negrisolo, Enrico ^a   Bailly, Xavier ^b   Bubacco, Luigi ^a   Beltramini, Mariano ^a   Salvato, Benedetto ^a  

^a UNIVERSITY OF PADOVA   (Italy)

^b STATION BIOLOGIQUE   (France)

Author keywords

Hemerythrin; Phylogeny; Respiratory proteins; Sipuncula

Indexed keywords

COMPLEMENTARY DNA; HEMERYTHRIN; MYOHEMERYTHRIN; PROTEIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ANIMAL CELL; ANNELID WORM; ARTICLE; BAYES THEOREM; CLADISTICS; GOLFINGIA VULGARIS VULGARIS; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SIPUNCULUS NUDUS; WORM;

AMINO ACID SEQUENCE; ANIMALS; EVOLUTION, MOLECULAR; HEMERYTHRIN; MOLECULAR SEQUENCE DATA; NEMATODA; PHYLOGENY; PROTEIN STRUCTURE, QUATERNARY; SEQUENCE ALIGNMENT;

ANIMALIA; ANNELIDA; GOLFINGIA VULGARIS VULGARIS; PHASCOLOPSIS GOULDII; SIPHONOSOMA CUMANENSE; SIPUNCULA; SIPUNCULUS NUDUS; THEMISTE; THEMISTE ZOSTERICOLA;

EID: 31844441323     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-004-0296-0     Document Type: Article

References (53)

1. Addison AW, Bruce RE (1977) Chemistry of Phascolosoma lurco hemerythrin. Arch Biochem Biophys 183:328-332
2. Bates G, Brunori M, Amiconi G, Antonini E, Wyman J (1968) Studies on hemerythrin. I. Thermodynamic and kinetic aspects of oxygen binding. Biochemistry 7:3016-3020
3. Burmester T (2002) Origin and evolution of arthropod hemocyanins and related proteins. J Comp Physiol B 172:95-107
4. Clark PE, Webb J (1981) Mossbauer spectroscopic studies of hemerythrin from Phascolosoma lurco (syn. Phascolosoma arcuatum). Biochemistry 20:4628-4632
5. Coutte L, Slomianny M-C, Malecha J, Baert J-L (2001) Cloning and expression analysis of a cDNA that encodes a leech hemerythrin. Biochim Biophys Acta 1518:282-286
6. Cutler EB (1994) The Sipuncula. Their systematics, biology and evolution. Cornell University Press, Ithaca, NY
7. Dayhoff MO, Schwartz RM, Orcutt BC (1978) A model of evolutionary change in proteins. In: Dayhoff MO (ed) Atlas of protein sequence structure. National Biomedical Research Foundation, Washington DC, pp 345-352
8. Demuynck S, Sautiere P, van Beeumen J , Dhainaut-Courtois N (1991) Homologies between hemerythrins of sipunculids and cadmium-binding metalloprotein (MP II) from a polychaete annelid, Nereis diversicolor. CR Acad Sci III 312:317-322
9. 2 binding pocket. J Biol Inorg Chem 6:418-429
10. Felsenstein J (1985) Confidence limits on phylogenies: an approach using bootstrap. Evolution 39:783-791
11. Felsenstein J (2002) PHYLIP (Phylogeny Inference Package), version 3.6a3. University of Washington, Seattle
12. Felsenstein (2003) Inferring phylogenies. Sinauer, Sunderland, MA
13. Ferrell RF, Kitto GB (1971) Structural studies on Dendrostomum pyroides hemerythrin. Biochemistry 10:2923-2929
14. Groskopf WR, Holleman JW, Klotz IM (1963) Amino acid composition of hemerythrin in relation to subunit structure. Science 141:166-167
15. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696-704
16. Hendrickson WA, Klippenstein GL, Ward KB (1975) Tertiary structure of myohemerythrin at low resolution. Proc Natl Acad Sci USA 72:2160-2164
17. Holmes MA, Stenkamp RE (1991) Structures of met and azidomet hemerythrin at 1.66 A resolution. J Mol Biol 220:723-737
18. Huelsenbeck JP, Ronquist F (2001) MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755
19. Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8:275-282
20. Jushi JG, Sullivan B (1973) Isolation and preliminary characterization of hemerythrin from Lingula unguis. Comp Biochem Physiol 44B:857-867
21. Klippenstein GL (1972) Molecular variants of Golfingia gouldii hemerythrin. The primary structure of the variants arising from five amino acid interchanges. Biochemistry 11:372-380
22. Klippenstein GL (1980) Structural aspects of hemerythin and myohemerythrin. Am Zool 20:39-51
23. Kurtz DM Jr (1999) Oxygen-carrying proteins: three solutions to a common problem. Essays Biochem 34:85-100
24. 2. J Exp Zool 244:59-65
25. Mangum CP, Kondon M (1975) The role of coelomic hemerythin in the sipunculid worm Phascolopsis gouldi. Comp Biochem Physiol 50A:777-785
26. Manwell C (1960) Histological specificity of respiratory pigments. II. Oxygen transfer system involving hemerythrins in sipunculid worms of different ecologies. Comp Biochem Physiol 1:277-285
27. Manwell C (1963) Genetic control of hemerythrin specificity in a marine worm. Science 139:755-758
28. Manwell C, Baker CMA (1988) Magellona papillicornis haemerythrin: tissue specificity, molecular weights and oxygen equilibria. Comp Biochem Physiol 89B:453-463
29. Maxmen AB, King BF, Cutler EB, Giribet G (2003) Evolutionary relationships within the protostome phylum Sipuncula: a molecular analysis of ribosomal genes and histone H3 sequence data. Mol Phylogenet Evol 27:489-503
30. Moens L, Vanfleteren J, Van de Peer Y, Peeters K, Kapp O, Czeluzniak J, Goodman M, Blaxter M, Vinogradov S (1996) Globins in nonvertebrate species: dispersal by horizontal gene transfer and evolution of the structure-function relationships. Mol Biol Evol 13:324-333
31. Page RDM (1996) TREEVIEW: An application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357-358
32. Perrière G, Gouy M (1996) WWW-Query: An on-line retrieval system for biological sequence banks. Biochimie 78:364-369
33. Richardson DE, Emad M, Reem RC, Solomon EI (1987) Allosteric interactions in sipunculid and brachiopod hemerythrins. Biochemistry 26:1003-1013
34. 2-carrying protein hemerythrin. Biochemistry 27:4458-4465
35. Roche A, Roche J (1935) Pression osmotique et poids moléculaire de l'hèmèrythrine du sipuncle. Bull Soc Chim Biol 17:1494-1508
36. Satake K, Yugi M, Kamo M, Kihara H, Tsugita A (1990) Hemerythrin from Lingula unguis consists of two different subunits, alpha and beta. Protein Seq Data Anal 3:1-5
37. Smith JL, Hendrickson WA, Addison AW (1983) Structure of trimeric hemerythrin. Nature 303:86-88
38. Staton JL (2003) Phylogenetic analysis of the mitochondrial cytochrome c oxidase subunit 1 gene from 13 sipunculan genera: intra- and interphylum relationships. Invertebr Biol 122:252-264
39. Tagagi T, Cox JA (1991) Primary structure of myohemerythrin fron the annelid Nereis diversicolor. FEBS Lett 285:25-27
40. Terwillinger RC (1998) Functional adaptations of oxygen-transport proteins. J Exp Biol 201:1085-1098
41. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
42. Uchida T, Yano H, Satake K, Kubota I, Tsugita A (1990) The amino acid sequence of hemerythrin from Siphonosoma cumanense. Protein Seq Data Anal 3:141-147
43. van Holde KE, Miller KI, Decker H (2001) Hemocyanins and invertebrate evolution. J Biol Chem 276:1553-1556
44. Vanin S (2001) Fisiologia molecolare di proteine con siti dinucleari. Doctoral thesis. University of Padua, Italy
45. Vergote D, Sautiere PE, Vandenbulcke F, Vieau D, Mitta G, Macagno ER, Salzet M (2004) Up-regulation of neurohemerythrin expression in the central nervous system of the medicinal leech, Hirudo medicinalis, following septic injury. J Biol Chem 279:43828-43837
46. Ward KB, Hendrickson WA, Klippenstein GL (1975) Quaternary and tertiary structure of hemerythrin. Nature 257:818-821
47. Wells RMG (1982) Respiratory characteristics of the blood pigments of three worms from an intertidal mudflat. NZ J Zool 9:243-248
48. Wilkins RG, Harrington PC (1983) The chemistry of hemerythrin. Adv Inorg Biochem 5:51-85
49. Yang Z (2002) PAML: Phylogenetic Analysis by Maximum Likelihood (PAML), version 3.13a. Available at: http://abacus.gene.ucl.ac.uk/software/paml.html
50. Yang Z, Bielawski JP (2000) Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15:496-503
51. Yang Z, Nielsen R, Goldman N, Pedersen A-MK (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449
52. 2 binding. Biochemistry 30:9121-9125
53. Zhang J, Kurtz DM Jr (1992) Metal substitutions at the diiron sites of hemerythrin and myohemerythrin: contributions of divalent metals to stability of a four-helix bundle protein. Proc Natl Acad Sci USA 89:7065-7069