Molecular determinants archetypical to the phylum Nematoda

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Yin, Yong ^a   Martin, John ^a   Abubucker, Sahar ^a   Wang, Zhengyuan ^a   Wyrwicz, Lucjan ^b,c   Rychlewski, Leszek ^c   McCarter, James P ^a,d   Wilson, Richard K ^a   Mitreva, Makedonka ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b INSTITUTE OF ONCOLOGY   (Poland)

^c BIOINFOBANK INSTITUTE   (Poland)

^d Divergence Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

POLYPEPTIDE; PEPTIDE;

AMINO ACID SEQUENCE; ARTICLE; CAENORHABDITIS ELEGANS; CLADISTICS; CONTROLLED STUDY; ELECTRON TRANSPORT; GENETIC CONSERVATION; NEMATODE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLUM; PREDICTION; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN FUNCTION; RNA INTERFERENCE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; ANIMAL; BIOLOGY; CLUSTER ANALYSIS; GENETICS; GENOMICS; MULTIGENE FAMILY; PROTEIN TERTIARY STRUCTURE; SPECIES DIFFERENCE;

ANIMALIA; CAENORHABDITIS ELEGANS; NEMATODA;

ANIMALS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; GENOMICS; MULTIGENE FAMILY; NEMATODA; PEPTIDES; PROTEIN STRUCTURE, TERTIARY; SEQUENCE HOMOLOGY; SPECIES SPECIFICITY;

EID: 64549160612     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-114     Document Type: Article

References (84)

1. Lambshead PJ Brown CJ Ferrero TJ Hawkins LE Smith CR Mitchell NJ Biodiversity of nematode assemblages from the region of the Clarion-Clipperton Fracture Zone, an area of commercial mining interest BMC ecology 2003, 3:1. 140317 12519466
2. Blaxter M Caenorhabditis elegans is a nematode Science 1998, 282(5396):2041-2046. 9851921
3. WHO Deworming for Health and Development The Third Global Meeting of the Partners for Parasite Control Geneva: World Health Organization 2004. http://whqlibdoc.who.int/hq/2005/WHO_CDS_CPE_PVC_2005.14.pdf
4. Barker KR Hussey RS Krusberg LR Bird GW Dunn RA Ferris VR Freckman DW Gabriel CJ Grewal PS Macguidwin AE et al Plant and soil nematodes-societal impact and focus for the future Journal of Nematology 1994, 26:127-137. 2619488 19279875
5. Ranjit N Jones MK Stenzel DJ Gasser RB Loukas A A survey of the intestinal transcriptomes of the hookworms, Necator americanus and Ancylostoma caninum, using tissues isolated by laser microdissection microscopy Int J Parasitol 2006, 36(6):701-710. 16545815
6. Rabelo EM Hall RS Loukas A Cooper L Hu M Ranganathan S Gasser RB Improved insights into the transcriptomes of the human hookworm Necator americanus - Fundamental and biotechnological implications Biotechnology advances 2009, 27(2):122-32. 18977428
7. Parkinson J Mitreva M Whitton C Thomson M Daub J Martin J Schmid R Hall N Barrell B Waterston RH et al A transcriptomic analysis of the phylum Nematoda Nat Genet 2004, 36(12):1259-1267. 15543149
8. The C. elegans Sequencing Consortium Genome Sequence of the Nematode C. elegans: A Platform for Investigating Biology Science 1998, 282(5396):2012-2018. 9851916
9. Stein LD Bao Z Blasiar D Blumenthal T Brent MR Chen N Chinwalla A Clarke L Clee C Coghlan A et al The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics PLoS Biol 2003, 1(2):E45. 261899 14624247
10. Givnish TJ Evans TM Zjhra ML Patterson TB Berry PE Sytsma KJ Molecular evolution, adaptive radiation, and geographic diversification in the amphiatlantic family Rapateaceae: Evidence from ndhF sequences and morphology Evolution; international journal of organic evolution 2000, 54(6):1915-1937. 11209770
11. Kocher TD Adaptive evolution and explosive speciation: The cichlid fish model Nature reviews 2004, 5(4):288-298. 15131652
12. Panhuis TM Clark NL Swanson WJ Rapid evolution of reproductive proteins in abalone and Drosophila Philos Trans R Soc Lond B Biol Sci 2006, 361(1466):261-268. 1569613 16612885
13. Peng J Huang CH Rh proteins vs Amt proteins: An organismal and phylogenetic perspective on CO2 and NH3 gas channels Transfus Clin Biol 2006, 13(1-2):85-94. 16564193
14. Jang CS Jung JH Yim WC Lee BM Seo YW Kim W Divergence of genes encoding non-specific lipid transfer proteins in the poaceae family Mol Cells 2007, 24(2):215-223. 17978574
15. Curtis RH Plant parasitic nematode proteins and the host parasite interaction Briefings in functional genomics & proteomics 2007, 6(1):50-58. 17525074
16. Davis EL Hussey RS Baum TJ Getting to the roots of parasitism by nematodes Trends Parasitol 2004, 20(3):134-141. 15036035
17. Lilley CJ Urwin PE Atkinson HJ Characterization of plant nematode genes: identifying targets for a transgenic defence Parasitology 1999, 118(Suppl):S63-72. 10466138
18. McCarter JP Genomic filtering: An approach to discovering novel antiparasitics Trends Parasitol 2004, 20(10):462-468. 15363439
19. Bateman A Birney E Cerruti L Durbin R Etwiller L Eddy SR Griffiths-Jones S Howe KL Marshall M Sonnhammer EL The Pfam protein families database Nucleic Acids Res 2002, 30(1):276-280. 99071 11752314
20. Sonnhammer EL Eddy SR Durbin R Pfam: A comprehensive database of protein domain families based on seed alignments Proteins 1997, 28(3):405-420. 9223186
21. Mitreva M Blaxter ML Bird DM McCarter JP Comparative genomics of nematodes Trends Genet 2005, 21(10):573-581. 16099532
22. McCarter JP Bird DM Mitreva M Nematode gene sequences: December 2005 update Journal of Nematology 2005, 37:417-421. 2620984 19262885
23. Wylie T Martin J Dante M Mitreva M Clifton SW Chinwalla A Waterston RH Wilson RK McCarter JP Nematode.net: A tool for navigating sequences from parasitic and free-living nematodes Nucleic Acids Res 2004, 32:D423-D426. 308745 14681448
24. Mitreva M Wendl MC Martin J Wylie T Yin Y Larson A Parkinson J Waterston RH McCarter JP Codon usage patterns in Nematoda: Analysis based on over 25 million codons in thirty-two species Genome Biol 2006, 7(8):R75. 1779591 16907990
25. Wasmuth J Schmid R Hedley A Blaxter M On the extent and origins of genic novelty in the phylum nematoda PLoS neglected tropical diseases 2008, 2(7):e258. 2432500 18596977
26. Martin J Abubucker S Wylie T Yin Y Wang Z Mitreva M Nematode.net update 2008: Improvements enabling more efficient data mining and comparative nematode genomics Nucl Acids Res 2009, 37:D571-578. 18940860
27. Enright AJ Van Dongen S Ouzounis CA An efficient algorithm for large-scale detection of protein families Nucleic Acids Res 2002, 30(7):1575-1584. 101833 11917018
28. Yin Y Martin J McCarter JP Clifton SW Wilson RK Mitreva M Identification and analysis of genes expressed in the adult filarial parasitic nematode Dirofilaria immitis Int J Parasitol 2006, 36(7):829-839. 16697384
29. McCarter J Dautova Mitreva M Martin J Dante M Wylie T Rao U Pape D Bowers Y Theising B Murphy CV et al Analysis and functional classification of transcripts from the nematode Meloidogyne incognita Genome Biol 2003, 4(4):R26. 12702207 154577
30. Mitreva M Elling AA Dante M Kloek AP Kalyanaraman A Aluru S Clifton SW Bird DM Baum TJ McCarter JP A survey of SL1-spliced transcripts from the root-lesion nematode Pratylenchus penetrans Mol Genet Genomics 2004, 272(2):138-148. 15338281
31. Mitreva M McCarter JP Martin J Dante M Wylie T Chiapelli B Pape D Clifton SW Nutman TB Waterston RH Comparative genomics of gene expression in the parasitic and free-living nematodes Strongyloides stercoralis and Caenorhabditis elegans Genome Res 2004, 14(2):209-220. 327096 14762059
32. Philippe H Lartillot N Brinkmann H Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia Mol Biol Evol 2005, 22(5):1246-1253. 15703236
33. Aguinaldo AM Turbeville JM Linford LS Rivera MC Garey JR Raff RA Lake JA Evidence for a clade of nematodes, arthropods and other moulting animals Nature 1997, 387(6632):489-493. 9168109
34. Geary TG Sangster NC Thompson DP Frontiers in anthelmintic pharmacology Vet Parasitol 1999, 84(3-4):275-295. 10456419
35. Bono H Ogata H Goto S Kanehisa M Reconstruction of amino acid biosynthesis pathways from the complete genome sequence Genome Res 1998, 8(3):203-210. 9521924
36. Kanehisa M Goto S KEGG: Kyoto encyclopedia of genes and genomes Nucleic Acids Res 2000, 28(1):27-30. 102409 10592173
37. Kanehisa M Goto S Kawashima S Okuno Y Hattori M The KEGG resource for deciphering the genome Nucleic Acids Res 2004, 32(Database):D277-280. 308797 14681412
38. Blaxter ML De Ley P Garey JR Liu LX Scheldeman P Vierstraete A Vanfleteren JR Mackey LY Dorris M Frisse LM et al A molecular evolutionary framework for the phylum Nematoda Nature 1998, 392(6671):71-75. 9510248
39. Fire A Xu S Montgomery MK Kostas SA Driver SE Mello CC Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans Nature 1998, 391(6669):806-811. 9486653
40. Kamath RS Fraser AG Dong Y Poulin G Durbin R Gotta M Kanapin A Le Bot N Moreno S Sohrmann M et al Systematic functional analysis of the Caenorhabditis elegans genome using RNAi Nature 2003, 421(6920):231-237. 12529635
41. Rual JF Ceron J Koreth J Hao T Nicot AS Hirozane-Kishikawa T Vandenhaute J Orkin SH Hill DE Heuvel van den S et al Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library Genome Res 2004, 14(10B):2162-2168. 528933 15489339
42. Sonnichsen B Koski LB Walsh A Marschall P Neumann B Brehm M Alleaume AM Artelt J Bettencourt P Cassin E et al Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans Nature 2005, 434(7032):462-469. 15791247
43. Mitreva M Zarlenga DS McCarter JP Jasmer DP Parasitic nematodes - from genomes to control Vet Parasitol 2007, 148(1):31-42. 17560034
44. Kita K Takamiya S Electron-transfer complexes in Ascaris mitochondria Adv Parasitol 2002, 51:95-131. 12238891
45. Tielens AG Rotte C van Hellemond JJ Martin W Mitochondria as we don't know them Trends Biochem Sci 2002, 27(11):564-572. 12417132
46. van Hellemond JJ Klei van der A van Weelden SW Tielens AG Biochemical and evolutionary aspects of anaerobically functioning mitochondria Philos Trans R Soc Lond B Biol Sci 2003, 358(1429):205-213. 1693107 12594928
47. Tielens AG Van Hellemond JJ The electron transport chain in anaerobically functioning eukaryotes Biochim Biophys Acta 1998, 1365(1-2):71-78. 9693724
48. Mulder NJ Apweiler R Attwood TK Bairoch A Bateman A Binns D Bradley P Bork P Bucher P Cerutti L et al InterPro, progress and status in 2005 Nucleic Acids Res 2005, 33(Database):D201-205. 540060 15608177
49. Ginalski K Grishin NV Godzik A Rychlewski L Practical lessons from protein structure prediction Nucleic Acids Res 2005, 33(6):1874-1891. 1074308 15805122
50. Stein LD Mungall C Shu S Caudy M Mangone M Day A Nickerson E Stajich JE Harris TW Arva A et al The generic genome browser: A building block for a model organism system database Genome Res 2002, 12(10):1599-1610. 187535 12368253
51. Berman HM Westbrook J Feng Z Gilliland G Bhat TN Weissig H Shindyalov IN Bourne PE The Protein Data Bank Nucleic Acids Res 2000, 28(1):235-242. 102472 10592235
52. Ginalski K von Grotthuss M Grishin NV Rychlewski L Detecting distant homology with Meta-BASIC Nucleic Acids Res 2004, 32(Web Server):W576-581. 441508 15215454
53. Jaroszewski L Rychlewski L Li Z Li W Godzik A FFAS03: A server for profile - profile sequence alignments Nucleic Acids Res 2005, 33(Web Server):W284-288. 1160179 15980471
54. Kelley LA MacCallum RM Sternberg MJ Enhanced genome annotation using structural profiles in the program 3D-PSSM J Mol Biol 2000, 299(2):499-520. 10860755
55. Fischer D Hybrid fold recognition: Combining sequence derived properties with evolutionary information Pacific Symposium on Biocomputing 2000:119-130. 10902162
56. Sanchez R Sali A Comparative protein structure modeling. Introduction and practical examples with modeller Methods Mol Biol 2000, 143:97-129. 11084904
57. Nagata Y Mori K Takagi M Murzin AG Damborsky J Identification of protein fold and catalytic residues of gamma-hexachlorocyclohexane dehydrochlorinase LinA Proteins 2001, 45(4):471-477. 11746694
58. Martin RJ Robertson AP Bjorn H Target sites of anthelmintics Parasitology 1997, 114(Suppl):S111-124. 9309773
59. Bethony J Loukas A Smout M Brooker S Mendez S Plieskatt J Goud G Bottazzi ME Zhan B Wang Y et al Antibodies against a secreted protein from hookworm larvae reduce the intensity of hookworm infection in humans and vaccinated laboratory animals Faseb J 2005, 19(12):1743-1745. 16037096
60. Loukas A Bethony JM Mendez S Fujiwara RT Goud GN Ranjit N Zhan B Jones K Bottazzi ME Hotez PJ Vaccination with recombinant aspartic hemoglobinase reduces parasite load and blood loss after hookworm infection in dogs PLoS medicine 2005, 2(10):e295. 1240050 16231975
61. Yin Y Martin J Abubucker S Scott AL McCarter JP Wilson RK Jasmer DP Mitreva M Intestinal Transcriptomes of Nematodes: Comparison of the Parasites Ascaris suum and Haemonchus contortus with the Free-living Caenorhabditis elegans PLoS neglected tropical diseases 2008, 2(8):e269. 2483350 18682827
62. Jasmer DP McGuire TC Protective immunity to a blood-feeding nematode (Haemonchus contortus) induced by parasite gut antigens Infect Immun 1991, 59(12):4412-4417. 259057 1937800
63. Knox DP Smith WD Vaccination against gastrointestinal nematode parasites of ruminants using gut-expressed antigens Vet Parasitol 2001, 100(1-2):21-32. 11522403
64. Loukas A Bethony J Brooker S Hotez P Hookworm vaccines: Past, present, and future Lancet Infect Dis 2006, 6(11):733-741. 17067922
65. Jasmer DP Yao C Rehman A Johnson S Multiple lethal effects induced by a benzimidazole anthelmintic in the anterior intestine of the nematode Haemonchus contortus Mol Biochem Parasitol 2000, 105(1):81-90. 10613701
66. Shompole S Yao C Cheng X Knox D Johnson S Jasmer DP Distinct characteristics of two intestinal protein compartments discriminated by using fenbendazole and a benzimidazole resistant isolate of Haemonchus contortus Exp Parasitol 2002, 101(4):200-209. 12594960
67. Shingles J Lilley CJ Atkinson HJ Urwin PE Meloidogyne incognita: molecular and biochemical characterisation of a cathepsin L cysteine proteinase and the effect on parasitism following RNAi Exp Parasitol 2007, 115(2):114-120. 16996059
68. Ghedin E Wang S Spiro D Caler E Zhao Q Crabtree J Allen JE Delcher AL Guiliano DB Miranda-Saavedra D et al. Draft genome of the filarial nematode parasite Brugia malayi Science 2007, 317(5845):1756-1760. 17885136 10.1126/science.1145406 2613796
69. Abad P Gouzy J Aury JM Castagnone-Sereno P Danchin EG Deleury E Perfus-Barbeoch L Anthouard V Artiguenave F Blok VC et al Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita Nat Biotechnol 2008, 26(8):909-915. 18660804
70. Mitreva M Jasmer DP Biology and genome of Trichinella spiralis WormBook, The C. elegans Research Community (Ed.) Wormbook 2006. http://www.wormbook.org
71. Wasmuth JD Blaxter ML prot4EST: Translating expressed sequence tags from neglected genomes BMC Bioinformatics 2004, 5(1):187. 543579 15571632
72. Parkinson J Anthony A Wasmuth J Schmid R Hedley A Blaxter M PartiGene - constructing partial genomes Bioinformatics 2004, 20(9):1398-1404. 14988115
73. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool J Mol Biol 1990, 215(3):403-410. 2231712
74. MCL http://micans.org/mcl/
75. Edgar RC MUSCLE: Multiple sequence alignment with high accuracy and high throughput Nucl Acids Res 2004, 32(5):1792-1797. 390337 15034147
76. Kall L Krogh A Sonnhammer EL A combined transmembrane topology and signal peptide prediction method J Mol Biol 2004, 338(5):1027-1036. 15111065
77. Quevillon E Silventoinen V Pillai S Harte N Mulder N Apweiler R Lopez R InterProScan: Protein domains identifier Nucleic Acids Res 2005, 33(Web Server):W116-120. 1160203 15980438
78. McGuffin LJ Bryson K Jones DT The PSIPRED protein structure prediction server Bioinformatics 2000, 16(4):404-405. 10869041
79. Gewehr JE Zimmer R SSEP-Domain: Protein domain prediction by alignment of secondary structure elements and profiles Bioinformatics 2006, 22(2):181-187. 16267083
80. Ward JJ McGuffin LJ Bryson K Buxton BF Jones DT The DISOPRED server for the prediction of protein disorder Bioinformatics 2004, 20(13):2138-2139. 15044227
81. Linding R Russell RB Neduva V Gibson TJ GlobPlot: Exploring protein sequences for globularity and disorder Nucleic Acids Res 2003, 31(13):3701-3708. 169197 12824398
82. Bujnicki JM Elofsson A Fischer D Rychlewski L Structure prediction meta server Bioinformatics 2001, 17(8):750-751. 11524381
83. Ginalski K Elofsson A Fischer D Rychlewski L 3D-Jury: A simple approach to improve protein structure predictions Bioinformatics 2003, 19(8):1015-1018. 12761065
84. von Grotthuss M Pas J Wyrwicz L Ginalski K Rychlewski L Application of 3D-Jury, GRDB, and Verify3D in fold recognition Proteins 2003, 53(Suppl 6):418-423. 14579330