Targets of the Entamoeba histolytica transcription factor URE3-BP

PLoS Neglected Tropical Diseases

Volumn 2, Issue 8, 2008, Pages

  Gilchrist, Carol A ^a   Baba, Duza J ^a   Zhang, Yan ^b   Crasta, Oswald ^b   Evans, Clive ^b   Caler, Elisabet ^c   Sobral, Bruno W S ^b   Bousquet, Christina ^a   Leo, Megan ^a   Hochreiter, Ameilia ^a   Connell, Sarah K ^a   Mann, Barbara J ^a,d   Petri Jr , William A ^a,d  

^a UNIVERSITY OF VIRGINIA   (United States)

^b VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

^c J CRAIG VENTER INSTITUTE   (United States)

^d UNIVERSITY OF VIRGINIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL PROTEIN; MEMBRANE PROTEIN; PROTOZOAL RNA; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; UPSTREAM REGULATORY ELEMENT 3 BINDING PROTEIN; DNA BINDING PROTEIN; URE3 BP PROTEIN, ENTAMOEBA HISTOLYTICA; URE3-BP PROTEIN, ENTAMOEBA HISTOLYTICA;

ARTICLE; CALCIUM SIGNALING; CELL MIGRATION; CONTROLLED STUDY; ENTAMOEBA HISTOLYTICA; GEL MOBILITY SHIFT ASSAY; GENE CONSTRUCT; GENE IDENTIFICATION; GENETIC REGULATION; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; PROMOTER REGION; PROTEIN FUNCTION; PROTEIN TARGETING; PROTOZOAL GENETICS; ANIMAL; DNA MICROARRAY; GENETICS; METABOLISM; PHYSIOLOGY; PROTEIN BINDING; REGULATORY SEQUENCE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TWO HYBRID SYSTEM;

ANIMALS; DNA-BINDING PROTEINS; ELECTROPHORETIC MOBILITY SHIFT ASSAY; ENTAMOEBA HISTOLYTICA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; REGULATORY SEQUENCES, NUCLEIC ACID; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; TWO-HYBRID SYSTEM TECHNIQUES;

EID: 56149096946     PISSN: None     EISSN: None     Source Type: Journal    
DOI: 10.1371/journal.pntd.0000282     Document Type: Article

References (54)

1. Haque R, Mondal D, Duggal P, Kabir M, Roy S, et al. (2006) Entamoeba histolytica infection in children and protection from subsequent amebiasis. Infect Immun 74: 904-909.
2. Gilchrist CA, Houpt E, Trapaidze N, Fei Z, Crasta O, et al. (2006) Impact of intestinal colonization and invasion on the Entamoeba histolytica transcriptome. Mol Biochem Parasitol 147: 163-176.
3. MacFarlane RC, Singh U (2006) Identification of differentially expressed genes in virulent and nonvirulent Entamoeba species: potential implications for amebic pathogenesis. Infect Immun 74: 340-351.
4. Ehrenkaufer GM, Haque R, Hackney JA, Eichinger DJ, Singh U (2007) Identification of developmentally regulated genes in Entamoeba histolytica: insights into mechanisms of stage conversion in a protozoan parasite. Cell Microbiol 9: 1426-1444.
5. Davis PH, Schulze J, Stanley SL Jr (2007) Transcriptomic comparison of two Entamoeba histolytica strains with defined virulence phenotypes identifies new virulence factor candidates and key differences in the expression patterns of cysteine proteases, lectin light chains, and calmodulin. Mol Biochem Parasitol 151: 118-128.
6. Davis PH, Zhang X, Guo J, Townsend RR, Stanley SL Jr (2006) Comparative proteomic analysis of two Entamoeba histolytica strains with different virulence phenotypes identifies peroxiredoxin as an important component of amoebic virulence. Mol Microbiol 61: 1523-1532.
7. Purdy JE, Pho LT, Mann BJ, Petri WA Jr (1996) Upstream regulatory elements controlling expression of the Entamoeba histolytica lectin. Mol Biochem Parasitol 78: 91-103.
8. Gilchrist CA, Mann BJ, Petri WA Jr (1998) Control of ferredoxin and Gal/ GalNAc lectin gene expression in Entamoeba histolytica by a cis-acting DNA sequence. Infect Immun 66: 2383-2386.
9. Gilchrist CA, Holm CF, Hughes MA, Schaenman JM, Mann BJ, et al. (2001) Identification and characterization of an Entamoeba histolytica upstream regulatory element 3 sequence-specific DNA-binding protein containing EF-hand motifs. J Biol Chems 276: 11838-11843.
10. Gilchrist CA, Leo M, Line CG, Mann BJ, Petri WA Jr (2003) Calcium modulates promoter occupancy by the Entamoeba histolytica Ca2+-binding transcription factor URE3-BP. J Biol Chem 278: 4646-4653.
11. Kolchanov NA, Merkulova TI, Ignatieva EV, Ananko EA, Oshchepkov DY, et al. (2007) Combined experimental and computational approaches to study the regulatory elements in eukaryotic genes. Brief Bioinform 8: 266-274.
12. Long X, Miano JM (2007) Remote control of gene expression. J Biol Chem 282: 15941-15945.
13. van Noort V, Huynen MA (2006) Combinatorial gene regulation in Plasmodium falciparum. Trends Genet 22: 73-78.
14. Hakimi MA, Deitsch KW (2007) Epigenetics in Apicomplexa: control of gene expression during cell cycle progression, differentiation and antigenic variation. Curr Opin Microbiol 10: 357-362.
15. Ramakrishnan G, Gilchrist CA, Musa H, Torok MS, Grant PA, et al. (2004) Histone acetyltransferases and deacetylase in Entamoeba histolytica. Mol Biochem Parasitol 138: 205-216.
16. Romero-Diaz M, Gomez C, Lopez-Reyes I, Martinez MB, Orozco E, et al. (2007) Structural and functional analysis of the Entamoeba histolytica EhrabB gene promoter. BMC Mol Biol 8: 82.
17. Ehrenkaufer GM, Eichinger DJ, Singh U (2007) Trichostatin A effects on gene expression in the protozoan parasite Entamoeba histolytica. BMC Genomics 8: 216.
18. Loftus B, Anderson I, Davies R, Alsmark UC, Samuelson J, et al. (2005) The genome of the protist parasite Entamoeba histolytica. Nature 433: 865-868.
19. Clark CG, Alsmark UCM, Tazreiter M, Saito-Nakano Y, Ali V, et al. (2007) Structure and content of the Entamoeba histolytica genome. Advances in Parasitology, Vol 65 65: 51-190.
20. Singh U, Gilchrist CA, Schaenman JM, Rogers JB, Hockensmith JW, et al. (2002) Context-dependent roles of the Entamoeba histolytica core promoter element GAAC in transcriptional activation and protein complex assembly. Mol Biochem Parasitol 120: 107-116.
21. Hackney JA, Ehrenkaufer GM, Singh U (2007) Identification of putative transcriptional regulatory networks in Entamoeba histolytica using Bayesian inference. Nucleic Acids Res 35: 2141-2152.
22. Diamond LS (1961) Axenic cultivation of Entamoeba hitolytica. Science 134: 336-337.
23. Gomez C, Perez DG, Lopez-Bayghen E, Orozco E (1998) Transcriptional analysis of the EhPgp1 promoter of Entamoeba histolytica multidrug-resistant mutant. J Biol Chem 273: 7277-7284.
24. Olvera A, Olvera F, Vines RR, Recillas-Targa F, Lizardi PM, et al. (1997) Stable transfection of Entamoeba histolytica trophozoites by lipofection. Arch Med Res 28 Spec No: 49-51.
25. Asgharpour A, Gilchrist C, Baba D, Hamano S, Houpt E (2005) Resistance to intestinal Entamoeba histolytica infection is conferred by innate immunity and Gr-1+ cells. Infect Immun 73: 4522-4529.
26. Vines RR, Ramakrishnan G, Rogers JB, Lockhart LA, Mann BJ, et al. (1998) Regulation of adherence and virulence by the Entamoeba histolytica lectin cytoplasmic domain, which contains a beta2 integrin motif. Mol Biol Cell 9: 2069-2079.
27. Ramakrishnan G, Vines RR, Mann BJ, Petri WA Jr (1997) A tetracycline-inducible gene expression system in Entamoeba histolytica. Mol Biochem Parasitol 84: 93-100.
28. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132: 365-386.
29. Ginzinger DG, Godfrey TE, Nigro J, Moore DH 2nd, Suzuki S, et al. (2000) Measurement of DNA copy number at microsatellite loci using quantitative PCR analysis. Cancer Res 60: 5405-5409.
30. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.
31. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
32. Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 98: 5116-5121.
33. Smyth GK, Michaud J, Scott HS (2005) Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 21: 2067-2075.
34. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society, Series B 57: 289-300.
35. Franco E, Vazquez-Prado J, Meza I (1997) Fibronectin-derived fragments as inducers of adhesion and chemotaxis of Entamoeba histolytica trophozoites. J Infect Dis 176: 1597-1602.
36. Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-210.
37. Eisenhaber B, Bork P, Yuan Y, Loffler G, Eisenhaber F (2000) Automated annotation of GPI anchor sites: case study C. elegans. Trends Biochem Sci 25: 340-341.
38. Hofmann K, Stoffel W (1993) TMBASE - A database of membrane spanning protein Segments; 166 p.
39. Emanuelsson O, Brunak S, von Heijne G, Nielsen H (2007) Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2: 953-971.
40. McCoy JJ, Mann BJ, Vedvick TS, Pak Y, Heimark DB, et al. (1993) Structural analysis of the light subunit of the Entamoeba histolytica galactose-specific adherence lectin. J Biol Chem 268: 24223-24231.
41. Knoll LJ, Johnson DR, Gordon JI (1994) Biochemical studies of three Saccharomyces cerevisiae acyl-CoA synthetases, Faa1p, Faa2p, and Faa3p. J Biol Chem 269: 16348-16356.
42. Stahl U, Carlsson AS, Lenman M, Dahlqvist A, Huang B, et al. (2004) Cloning and functional characterization of a phospholipid:diacylglycerol acyltransferase from Arabidopsis. Plant Physiol 135: 1324-1335.
43. Willhoeft U, Buss H, Tannich E (1999) DNA sequences corresponding to the ariel gene family of Entamoeba histolytica are not present in E. dapar. Parasitol Res 85: 787-789.
44. Mai Z, Samuelson J (1998) A new gene family (ariel) encodes asparagine-rich Entamoeba histolytica antigens, which resemble the amebic vaccine candidate serine-rich E. histolytica protein. Infect Immun 66: 353-355.
45. Nixon JE, Field J, McArthur AG, Sogin ML, Yarlett N, et al. (2003) Iron-dependent hydrogenases of Entamoeba histolytica and Giardia lamblia: activity of the recombinant entamoebic enzyme and evidence for lateral gene transfer. Biol Bull 204: 1-9.
46. Grogan DW, Cronan JE Jr (1984) Cloning and manipulation of the Escherichia coli cyclopropane fatty acid synthase gene: physiological aspects of enzyme overproduction. J Bacteriol 158: 286-295.
47. Lopez-Camarillo C, Luna-Arias JP, Marchat LA, Orozco E (2003) EhPgp5 mRNA stability is a regulatory event in the Entamoeba histolytica multidrug resistance phenotype. J Biol Chem 278: 11273-11280.
48. Davis CA, Brown MP, Singh U (2007) Functional characterization of spliceosomal introns and identification of U2, U4, and US snRNAs in the deep-branching eukaryote Entamoeba histolytica. Eukaryot Cell 6: 940-948.
49. Dillner NB, Sanders MM (2002) Upstream stimulatory factor (USF) is recruited into a steroid hormone-triggered regulatory circuit by the estrogen-inducible transcription factor delta EF1. J Biol Chem 277: 33890-33894.
50. Macfarlane RC, Singh U (2007) Identification of an Entamoeba histolytica serine, threonine, isoleucine, rich protein with roles in adhesion and cytotoxicity. Eukaryot Cell.
51. Thomas R, Paredes CJ, Mehrotra S, Hatzimanikatis V, Papoutsakis ET (2007) A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data. BMC Bioinformatics 8: 228.
52. Margolin AA, Califano A (2007) Theory and limitations of genetic network inference from microarray data. Ann N Y Acad Sci.
53. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188-1190.
54. Borggreve SE, De Vries K, Dullaart RP (2003) Alterations in high-density lipoprotein metabolism and reverse cholesterol transport in insulin resistance and type 2 diabetes mellitus: role of lipolytic enzymes, lecithin:cholesterol acyltransferase and lipid transfer proteins. Eur J Clin Invest 33: 1051-1069.