Genomic characterization of Tv-ant-1, a Caenorhabditis elegans tag-61 homologue from the parasitic nematode Trichostrongylus vitrinus

Gene

Volumn 397, Issue 1-2, 2007, Pages 12-25

  Hu, Min ^a   Campbell, Bronwyn E ^a   Pellegrino, Mark ^a   Loukas, Alex ^b   Beveridge, Ian ^a   Ranganathan, Shoba ^c,d   Gasser, Robin B ^a  

^a UNIVERSITY OF MELBOURNE   (Australia)

^b QIMR BERGHOFER MEDICAL RESEARCH INSTITUTE   (Australia)

^c MACQUARIE UNIVERSITY   (Australia)

^d NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Adenine nucleotide translocator; ADP ATP translocase; Caenorhabditis elegans; Genomic structure; Promoter elements; Transcription; Trichostrongylus vitrinus

Indexed keywords

ADENINE NUCLEOTIDE TRANSLOCASE; CCAAT BINDING FACTOR; COMPLEMENTARY DNA; DOUBLE STRANDED RNA; TRANSCRIPTION FACTOR GATA;

5' UNTRANSLATED REGION; ALPHA HELIX; AMINO ACID SEQUENCE; ARTICLE; BASE PAIRING; CAENORHABDITIS ELEGANS; CONSENSUS SEQUENCE; E BOX ELEMENT; GENE; GENE SILENCING; GENETIC TRANSCRIPTION; HYDROPHOBICITY; LARVA; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; ORTHOLOGY; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN MOTIF; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA INTERFERENCE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; TAG 61 GENE; TRICHOSTRONGYLUS; TRICHOSTRONGYLUS VITRINUS; TV ANT 1 GENE;

ADENINE NUCLEOTIDE TRANSLOCATOR 1; AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; DNA, COMPLEMENTARY; DNA, HELMINTH; FEMALE; GENES, HELMINTH; HELMINTH PROTEINS; MALE; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROMOTER REGIONS (GENETICS); RNA INTERFERENCE; SEQUENCE HOMOLOGY, AMINO ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY; TRICHOSTRONGYLUS;

BOS; CAENORHABDITIS ELEGANS; NEMATODA; STRONGYLIDA; TRICHOSTRONGYLIDAE; TRICHOSTRONGYLUS VITRINUS;

EID: 34250882200     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2007.03.011     Document Type: Article

References (89)

1. Aboobaker A.A., and Blaxter M.L. Functional genomics for parasitic nematodes and platyhelminths. Trends Parasitol. 20 (2004) 178-184
2. Adrian G.S., McCammon M.T., Montgomery D.L., and Douglas M.G. Sequences required for delivery and localization of the ADP/ATP translocator to the mitochondrial inner membrane. Mol. Cell. Biol. 6 (1986) 626-634
3. Altschul S.F., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
4. Atchley W.R., and Fitch W.M. A natural classification of the basic helix-loop-helix class of transcription factors. Proc. Natl. Acad. Sci. U. S. A. 94 (1997) 5172-5176
5. Bairoch A. The PROSITE dictionary of sites and patterns in proteins, its current status. Nucleic Acids Res. 21 (1993) 3097-3103
6. Bateman A., Birney E., Durbin R., Eddy S.R., Howe K.L., and Sonnhammer E.L. The Pfam protein families database. Nucleic Acids Res. 28 (2000) 263-266
7. Battini R., Ferrari S., Kaczmarek L., Calabretta B., Chen S., and Baserga T.R. Molecular cloning of a cDNA for a human ADP/ATP carrier which is growth-regulated. J. Biol. Chem. 262 (1987) 4355-4359
8. Blaxter M.L., et al. A molecular evolutionary framework for the phylum Nematoda. Nature 392 (1998) 71-75
9. Blumenthel T., and Steward K. RNA processing and gene structure. In: Riddle D.L., Blumenthal T., Meyer B.J., and Priess J.R. (Eds). C. ELEGANS II (1997), Cold Spring Harbor Laboratory Press, Cold Spring Harbor 117-146
10. Boag P.R., Ren P., Newton S.E., and Gasser R.B. Molecular characterisation of a male-specific serine/threonine phosphatase from Oesophagostomum dentatum (Nematoda; Strongylida) and functional analysis of homologues in Caenorhaboditis elegans. Int. J. Parasitol. 33 (2003) 313-325
11. Brandeis M., et al. SP1 elements protect a CpG island from de novo methylation. Nature 371 (1994) 435-438
12. Breathnach R., and Chambon P. Organization and expression of eucaryotic split genes coding for proteins. Annu. Rev. Biochem. 50 (1981) 349-383
13. Brenner S. The genetics of Caenorhabditis elegans. Genetics 77 (1974) 71-94
14. Bresnick E.H., Martowicz M.L., Pal S., and Johnson K.D. Developmental control via GATA factor interplay at chromatin domain. J. Cell. Physiol. 205 (2005) 1-9
15. Britton C., and Murray L. Using Caenorhabditis elegans for functional analysis of genes of parasitic nematodes. Int. J. Parasitol. 36 (2006) 651-659
16. Britton C., McKerrow J.H., and Johnstone I.L. Regulation of the Caenorhabditis elegans gut cysteine protease gene cpr-1: requirement for GATA motifs. J. Mol. Biol. 283 (1998) 15-27
17. Britton C., Redmond D.L., Knox D.P., McKerrow J.H., and Barry J.D. Identification of promoter elements of parasitic nematode genes in transgenic Caenorhabditis elegans. Mol. Biochem. Parasitol. 103 (1999) 171-181
18. Bucher P. Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol. 212 (1990) 563-578
19. Bürglin T.R., Lobos E., and Blaxter M.L. Caenorhabditis elegans as a model for parasitic nematodes. Int. J. Parasitol. 28 (1998) 395-411
20. Cottee P.A., Nisbet A.J., Boag P.R., Larsen M., and Gasser R.B. Characterisation of major sperm protein genes and their expression in Oesophagostomum dentatum (Nematoda: Strongylida). Parasitology 129 (2004) 479-490
21. Cottee P.A., Abs EL-Osta Y.G., Nisbet A.J., and Gasser R.B. Ubiquitin-conjugating enzyme genes in Oesophagostomum dentatum. Parasitol. Res. 99 (2006) 119-125
22. Couthier A., Smith J., McGarr P., Craig B., and Gilleard J.S. Ectopic expression of a Haemonchus contortus GATA transcription factor in Caenorhabditis elegans reveals conserved function in spite of extensive sequence divergence. Mol. Biochem. Parasitol. 133 (2004) 241-253
23. Cozens A.L., Runswick M.J., and Walker J.E. DNA sequences of two expressed nuclear genes for human mitochondrial ADP/ATP translocase. J. Mol. Biol. 206 (1989) 261-280
24. Dahout-Gonzalez C., Nury H., Trézéguet V., Lauquin G.J., Pebay-Peyroula E., and Brandolin G. Molecular, functional, and pathological aspects of the mitochondrial ADP/ATP carrier. Physiology 21 (2006) 242-249
25. Dolce V., Scarcia P., Iacopetta D., and Palmieri F. A fourth ADP/ATP carrier isoform in man: identification, bacterial expression, functional characterization and tissue distribution. FEBS Lett. 579 (2005) 633-637
26. Fiore C., et al. The mitochondrial ADP/ATP carrier: structural, physiological and pathological aspects. Biochimie 80 (1998) 137-150
27. Fire A., Xu S., Montgomery M.K., Kostas S.A., Driver S.E., and Mello C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391 (1998) 806-811
28. Gao G., et al. Cross-species RNAi: selected Ascaris suum dsRNAs can sterilize Caenorhabditis elegans. Mol. Biochem. Parasitol. 146 (2006) 124-128
29. Gasser R.B., Chilton N.B., Hoste H., and Beveridge I. Rapid sequencing of rDNA from single worms and eggs of parasitic helminths. Nucleic Acids Res. 21 (1993) 2525-2526
30. Geldhof P., et al. Testing the efficacy of RNA interference in Haemonchus contortus. Int. J. Parasitol. 36 (2006) 801-810
31. Geldhof P., Visser A., Clark D., Saunders G., Britton C., Gilleard J., Berriman M., and Knox D. RNA interference in parasitic helminths: current situation, potential pitfalls and future prospects. Parasitology 134 (2007) 609-619
32. Gilleard J.S., Woods D.J., and Dow J.A. Model-organism genomics in veterinary parasite drug-discovery. Trends Parasitol. 21 (2005) 302-305
33. Giraud S., Bonod-Bidaud C., Wesolowski-Louvel M., and Stepien G. Expression of human ANT2 gene in highly proliferative cells: GRBOX, a new transcriptional element, is involved in the regulation of glycolytic ATP import into mitochondria. J. Mol. Biol. 281 (1998) 409-418
34. Grant W.N., et al. Heritable transgenesis of Parastrongyloides trichosuri: a nematode parasite of mammals. Int. J. Parasitol. 36 (2006) 475-483
35. Gönczy P., et al. Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III. Nature 408 (2000) 331-336
36. Halestrap A.P., and Brennerb C. The adenine nucleotide translocase: a central component of the mitochondrial permeability transition pore and key player in cell death. Curr. Med. Chem. 10 (2003) 1507-1525
37. Hoste H., Chilton N.B., Gasser R.B., and Beveridge I. Differences in the second internal transcribed spacer (ribosomal DNA) between five species of Trichostrongylus (Nematoda: Trichostrongylidae). Int. J. Parasitol. 25 (1995) 75-80
38. Houldsworth J., and Attardi G. Two distinct genes for ADP/ATP translocase are expressed at the mRNA level in adult human liver. Proc. Natl. Acad. Sci. U. S. A. 85 (1988) 377-381
39. Hu M., Gasser R.B., Chilton N.B., and Beveridge I. Genetic variation in the mitochondrial cytochrome c oxidase subunit 1 within three species of Progamotaenia (Cestoda: Anoplocephalidae) from macropodid marsupials. Parasitology 130 (2005) 117-129
40. Huang X. A contig assembly program based on sensitive detection of fragment overlaps. Genomics 14 (1992) 18-25
41. Hussein A.S., Kichenin K., and Selkirk M.E. Suppression of secreted acetylcholinesterase expression in Nippostrongylus brasiliensis by RNA interference. Mol. Biochem. Parasitol. 122 (2002) 91-94
42. Islam M.K., Miyoshi T., Yamada M., and Tsuji N. Pyrophosphatase of the roundworm Ascaris suum plays an essential role in the worm's molting and development. Infect. Immun. 73 (2005) 1995-2004
43. Issa Z., Grant W.N., Stasiuk S., and Shoemaker C.B. Development of methods for RNA interference in the sheep gastrointestinal parasite, Trichostrongylus colubriformis. Int. J. Parasitol. 35 (2005) 935-940
44. Kageyama R., Ohtsuka T., Hatakeyama J., and Ohsawa R. Roles of bHLH genes in neural stem cell differentiation. Exp. Cell Res. 306 (2005) 343-348
45. Kamath R.S., et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421 (2003) 231-237
46. Kewley R.J., Whitelaw M.L., and Chapman-Smith A. The mammalian basic helix-loop-helix/PAS family of transcriptional regulators. Int. J. Biochem. Cell Biol. 36 (2004) 189-204
47. Kim S.K., et al. A gene expression map for Caenorhabditis elegans. Science 293 (2001) 2087-2092
48. Kotze A.C., and Bagnall N.H. RNA interference in Haemonchus contortus: suppression of beta-tubulin gene expression in L3, L4 and adult worms in vitro. Mol. Biochem. Parasitol. 145 (2006) 101-110
49. Larsen F., Gundersen G., Lopez R., and Prydz H. CpG islands as gene markers in the human genome. Genomics 13 (1992) 1095-1107
50. LaVoie H.A. The role of GATA in mammalian reproduction. Exp. Biol. Med. 228 (2003) 1282-1290
51. Levy S.E., Chen Y.S., Graham B.H., and Wallace D.C. Expression and sequence analysis of the mouse adenine nucleotide translocase 1 and 2 genes. Gene 254 (2000) 57-66
52. Li K., et al. A human muscle adenine nucleotide translocator gene has four exons, is located on chromosome 4 and is differentially expressed. J. Biol. Chem. 264 (1989) 13998-14004
53. Li R., Hodny Z., Luciakova K., Barath P., and Nelson B.D. Sp1 activates and inhibits transcription from separate elements in the proximal promoter of the human adenine nucleotide translocase 2 (ANT2) gene. J. Biol. Chem. 271 (1996) 18925-18930
54. Li S., et al. A map of the interactome network of the metazoan C. elegans. Science 303 (2004) 540-543
55. Li X., et al. Successful transgenesis of the parasitic nematode Strongyloides stercoralis requires endogenous non-coding control elements. Int. J. Parasitol. 36 (2006) 671-679
56. Lowry J.A., and Atchley W.R. Molecular evolution of the GATA family of transcription factors: conservation within the DNA-binding domain. J. Mol. Evol. 50 (2000) 103-115
57. Lustigman S., Zhang J., Liu J., Oksov Y., and Hashmi S. RNA interference targeting cathepsin L and Z-like cysteine proteases of Onchocerca volvulus confirmed their essential function during L3 molting. Mol. Biochem. Parasitol. 138 (2004) 165-170
58. Macleod D., Charlton J., Mullin J., and Bird A.P. Sp1 sites in the mouse aprt gene promoter are required to prevent methylation of the CpG island. Genes Dev. 8 (1994) 2282-2292
59. MacRae I.J., et al. Structural basis for double-stranded RNA processing by dicer. Science 311 (2006) 195-198
60. MAFF. Manual of Veterinary Parasitological Laboratory Techniques. Technical Bulletin vol. 18 (1977), Her Majesty's Stationary Office, London, UK
61. Massari M.E., and Murre C. Helix-loop-helix proteins: regulators of transcription in eukaryotic organisms. Mol. Cell. Biol. 20 (2000) 429-440
62. Mckay S.J., et al. Gene expression profiling of cells, tissues, and developmental stages of the nematode C. elegans. Cold Spring Harbor Symp. Quant. Biol. 68 (2003) 159-169
63. McMiller T.L., and Johnson C.M. Molecular characterization of HLH-17, a C. elegans bHLH protein required for normal larval development. Gene 356 (2005) 1-10
64. Murakami R., Okumura T., and Uchiyama H. GATA factors as key regulatory molecules in the development of Drosophila endoderm. Dev. Growth Differ. 47 (2005) 581-589
65. Neckelmann N., Li K., Wade R., Shuster P.R., and Wallace D.C. cDNA sequence of a human skeletal muscle ADP/ATP translocator: lack of a leader peptide, divergence from a fibroblast translocator cDNA, and coevolution with mitochondrial DNA genes. Proc. Natl. Acad. Sci. U. S. A. 84 (1987) 7580-7584
66. Nelson D.R., Felix C.M., and Swanson J.M. Highly conserved charge-pair networks in the mitochondrial carrier family. J. Mol. Biol. 277 (1998) 285-308
67. Nielsen H., Engelbrecht J., Brunak S., and von Heijne G. A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Int. J. Neural Syst. 8 (1997) 581-599
68. Nisbet A.J., and Gasser R.B. Profiling of gender-specific gene expression for Trichostrongylus vitrinus (Nematoda: Strongylida) by microarray analysis of expressed sequence tag libraries constructed by suppressive-subtractive hybridisation. Int. J. Parasitol. 34 (2004) 633-643
69. Pabo C.O., and Sauer R.T. Transcription factors: structural families and principles of DNA recognition. Annu. Rev. Biochem. 61 (1992) 1053-1059
70. Patient R.K., and McGhee J.D. The GATA family (vertebrates and invertebrates). Curr. Opin. Genet. Dev. 12 (2002) 416-422
71. Pebay-Peyroula E., Dahout-Gonzalez C., Kahn R., Trézéguet V., Lauquin G.J., and Brandolin G. Structure of mitochondrial ADP/ATP carrier in complex with carboxyatractyloside. Nature 426 6962 (2003) 39-44
72. Pikkarainen S., Tokola H., Kerkelä R., and Ruskoaho H. GATA transcription factors in the developing and adult heart. Cardiovasc. Res. 63 (2004) 196-207
73. Robinson A.J., and Kunji E.R. Mitochondrial carriers in the cytoplasmic state have a common substrate binding site. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 2617-2622
74. Robinson K.A., and Lopes J.M. SURVER AND SUMMARY: Saccharomyces cerevisiae basic helix-loop-helix proteins regulate diverse biological processes. Nucleic Acids Res. 28 (2000) 1499-1505
75. Ross S.E., Greenberg M.E., and Stiles C.D. Basic helix-loop-helix factors in cortical development. Neuron 39 (2003) 13-25
76. Rual J.F., et al. Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. Genome Res. 14 (2004) 2162-2168
77. Santamaria M., Lanave C., and Saccone C. The evolution of the adenine nucleotide translocase family. Gene 333 (2004) 51-59
78. Shim Y.H. elt-1, a gene encoding a Caenorhabditis elegans GATA transcription factor, is highly expressed in the germ lines with msp genes as potential targets. Mol. Cells 9 (1999) 535-541
79. Simmer F., et al. Genome-wide RNAi of C. elegans using the hypersensitive rrf-3 strain reveals novel gene functions. PLoS Biol. 1 (2003) 77-84
80. Sonnichsen B., et al. Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature 434 (2005) 462-469
81. Stein L., Sternberg P., Durbin R., Thierry-Mieg J., and Spieth J. WormBase: network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Res. 29 (2001) 82-86
82. Stepien G., Torroni A., Chung A.B., Hodge J.A., and Wallace D.C. Differential expression of adenine nucleotide translocator isoforms in mammalian tissues and during muscle cell differentiation. J. Biol. Chem. 267 (1992) 14592-14597
83. *4.0b10 (1999), Sinauer Associates, Sunderland
84. The C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282 (1998) 2012-2018
85. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
86. Timmons L., and Fire A. Specific interference by ingested dsRNA. Nature 395 (1998) 854
87. Walker J.E., and Runswick M.J. The mitochondrial transport protein superfamily. J. Bioenerg. Biomembranes 25 (1993) 435-446
88. Yan Y., et al. Genomic organization of four β-1,4-endoglucanase genes in plant-parasitic cyst nematodes and its evolutionary implications. Gene 220 (1998) 61-70
89. Zhong W., and Sternberg P.W. Genome-wide prediction of C. elegans genetic interactions. Science 311 (2006) 1481-1484