51
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Rawling JM, Alvarez-Gonzalez R. TFIIF, a basal eukaryotic transcription factor, is a substrate for poly(ADP-ribosyl)ation. Biochem J 1997; 324 ( Pt 1):249-53. [PMID: 9164864 PMCID: PMC1218424 DOI: 10.1042/bj3240249] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have examined the susceptibility of some of the basal eukaryotic transcription factors as covalent targets for poly(ADP-ribosyl)ation. Human recombinant TATA-binding protein, transcription factor (TF)IIB and TFIIF (made up of the 30 and 74 kDa RNA polymerase II-associated proteins RAP30 and RAP74) were incubated with calf thymus poly(ADP-ribose) polymerase and [32P]NAD+ at 37 degrees C. On lithium dodecyl sulphate/PAGE and autoradiography, two bands of radioactivity, coincident with RAP30 and RAP74, were observed. No radioactivity co-migrated with TATA-binding protein or TFIIB. The phenomenon was dependent on the presence of nicked DNA, which is essential for poly(ADP-ribose) polymerase activity. Covalent modification of TFIIF increased with time of incubation, with increasing TFIIF concentration and with increasing NAD+ concentration. High-resolution PAGE confirmed that the radioactive species associated with RAP30 and RAP74 were ADP-ribose polymers. From these observations, we conclude that both TFIIF subunits are highly specific substrates for covalent poly(ADP-ribosyl)ation.
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Affiliation(s)
- J M Rawling
- Department of Microbiology and Immunology, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107-2699, USA
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52
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Nikolov DB, Burley SK. RNA polymerase II transcription initiation: a structural view. Proc Natl Acad Sci U S A 1997; 94:15-22. [PMID: 8990153 PMCID: PMC33652 DOI: 10.1073/pnas.94.1.15] [Citation(s) in RCA: 170] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In eukaryotes, RNA polymerase II transcribes messenger RNAs and several small nuclear RNAs. Like RNA polymerases I and III, polymerase II cannot act alone. Instead, general initiation factors [transcription factor (TF) IIB, TFIID, TFIIE, TFIIF, and TFIIH] assemble on promoter DNA with polymerase II, creating a large multiprotein-DNA complex that supports accurate initiation. Another group of accessory factors, transcriptional activators and coactivators, regulate the rate of RNA synthesis from each gene in response to various developmental and environmental signals. Our current knowledge of this complex macromolecular machinery is reviewed in detail, with particular emphasis on insights gained from structural studies of transcription factors.
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Affiliation(s)
- D B Nikolov
- Laboratories of Molecular Biophysics, The Rockefeller University, New York, NY 10021, USA
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53
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Conaway RC, Conaway JW. General transcription factors for RNA polymerase II. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1997; 56:327-46. [PMID: 9187058 DOI: 10.1016/s0079-6603(08)61009-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- R C Conaway
- Program in Molecular and Cell Biology, Oklahoma Medical Research Foundation, Oklahoma City 73104, USA
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54
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Abstract
Ternary complexes of DNA-dependent RNA polymerase with its DNA template and nascent transcript are central intermediates in transcription. In recent years, several unusual biochemical reactions have been discovered that affect the progression of RNA polymerase in ternary complexes through various transcription units. These reactions can be signaled intrinsically, by nucleic acid sequences and the RNA polymerase, or extrinsically, by protein or other regulatory factors. These factors can affect any of these processes, including promoter proximal and promoter distal pausing in both prokaryotes and eukaryotes, and therefore play a central role in regulation of gene expression. In eukaryotic systems, at least two of these factors appear to be related to cellular transformation and human cancers. New models for the structure of ternary complexes, and for the mechanism by which they move along DNA, provide plausible explanations for novel biochemical reactions that have been observed. These models predict that RNA polymerase moves along DNA without the constant possibility of dissociation and consequent termination. A further prediction of these models is that the polymerase can move in a discontinuous or inchworm-like manner. Many direct predictions of these models have been confirmed. However, one feature of RNA chain elongation not predicted by the model is that the DNA sequence can determine whether the enzyme moves discontinuously or monotonically. In at least two cases, the encounter between the RNA polymerase and a DNA block to elongation appears to specifically induce a discontinuous mode of synthesis. These findings provide important new insights into the RNA chain elongation process and offer the prospect of understanding many significant biological regulatory systems at the molecular level.
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Affiliation(s)
- S M Uptain
- Department of Molecular and Cell Biology, University of California at Berkeley 94720, USA.
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55
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Orphanides G, Lagrange T, Reinberg D. The general transcription factors of RNA polymerase II. Genes Dev 1996; 10:2657-83. [PMID: 8946909 DOI: 10.1101/gad.10.21.2657] [Citation(s) in RCA: 770] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- G Orphanides
- Howard Hughes Medical Institute, Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway 08854-5635, USA
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56
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Gnarra JR, Zhou S, Merrill MJ, Wagner JR, Krumm A, Papavassiliou E, Oldfield EH, Klausner RD, Linehan WM. Post-transcriptional regulation of vascular endothelial growth factor mRNA by the product of the VHL tumor suppressor gene. Proc Natl Acad Sci U S A 1996; 93:10589-94. [PMID: 8855222 PMCID: PMC38197 DOI: 10.1073/pnas.93.20.10589] [Citation(s) in RCA: 375] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The VHL tumor suppressor gene is inactivated in patients with von Hippel-Lindau disease and in most sporadic clear cell renal carcinomas. Although VHL protein function remains unclear, VHL does interact with the elongin BC subunits in vivo and regulates RNA polymerase II elongation activity in vitro by inhibiting formation of the elongin ABC complex. Expression of wild-type VHL in renal carcinoma cells with inactivated endogenous VHL resulted in unaltered in vitro cell growth and decreased vascular endothelial growth factor (VEGF) mRNA expression and responsiveness to serum deprivation. VEGF is highly expressed in many tumors, including VHL-associated and sporadic renal carcinomas, and it stimulates neoangiogenesis in growing solid tumors. Despite 5-fold differences in VEGF mRNA levels, VHL overexpression did not affect VEGF transcription initiation or elongation as would have been suggested by VHL-elongin association. These results suggest that VHL regulates VEGF expression at a post-transcriptional level and that VHL inactivation in target cells causes a loss of VEGF suppression, leading to formation of a vascular stroma.
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Affiliation(s)
- J R Gnarra
- Urologic Oncology Section, National Cancer Institute, Bethesda, MD 20892, USA
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57
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Reines D, Conaway JW, Conaway RC. The RNA polymerase II general elongation factors. Trends Biochem Sci 1996; 21:351-5. [PMID: 8870500 PMCID: PMC3374595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Synthesis of eukaryotic messenger RNA by RNA polymerase II is governed by the concerted action of a set of general transcription factors that control the activity of polymerase during both the initiation and elongation stages of transcription. To date, five general elongation factors [P-TEFb, SII, TFIIF, Elongin (SIII) and ELL] have been defined biochemically. Here, we discuss these transcription factors and their roles in controlling the activity of the RNA polymerase II elongation complex.
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Affiliation(s)
- D Reines
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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58
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Leuther KK, Bushnell DA, Kornberg RD. Two-dimensional crystallography of TFIIB- and IIE-RNA polymerase II complexes: implications for start site selection and initiation complex formation. Cell 1996; 85:773-9. [PMID: 8646784 DOI: 10.1016/s0092-8674(00)81242-8] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
SUMMARY Transcription factors IIB (TFIIB) and IIE (TFIIE) bound to RNA polymerase II have been revealed by electron crystallography in projection at 15.7 A resolution. The results lead to simple hypotheses for the roles of these factors in the initiation of transcription. TFIIB is suggested to define the distance from TATA box to transcription start site by bringing TATA DNA in contact with polymerase at that distance from the active center of the enzyme. TFIIE is suggested to participate in a key conformational switch occurring at the active center upon polymerase-DNA interaction.
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Affiliation(s)
- K K Leuther
- Department of Structural Biology, Stanford University School of Medicine, California 94305-5400, USA
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59
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Fang SM, Burton ZF. RNA polymerase II-associated protein (RAP) 74 binds transcription factor (TF) IIB and blocks TFIIB-RAP30 binding. J Biol Chem 1996; 271:11703-9. [PMID: 8662660 DOI: 10.1074/jbc.271.20.11703] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A set of deletion mutants of human RNA polymerase II-associated protein (RAP) 30, the small subunit of transcription factor IIF (TFIIF; RAP30/74), was constructed to map functional domains. Mutants were tested for accurate transcriptional activity, RAP74 binding, and TFIIB binding. Transcription assays indicate the importance of both N- and C-terminal sequences for RAP30 function. RAP74 binds to the N-terminal region of RAP30 between amino acids 1 and 98. TFIIB binds to an overlapping region of RAP30, localized to amino acids 1-176 (amino acids 27-152 comprise a minimal binding region). The C-terminal region of RAP74 (amino acids 358-517) binds directly and independently to TFIIB. Interestingly, RAP74 blocks TFIIB-RAP30 binding, both by binding TFIIB and by binding RAP30. When the TFIIF complex is intact, therefore, TFIIB-TFIIF contact is maintained through RAP74. If the TFIIB-RAP30 interaction is physiologically important, the TFIIF complex must dissociate within some transcription complexes.
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Affiliation(s)
- S M Fang
- Department of Biochemistry, Michigan State University, East Lansing 48824, USA
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60
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Aso T, Shilatifard A, Conaway JW, Conaway RC. Transcription syndromes and the role of RNA polymerase II general transcription factors in human disease. J Clin Invest 1996; 97:1561-9. [PMID: 8601619 PMCID: PMC507218 DOI: 10.1172/jci118580] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
MESH Headings
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Elongin
- Gene Expression
- Genes, Tumor Suppressor
- Genetic Diseases, Inborn/genetics
- Genetic Diseases, Inborn/metabolism
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Neoplasm Proteins
- Peptide Elongation Factors
- Promoter Regions, Genetic
- RNA Polymerase II/metabolism
- RNA, Messenger/biosynthesis
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic
- Transcriptional Elongation Factors
- von Hippel-Lindau Disease/genetics
- von Hippel-Lindau Disease/metabolism
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Affiliation(s)
- T Aso
- Program in Molecular and Cell Biology, Oklahoma Medical Research Foundation, Oklahoma City, 73104, USA
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61
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Powell W, Reines D. Mutations in the second largest subunit of RNA polymerase II cause 6-azauracil sensitivity in yeast and increased transcriptional arrest in vitro. J Biol Chem 1996; 271:6866-73. [PMID: 8636112 PMCID: PMC3371610 DOI: 10.1074/jbc.271.12.6866] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Yeast RNA polymerase II enzymes containing single amino acid substitutions in the second largest subunit were analyzed in vitro for elongation-related defects. Mutants were chosen for analysis based on their ability to render yeast cells sensitive to growth on medium containing 6-azauracil. RNA polymerase II purified from three different 6-azauracil-sensitive yeast strains displayed increased arrest at well characterized arrest sites in vitro. The extent of this defect did not correlate with sensitivity to growth in the presence of 6-azauracil. The most severe effect resulted from mutation rpb2 10 (P1018S), which occurs in region H, a domain highly conserved between prokaryotic and eukaryotic RNA polymerases that is associated with nucleotide binding. The average elongation rate of this mutant enzyme is also slower than wild type. We suggest that the slowed elongation rate and an increase in dwell time of elongating pol II leads to rpb2 10's arrest-prone phenotype. This mutant enzyme can respond to SII for transcriptional read-through and carry out SII-activated nascent RNA cleavage.
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Affiliation(s)
- W Powell
- Graduate Program in Biochemistry and Molecular Biology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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62
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Mavankal G, Ignatius Ou SH, Oliver H, Sigman D, Gaynor RB. Human immunodeficiency virus type 1 and 2 Tat proteins specifically interact with RNA polymerase II. Proc Natl Acad Sci U S A 1996; 93:2089-94. [PMID: 8700889 PMCID: PMC39914 DOI: 10.1073/pnas.93.5.2089] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The Tat-responsive region (TAR) element is a critical RNA regulatory element in the human immunodeficiency virus (HIV) long terminal repeat, which is required for activation of gene expression by the transactivator protein Tat. Recently, we demonstrated by gel-retardation analysis that RNA polymerase II binds to TAR RNA and that Tat prevents this binding even when Tat does not bind to TAR RNA. These results suggested that direct interactions between Tat and RNA polymerase II may prevent RNA polymerase II pausing and lead to Tat-mediated increases in transcriptional elongation. To test this possibility, we performed protein interaction studies with RNA polymerase II and both the HIV-1 and the closely related HIV-2 Tat protein. These studies indicated that both the HIV-1 and HIV-2 Tat proteins could specifically interact with RNA polymerase II. Mutagenesis of both HIV-1 and HIV-2 Tat demonstrated that the basic domains of both the HIV-1 and HIV-2 Tat proteins were required for this interaction. Furthermore, "far Western" analysis suggested that the largest subunit of RNA polymerase II was the site for interaction with Tat. The interactions between Tat and RNA polymerase II were of similar magnitude to those detected between RNA polymerase II and the cellular transcription factor RAP30, which stably associates with RNA polymerase II during transcriptional elongation. These studies are consistent with the model that RNA polymerase II is a cellular target for Tat resulting in Tat-mediated increases in transcriptional elongation from the HIV long terminal repeat.
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Affiliation(s)
- G Mavankal
- Division of Molecular Virology, University of Texas Southwestern Medical Center, Dallas 75235-8594, USA
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