Abstract
To identify regulatory elements that play a role in transcription initiation in ancient eukaryotes, we have analyzed the upstream regions of protein-coding genes from Trichomonas vaginalis, one of the most ancient eukaryotes studied to date. Characterization of seven protein-coding genes from this protist invariably revealed the presence of a highly conserved DNA sequence motif immediately upstream of the coding region. This 13-nt motif was shown to surround and contain precise sites for transcription initiation. No typical TATA boxes, positioned at 25-30 nt upstream of the transcription start sites of these genes, were found. The start-site regions from all seven T. vaginalis genes impart strong specific initiation of transcription in a mammalian in vitro transcription assay. This consensus promoter element in an ancient eukaryote is similar, both structurally and functionally, to initiator elements found in promoters of higher eukaryotes.
Full text
PDF




Images in this article
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Alonso R. A., Peattie D. A. Nucleotide sequence of a second alpha giardin gene and molecular analysis of the alpha giardin genes and transcripts in Giardia lamblia. Mol Biochem Parasitol. 1992 Jan;50(1):95–104. doi: 10.1016/0166-6851(92)90247-h. [DOI] [PubMed] [Google Scholar]
- Baroin A., Perasso R., Qu L. H., Brugerolle G., Bachellerie J. P., Adoutte A. Partial phylogeny of the unicellular eukaryotes based on rapid sequencing of a portion of 28S ribosomal RNA. Proc Natl Acad Sci U S A. 1988 May;85(10):3474–3478. doi: 10.1073/pnas.85.10.3474. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Breathnach R., Chambon P. Organization and expression of eucaryotic split genes coding for proteins. Annu Rev Biochem. 1981;50:349–383. doi: 10.1146/annurev.bi.50.070181.002025. [DOI] [PubMed] [Google Scholar]
- Brown S. D., Huang J., Van der Ploeg L. H. The promoter for the procyclic acidic repetitive protein (PARP) genes of Trypanosoma brucei shares features with RNA polymerase I promoters. Mol Cell Biol. 1992 Jun;12(6):2644–2652. doi: 10.1128/mcb.12.6.2644. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bucher P. Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J Mol Biol. 1990 Apr 20;212(4):563–578. doi: 10.1016/0022-2836(90)90223-9. [DOI] [PubMed] [Google Scholar]
- Cohen S. M., Knecht D., Lodish H. F., Loomis W. F. DNA sequences required for expression of a Dictyostelium actin gene. EMBO J. 1986 Dec 1;5(12):3361–3366. doi: 10.1002/j.1460-2075.1986.tb04651.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Edman U., Meraz M. A., Rausser S., Agabian N., Meza I. Characterization of an immuno-dominant variable surface antigen from pathogenic and nonpathogenic Entamoeba histolytica. J Exp Med. 1990 Sep 1;172(3):879–888. doi: 10.1084/jem.172.3.879. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Edman U., Meza I., Agabian N. Genomic and cDNA actin sequences from a virulent strain of Entamoeba histolytica. Proc Natl Acad Sci U S A. 1987 May;84(9):3024–3028. doi: 10.1073/pnas.84.9.3024. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ey P. L., Khanna K. K., Manning P. A., Mayrhofer G. A gene encoding a 69-kilodalton major surface protein of Giardia intestinalis trophozoites. Mol Biochem Parasitol. 1993 Apr;58(2):247–257. doi: 10.1016/0166-6851(93)90046-z. [DOI] [PubMed] [Google Scholar]
- Fitch W. M., Margoliash E. Construction of phylogenetic trees. Science. 1967 Jan 20;155(3760):279–284. doi: 10.1126/science.155.3760.279. [DOI] [PubMed] [Google Scholar]
- Huber M., Garfinkel L., Gitler C., Mirelman D., Revel M., Rozenblatt S. Entamoeba histolytica: cloning and characterization of actin cDNA. Mol Biochem Parasitol. 1987 Jul;24(3):227–235. doi: 10.1016/0166-6851(87)90154-x. [DOI] [PubMed] [Google Scholar]
- Huber M., Garfinkel L., Gitler C., Mirelman D., Revel M., Rozenblatt S. Nucleotide sequence analysis of an Entamoeba histolytica ferredoxin gene. Mol Biochem Parasitol. 1988 Oct;31(1):27–33. doi: 10.1016/0166-6851(88)90142-9. [DOI] [PubMed] [Google Scholar]
- Javahery R., Khachi A., Lo K., Zenzie-Gregory B., Smale S. T. DNA sequence requirements for transcriptional initiator activity in mammalian cells. Mol Cell Biol. 1994 Jan;14(1):116–127. doi: 10.1128/mcb.14.1.116. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Johnson P. F., McKnight S. L. Eukaryotic transcriptional regulatory proteins. Annu Rev Biochem. 1989;58:799–839. doi: 10.1146/annurev.bi.58.070189.004055. [DOI] [PubMed] [Google Scholar]
- Johnson P. J., Lahti C. J., Bradley P. J. Biogenesis of the hydrogenosome in the anaerobic protist Trichomonas vaginalis. J Parasitol. 1993 Oct;79(5):664–670. [PubMed] [Google Scholar]
- Johnson P. J., d'Oliveira C. E., Gorrell T. E., Müller M. Molecular analysis of the hydrogenosomal ferredoxin of the anaerobic protist Trichomonas vaginalis. Proc Natl Acad Sci U S A. 1990 Aug;87(16):6097–6101. doi: 10.1073/pnas.87.16.6097. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kimmel A. R., Firtel R. A. Sequence organization in Dictyostelium: unique structure at the 5'-ends of protein coding genes. Nucleic Acids Res. 1983 Jan 25;11(2):541–552. doi: 10.1093/nar/11.2.541. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kirk-Mason K. E., Turner M. J., Chakraborty P. R. Evidence for unusually short tubulin mRNA leaders and characterization of tubulin genes in Giardia lamblia. Mol Biochem Parasitol. 1989 Aug;36(1):87–99. doi: 10.1016/0166-6851(89)90204-1. [DOI] [PubMed] [Google Scholar]
- Kollmar R., Farnham P. J. Site-specific initiation of transcription by RNA polymerase II. Proc Soc Exp Biol Med. 1993 Jun;203(2):127–139. doi: 10.3181/00379727-203-43583. [DOI] [PubMed] [Google Scholar]
- Lahti C. J., d'Oliveira C. E., Johnson P. J. Beta-succinyl-coenzyme A synthetase from Trichomonas vaginalis is a soluble hydrogenosomal protein with an amino-terminal sequence that resembles mitochondrial presequences. J Bacteriol. 1992 Nov;174(21):6822–6830. doi: 10.1128/jb.174.21.6822-6830.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Laird P. W., Zomerdijk J. C., de Korte D., Borst P. In vivo labelling of intermediates in the discontinuous synthesis of mRNAs in Trypanosoma brucei. EMBO J. 1987 Apr;6(4):1055–1062. doi: 10.1002/j.1460-2075.1987.tb04858.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lanzer M., de Bruin D., Ravetch J. V. A sequence element associated with the Plasmodium falciparum KAHRP gene is the site of developmentally regulated protein-DNA interactions. Nucleic Acids Res. 1992 Jun 25;20(12):3051–3056. doi: 10.1093/nar/20.12.3051. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lanzer M., de Bruin D., Ravetch J. V. Transcription mapping of a 100 kb locus of Plasmodium falciparum identifies an intergenic region in which transcription terminates and reinitiates. EMBO J. 1992 May;11(5):1949–1955. doi: 10.1002/j.1460-2075.1992.tb05248.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Leipe D. D., Gunderson J. H., Nerad T. A., Sogin M. L. Small subunit ribosomal RNA+ of Hexamita inflata and the quest for the first branch in the eukaryotic tree. Mol Biochem Parasitol. 1993 May;59(1):41–48. doi: 10.1016/0166-6851(93)90005-i. [DOI] [PubMed] [Google Scholar]
- McAndrew M. B., Read M., Sims P. F., Hyde J. E. Characterisation of the gene encoding an unusually divergent TATA-binding protein (TBP) from the extremely A+T-rich human malaria parasite Plasmodium falciparum. Gene. 1993 Feb 28;124(2):165–171. doi: 10.1016/0378-1119(93)90390-o. [DOI] [PubMed] [Google Scholar]
- McKnight S. L., Kingsbury R. Transcriptional control signals of a eukaryotic protein-coding gene. Science. 1982 Jul 23;217(4557):316–324. doi: 10.1126/science.6283634. [DOI] [PubMed] [Google Scholar]
- Means A. L., Farnham P. J. Transcription initiation from the dihydrofolate reductase promoter is positioned by HIP1 binding at the initiation site. Mol Cell Biol. 1990 Feb;10(2):653–661. doi: 10.1128/mcb.10.2.653. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Murphy W. J., Watkins K. P., Agabian N. Identification of a novel Y branch structure as an intermediate in trypanosome mRNA processing: evidence for trans splicing. Cell. 1986 Nov 21;47(4):517–525. doi: 10.1016/0092-8674(86)90616-1. [DOI] [PubMed] [Google Scholar]
- Müller M. Energy metabolism of protozoa without mitochondria. Annu Rev Microbiol. 1988;42:465–488. doi: 10.1146/annurev.mi.42.100188.002341. [DOI] [PubMed] [Google Scholar]
- Nellen W., Gallwitz D. Actin genes and actin messenger RNA in Acanthamoeba castellanii. Nucleotide sequence of the split actin gene I. J Mol Biol. 1982 Jul 25;159(1):1–18. doi: 10.1016/0022-2836(82)90028-6. [DOI] [PubMed] [Google Scholar]
- Nellen W., Silan C., Saur U., Firtel R. A. Regulatory sequences in the promoter of the Dictyostelium Actin 6 gene. EMBO J. 1986 Dec 1;5(12):3367–3372. doi: 10.1002/j.1460-2075.1986.tb04652.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- O'Shea-Greenfield A., Smale S. T. Roles of TATA and initiator elements in determining the start site location and direction of RNA polymerase II transcription. J Biol Chem. 1992 Jan 15;267(2):1391–1402. [PubMed] [Google Scholar]
- Reiter W. D., Hüdepohl U., Zillig W. Mutational analysis of an archaebacterial promoter: essential role of a TATA box for transcription efficiency and start-site selection in vitro. Proc Natl Acad Sci U S A. 1990 Dec;87(24):9509–9513. doi: 10.1073/pnas.87.24.9509. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sherman D. R., Janz L., Hug M., Clayton C. Anatomy of the parp gene promoter of Trypanosoma brucei. EMBO J. 1991 Nov;10(11):3379–3386. doi: 10.1002/j.1460-2075.1991.tb04902.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Smale S. T., Baltimore D. The "initiator" as a transcription control element. Cell. 1989 Apr 7;57(1):103–113. doi: 10.1016/0092-8674(89)90176-1. [DOI] [PubMed] [Google Scholar]
- Smale S. T., Schmidt M. C., Berk A. J., Baltimore D. Transcriptional activation by Sp1 as directed through TATA or initiator: specific requirement for mammalian transcription factor IID. Proc Natl Acad Sci U S A. 1990 Jun;87(12):4509–4513. doi: 10.1073/pnas.87.12.4509. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sogin M. L. Early evolution and the origin of eukaryotes. Curr Opin Genet Dev. 1991 Dec;1(4):457–463. doi: 10.1016/s0959-437x(05)80192-3. [DOI] [PubMed] [Google Scholar]
- Struhl K. Promoters, activator proteins, and the mechanism of transcriptional initiation in yeast. Cell. 1987 May 8;49(3):295–297. doi: 10.1016/0092-8674(87)90277-7. [DOI] [PubMed] [Google Scholar]
- Sutton R. E., Boothroyd J. C. Evidence for trans splicing in trypanosomes. Cell. 1986 Nov 21;47(4):527–535. doi: 10.1016/0092-8674(86)90617-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Thomashow L. S., Milhausen M., Rutter W. J., Agabian N. Tubulin genes are tandemly linked and clustered in the genome of trypanosoma brucei. Cell. 1983 Jan;32(1):35–43. doi: 10.1016/0092-8674(83)90494-4. [DOI] [PubMed] [Google Scholar]
- Weis L., Reinberg D. Transcription by RNA polymerase II: initiator-directed formation of transcription-competent complexes. FASEB J. 1992 Nov;6(14):3300–3309. doi: 10.1096/fasebj.6.14.1426767. [DOI] [PubMed] [Google Scholar]
- Wong J. M., Liu F., Bateman E. Isolation of genomic DNA encoding transcription factor TFIID from Acanthamoeba castellanii: characterization of the promoter. Nucleic Acids Res. 1992 Sep 25;20(18):4817–4824. doi: 10.1093/nar/20.18.4817. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zawel L., Reinberg D. Advances in RNA polymerase II transcription. Curr Opin Cell Biol. 1992 Jun;4(3):488–495. doi: 10.1016/0955-0674(92)90016-6. [DOI] [PubMed] [Google Scholar]
- Zenzie-Gregory B., O'Shea-Greenfield A., Smale S. T. Similar mechanisms for transcription initiation mediated through a TATA box or an initiator element. J Biol Chem. 1992 Feb 5;267(4):2823–2830. [PubMed] [Google Scholar]
- Zomerdijk J. C., Kieft R., Shiels P. G., Borst P. Alpha-amanitin-resistant transcription units in trypanosomes: a comparison of promoter sequences for a VSG gene expression site and for the ribosomal RNA genes. Nucleic Acids Res. 1991 Oct 11;19(19):5153–5158. doi: 10.1093/nar/19.19.5153. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zomerdijk J. C., Ouellette M., ten Asbroek A. L., Kieft R., Bommer A. M., Clayton C. E., Borst P. The promoter for a variant surface glycoprotein gene expression site in Trypanosoma brucei. EMBO J. 1990 Sep;9(9):2791–2801. doi: 10.1002/j.1460-2075.1990.tb07467.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zuber P., Healy J., Carter H. L., 3rd, Cutting S., Moran C. P., Jr, Losick R. Mutation changing the specificity of an RNA polymerase sigma factor. J Mol Biol. 1989 Apr 20;206(4):605–614. doi: 10.1016/0022-2836(89)90569-x. [DOI] [PubMed] [Google Scholar]