Intestinal transcriptomes of nematodes: Comparison of the parasites Ascaris suum and Haemonchus contortus with the free-living Caenorhabditis elegans

PLoS Neglected Tropical Diseases

Volumn 2, Issue 8, 2008, Pages

  Yin, Yong ^a   Martin, John ^a   Abubucker, Sahar ^a   Scott, Alan L ^b   McCarter, James P ^a,c   Wilson, Richard K ^a   Jasmer, Douglas P ^d   Mitreva, Makedonka ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^c Divergence Inc   (United States)

^d WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN KINASE; PROTEINASE; TRANSCRIPTOME;

AMINO ACID SEQUENCE; ARTICLE; ASCARIS SUUM; CAENORHABDITIS ELEGANS; CARBOHYDRATE METABOLISM; CONTROLLED STUDY; ENERGY METABOLISM; EVOLUTIONARY ADAPTATION; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENETIC CONSERVATION; GENETIC VARIABILITY; GENOME ANALYSIS; HAEMONCHUS CONTORTUS; INTESTINE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PROTEIN FUNCTION; RNA INTERFERENCE; RNA TRANSLATION; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; UNINDEXED SEQUENCE; ANIMAL; GENE; GENETICS; HAEMONCHUS; METABOLISM; MOLECULAR GENETICS;

ANIMALS; ASCARIS SUUM; CAENORHABDITIS ELEGANS; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENES, HELMINTH; HAEMONCHUS; INTESTINES; MOLECULAR SEQUENCE DATA;

EID: 56149121546     PISSN: None     EISSN: None     Source Type: Journal    
DOI: 10.1371/journal.pntd.0000269     Document Type: Article

References (52)

1. McGhee JD (2007) The C. elegans Intestine. WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/ wormbook.1.133.1, http://www.wormbook.org.
2. Ghafouri S, McGhee JD (2007) Bacterial residence time in the intestine of Caenorhabditis elegans. Nematology 9: 87-91.
3. Jasmer DP, McGuire TC (1991) Protective immunity to a blood-feeding nematode (Haemonchus contortus) induced by parasite gut antigens. Infect Immun 59: 4412-4417.
4. Tavernor AS, Smith TS, Langford CF, Munn EA, Graham M (1992) Vaccination of young Dorset lambs against haemonchosis. Parasite Immunol 14: 645-655.
5. Smith WD (1993) Protection in lambs immunised with Haemonchus contortus gut membrane proteins. Res Vet Sci 54: 94-101.
6. Smith SK, Pettit D, Newlands GF, Redmond DL, Skuce PJ, et al. (1999) Further immunization and biochemical studies with a protective antigen complex from the microvillar membrane of the intestine of Haemonchus contortus. Parasite Immunol 21: 187-199.
7. Knox DP, Smith WD (2001) Vaccination against gastrointestinal nematode parasites of ruminants using gut-expressed antigens. Vet Parasitol 100: 21-32.
8. Loukas A, Bethony J, Brooker S, Hotez P (2006) Hookworm vaccines: past, present, and future. Lancet Infect Dis 6: 733-741.
9. Jasmer DP, Yao C, Rehman A, Johnson S (2000) Multiple lethal effects induced by a benzimidazole anthelmintic in the anterior intestine of the nematode Haemonchus contortus. Mol Biochem Parasitol 105: 81-90.
10. Shompole S, Yao C, Cheng X, Knox D, Johnson S, et al. (2002) Distinct characteristics of two intestinal protein compartments discriminated by using fenbendazole and a benzimidazole resistant isolate of Haemonchus contortus. Exp Parasitol 101: 200-209.
11. Shingles J, Lilley CJ, Atkinson HJ, Urwin PE (2007) Meloidogyne incognita: molecular and biochemical characterisation of a cathepsin L cysteine proteinase and the effect on parasitism following RNAi. Exp Parasitol 115: 114-120.
12. Meldal BH, Debenham NJ, De Ley P, De Ley IT, Vanfleteren JR, et al. (2007) An improved molecular phylogeny of the Nematoda with special emphasis on marine taxa. Mol Phylogenet Evol 42: 622-636.
13. Blaxter ML, De Ley P, Garey JR, Liu LX, Scheldeman P, et al. (1998) A molecular evolutionary framework for the phylum Nematoda. Nature 392: 71-75.
14. Jasmer DP, Roth J, Myler PJ (2001) Cathepsin B-like cysteine proteases and Caenorhabditis elegans homologues dominate gene products expressed in adult Haemonchus contortus intestine. Mol Biochem Parasitol 116: 159-169.
15. Williamson AL, Brindley PJ, Knox DP, Hotez PJ, Loukas A (2003) Digestive proteases of blood-feeding nematodes. Trends Parasitol 19: 417-423.
16. Ranjit N, Jones MK, Stenzel DJ, Gasser RB, Loukas A (2006) A survey of the intestinal transcriptomes of the hookworms, Necator americanus and Ancylostoma caninum, using tissues isolated by laser microdissection microscopy. Int J Parasitol 36: 701-710.
17. McKay SJ, Johnson R, Khattra J, Asano J, Baillie DL, et al. (2004) Gene expression profiling of cells, tissues and developmental stages of the nematode C. elegans. Cold Spring Harb Symp Quant Biol 68: 159-170.
18. McGhee JD, Sleumer MC, Bilenky M, Wong K, McKay SJ, et al. (2007) The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine. Dev Biol 302: 627-645.
19. Pauli F, Liu Y, Kim YA, Chen PJ, Kim SK (2006) Chromosomal clustering and GATA transcriptional regulation of intestine-expressed genes in C. elegans. Development 133: 287-295.
20. Rehman A, Jasmer DP (1999) Defined characteristics of cathepsin B-like proteins from nematodes: inferred functional diversity and phylogenetic relatedness. Mol Biochem Parasitol 102: 297-310.
21. Rehman A, Jasmer DP (1998) A tissue specific approach for analysis of membrane and secreted protein antigens from Haemonchus contortus gut and its application to diverse nematode species. Mol Biochem Parasitol 97: 55-68.
22. Yin Y, Martin J, McCarter JP, Clifton SW, Wilson RK, et al. (2006) Identification and analysis of genes expressed in the adult filarial parasitic nematode Dirofilaria immitis. Int J Parasitol 36: 829-839.
23. McCarter J, Dautova Mitreva M, Martin J, Dante M, Wylie T, et al. (2003) Analysis and functional classification of transcripts from the nematode Meloidogyne incognita. Genome Biology 4: R26: 21-19.
24. Mitreva M, Elling AA, Dante M, Kloek AP, Kalyanaraman A, et al. (2004) A survey of SL1-spliced transcripts from the root-lesion nematode Pratylenchus penetrans. Mol Genet Genomics 272: 138-148.
25. Mitreva M, McCarter JP, Martin J, Dante M, Wylie T, et al. (2004) Comparative genomics of gene expression in the parasitic and free-living nematodes Strongyloides stercoralis and Caenorhabditis elegans. Genome Res 14: 209-220.
26. Wasmuth JD, Blaxter ML (2004) prot4EST: translating expressed sequence tags from neglected genomes. BMC Bioinformatics 5: 187.
27. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
28. Audic S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Res 7: 986-995.
29. Kall L, Krogh A, Sonnhammer EL (2004) A combined transmembrane topology and signal peptide prediction method. J Mol Biol 338: 1027-1036.
30. Remm M, Storm CE, Sonnhammer EL (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 314: 1041-1052.
31. Enright AJ, Van Dongen S, Ouzounis CA (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30: 1575-1584.
32. Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, et al. (2005) InterProScan: protein domains identifier. Nucleic Acids Res 33: W116-120.
33. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, et al. (2005) InterPro, progress and status in 2005. Nucleic Acids Res 33 Database Issue. pp D201-205.
34. Consortium TGO (2000) Gene ontology: Tool for the unification of biology. Nat Genet 25: 25-29.
35. Bono H, Ogata H, Goto S, Kanehisa M (1998) Reconstruction of amino acid biosynthesis pathways from the complete genome sequence. Genome Res 8: 203-210.
36. Kanehisa M, Goto S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30.
37. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32: D277-280.
38. Mao X, Cai T, Olyarchuk JG, Wei L (2005) Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21: 3787-3793.
39. Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, et al. (2007) Draft genome of the filarial nematode parasite Brugia malayi. Science 317: 1756-1760.
40. Mitreva M, Jasmer DP, Appleton J, Martin J, Dante M, et al. (2004) Gene discovery in the adenophorean nematode Trichinella spiralis: an analysis of transcription from three life cycle stages. Mol Biochem Parasitol 137: 277-291.
41. Vanfleteren JR, Van de Peer Y, Blaxter ML, Tweedie SA, Trotman C, et al. (1994) Molecular genealogy of some nematode taxa as based on cytochrome c and globin amino acid sequences. Mol Phylogenet Evol 3: 92-101.
42. Jasmer DP, Mitreva MD, McCarter JP (2004) mRNA sequences for Haemonchus contortus intestinal cathepsin B-like cysteine proteases display an extreme in abundance and diversity compared with other adult mammalian parasitic nematodes. Mol Biochem Parasitol 137: 297-305.
43. Steel RGD, Torrie JH (1960) Principles and procedures of statistics: McGraw-Hill Book Company, Inc. New York Toronto London.
44. Gu X, Su Z (2007) Tissue-driven hypothesis of genomic evolution and sequence-expression correlations. Proc Natl Acad Sci U S A 104: 2779-2784.
45. Camon E, Magrane M, Barrell D, Binns D, Fleischmann W, et al. (2003) The Gene Ontology Annotation (GOA) project: Implementation of GO in SWISSPROT, TrEMBL, and InterPro. Genome Res 13: 662-672.
46. Wylie T, Martin J, Dante M, Mitreva M, Clifton SW, et al. (2004) Nematode.net: A tool for navigating sequences from parasitic and free-living nematodes. Nucleic Acids Res 32: D423-D426.
47. Plowman GD, Sudarsanam S, Bingham J, Whyte D, Hunter T (1999) The protein kinases of Caenorhabditis elegans: a model for signal transduction in multicellular organisms. Proc Natl Acad Sci U S A 96: 13603-13610.
48. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, et al. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806-811.
49. Kamath RS, Fraser AG, Dong Y, Poulin G, Durbin R, et al. (2003) Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421: 231-237.
50. Rual JF, Ceron J, Koreth J, Hao T, Nicot AS, et al. (2004) Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. Genome Res 14: 2162-2168.
51. Sonnichsen B, Koski LB, Walsh A, Marschall P, Neumann B, et al. (2005) Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature 434: 462-469.
52. Mitreva M, Blaxter ML, Bird DM, McCarter JP (2005) Comparative genomics of nematodes. Trends Genet 21: 573-581.