Identification of proteins involved in the functioning of Riftia pachyptila symbiosis by Subtractive Suppression Hybridization

BMC Genomics

Volumn 8, Issue , 2007, Pages

  Sanchez, Sophie ^a   Hourdez, Stéphane ^a   Lallier, François H ^a  

^a STATION BIOLOGIQUE DE ROSCOFF   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CARBONATE DEHYDRATASE; CATHEPSIN; CHITINASE; LUNG RESISTANCE PROTEIN; MYOHEMERYTHRIN; T LYMPHOCYTE RECEPTOR; UNCLASSIFIED DRUG; PROTEIN;

ANNELID WORM; ARTICLE; DNA LIBRARY; DNA SEQUENCE; GENETIC DATABASE; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEOBACTERIA; QUANTITATIVE ANALYSIS; SEQUENCE ANALYSIS; SUPPRESSION SUBTRACTIVE HYBRIDIZATION; SYMBIOSIS; ANIMAL; IMAGE SUBTRACTION; NUCLEIC ACID HYBRIDIZATION; PHYSIOLOGY;

GAMMAPROTEOBACTERIA; RIFTIA PACHYPTILA; TUBICOLAE;

ANIMALS; ANNELIDA; NUCLEIC ACID HYBRIDIZATION; POLYMERASE CHAIN REACTION; PROTEINS; SUBTRACTION TECHNIQUE; SYMBIOSIS;

EID: 37849050200     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-337     Document Type: Article

References (49)

1. Van Dover CL The ecology of deep sea hydrothermal vents Princeton Univeristy Press 2000. 11001053
2. Jones ML On the Vestimentifera, new phylum: Six new species, and other taxa, from hydrothermal vents and elsewhere Biol Soc Wash Bull 1985, 6:117-158.
3. Childress JJ Fischer CR Favuzzi JA Kochevar R Sanders NK Alayse AM Sulfide-driven autotrophic balance in the bacterial symbiont-containing hydrothermal vent tubeworm, Riftia pachyptila Jones Biol Bull 1991, 180:135-153. 10.2307/1542437
4. Jones ML Gardiner SL Evidence for a transient digestive tract in Vestimentifera Proc Biol Soc Wash 1988, 101(2):423-433.
5. Nussbaumer AD Fisher CR Bright M Horizontal endosymbiont transmission in hydrothermal vent tubeworms Nature 2006, 441:345-348. 10.1038/ nature04793 16710420
6. Goffredi SK Physiological Adaptations of the Hydrothermal Vent Tubeworm Riftia pachyptila; Including the Uptake of Carbon Dioxide and Hydrogen Sulfide, Unprecedented pH Regulation, and a Reverse Chloride Shift PhD Dissertation Univ. California Santa Barbara 1999
7. 2S J Exp Biol 1997, 200(20):2609-2616. 9359367
8. Arp AJ Childress JJ Vetter RD The sulfide-binding protein in the blood of the vestimentiferan tube worm, Riftia pachyptila, is the extracellular haemoglobin J Exp Biol 1987, 128:139-158.
9. Flores JF Fisher CR Carney SL Green BN Freytag JK Schaeffer SW Royer WE Jr Sulfide binding is mediated by zinc ions discovered in the crystal structure of a hydrothermal vent tubeworm hemoglobin Proc Natl Acad Sci USA 2005, 102(8):2713-2718. 549462 15710902 10.1073/pnas.0407455102
10. Zal F Leize E Lallier FH Toulmond A Van Dorsselaer A Childress JJ S-Sulfohemoglobin and disulfide exchange: The mechanisms of sulfide binding by Riftia pachyptila hemoglobins Proc Natl Acad Sci USA 1998, 95(15):8997-9002. 21191 9671793 10.1073/pnas.95.15.8997
11. Goffredi S Childress J Desaulniers N Lee R Lallier F Hammond D Inorganic carbon acquisition by the hydrothermal vent tubeworm Riftia pachyptila depends upon high external PCO2 and upon proton-equivalent ion transport by the worm J Exp Biol 1997 200 Pt 5 883 896 9318669
12. De Cian MC Bailly X Morales J Strub JM Van Dorsselaer A Lallier FH Characterization of carbonic anhydrases from Riftia pachyptila, a symbiotic invertebrate from deep-sea hydrothermal vents Proteins 2003, 51:327-339. 10.1002/prot.10295 12696045
13. Kochevar RE Govind NS Childress JJ Identification and characterization of two carbonic anhydrases from the hydrothermal vent tubeworm Riftia pachyptila Jones Molec Mar Biol Biotechnol 1993, 2(1):10-19.
14. De Cian MC Andersen AC Bailly X Lallier FH Expression and localization of carbonic anhydrase and ATPases in the symbiotic tubeworm Riftia pachyptila J Exp Biol 2003, 206(Pt 2)399-409. 10.1242/jeb.00074 12477910
15. Markert S Arndt C Felbeck H Becher D Sievert SM Hügler M Albrecht D Robidart J Bench S Feldman RA Physiological Proteomics of the Uncultured Endosymbiont of Riftia pachyptila Science 2007, 315:247-250. 10.1126/ science.1132913 17218528
16. 5Lievens S Goormachtig S Holsters M A critical evaluation of differential display as a tool to identify genes involved in legume nodulation: Looking back and looking forward Nucleic Acids Res 2001, 29(17):3459-3468. 55879 11522814 10.1093/nar/29.17.3459
17. Morel M Jacob C Kohler A Johansson T Martin F Chalot M Brun A Identification of Genes Differentially Expressed in Extraradical Mycelium and Ectomycorrhizal Roots during Paxillus involutus-Betula pendula Ectomycorrhizal Symbiosis Appl Environ Microbiol 2005, 71(1):382-391. 544268 15640212 10.1128/AEM.71.1.382-391.2005
18. Rodriguez-Lanetty M Phillips WS Weis VM Transcriptome analysis of a cnidarian-dinoflagellate mutualism reveals complex modulation of host gene expression BMC Genomics 2006, 7:23. 1408080 16472376
19. Sanchez S Andersen AC Hourdez S Lallier FH Identification, sequencing, and localization of new carbonic anhydrase transcripts from the hydrothermal vent tubeworm Riftia pachyptila FEBS J 2007. 17892492
20. Chamoy L Nicolaï M Ravaux J Quennedey B Gaill F Delachambre J A Novel Chitin-binding Protein from the Vestimentiferan Riftia pachyptila Interacts Specifically with b-Chitin. Cloning, expression, and characterization J Biol Chem 2001, 276(11):8051-8058. 10.1074/ jbc.M009244200 11113138
21. Chabasse C Bailly X Sanchez S Rousselot M Zal F Gene Structure and Molecular Phylogeny of the Linker Chains from the Giant Annelid Hexagonal Bilayer Hemoglobins J Mol Evol 2006, 63:365-374. 10.1007/ s00239-005-0198-9 16838215
22. Zal F Lallier FH Wall JS Vinogradov SN Toulmond A The multi-hemoglobin system of the hydrothermal vent tube worm Riftia pachyptila. I. Reexamination of the number and masses of its constituents J Biol Chem 1996, 271:8869-8874. 10.1074/jbc.271.15.8869 8621528
23. Ji W Wright MB Cai L Flament A Lindpaintner K Efficacy of SSH PCR in isolating differentially expressed genes BMC Genomics 2002, 3:12. 115870 12033988
24. Menon J Willsie JK Tauscher A Arp AJ Epidermal ultrastructure and implications for sulfide tolerance in six species of deep-sea polychaetes Invertebr Biol 2003, 122(4):334-346.
25. Arp AJ Menon JG Julian D Multiple mechanisms for sulfide tolerance in Urechis caupo Amer Zool 1995, 35:132-144.
26. Julian D April KL Patel S Stein JR Wohlgemuth SE Mitochondrial depolarization following hydrogen sulfide exposure in erythrocytes from a sulfide-tolerant marine invertebrate J Exp Biol 2005, 208:4109-4122. 10.1242/jeb.01867 16244170
27. Dai RM Li C-CH Valosin-containing protein is a multiubiquitin chain-targeting factor required in ubiquitin-proteasome degradation Nat Cell Biol 2001, 3:740-744. 10.1038/35087056 11483959
28. Suzuki T Honda M Matsumoto S Stürzenbaum SR Gamou S Valosine-containing proteins (VCP) in an annelid: Identification of a novel spermatogenesis related factor Gene 2005, 362:11-18. 10.1016/ j.gene.2005.07.039 16216447
29. Wohlgemuth S Arp A Bergquist D Julian D Rapid induction and disappearance of electron-dense organelles following sulfide exposure in the marine annelid Branchioasychis americana Invertebr Biol 2007, 126(2):163-172. 10.1111/j.1744-7410.2007.00086.x
30. Völkel S Grieshaber MK Sulphide oxidation and oxidative phosphorylation in the mitochondria of the lugworm Arenicola marina J Exp Biol 1997, 200:83-92. 9317382
31. Bernheim MLC The Hydroxylamine Reductase of Mitochondria Arch Biochem Biophys 1969, 134:408-413. 10.1016/0003-9861(69)90300-2 4311180
32. Wikström MKF L SN-E Effect of Hydroxylamine on Respiration and Oxidative Phosphorylation Eur J Biochem 1969, 9:160-166. 10.1111/ j.1432-1033.1969.tb00590.x 4308616
33. Hamill DR Suprenant KA Characterization of the Sea Urchin Major Vault Protein: A Possible Role for Vault Ribonucleoprotein Particles in Nucleocytoplasmic Transport Dev Biol 1997, 190:117-128. 10.1006/ dbio.1997.8676 9331335
34. Scheffer GL Wijingaard PLJ Flens MJ Izquierdo MA Slovak ML Pinedo HM Meijer CJLM Clevers HC Scheper RJ The drug resistance-related protein LRP is the human major vault protein Nat Med 1995, 1(6):578-582. 10.1038/ nm0695-578 7585126
35. Mossink MH van Zon A Scheper RJ Sonneveld P Wiemer EA Vaults: A ribonucleoprotein particle involved in drug resistance? Oncogene 2003, 22:7458-7467. 10.1038/sj.onc.1206947 14576851
36. Lüdeking A Köhler A Identification of six mRNA sequences of genes to multixenobiotic resistance (MXR) and biotransformation in Mytilus edulis Mar Ecol Prog Ser 2002, 238:115-124. 10.3354/meps238115
37. Ravaux J Gay L Voss-Foucart MF Gaill F Tube growth process in the deep-sea hydrothermal vent tubeworm Riftia pachyptila (Vestimentifera): synthesis and degradation of chitin Cah Biol Mar 1998, 39(2):99-107.
38. Shillito B Lubbering B Lechaire JP Childress JJ Gaill F Chitin Localization in the Tube Secretion System of a Repressurized Deep-Sea Tube Worm J Struct Biol 1995, 114(1):67-75. 10.1006/jsbi.1995.1006
39. Mali B Möhrlen F Frohme M Frank U A putative double role of a chitinase in a cnidarian: Pattern formation and immunity Dev Comp Immunol 2004, 28:973-981. 10.1016/j.dci.2004.04.002 15236928
40. Demuynck S Bocquet-Muchembled B Deloffre L Grumiaux F Leprêtre A Stimulation by cadmium of myohemerythrin-like cells in the gut of the annelid Nereis diversicolor J Exp Biol 2004, 207:1101-1111. 10.1242/ jeb.00858 14978053
41. Vergote D Sautière P-E Vandenbulcke F Vieau D Mitta G Macagno ER Salzet M Up-regulation of Neurohemerythrin Expression in the Central Nervous System of the Medicinal Leech, Hirudo medicinalis, following Septic Injury J Biol Chem 2004, 279(42):43828-43837. 10.1074/ jbc.M403073200 15258158
42. Diatchenko L Lau Y-FC Campbell AP Chenchik A Moqadam F Huang B Lukyanov S Lukyanov K Gurskaya N Sverdlov ED Suppression substractive hydridization: A method for generating differentially regulated or tissue-specific cDNA probes and libraries Proc Natl Acad Sci USA 1996, 93:6025-6030. 39182 8650213 10.1073/pnas.93.12.6025
43. Gurskaya NG Diatchenko L Chenchik A Siebert PD Khaspekov GL Lukyanov SA Sverdlov ED Equalizing cDNA Substraction Based on Selective Suppression of Polymerase Chain Reaction: Cloning of Jurkat Cell Transcripts Induced by Phytohemaglutinin and Phorbol 12-Myristate 13-Acetate Anal Biochem 1996, 240:90-97. 10.1006/abio.1996.0334 8811883
44. Ewing B Hillier L Wendl M Green P Base calling of automated sequencer traces using phred. I. Accuracy assessment Genome Res 1998, 8:175-185. 9521921
45. Pertea G Huang X Liang F Antonescu V Sultana R Karamycheva S Lee Y White J Cheung F Parvizi B Jennifer J TIGR Gene Indices clustering tools (TGICL): A software system for fast clustering of large EST data sets Bioinformatics 2003, 19:651-652. 10.1093/bioinformatics/btg034 12651724
46. BLAST: Basic Local Alignment and Search Tool http://www.ncbi.nlm.nih.gov/ BLAST/
47. Hanekamp K Bohnebeck U Beszteri B Valentin K PhyloGena - a user-friendly system for automated phylogenetic annotation of unknown sequences Bioinformatics 2007, 23(7)793-801. 10.1093/bioinformatics/btm016 17332025
48. Halanych KM Lutz RA Vrijenhoek RC Evolutionary origins and age of vestimentiferan tube-worms Cah Biol Mar 1998, 39:355-358.
49. Livak KJ Schmittgen TD Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2-ΔΔCT Method Methods 2001, 25:402-408. 10.1006/meth.2001.1262 11846609