1
|
Belcher DJ, Guitart M, Hain B, Kim HG, Waning D, Barreiro E, Nader GA. LP07 and LLC preclinical models of lung cancer induce divergent anabolic deficits and expression of pro-inflammatory effectors of muscle wasting. J Appl Physiol (1985) 2022; 133:1260-1272. [PMID: 36201324 PMCID: PMC9678411 DOI: 10.1152/japplphysiol.00246.2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 09/12/2022] [Accepted: 09/29/2022] [Indexed: 11/22/2022] Open
Abstract
Preclinical models have been instrumental to elucidate the mechanisms underlying muscle wasting in lung cancer (LC). We investigated anabolic deficits and the expression of proinflammatory effectors of muscle wasting in the LP07 and Lewis lung carcinoma (LLC) tumor models. Tumor growth resulted in significant weakness in LP07 but not in LLC mice despite similar reductions in gastrocnemius muscle mass in both models. The LP07 tumors caused a reduction in ribosomal (r)RNA and a decrease in rRNA gene (rDNA) transcription elongation, whereas no changes in ribosomal capacity were evident in LLC tumor-bearing mice. Expression of RNA Polymerase I (Pol I) elongation-associated subunits Polr2f, PAF53, and Znrd1 mRNAs was significantly elevated in the LP07 model, whereas Pol I elongation-related factors FACT and Spt4/5 mRNAs were elevated in the LLC mice. Reductions in RPS6 and 4E-BP1 phosphorylation were similar in both models but were independent of mTOR phosphorylation in LP07 mice. Muscle inflammation was also tumor-specific, IL-6 and TNF-α mRNA increased with LLC tumors, and upregulation of NLRP3 mRNA was independent of tumor type. In summary, although both models caused muscle wasting, only the LP07 model displayed muscle weakness with reductions in ribosomal capacity. Intracellular signaling diverged at the mTOR level with similar reductions in RPS6 and 4E-BP1 phosphorylation regardless of tumor type. The increase in proinflammatory factors was more pronounced in the LLC model. Our results demonstrate novel divergent anabolic deficits and expression of proinflammatory effectors of muscle wasting in the LP07 and LLC preclinical models of lung cancer.NEW & NOTEWORTHY We provide novel data demonstrating significant divergence in anabolic deficits and the expression of proinflammatory effectors of muscle wasting consequent to different lung-derived tumors.
Collapse
Affiliation(s)
- Daniel J Belcher
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania
| | - Maria Guitart
- Pulmonology Department-Muscle Wasting and Cachexia in Chronic Respiratory Diseases and Lung Cancer Research Group, IMIM-Hospital del Mar, Barcelona, Spain
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Network of Excellence in Lung Diseases (CIBERES), Instituto de Salud Carlos III (ISCIII), Barcelona, Spain
| | - Brian Hain
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Hyo-Gun Kim
- Department of Kinesiology, The Pennsylvania State University, University Park, Pennsylvania
| | - David Waning
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania
- Penn State Cancer Institute, The Pennsylvania State University, University Park, Pennsylvania
| | - Esther Barreiro
- Pulmonology Department-Muscle Wasting and Cachexia in Chronic Respiratory Diseases and Lung Cancer Research Group, IMIM-Hospital del Mar, Barcelona, Spain
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Network of Excellence in Lung Diseases (CIBERES), Instituto de Salud Carlos III (ISCIII), Barcelona, Spain
| | - Gustavo A Nader
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania
- Department of Kinesiology, The Pennsylvania State University, University Park, Pennsylvania
- Penn State Cancer Institute, The Pennsylvania State University, University Park, Pennsylvania
| |
Collapse
|
2
|
Fernández-Parras I, Ramírez-Tejero JA, Luque F, Navarro F. Several Isoforms for Each Subunit Shared by RNA Polymerases are Differentially Expressed in the Cultivated Olive Tree ( Olea europaea L.). Front Mol Biosci 2022; 8:679292. [PMID: 34988111 PMCID: PMC8721170 DOI: 10.3389/fmolb.2021.679292] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 10/07/2021] [Indexed: 11/13/2022] Open
Abstract
Plants contain five nuclear RNA polymerases, with RNA pols IV and V in addition to conserved eukaryotic RNA pols I, II, and III. These transcriptional complexes share five common subunits, which have been extensively analyzed only in yeasts. By taking advantage of the recently published olive tree cultivar (Olea europaea L. cv. Picual) genome, we performed a genome-wide analysis of the genomic composition corresponding to subunits common to RNA pols. The cultivated olive tree genome is quite complex and contains many genes with several copies. We also investigated, for the first time, gene expression patterns for subunits common to RNA pols using RNA-Seq under different economically and biologically relevant conditions for the cultivar "Picual": tissues/organs, biotic and abiotic stresses, and early development from seeds. Our results demonstrated the existence of a multigene family of subunits common to RNA pols, and a variable number of paralogs for each subunit in the olive cultivar "Picual." Furthermore, these isoforms display specific and differentiated expression profiles depending on the isoform and growth conditions, which may be relevant for their role in olive tree biology.
Collapse
Affiliation(s)
| | | | - Francisco Luque
- Departamento de Biología Experimental-Genética, Jaén, Spain.,Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Jaén, Jaén, Spain
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Jaén, Spain.,Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Jaén, Jaén, Spain
| |
Collapse
|
3
|
Viktorovskaya OV, Schneider DA. Functional divergence of eukaryotic RNA polymerases: unique properties of RNA polymerase I suit its cellular role. Gene 2014; 556:19-26. [PMID: 25445273 DOI: 10.1016/j.gene.2014.10.035] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 10/16/2014] [Accepted: 10/17/2014] [Indexed: 02/08/2023]
Abstract
Eukaryotic cells express at least three unique nuclear RNA polymerases. The selective advantage provided by this enhanced complexity is a topic of fundamental interest in cell biology. It has long been known that the gene targets and transcription initiation pathways for RNA polymerases (Pols) I, II and III are distinct; however, recent genetic, biochemical and structural data suggest that even the core enzymes have evolved unique properties. Among the three eukaryotic RNA polymerases, Pol I is considered the most divergent. Transcription of the ribosomal DNA by Pol I is unmatched in its high rate of initiation, complex organization within the nucleolus and functional connection to ribosome assembly. Furthermore, ribosome synthesis is intimately linked to cell growth and proliferation. Thus, there is intense selective pressure on Pol I. This review describes key features of Pol I transcription, discusses catalytic activities of the enzyme and focuses on recent advances in understanding its unique role among eukaryotic RNA polymerases.
Collapse
Affiliation(s)
- Olga V Viktorovskaya
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, United States
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, United States.
| |
Collapse
|
4
|
Gerber J, Reiter A, Steinbauer R, Jakob S, Kuhn CD, Cramer P, Griesenbeck J, Milkereit P, Tschochner H. Site specific phosphorylation of yeast RNA polymerase I. Nucleic Acids Res 2007; 36:793-802. [PMID: 18084032 PMCID: PMC2241885 DOI: 10.1093/nar/gkm1093] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
All nuclear RNA polymerases are phosphoprotein complexes. Yeast RNA polymerase I (Pol I) contains approximately 15 phosphate groups, distributed to 5 of the 14 subunits. Information about the function of the single phosphosites and their position in the primary, secondary and tertiary structure is lacking. We used a rapid and efficient way to purify yeast RNA Pol I to determine 13 phosphoserines and –threonines. Seven of these phosphoresidues could be located in the 3D-homology model for Pol I, five of them are more at the surface. The single phosphorylated residues were systematically mutated and the resulting strains and Pol I preparations were analyzed in cellular growth, Pol I composition, stability and genetic interaction with non-essential components of the transcription machinery. Surprisingly, all Pol I phosphorylations analyzed were found to be non-essential post-translational modifications. However, one mutation (subunit A190 S685D) led to higher growth rates in the presence of 6AU or under environmental stress conditions, and was synthetically lethal with a deletion of the Pol I subunit A12.2, suggesting a role in RNA cleavage/elongation or termination. Our results suggest that individual major or constitutively phosphorylated residues contribute to non-essential Pol I-functions.
Collapse
Affiliation(s)
- Jochen Gerber
- Institut für Biochemie, Mikrobiologie und Genetik, Universität Regensburg, Munich, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Devaux S, Kelly S, Lecordier L, Wickstead B, Perez-Morga D, Pays E, Vanhamme L, Gull K. Diversification of function by different isoforms of conventionally shared RNA polymerase subunits. Mol Biol Cell 2007; 18:1293-301. [PMID: 17267688 PMCID: PMC1838988 DOI: 10.1091/mbc.e06-09-0841] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Eukaryotic nuclei contain three classes of multisubunit DNA-directed RNA polymerase. At the core of each complex is a set of 12 highly conserved subunits of which five--RPB5, RPB6, RPB8, RPB10, and RPB12--are thought to be common to all three polymerase classes. Here, we show that four distantly related eukaryotic lineages (the higher plant and three protistan) have independently expanded their repertoire of RPB5 and RPB6 subunits. Using the protozoan parasite Trypanosoma brucei as a model organism, we demonstrate that these distinct RPB5 and RPB6 subunits localize to discrete subnuclear compartments and form part of different polymerase complexes. We further show that RNA interference-mediated depletion of these discrete subunits abolishes class-specific transcription and hence demonstrates complex specialization and diversification of function by conventionally shared subunit groups.
Collapse
Affiliation(s)
- Sara Devaux
- *Institute for Molecular Biology and Medicine, Université Libre de Bruxelles, 6041 Gosselies, Belgium; and
| | - Steven Kelly
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Laurence Lecordier
- *Institute for Molecular Biology and Medicine, Université Libre de Bruxelles, 6041 Gosselies, Belgium; and
| | - Bill Wickstead
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - David Perez-Morga
- *Institute for Molecular Biology and Medicine, Université Libre de Bruxelles, 6041 Gosselies, Belgium; and
| | - Etienne Pays
- *Institute for Molecular Biology and Medicine, Université Libre de Bruxelles, 6041 Gosselies, Belgium; and
| | - Luc Vanhamme
- *Institute for Molecular Biology and Medicine, Université Libre de Bruxelles, 6041 Gosselies, Belgium; and
| | - Keith Gull
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| |
Collapse
|
6
|
Imazawa Y, Hisatake K, Mitsuzawa H, Matsumoto M, Tsukui T, Nakagawa K, Nakadai T, Shimada M, Ishihama A, Nogi Y. The Fission Yeast Protein Ker1p Is an Ortholog of RNA Polymerase I Subunit A14 in Saccharomyces cerevisiae and Is Required for Stable Association of Rrn3p and RPA21 in RNA Polymerase I. J Biol Chem 2005; 280:11467-74. [PMID: 15647272 DOI: 10.1074/jbc.m411150200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A heterodimer formed by the A14 and A43 subunits of RNA polymerase (pol) I in Saccharomyces cerevisiae is proposed to correspond to the Rpb4/Rpb7 and C17/C25 heterodimers in pol II and pol III, respectively, and to play a role(s) in the recruitment of pol I to the promoter. However, the question of whether the A14/A43 heterodimer is conserved in eukaryotes other than S. cerevisiae remains unanswered, although both Rpb4/Rpb7 and C17/C25 are conserved from yeast to human. To address this question, we have isolated a Schizosaccharomyces pombe gene named ker1+ using a yeast two-hybrid system, including rpa21+, which encodes an ortholog of A43, as bait. Although no homolog of A14 has previously been found in the S. pombe genome, functional characterization of Ker1p and alignment of Ker1p and A14 showed that Ker1p is an ortholog of A14. Disruption of ker1+ resulted in temperature-sensitive growth, and the temperature-sensitive deficit of ker1delta was suppressed by overexpression of either rpa21+ or rrn3+, which encodes the rDNA transcription factor Rrn3p, suggesting that Ker1p is involved in stabilizing the association of RPA21 and Rrn3p in pol I. We also found that Ker1p dissociated from pol I in post-log-phase cells, suggesting that Ker1p is involved in growth-dependent regulation of rDNA transcription.
Collapse
Affiliation(s)
- Yukiko Imazawa
- Department of Molecular Biology, Saitama Medical School, 38 Morohongo, Moroyama, Iruma-gun, Saitama 350-0495, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
De Carlo S, Carles C, Riva M, Schultz P. Cryo-negative staining reveals conformational flexibility within yeast RNA polymerase I. J Mol Biol 2003; 329:891-902. [PMID: 12798680 DOI: 10.1016/s0022-2836(03)00510-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The structure of the yeast DNA-dependent RNA polymerase I (RNA Pol I), prepared by cryo-negative staining, was studied by electron microscopy. A structural model of the enzyme at a resolution of 1.8 nm was determined from the analysis of isolated molecules and showed an excellent fit with the atomic structure of the RNA Pol II Delta4/7. The high signal-to-noise ratio (SNR) of the stained molecular images revealed a conformational flexibility within the image data set that could be recovered in three-dimensions after implementation of a novel strategy to sort the "open" and "closed" conformations in our heterogeneous data set. This conformational change mapped in the "wall/flap" domain of the second largest subunit (beta-like) and allows a better accessibility of the DNA-binding groove. This displacement of the wall/flap domain could play an important role in the transition between initiation and elongation state of the enzyme. Moreover, a protrusion was apparent in the cryo-negatively stained model, which was absent in the atomic structure and was not detected in previous 3D models of RNA Pol I. This structure could, however, be detected in unstained views of the enzyme obtained from frozen hydrated 2D crystals, indicating that this novel feature is not induced by the staining process. Unexpectedly, negatively charged molybdenum compounds were found to accumulate within the DNA-binding groove, which is best explained by the highly positive electrostatic potential of this region of the molecule, thus, suggesting that the stain distribution reflects the overall surface charge of the molecule.
Collapse
Affiliation(s)
- Sacha De Carlo
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 rue Laurent Fries, BP163, F-67404 Illkirch Cedex, C.U. de Strasbourg, France.
| | | | | | | |
Collapse
|
8
|
Peyroche G, Levillain E, Siaut M, Callebaut I, Schultz P, Sentenac A, Riva M, Carles C. The A14-A43 heterodimer subunit in yeast RNA pol I and their relationship to Rpb4-Rpb7 pol II subunits. Proc Natl Acad Sci U S A 2002; 99:14670-5. [PMID: 12407181 PMCID: PMC137477 DOI: 10.1073/pnas.232580799] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2002] [Accepted: 09/25/2002] [Indexed: 11/18/2022] Open
Abstract
A43, an essential subunit of yeast RNA polymerase I (pol I), interacts with Rrn3, a class I general transcription factor required for rDNA transcription. The pol I-Rrn3 complex is the only form of enzyme competent for promoter-dependent transcription initiation. In this paper, using biochemical and genetic approaches, we demonstrate that the A43 polypeptide forms a stable heterodimer with the A14 pol I subunit and interacts with the common ABC23 subunit, the yeast counterpart of the omega subunit of bacterial RNA polymerase. We show by immunoelectronic microscopy that A43, ABC23, and A14 colocalize in the three-dimensional structure of the pol I, and we demonstrate that the presence of A43 is required for the stabilization of both A14 and ABC23 within the pol I. Because the N-terminal half of A43 is clearly related to the pol II Rpb7 subunit, we propose that the A43-A14 pair is likely the pol I counterpart of the Rpb7-Rpb4 heterodimer, although A14 distinguishes from Rpb4 by specific sequence and structure features. This hypothesis, combined with our structural data, suggests a new localization of Rpb7-Rpb4 subunits in the three-dimensional structure of yeast pol II.
Collapse
Affiliation(s)
- Gerald Peyroche
- Laboratoire de Transcription des Gènes, Commissariat à l'Energie Atomique/Saclay, 91191 Gif sur Yvette Cedex, France
| | | | | | | | | | | | | | | |
Collapse
|
9
|
Bischler N, Brino L, Carles C, Riva M, Tschochner H, Mallouh V, Schultz P. Localization of the yeast RNA polymerase I-specific subunits. EMBO J 2002; 21:4136-44. [PMID: 12145213 PMCID: PMC126139 DOI: 10.1093/emboj/cdf392] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The spatial distribution of four subunits specifically associated to the yeast DNA-dependent RNA polymerase I (RNA pol I) was studied by electron microscopy. A structural model of the native enzyme was determined by cryo-electron microscopy from isolated molecules and was compared with the atomic structure of RNA pol II Delta 4/7, which lacks the specific polypeptides. The two models were aligned and a difference map revealed four additional protein densities present in RNA pol I, which were characterized by immunolabelling. A protruding protein density named stalk was found to contain the RNA pol I-specific subunits A43 and A14. The docking with the atomic structure showed that the stalk protruded from the structure at the same site as the C-terminal domain (CTD) of the largest subunit of RNA pol II. Subunit A49 was placed on top of the clamp whereas subunit A34.5 bound at the entrance of the DNA binding cleft, where it could contact the downstream DNA. The location of the RNA pol I-specific subunits is correlated with their biological activity.
Collapse
Affiliation(s)
- Nicolas Bischler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 rue Laurent Fries, BP163, F-67404 Illkirch Cedex, France
| | | | | | | | | | | | | |
Collapse
|
10
|
Imazawa Y, Hisatake K, Nakagawa K, Muramatsu M, Nogi Y. The fission yeast RPA21 subunit of RNA polymerase I: an evolutionarily conserved subunit interacting with ribosomal DNA (rDNA) transcription factor Rrn3p for recruitment to rDNA promoter. Genes Genet Syst 2002; 77:147-57. [PMID: 12207036 DOI: 10.1266/ggs.77.147] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Recruitment of RNA polymerases to the cognate promoter is a key step for the transcription initiation of specific genes in eukaryotes. Recently, RNA polymerase I (pol I) of Saccharomyces cerevisiae was shown to be recruited to the rDNA promoter via interaction between Rrn3p, a conserved transcription factor for rDNA, and A43, a subunit specific to pol I. The question of whether a similar interaction for pol I recruitment is conserved in other eukaryotes remains to be answered. We show here that Schizosaccharomyces pombe rpa21(+) encodes a protein of apparent molecular mass 21 kD which shows 36% identity to the A43 subunit of pol I in S. cerevisiae, and that rpa21(+) is essential for cell growth. To gain further insight into the functions of RPA21, we isolated a total of 22 temperature-sensitive (ts) mutants of rpa21(+) and found that most of the substitutions causing the ts phenotype are clustered in the N-terminal half of RPA21. The ts mutants showed a markedly reduced amount of primary transcripts of rDNA immediately after temperature shift-up. Over-expression of S. pombe rrn3(+) in the ts mutants suppressed the growth defect in an allele-specific manner. Therefore, we conclude that S. pombe RPA21 plays a functional role similar to that of A43 in S. cerevisiae and that the mechanism of recruitment of pol I to the rDNA promoter by the interaction of a specific pol I subunit with Rrn3p is evolutionarily conserved.
Collapse
Affiliation(s)
- Yukiko Imazawa
- CREST, Japan Science and Technology Corporation Center, Kawaguchi, Saitama, 332-0012, Japan
| | | | | | | | | |
Collapse
|
11
|
Peyroche G, Milkereit P, Bischler N, Tschochner H, Schultz P, Sentenac A, Carles C, Riva M. The recruitment of RNA polymerase I on rDNA is mediated by the interaction of the A43 subunit with Rrn3. EMBO J 2000; 19:5473-82. [PMID: 11032814 PMCID: PMC314014 DOI: 10.1093/emboj/19.20.5473] [Citation(s) in RCA: 140] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
RNA polymerase I (Pol I) is dedicated to transcription of the large ribosomal DNA (rDNA). The mechanism of Pol I recruitment onto rDNA promoters is poorly understood. Here we present evidence that subunit A43 of Pol I interacts with transcription factor Rrn3: conditional mutations in A43 were found to disrupt the transcriptionally competent Pol I-Rrn3 complex, the two proteins formed a stable complex when co-expressed in Escherichia coli, overexpression of Rrn3 suppressed the mutant phenotype, and A43 and Rrn3 mutants showed synthetic lethality. Consistently, immunoelectron microscopy data showed that A43 and Rrn3 co-localize within the Pol I-Rrn3 complex. Rrn3 has several protein partners: a two-hybrid screen identified the C-terminus of subunit Rrn6 of the core factor as a Rrn3 contact, an interaction supported in vitro by affinity chromatography. Our results suggest that Rrn3 plays a central role in Pol I recruitment to rDNA promoters by bridging the enzyme to the core factor. The existence of mammalian orthologues of A43 and Rrn3 suggests evolutionary conservation of the molecular mechanisms underlying rDNA transcription in eukaryotes.
Collapse
MESH Headings
- Amino Acid Sequence
- Binding Sites
- DNA, Fungal/genetics
- DNA, Fungal/metabolism
- DNA, Ribosomal/genetics
- DNA, Ribosomal/metabolism
- Epistasis, Genetic
- Fungal Proteins/genetics
- Fungal Proteins/metabolism
- Gene Expression Regulation, Fungal
- Image Processing, Computer-Assisted
- Macromolecular Substances
- Microscopy, Electron
- Models, Molecular
- Molecular Sequence Data
- Mutation/genetics
- Pol1 Transcription Initiation Complex Proteins
- Promoter Regions, Genetic
- Protein Binding
- Protein Subunits
- RNA Polymerase I/chemistry
- RNA Polymerase I/genetics
- RNA Polymerase I/metabolism
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Saccharomyces cerevisiae/enzymology
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins
- Sequence Alignment
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic
- Two-Hybrid System Techniques
Collapse
Affiliation(s)
- G Peyroche
- Service de Biochimie et de Génétique Moléculaire, CEA/Saclay, F-91191 Gif sur Yvette Cedex, France
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Norris JS, Hoel B, Voeks D, Maggouta F, Dahm M, Pan W, Clawson G. Design and testing of ribozymes for cancer gene therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2000; 465:293-301. [PMID: 10810634 DOI: 10.1007/0-306-46817-4_25] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
This chapter describes procedural aspects for development of ribozymes in general, and specifically, that cleave mRNA to an essential cellular gene, the AC40 subunit of RNA pol I. Ribozyme design includes functional selection of binding sites followed by computer modeling. These ribozymes are being used in vectors that target expression to the prostate via tissue specific promoters (Voeks, Norris, and Clawson, 1998) and have demonstrated efficacy.
Collapse
Affiliation(s)
- J S Norris
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston 29425, USA
| | | | | | | | | | | | | |
Collapse
|
13
|
Kimura M, Ishihama A. Involvement of multiple subunit-subunit contacts in the assembly of RNA polymerase II. Nucleic Acids Res 2000; 28:952-9. [PMID: 10648788 PMCID: PMC102587 DOI: 10.1093/nar/28.4.952] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
RNA polymerase II from the fission yeast Schizo-saccharomyces pombe consists of 12 species of subunits, Rpb1-Rpb12. We expressed these subunits, except Rpb4, simultaneously in cultured insect cells with baculovirus expression vectors. For the isolation of subunit complexes formed in the virus-infected cells, a glutathione S -transferase (GST) sequence was fused to the rpb3 cDNA to produce GST-Rpb3 fusion protein and a decahistidine-tag sequence was inserted into the rpb1 cDNA to produce Rpb1H protein. After successive affinity chromatography on glutathione and Ni(2+)columns, complexes consisting of the seven subunits, Rpb1H, Rpb2, GST-Rpb3, Rpb5, Rpb7, Rpb8 and Rpb11, were identified. Omission of the GST-Rpb3 expression resulted in reduced assembly of the Rpb11 into the complex. Direct interaction between Rpb3 and the other six subunits was detected by pairwise coexpression experiments. Coexpression of various combinations of a few subunits revealed that Rpb11 enhances Rpb3-Rpb8 interaction and consequently Rpb8 enhances Rpb1-Rpb3 interaction to some extent. We propose a mechanism in which the assembly of RNA poly-merase II is stabilized through multiple subunit-subunit contacts.
Collapse
Affiliation(s)
- M Kimura
- Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
| | | |
Collapse
|
14
|
Ishiguro A, Nogi Y, Hisatake K, Muramatsu M, Ishihama A. The Rpb6 subunit of fission yeast RNA polymerase II is a contact target of the transcription elongation factor TFIIS. Mol Cell Biol 2000; 20:1263-70. [PMID: 10648612 PMCID: PMC85260 DOI: 10.1128/mcb.20.4.1263-1270.2000] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Rpb6 subunit of RNA polymerase II is one of the five subunits common to three forms of eukaryotic RNA polymerase. Deletion and truncation analyses of the rpb6 gene in the fission yeast Schizosaccharomyces pombe indicated that Rpb6, consisting of 142 amino acid residues, is an essential protein for cell viability, and the essential region is located in the C-terminal half between residues 61 and 139. After random mutagenesis, a total of 14 temperature-sensitive mutants were isolated, each carrying a single (or double in three cases and triple in one) mutation. Four mutants each carrying a single mutation in the essential region were sensitive to 6-azauracil (6AU), which inhibits transcription elongation by depleting the intracellular pool of GTP and UTP. Both 6AU sensitivity and temperature-sensitive phenotypes of these rpb6 mutants were suppressed by overexpression of TFIIS, a transcription elongation factor. In agreement with the genetic studies, the mutant RNA polymerases containing the mutant Rpb6 subunits showed reduced affinity for TFIIS, as measured by a pull-down assay of TFIIS-RNA polymerase II complexes using a fusion form of TFIIS with glutathione S-transferase. Moreover, the direct interaction between TFIIS and RNA polymerase II was competed by the addition of Rpb6. Taken together, the results lead us to propose that Rpb6 plays a role in the interaction between RNA polymerase II and the transcription elongation factor TFIIS.
Collapse
Affiliation(s)
- A Ishiguro
- School of Life Science, Graduate University for Advanced Studies, Mishima, Shizuoka 411-8540, Japan
| | | | | | | | | |
Collapse
|
15
|
Jones E, Kimura H, Vigneron M, Wang Z, Roeder RG, Cook PR. Isolation and characterization of monoclonal antibodies directed against subunits of human RNA polymerases I, II, and III. Exp Cell Res 2000; 254:163-72. [PMID: 10623476 DOI: 10.1006/excr.1999.4739] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Human nuclei contain three different RNA polymerases: polymerases I, II, and III. Each polymerase is a multi-subunit enzyme with 12-17 subunits. The localization of these subunits is limited by the paucity of antibodies suitable for immunofluorescence. We now describe eight different monoclonal antibodies that react specifically with RPB6 (also known as RPA20, RPB14.4, or RPC20), RPB8 (RPA18, RPB17, or RPC18), RPC32, or RPC39 and which are suitable for such studies. Each antibody detects one specific band in immunoblots of nuclear extracts; each also immunoprecipitates large complexes containing many other subunits. When used for immunofluorescence, antibodies against the subunits shared by all three polymerases (i.e., RPB6, RPB8) gave a few bright foci in nucleoli and nucleoplasm, as well as many fainter nucleoplasmic foci; all the bright foci were generally distinct from speckles containing Sm antigen. Antibodies against the two subunits found only in polymerase III (i.e., RPC32, RPC39) gave a few bright and many faint nucleoplasmic foci, but no nucleolar foci. Growth in two transcriptional inhibitors-5, 6-dichloro-1-beta-d-ribofuranosylbenzimidazole and actinomycin D-led to the redistribution of each subunit in a characteristic manner.
Collapse
Affiliation(s)
- E Jones
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, United Kingdom
| | | | | | | | | | | |
Collapse
|
16
|
Rubbi L, Labarre-Mariotte S, Chédin S, Thuriaux P. Functional characterization of ABC10alpha, an essential polypeptide shared by all three forms of eukaryotic DNA-dependent RNA polymerases. J Biol Chem 1999; 274:31485-92. [PMID: 10531351 DOI: 10.1074/jbc.274.44.31485] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ABC10alpha is a small polypeptide shared by the three yeast RNA polymerases. Homologous polypeptides in higher eukaryotes have a zinc-binding CX(2)C. CX(2)C motif and a conserved basic C-terminal end. These features are also found in archaeal gene products that may encode an RNA polymerase subunit. The CX(2)C. CX(2)C motif is partly dispensable, since only its first cysteine is essential for growth, whereas the basic C-terminal end is critical in vivo. A mutant in the latter domain has an RNA polymerase III-specific defect and, in vitro, impairs RNA polymerase III assembly. Polymerase activity was, however, not affected in various faithful transcription assays. The mutant is suppressed by a high gene dosage of the second largest subunit of RNA polymerase III, whereas the homologous subunits of RNA polymerase I and II have aggravating effects. In a two-hybrid assay, ABC10alpha binds to the C-terminal half of the second largest subunit of RNA polymerase I, in a way that requires the integrity of the CX(2)C. CX(2)C motif. Thus, ABC10alpha appears to interact directly with the second largest subunit during polymerase assembly. This interaction is presumably a major rate-limiting step in assembly, since diploid cells containing only one functional gene copy for ABC10alpha have a partial growth defect.
Collapse
Affiliation(s)
- L Rubbi
- Service de Biochimie et Génétique Moléculaire, Bât. 142, Commissariat à l'Energie Atomique, CEA/Saclay, Gif sur Yvette, F-91191 Cedex, France
| | | | | | | |
Collapse
|
17
|
Gadal O, Shpakovski GV, Thuriaux P. Mutants in ABC10beta, a conserved subunit shared by all three yeast RNA polymerases, specifically affect RNA polymerase I assembly. J Biol Chem 1999; 274:8421-7. [PMID: 10085073 DOI: 10.1074/jbc.274.13.8421] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ABC10beta, a small polypeptide common to the three yeast RNA polymerases, has close homology to the N subunit of the archaeal enzyme and is remotely related to the smallest subunit of vaccinial RNA polymerase. The eucaryotic, archaeal, and viral polypeptides share an invariant motif CX2C. CC that is strictly essential for yeast growth, as shown by site-directed mutagenesis, whereas the rest of the ABC10beta sequence is fairly tolerant to amino acid replacements. ABC10beta has Zn2+ binding properties in vitro, and the CX2C. CC motif may therefore define an atypical metal-chelating site. Hybrid subunits that derive most of their amino acids from the archaeal subunit are functional in yeast, indicating that the archaeal and eucaryotic polypeptides have a largely equivalent role in the organization of their respective transcription complexes. However, all eucaryotic forms of ABC10beta harbor a HVDLIEK motif that, when mutated or replaced by its archaeal counterpart, leads to a polymerase I-specific lethal defect in vivo. This is accompanied by a specific lack in the largest subunit of RNA polymerase I (A190) in cell-free extracts, showing that the mutant enzyme is not properly assembled in vivo.
Collapse
Affiliation(s)
- O Gadal
- Service de Biochimie et Génétique Moléculaire, Bât. 142, Commissariat à l'Energie Atomique-Saclay. Gif sur Yvette, F 91191 cedex, France
| | | | | |
Collapse
|
18
|
Abstract
Following isolation of the genes encoding the putative subunits of RNA polymerase in both budding and fission yeasts, combined biochemical and genetic studies, together with a structural approach applicable to large assemblies, have begun to reveal the protein-protein interactions not only between RNA polymerase subunits but also between the RNA polymerases and transcription factors. These protein-protein interactions ultimately lead to control of the activity and specificity of the RNA polymerases.
Collapse
Affiliation(s)
- A Ishihama
- Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411, Japan.
| | | | | |
Collapse
|
19
|
Dammann R, Pfeifer GP. Cloning and characterization of the human RNA polymerase I subunit hRPA40. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1396:153-7. [PMID: 9540830 DOI: 10.1016/s0167-4781(97)00206-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The cloning of the human RNA polymerase I 40 kDa subunit, and the comparison of its amino acid sequence to other related RNA polymerase subunits are described. The amino acid sequence of hRPA40 has high homology to the mouse RNA polymerase I 40 kDa subunit (93%), to two Arabidopsis thaliana subunits (47%), the yeast RPC40 subunit (46%) and the human RNA polymerase II hRPB33 subunit (40%). Southern blot analysis shows that this gene is single copy and Northern blot analysis indicates that the mRNA of 1.3 kb is expressed in different cell types.
Collapse
Affiliation(s)
- R Dammann
- Department of Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
| | | |
Collapse
|
20
|
Bischler N, Balavoine F, Milkereit P, Tschochner H, Mioskowski C, Schultz P. Specific interaction and two-dimensional crystallization of histidine tagged yeast RNA polymerase I on nickel-chelating lipids. Biophys J 1998; 74:1522-32. [PMID: 9512048 PMCID: PMC1299498 DOI: 10.1016/s0006-3495(98)77864-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Nickel-chelating lipid monolayers were used to generate two-dimensional crystals from yeast RNA polymerase I that was histidine-tagged on one of its subunits. The interaction of the enzyme with the spread lipid layers was found to be imidazole dependent, and the formation of two-dimensional crystals required small amounts of imidazole, probably to select the specific interaction of the engineered tag with the nickel. Two distinct preparations of RNA polymerase I tagged on different subunits yielded two different crystal forms, indicating that the position of the tag determines the crystallization process. The orientation of the enzyme in both crystal forms is correlated with the location of the tagged subunits in a three-dimensional model which shows that the tagged subunits are in contact with the lipid layer.
Collapse
Affiliation(s)
- N Bischler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP 1, C.U. de Strasbourg, France
| | | | | | | | | | | |
Collapse
|