51
|
Matsuda T, Morikawa M, Haruki M, Higashibata H, Imanaka T, Kanaya S. Isolation of TBP-interacting protein (TIP) from a hyperthermophilic archaeon that inhibits the binding of TBP to TATA-DNA. FEBS Lett 1999; 457:38-42. [PMID: 10486559 DOI: 10.1016/s0014-5793(99)01005-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We have isolated TBP (TATA-binding protein)-interacting protein (TIP) from cell lysates of a hyperthermophilic archaeon, Pyrococcus kodakaraensis KOD1, by affinity chromatography with TBP-agarose. Based on the internal amino acid sequence information, PCR primers were synthesized and used to amplify the gene encoding this protein (Pk-TIP). Determination of the nucleotide sequence and characterization of the recombinant protein revealed that Pk-TIP is composed of 224 amino acid residues (molecular weight of 25,558) and exists in a dimeric form. BIAcore analyses for the interaction between recombinant Pk-TIP and recombinant Pk-TBP indicated that they interact with each other with an equilibrium dissociation constant, KD, of 1.24-1.46 microM. A gel mobility shift assay indicated that Pk-TIP inhibited the interaction between Pk-TBP and a TATA-DNA. Pk-TIP may be one of the archaeal factors which negatively regulate transcription.
Collapse
Affiliation(s)
- T Matsuda
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Japan
| | | | | | | | | | | |
Collapse
|
52
|
Hethke C, Bergerat A, Hausner W, Forterre P, Thomm M. Cell-free transcription at 95 degrees: thermostability of transcriptional components and DNA topology requirements of Pyrococcus transcription. Genetics 1999; 152:1325-33. [PMID: 10430563 PMCID: PMC1460703 DOI: 10.1093/genetics/152.4.1325] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cell-free transcription of archaeal promoters is mediated by two archaeal transcription factors, aTBP and TFB, which are orthologues of the eukaryotic transcription factors TBP and TFIIB. Using the cell-free transcription system described for the hyperthermophilic Archaeon Pyrococcus furiosus by Hethke et al., the temperature limits and template topology requirements of archaeal transcription were investigated. aTBP activity was not affected after incubation for 1 hr at 100 degrees. In contrast, the half-life of RNA polymerase activity was 23 min and that of TFB activity was 3 min. The half-life of a 328-nt RNA product was 10 min at 100 degrees. Best stability of RNA was observed at pH 6, at 400 mm K-glutamate in the absence of Mg(2+) ions. Physiological concentrations of K-glutamate were found to stabilize protein components in addition, indicating that salt is an important extrinsic factor contributing to thermostability. Both RNA and proteins were stabilized by the osmolyte betaine at a concentration of 1 m. The highest activity for RNA synthesis at 95 degrees was obtained in the presence of 1 m betaine and 400 mm K-glutamate. Positively supercoiled DNA, which was found to exist in Pyrococcus cells, can be transcribed in vitro both at 70 degrees and 90 degrees. However, negatively supercoiled DNA was the preferred template at all temperatures tested. Analyses of transcripts from plasmid topoisomers harboring the glutamate dehydrogenase promoter and of transcription reactions conducted in the presence of reverse gyrase indicate that positive supercoiling of DNA inhibits transcription from this promoter.
Collapse
MESH Headings
- Archaeal Proteins/metabolism
- Cell-Free System
- DNA Topoisomerases, Type I
- DNA Topoisomerases, Type II/metabolism
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- DNA-Directed RNA Polymerases/metabolism
- Gene Expression Regulation, Archaeal
- Half-Life
- Hot Temperature
- Nucleic Acid Conformation
- Protein Denaturation
- Pyrococcus furiosus/genetics
- Pyrococcus furiosus/physiology
- RNA, Archaeal/biosynthesis
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Messenger/biosynthesis
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- Transcription, Genetic
Collapse
Affiliation(s)
- C Hethke
- Institut für Allgemeine Mikrobiologie, Universität Kiel, D-24118 Kiel, Germany
| | | | | | | | | |
Collapse
|
53
|
Tsai FT, Littlefield O, Kosa PF, Cox JM, Schepartz A, Sigler PB. Polarity of transcription on Pol II and archaeal promoters: where is the "one-way sign" and how is it read? COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 1999; 63:53-61. [PMID: 10384270 DOI: 10.1101/sqb.1998.63.53] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
MESH Headings
- Archaea/enzymology
- Archaea/genetics
- Base Sequence
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- Gene Expression Regulation, Archaeal
- Models, Genetic
- Models, Molecular
- Nucleic Acid Conformation
- Promoter Regions, Genetic
- Protein Conformation
- Protein Structure, Secondary
- RNA Polymerase II/metabolism
- TATA Box
- Transcription Factor TFIID
- Transcription Factors/chemistry
- Transcription Factors/metabolism
- Transcription Factors, TFII/chemistry
- Transcription Factors, TFII/metabolism
- Transcription, Genetic
Collapse
Affiliation(s)
- F T Tsai
- Department of Molecular Biophysics, Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06511, USA
| | | | | | | | | | | |
Collapse
|
54
|
Bell SD, Jackson SP. Transcription in Archaea. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 1999; 63:41-51. [PMID: 10384269 DOI: 10.1101/sqb.1998.63.41] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- S D Bell
- Wellcome Trust/Cancer Research Campaign Institute, Cancer and Developmental Biology, Cambridge, England, United Kingdom
| | | |
Collapse
|
55
|
Voorhorst WG, Gueguen Y, Geerling AC, Schut G, Dahlke I, Thomm M, van der Oost J, de Vos WM. Transcriptional regulation in the hyperthermophilic archaeon Pyrococcus furiosus: coordinated expression of divergently oriented genes in response to beta-linked glucose polymers. J Bacteriol 1999; 181:3777-83. [PMID: 10368153 PMCID: PMC93856 DOI: 10.1128/jb.181.12.3777-3783.1999] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/1999] [Accepted: 04/19/1999] [Indexed: 11/20/2022] Open
Abstract
The genetic organization, expression, and regulation of the celB locus of the hyperthermophilic archaeon Pyrococcus furiosus were analyzed. This locus includes the celB gene, which codes for an intracellular beta-glucosidase, and a divergently orientated gene cluster, adhA-adhB-lamA, which codes for two alcohol dehydrogenases and an extracellular beta-1,3-endoglucanase that is transcribed as a polycistronic messenger (the lamA operon). During growth of P. furiosus on either the beta-1,4-linked glucose dimer cellobiose or the beta-1,3-linked glucose polymer laminarin, the activities of both beta-glucosidase and endoglucanase were increased at least fivefold compared with levels during growth on maltose or pyruvate. Northern blot analysis revealed an enhanced transcription of both the celB gene and the lamA operon in the presence of these glucose-containing substrates. The in vivo and in vitro transcription initiation sites of both the celB gene and the lamA operon were identified 25 nucleotides downstream of conserved TATA box motifs. A number of repeating sequences have been recognized in the celB-adhA intergenic region, some of which might be part of a transcriptional regulator-binding site.
Collapse
Affiliation(s)
- W G Voorhorst
- Laboratory of Microbiology, Department of Biomolecular Sciences, Wageningen Agricultural University, NL-6703 CT Wageningen, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
56
|
Abstract
Information regarding transcriptional regulation in Archaea has begun to emerge from in vivo genetic studies. Evidence to date suggests a varied repertoire of regulatory mechanisms in Archaea that invokes both bacterial and eukaryal paradigms, as well as some novel features. Overall simplicity of mechanisms may reflect the prokaryotic lifestyle. Sequencing projects suggest the existence of certain classes of regulators, but experimental verification is needed.
Collapse
Affiliation(s)
- J A Leigh
- Department of Microbiology, University of Washington, Seattle, WA 98195-7242, USA.
| |
Collapse
|
57
|
Bell SD, Jaxel C, Nadal M, Kosa PF, Jackson SP. Temperature, template topology, and factor requirements of archaeal transcription. Proc Natl Acad Sci U S A 1998; 95:15218-22. [PMID: 9860949 PMCID: PMC28023 DOI: 10.1073/pnas.95.26.15218] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although Archaea are prokaryotic and resemble Bacteria morphologically, their transcription apparatus is remarkably similar to those of eukaryotic cell nuclei. Because some Archaea exist in environments with temperatures of around 100 degreesC, they are likely to have evolved unique strategies for transcriptional control. Here, we investigate the effects of temperature and DNA template topology in a thermophilic archaeal transcription system. Significantly, and in marked contrast with characterized eucaryal systems, archaeal DNA template topology has negligible effect on transcription levels at physiological temperatures using highly purified polymerase and recombinant transcription factors. Furthermore, archaeal transcription does not require hydrolysis of the beta-gamma phosphoanhydride bond of ATP. However, at lower temperatures, negatively supercoiled templates are transcribed more highly than those that are positively supercoiled. Notably, the block to transcription on positively supercoiled templates at lowered temperatures is at the level of polymerase binding and promoter opening. These data imply that Archaea do not possess a functional homologue of transcription factor TFIIH, and that for the promoters studied, transcription is mediated by TATA box-binding protein, transcription factor TFB, and RNA polymerase alone. Furthermore, they suggest that the reduction of plasmid linking number by hyperthermophilic Archaea in vivo in response to cold shock is a mechanism to maintain gene expression under these adverse circumstances.
Collapse
Affiliation(s)
- S D Bell
- Wellcome Trust/Cancer Research Campaign Institute of Cancer and Developmental Biology, and Department of Zoology Cambridge University, Tennis Court Road, Cambridge CB2 1QR United Kingdom
| | | | | | | | | |
Collapse
|
58
|
van der Oost J, Schut G, Kengen SW, Hagen WR, Thomm M, de Vos WM. The ferredoxin-dependent conversion of glyceraldehyde-3-phosphate in the hyperthermophilic archaeon Pyrococcus furiosus represents a novel site of glycolytic regulation. J Biol Chem 1998; 273:28149-54. [PMID: 9774434 DOI: 10.1074/jbc.273.43.28149] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The fermentative conversion of glucose in anaerobic hyperthermophilic Archaea is a variant of the classical Embden-Meyerhof pathway found in Bacteria and Eukarya. A major difference of the archaeal glycolytic pathway concerns the conversion of glyceraldehyde-3-phosphate. In the hyperthermophilic archaeon Pyrococcus furiosus, this reaction is catalyzed by an unique enzyme, glyceraldehyde-3-phosphate ferredoxin oxidoreductase (GAPOR). Here, we report the isolation, characterization, and transcriptional analysis of the GAPOR-encoding gene. GAPOR is related to a family of ferredoxin-dependent tungsten enzymes in (hyper)thermophilic Archaea and, in addition, to a hypothetical protein in Escherichia coli. Electron paramagnetic resonance analysis of the purified P. furiosus GAPOR protein confirms the anticipated involvement of tungsten in catalysis. During glycolysis in P. furiosus, GAPOR gene expression is induced, whereas the activity of glyceraldehyde-3-phosphate dehydrogenase is repressed. It is discussed that this unprecedented unidirectional reaction couple in the pyrococcal glycolysis and gluconeogenesis gives rise to a novel site of glycolytic regulation that might be widespread among Archaea.
Collapse
Affiliation(s)
- J van der Oost
- Laboratory of Microbiology, Wageningen Agricultural University, Hesselink van Suchtelenweg 4, NL-6307 CT Wageningen, The Netherlands.
| | | | | | | | | | | |
Collapse
|
59
|
van der Oost J, Ciaramella M, Moracci M, Pisani FM, Rossi M, de Vos WM. Molecular biology of hyperthermophilic Archaea. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 1998; 61:87-115. [PMID: 9670798 DOI: 10.1007/bfb0102290] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The sequences of a number of archaeal genomes have recently been completed, and many more are expected shortly. Consequently, the research of Archaea in general and hyperthermophiles in particular has entered a new phase, with many exciting discoveries to be expected. The wealth of sequence information has already led, and will continue to lead to the identification of many enzymes with unique properties, some of which have potential for industrial applications. Subsequent functional genomics will help reveal fundamental matters such as details concerning the genetic, biochemical and physiological adaptation of extremophiles, and hence give insight into their genomic evolution, polypeptide structure-function relations, and metabolic regulation. In order to optimally exploit many unique features that are now emerging, the development of genetic systems for hyperthermophilic Archaea is an absolute requirement. Such systems would allow the application of this class of Archaea as so-called "cell factories": (i) expression of certain archaeal enzymes for which no suitable conventional (mesophilic bacterial or eukaryal) systems are available, (ii) selection for thermostable variants of potentially interesting enzymes from mesophilic origin, and (iii) the development of in vivo production systems by metabolic engineering. An overview is given of recent insight in the molecular biology of hyperthermophilic Archaea, as well as of a number of promising developments that should result in the generation of suitable genetic systems in the near future.
Collapse
Affiliation(s)
- J van der Oost
- Department of Microbiology, Wageningen Agricultural University, The Netherlands
| | | | | | | | | | | |
Collapse
|
60
|
Bell SD, Jackson SP. Transcription and translation in Archaea: a mosaic of eukaryal and bacterial features. Trends Microbiol 1998; 6:222-8. [PMID: 9675798 DOI: 10.1016/s0966-842x(98)01281-5] [Citation(s) in RCA: 159] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The principal components involved in the processes of transcription and translation in Archaea have been identified by a combination of biochemistry and genome sequencing. In many cases, these factors are closely related to previously characterized proteins from Eukarya and Bacteria. Elucidating the function of these proteins will shed considerable light on the evolution of gene regulatory processes.
Collapse
Affiliation(s)
- S D Bell
- Wellcome/CRC Institute of Cancer and Developmental Biology, University of Cambridge, UK
| | | |
Collapse
|
61
|
Qureshi SA, Jackson SP. Sequence-specific DNA binding by the S. shibatae TFIIB homolog, TFB, and its effect on promoter strength. Mol Cell 1998; 1:389-400. [PMID: 9660923 DOI: 10.1016/s1097-2765(00)80039-8] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Previous studies have established that Archaea possess a homolog of the eukaryotic basal transcription factor TFIIB, termed TFB, that functions together with the archaeal TATA-binding protein (TBP) to direct transcription by RNA polymerase. Here, we analyze the strong S. shibatae viral (SSV) T6 promoter and show that the region of DNA immediately upstream of the TATA-like A box influences promoter strength. When placed upstream of the much weaker rRNA promoter, this sequence makes it as strong as the T6 promoter. By using a combination of approaches, we show that S. shibatae TFB mediates sequence-specific interactions with DNA flanking the A box. Thus, sequence-specific DNA recognition by TFB and TBP are codeterminants of promoter strength in Archaea.
Collapse
MESH Headings
- Base Sequence
- DNA Footprinting
- DNA Mutational Analysis
- DNA, Archaeal/metabolism
- DNA, Viral/genetics
- DNA-Binding Proteins/metabolism
- Evolution, Molecular
- Gene Expression Regulation, Archaeal
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Oligonucleotides/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- Sulfolobus/genetics
- TATA Box/physiology
- Transcription Factor TFIIB
- Transcription Factors/metabolism
- Transcription, Genetic/physiology
Collapse
Affiliation(s)
- S A Qureshi
- Wellcome/CRC Institute, Cambridge, United Kingdom
| | | |
Collapse
|
62
|
Roovers M, Hethke C, Legrain C, Thomm M, Glansdorff N. Isolation of the gene encoding Pyrococcus furiosus ornithine carbamoyltransferase and study of its expression profile in vivo and in vitro. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 247:1038-45. [PMID: 9288929 DOI: 10.1111/j.1432-1033.1997.01038.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The gene coding for ornithine carbamoyltransferase (OTCase, argF) in the hyperthermophilic archaea Pyrococcus furiosus was cloned by complementation of an OTCase mutant of Escherichia coli. The cloned P. furiosus argF gene also complemented a similar mutant of Saccharomyces cerevisiae. Sequencing revealed an open reading frame of 314 amino acids homologous to known OTCases and preceded by a TATA box showing only limited similarity with the Euryarchaeota consensus sequence. This is in accordance with the comparatively low in vitro promoter activity observed in a cell-free purified transcription system. Transcription initiates in vivo as well as in vitro at a guanine, 22 nucleotides downstream of the TATA box. Upstream from argF is a putative gene for diphthine synthetase, a eukaryotic enzyme assumed to occur also in archaea but not in bacteria.
Collapse
Affiliation(s)
- M Roovers
- Laboratorium voor Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussel, Brussels, Belgium
| | | | | | | | | |
Collapse
|
63
|
Qureshi SA, Bell SD, Jackson SP. Factor requirements for transcription in the Archaeon Sulfolobus shibatae. EMBO J 1997; 16:2927-36. [PMID: 9184236 PMCID: PMC1169900 DOI: 10.1093/emboj/16.10.2927] [Citation(s) in RCA: 116] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Archaea (archaebacteria) constitute a domain of life that is distinct from Bacteria (eubacteria) and Eucarya (eukaryotes). Although archaeal cells share many morphological features with eubacteria, their transcriptional apparatus is more akin to eukaryotic RNA polymerases I, II and III than it is to eubacterial transcription systems. Thus, in addition to possessing a 10 subunit RNA polymerase and a homologue of the TATA-binding protein (TBP), Archaea possess a polypeptide termed TFB that is homologous to eukaryotic TFIIB. Here, we investigate the factor requirements for transcription of several promoters of the archaeon Sulfolobus shibatae and its associated virus SSV. Through in vitro transcription and immunodepletion, we demonstrate that S. shibatae TBP, TFB and RNA polymerase are not complexed tightly with one another and that each is required for efficient transcription of all promoters tested. Furthermore, full transcription is restored by supplementing respective depleted extracts with recombinant TBP or TFB, indicating that TBP-associated factors or TFB-associated factors are not required. Indeed, gel-filtration suggests that Sulfolobus TBP and TFB are not associated stably with other proteins. Finally, all promoters analysed are transcribed accurately and efficiently in an in vitro system comprising recombinant TBP and TFB, together with essentially homogeneous preparation of RNA polymerase. Transcription in Archaea is therefore fundamentally homologous to that in eukaryotes, although factor requirements appear to be much less complex.
Collapse
Affiliation(s)
- S A Qureshi
- Wellcome/CRC Institute, and Department of Zoology, University of Cambridge, UK
| | | | | |
Collapse
|
64
|
Hausner W, Wettach J, Hethke C, Thomm M. Two transcription factors related with the eucaryal transcription factors TATA-binding protein and transcription factor IIB direct promoter recognition by an archaeal RNA polymerase. J Biol Chem 1996; 271:30144-8. [PMID: 8939964 DOI: 10.1074/jbc.271.47.30144] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We reported previously that cell-free transcription in the Archaea Methanococcus and Pyrococcus depends upon two archaeal transcription factors, archaeal transcription factor A (aTFA) and archaeal transcription factor B (aTFB). In the genome of Pyrococcus genes encoding putative homologues of eucaryal transcription factors TATA-binding protein (TBP) and TFIIB have been detected. Here, we report that Escherichia coli synthesized Pyrococcus homologues of TBP and TFIIB are able to replace endogenous aTFB and aTFA in cell-free transcription reactions. Antibodies raised against archaeal TBP and TFIIB bind to polypeptides of identical molecular mass in the aTFB and aTFA fraction. These data identify aTFB as archaeal TBP and aTFA as the archaeal homologue of TFIIB. At the Pyrococcus glutamate dehydrogenase (gdh) promoter these two bacterially produced transcription factors and endogenous RNA polymerase are sufficient to direct accurate and active initiation of transcription. DNase I protection experiments revealed Pyrococcus-TBP producing a characteristic footprint between position -20 and -34 centered around the TATA box of gdh promoter. Pyrococcus-TFIIB did not bind to the TATA box but bound cooperatively with Pyrococcus-TBP generating an extended DNase I footprinting pattern ranging from position -19 to -42. These data suggest that the Pyrococcus homologue of TFIIB associates with the TBP-promoter binary complex as its eucaryal counterpart, but in contrast to eucaryal TFIIB, it causes an extension of the protection to the region upstream of the TATA box.
Collapse
Affiliation(s)
- W Hausner
- Institut für Allgemeine Mikrobiologie, Universität Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Federal Republic of Germany
| | | | | | | |
Collapse
|