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Bric A, Radebaugh CA, Paule MR. Photocross-linking of the RNA Polymerase I Preinitiation and Immediate Postinitiation Complexes. J Biol Chem 2004; 279:31259-67. [PMID: 15161919 DOI: 10.1074/jbc.m311828200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The architecture of eukaryotic rRNA transcription complexes was analyzed, revealing facts significant to the RNA polymerase (pol) I initiation process. Functional initiation and elongation complexes were mapped by site-specific photocross-linking to template DNA. Polymerase I is recruited to the promoter via protein-protein interactions with DNA-bound transcription initiation factor-IB. The latter's TATA-binding protein (TBP) and TAFs photocross-link to the promoter from -78 to +10 relative to the tis (+1). Although TBP does not bind DNA using its TATA-binding saddle, it does photocross-link to a 22-bp sequence that does not resemble a TATA box. Only TAF(I)96 (the mammalian TAF(I) 68, yeast Rrn7p homolog) overlaps significantly with the DNA interaction cleft of pol I based on modeling to the pol II crystal structure. None of the pol I-specific subunits that are localized on the lips of the cleft (A49 and A34.5) or the pol I-specific stalk (A43 and A14) cross-link to DNA. Pol I does not extend significantly upstream of the promoter-proximal border of the factor complex (-11 to -14), and similarly in the promoter proximal elongation complex, the enzyme does not contact DNA upstream of its normal exit from the cleft.
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Affiliation(s)
- Anka Bric
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA
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2
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Al-Khouri AM, Paule MR. A novel RNA polymerase I transcription initiation factor, TIF-IE, commits rRNA genes by interaction with TIF-IB, not by DNA binding. Mol Cell Biol 2002; 22:750-61. [PMID: 11784852 PMCID: PMC133551 DOI: 10.1128/mcb.22.3.750-761.2002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the small, free-living amoeba Acanthamoeba castellanii, rRNA transcription requires, in addition to RNA polymerase I, a single DNA-binding factor, transcription initiation factor IB (TIF-IB). TIF-IB is a multimeric protein that contains TATA-binding protein (TBP) and four TBP-associated factors that are specific for polymerase I transcription. TIF-IB is required for accurate and promoter-specific initiation of rRNA transcription, recruiting and positioning the polymerase on the start site by protein-protein interaction. In A. castellanii, partially purified TIF-IB can form a persistent complex with the ribosomal DNA (rDNA) promoter while homogeneous TIF-IB cannot. An additional factor, TIF-IE, is required along with homogeneous TIF-IB for the formation of a stable complex on the rDNA core promoter. We show that TIF-IE by itself, however, does not bind to the rDNA promoter and thus differs in its mechanism from the upstream binding factor and upstream activating factor, which carry out similar complex-stabilizing functions in vertebrates and yeast, respectively. In addition to its presence in impure TIF-IB, TIF-IE is found in highly purified fractions of polymerase I, with which it associates. Renaturation of polypeptides excised from sodium dodecyl sulfate-polyacrylamide gels showed that a 141-kDa polypeptide possesses all the known activities of TIF-IE.
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Affiliation(s)
- Anna Maria Al-Khouri
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA
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3
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Radebaugh CA, Kubaska WM, Hoffman LH, Stiffler K, Paule MR. A novel transcription initiation factor (TIF), TIF-IE, is required for homogeneous Acanthamoeba castellanii TIF-IB (SL1) to form a committed complex. J Biol Chem 1998; 273:27708-15. [PMID: 9765308 DOI: 10.1074/jbc.273.42.27708] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The fundamental transcription initiation factor (TIF) for ribosomal RNA expression by eukaryotic RNA polymerase I, TIF-IB, has been purified to near homogeneity from Acanthamoeba castellanii using standard techniques. The purified factor consists of the TATA-binding protein and four TATA-binding protein-associated factors with relative molecular weights of 145,000, 99,000, 96,000, and 91,000. This yields a calculated native molecular weight of 460, 000, which compares well with its mass determined by scanning transmission electron microscopy (493,000) and its sedimentation rate, which is close to RNA polymerase I (515,000). Both impure and nearly homogeneous TIF-IB exhibit an apparent equilibrium dissociation constant of 56 +/- 3 pM. However, although impure TIF-IB can form a promoter-DNA complex resistant to challenge by other promoter-containing DNAs, near homogeneous TIF-IB cannot do so. An additional transcription factor, dubbed TIF-IE, restores the ability of near homogeneous TIF-IB to sequester DNA into a committed complex.
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Affiliation(s)
- C A Radebaugh
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA
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An exonuclease requiring an intact helical stem for specificity produces the 3' end of Acanthamoeba castellanii 5 S RNA. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)35807-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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5
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Liu F, Bateman E. Acanthamoeba castellanii RNA polymerase II transcription in vitro: accurate initiation at the adenovirus major late promoter. Gene X 1992; 120:143-9. [PMID: 1398130 DOI: 10.1016/0378-1119(92)90087-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We have developed and characterized an efficient in vitro system from the protozoan, Acanthamoeba castellanii, that accurately initiates transcription from the adenovirus-2 major late promoter (AdMLP). Transcription by A. castellanii RNA polymerase II (pol II) is initiated at the same nucleotide (nt) that is used by HeLa extracts and is dependent upon adenovirus sequences located between nt -51 and the region around the transcription start point (tsp). The results suggest that the A. castellanii transcription factors for pol II which determine the tsp and the promoter elements that they recognize have been functionally conserved during evolution.
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Affiliation(s)
- F Liu
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington 05405-0068
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6
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Abstract
A comparative overview of the subunit taxonomy and sequences of eukaryotic and prokaryotic RNA polymerases indicates the presence of a core structure conserved between both sets of enzymes. The differentiation between prokaryotic and eukaryotic polymerases is ascribed to domains and subunits peripheral to the largely conserved central structure. Possible subunit and domain functions are outlined. The core's flexible shape is largely determined by the elongated architecture of the two largest subunits, which can be oriented along the DNA axis with their bulkier amino-terminal head regions looking towards the 3' end of the gene to be transcribed and their more slender carboxyl-terminal domains at the tail end of the enzyme. The two largest prokaryotic subunits appear originally derived from a single gene.
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Affiliation(s)
- D Armaleo
- Department of Microbiology, Duke University Medical Center, Durham, North Carolina 27710
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7
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Garcia-Carranca A, Miguel F, Dahmus ME, Gariglio P. Structure of monkey kidney cell RNA polymerase II: characterization of RNA polymerase associated with SV40 late transcriptional complexes. Arch Biochem Biophys 1986; 251:232-8. [PMID: 3024573 DOI: 10.1016/0003-9861(86)90070-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Three subspecies of RNA polymerase II have been described in eucaryotic cells and designated IIO, IIA, and IIB. Although their relative proportions vary among different sources, RNA polymerases IIA and IIB constitute the bulk of most purified RNA polymerase II preparations. Antibodies against calf thymus RNA polymerase II were used to estimate the amount of polymerase II subspecies in monkey kidney cells, isolated nuclei, and SV40 late transcriptional complexes. We have found that RNA polymerase IIO is present in whole cells and isolated nuclei in higher proportions than previously reported. Subspecies IIO was found associated with SV40 minichromosomes engaged in transcription during late lytic infection. The observation that RNA polymerase IIO is associated with the cellular chromatin and SV40 minichromosomes suggest that this form of the enzyme is the subspecies active in in vivo transcription.
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8
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Immunochemical analysis of mammalian RNA polymerase II subspecies. Stability and relative in vivo concentration. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)67007-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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9
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Lonigro RI, Altieri F, Allegra P, Caiafa P. Distribution of tightly bound non-histone proteins in chromatin fractions obtained by DNAase II digestion. Cell Biochem Funct 1985; 3:223-33. [PMID: 2424632 DOI: 10.1002/cbf.290030310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Digestion of pig liver chromatin with DNAse II afforded three different fractions which were characterized in terms of their DNA, RNA and tightly bound non-histone protein content, their DNA fragment size and their template activity. Two of these fractions are soluble after digestion with DNAase II and have been separated on the basis of their different solubility in MgCl2. A third fraction is not solubilized even after extensive digestion, although the size of its DNA is comparable to that of the enzyme solubilized fractions. The three fractions show qualitatively and quantitatively different distribution of tightly bound non-histone proteins, with specific protein components in each fraction; furthermore the non-solubilized fraction is greatly enriched in proteins tightly bound to DNA. From all the data obtained it can be suggested that the tightly bound proteins of the insoluble fraction may play, directly or indirectly, a role in maintaining an organized chromatin structure.
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Abstract
This review will attempt to cover the present information on the multiple forms of eukaryotic DNA-dependent RNA polymerases, both at the structural and functional level. Nuclear RNA polymerases constitute a group of three large multimeric enzymes, each with a different and complex subunit structure and distinct specificity. The review will include a detailed description of their molecular structure. The current approaches to elucidate subunit function via chemical modification, phosphorylation, enzyme reconstitution, immunological studies, and mutant analysis will be described. In vitro reconstituted systems are available for the accurate transcription of cloned genes coding for rRNA, tRNA, 5 SRNA, and mRNA. These systems will be described with special attention to the cellular factors required for specific transcription. A section on future prospects will address questions concerning the significance of the complex subunit structure of the nuclear enzymes; the organization and regulation of the gene coding for RNA polymerase subunits; the obtention of mutants affected at the level of factors, or RNA polymerases; the mechanism of template recognition by factors and RNA polymerase.
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11
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Guilfoyle TJ, Hagen G, Malcolm S. Size heterogeneity of the largest subunit of nuclear RNA polymerase II. An immunological analysis. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)43710-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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12
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Paule MR. Regulation of ribosomal RNA transcription during differentiation of Acanthamoeba castellanii: a review. THE JOURNAL OF PROTOZOOLOGY 1983; 30:211-4. [PMID: 6355452 DOI: 10.1111/j.1550-7408.1983.tb02905.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
During the cellular differentiation induced by starvation of Acanthamoeba castellanii, the expression of a number of genes is regulated. Evidence is reviewed that at least one of these, the precursor ribosomal RNA transcription unit, is regulated at the level of transcription. The structure of the rRNA transcription unit and of the RNA polymerases responsible for transcription in Acanthamoeba are reviewed. Utilizing an in vitro transcription system constructed from these components, preliminary evidence has been obtained that pre-rRNA gene expression is regulated by a modification of RNA polymerase I that affects the enzyme's ability to participate efficiently in the initiation of transcription. These results are reviewed in relation to other known mechanisms of transcriptional regulation in eukaryotes.
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13
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Engelke DR, Shastry BS, Roeder RG. Multiple forms of DNA-dependent RNA polymerases in Xenopus laevis. Rapid purification and structural and immunological properties. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(18)33077-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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14
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Ferraro A, D'Erme M, Cinquepalmi M, Noce A, Padula F, Turano C. Isolation of chromatin fragments carrying nascent RNA chains. Biochem Biophys Res Commun 1982; 106:961-6. [PMID: 6180746 DOI: 10.1016/0006-291x(82)91804-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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15
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Hahn H. Isolation of RNA polymerases from the water mold Achlya. PLANTA 1982; 154:53-59. [PMID: 24275917 DOI: 10.1007/bf00385496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/1981] [Accepted: 10/08/1981] [Indexed: 06/02/2023]
Abstract
The DNA-dependent RNA polymerases I, II, and III (ribonucleosidetriphosphate: RNA nucleotidyl-transferase, EC 2.7.7.6) from Achlya ambisexualis E87 (male), have been isolated. The highly purified RNA polymerase I was found to be composed of polypeptides with the following molecular weights (·10(-4)): 18.5, 14, 11.8, 7.3, 6.1, 4.9, 4.4, 2.8. RNA polymerase II showed a 400-fold higher resistance against α-amanitin than mammalian or higher plant RNA polymerase II.
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Affiliation(s)
- H Hahn
- Botanisches Institut der Universität, Meckenheimer Allee 170, D-5300, Bonn 1, Federal Republic of Germany
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16
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Spot-immunodetection of conserved determinants in eukaryotic RNA polymerases. Study with antibodies to yeast RNA polymerases subunits. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34968-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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17
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Lewis MK, Burgess RR. 5 Eukaryotic RNA Polymerases. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/s1874-6047(08)60277-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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18
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D'Alessio J, Perna P, Paule M. DNA-dependent RNA polymerases from Acanthamoeba castellanii. Comparative subunit structures of the homogeneous enzymes. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(19)86482-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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