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Marygold SJ, Alic N, Gilmour DS, Grewal SS. In silico identification of Drosophila melanogaster genes encoding RNA polymerase subunits. MICROPUBLICATION BIOLOGY 2020; 2020. [PMID: 33274328 PMCID: PMC7704258 DOI: 10.17912/micropub.biology.000320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Steven J Marygold
- FlyBase, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, U.K
| | - Nazif Alic
- Institute of Healthy Ageing and the Research Department of Genetics, Evolution, and Environment, University College London, London, U.K
| | - David S Gilmour
- Pennsylvania State University, Center for Eukaryotic Gene Regulation, University Park, PA, U.S.A
| | - Savraj S Grewal
- Clark H Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, & Department of Biochemistry and Molecular Biology, University of Calgary, Alberta, Canada
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2
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Flora P, McCarthy A, Upadhyay M, Rangan P. Role of Chromatin Modifications in Drosophila Germline Stem Cell Differentiation. Results Probl Cell Differ 2017; 59:1-30. [PMID: 28247044 DOI: 10.1007/978-3-319-44820-6_1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
During Drosophila oogenesis, germline stem cells (GSCs) self-renew and differentiate to give rise to a mature egg. Self-renewal and differentiation of GSCs are regulated by both intrinsic mechanisms such as regulation of gene expression in the germ line and extrinsic signaling pathways from the surrounding somatic niche. Epigenetic mechanisms, including histone-modifying proteins, nucleosome remodeling complexes, and histone variants, play a critical role in regulating intrinsic gene expression and extrinsic signaling cues from the somatic niche. In the GSCs, intrinsic epigenetic modifiers are required to maintain a stem cell fate by promoting expression of self-renewal factors and repressing the differentiation program. Subsequently, in the GSC daughters, epigenetic regulators activate the differentiation program to promote GSC differentiation. During differentiation, the GSC daughter undergoes meiosis to give rise to the developing egg, containing a compacted chromatin architecture called the karyosome. Epigenetic modifiers control the attachment of chromosomes to the nuclear lamina to aid in meiotic recombination and the release from the lamina for karyosome formation. The germ line is in close contact with the soma for the entirety of this developmental process. This proximity facilitates signaling from the somatic niche to the developing germ line. Epigenetic modifiers play a critical role in the somatic niche, modulating signaling pathways in order to coordinate the transition of GSC to an egg. Together, intrinsic and extrinsic epigenetic mechanisms modulate this exquisitely balanced program.
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Affiliation(s)
- Pooja Flora
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY, USA
- University at Albany SUNY, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Alicia McCarthy
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY, USA
- University at Albany SUNY, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Maitreyi Upadhyay
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY, USA
- University at Albany SUNY, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Prashanth Rangan
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY, USA.
- University at Albany SUNY, 1400 Washington Avenue, Albany, NY, 12222, USA.
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3
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Zhang Q, Shalaby NA, Buszczak M. Changes in rRNA transcription influence proliferation and cell fate within a stem cell lineage. Science 2014; 343:298-301. [PMID: 24436420 DOI: 10.1126/science.1246384] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Ribosome biogenesis drives cell growth and proliferation, but mechanisms that modulate this process within specific lineages remain poorly understood. Here, we identify a Drosophila RNA polymerase I (Pol I) regulatory complex composed of Under-developed (Udd), TAF1B, and a TAF1C-like factor. Disruption of udd or TAF1B results in reduced ovarian germline stem cell (GSC) proliferation. Female GSCs display high levels of ribosomal RNA (rRNA) transcription, and Udd becomes enriched in GSCs relative to their differentiating daughters. Increasing Pol I transcription delays differentiation, whereas reducing rRNA production induces both morphological changes that accompany multicellular cyst formation and specific decreased expression of the bone morphogenetic protein (BMP) pathway component Mad. These findings demonstrate that modulating rRNA synthesis fosters changes in the cell fate, growth, and proliferation of female Drosophila GSCs and their daughters.
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Affiliation(s)
- Qiao Zhang
- Department of Molecular Biology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9148, USA
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4
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Gaur K, Li J, Wang D, Dutta P, Yan SJ, Tsurumi A, Land H, Wu G, Li WX. The Birt-Hogg-Dubé tumor suppressor Folliculin negatively regulates ribosomal RNA synthesis. Hum Mol Genet 2012; 22:284-99. [PMID: 23077212 DOI: 10.1093/hmg/dds428] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Birt-Hogg-Dubé syndrome (BHD) is a human cancer disorder caused by mutations in the tumor suppressor gene Folliculin (FLCN) with unknown biological functions. Here, we show that the Drosophila homolog of FLCN, dFLCN (a.k.a. dBHD) localizes to the nucleolus and physically interacts with the 19S proteasomal ATPase, Rpt4, a nucleolar resident and known regulator of rRNA transcription. Downregulation of dFLCN resulted in an increase in nucleolar volume and upregulation of rRNA synthesis, whereas dFLCN overexpression reduced rRNA transcription and counteracted the effects of Rpt4 on rRNA production by preventing the association of Rpt4 with the rDNA locus. We further show that human FLCN exhibited evolutionarily conserved function and that Rpt4 knockdown inhibits the growth of FLCN-deficient human renal cancer cells in mouse xenografts. Our study suggests that FLCN functions as a tumor suppressor by negatively regulating rRNA synthesis.
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Affiliation(s)
- Kriti Gaur
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
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5
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ZANOTTI GIANCARLO, PETERSEN GABRIELE, WIELAND THEODOR. Structure-toxicity relationships in the amatoxin series. ACTA ACUST UNITED AC 2009. [DOI: 10.1111/j.1399-3011.1992.tb00440.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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6
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Li H, Pellegrini M, Eisenberg D. Detection of parallel functional modules by comparative analysis of genome sequences. Nat Biotechnol 2005; 23:253-60. [PMID: 15696156 DOI: 10.1038/nbt1065] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Parallel functional modules are separate sets of proteins in an organism that catalyze the same or similar biochemical reactions but act on different substrates or use different cofactors. They originate by gene duplication during evolution. Parallel functional modules provide versatility and complexity to organisms, and increase cellular flexibility and robustness. We have developed a four-step approach for genome-wide discovery of parallel modules from protein functional linkages. From ten genomes, we identified 37 cellular systems that consist of parallel functional modules. This approach recovers known parallel complexes and pathways, and discovers new ones that conventional homology-based methods did not previously reveal, as illustrated by examples of peptide transporters in Escherichia coli and nitrogenases in Rhodopseudomonas palustris. The approach untangles intertwined functional linkages between parallel functional modules and expands our ability to decode protein functions from genome sequences.
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Affiliation(s)
- Huiying Li
- Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, 90095-1570, USA
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7
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Grewal SS, Li L, Orian A, Eisenman RN, Edgar BA. Myc-dependent regulation of ribosomal RNA synthesis during Drosophila development. Nat Cell Biol 2005; 7:295-302. [PMID: 15723055 DOI: 10.1038/ncb1223] [Citation(s) in RCA: 310] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2004] [Accepted: 01/05/2005] [Indexed: 01/02/2023]
Abstract
Regulating ribosome number is thought to control cellular growth. Synthesis of ribosomal RNA (rRNA) is a limiting step in ribosome biogenesis and rates of rRNA synthesis are generally altered depending on the growth status of a cell. Although studies in unicellular systems have addressed the mechanisms by which this occurs, few studies have applied a genetic approach to examine growth-dependent control of rRNA synthesis in metazoans. Here, we show that in Drosophila melanogaster Myc (dMyc) is a regulator of rRNA synthesis. Expression of dMyc is both necessary and sufficient to control rRNA synthesis and ribosome biogenesis during larval development. Stimulation of rRNA synthesis by dMyc is mediated through a rapid, coordinated increase in the levels of the Pol I transcriptional machinery. In addition, the growth effects of dMyc in larval wing imaginal discs require de novo rRNA synthesis. We suggest that during animal development, the control of rRNA synthesis and ribosome biogenesis is an essential Myc function.
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Affiliation(s)
- Savraj S Grewal
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA
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8
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Oxelman B, Bremer B. Discovery of paralogous nuclear gene sequences coding for the second-largest subunit of RNA polymerase II (RPB2) and their phylogenetic utility in gentianales of the asterids. Mol Biol Evol 2000; 17:1131-45. [PMID: 10908634 DOI: 10.1093/oxfordjournals.molbev.a026396] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Paralogous sequences of the RPB2 gene are demonstrated in the angiosperm order Gentianales. Two different copies were found by using different PCR primer pairs targeting a region that corresponds to exons 22-24 in the Arabidopsis RPB2 gene. One of the copies (RPB2-d) lacks introns in this region, whereas the other has introns at locations corresponding to those of green plants previously investigated. When analyzed with other available RPB2 sequences from this region, all 28 RPB2-d sequences obtained from the Gentianales and the four sequences from the Lamiales form a monophyletic group, together with a previously published tomato cDNA sequence. The substitution patterns, relative rates of change, and nucleotide compositions of the two paralogous RPB2 exon regions are similar, and none of them shows any signs of being a pseudogene. Although multiple copies of similar, paralogous sequences can confound phylogenetic interpretations, the lack of introns in RPB2-d make a priori homology assessment easy. The phylogenetic utility of RPB2-d within the Gentianales is evaluated in comparison with the chloroplast genes ndhF and rbcL. The hierarchical information in the RPB2-d region sequenced is more incongruent with that of the plastid genes than the plastid genes are with each other as determined by incongruence length difference tests. In contrast to the plastid genes, parsimony-informative third codon positions of RPB2 have a significantly higher rate of change than first and second positions. Topologically, the trees from the three genes are similar, and the differences are usually only weakly supported. In terms of support, RPB2 gives the highest jackknife support per sequenced nucleotide, whereas ndhF gives the highest Bremer support per sequenced nucleotide. The RPB2-d locus has the potential to be a valuable nuclear marker for determination of phylogenetic relationships within the euasterid I group of plants.
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Affiliation(s)
- B Oxelman
- Department of Systematic Botany, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
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Wiedemann M, Oldenburg I, Sitzler S, Petersen G. Transcription of DmRP140, the gene coding for the second-largest subunit of RNA polymerase II. BIOCHIMICA ET BIOPHYSICA ACTA 1997; 1350:282-6. [PMID: 9061024 DOI: 10.1016/s0167-4781(96)00230-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
To analyze transcriptional control regions of Drosophila melanogaster housekeeping genes, we have characterized the promoter of the gene coding for the second-largest subunit of RNA polymerase II (DmRP140). Upstream of DmRP140 the genomic region harbors a gene which is transcribed in the opposite direction (DmRP140up). By determination of the transcription start sites of both genes we found a short non-transcribed intergenic region of 220 bp. Functional analysis of various promoter reportergene constructs by transient transfection of cultured cells revealed that sequences important for transcription of DmRP140 are located in the untranslated leader of the upstream gene. The onset of DmRP140 transcription during embryonic development was studied in transgenic flies using beta-galactosidase as reportergene. To distinguish between the maternally provided DmRP140 transcripts and the embryonically transcribed RNA the offspring of nontransformed females and male transformants was examined. The development of a sensitive detection assay based on a chemiluminescent substrate for beta-galactosidase allowed us to determine the onset of DmRP140 transcription to between 8-10 h after oviposition. Thus, DmRP140 transcription does not start following the transcriptional transition period between 2-3 h of development but occurs much later in embryogenesis coinciding with decreasing DNA synthesis and cell division rates.
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Affiliation(s)
- M Wiedemann
- Institute of Molecular Genetics, University Heidelberg, Germany
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10
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Kontermann RE, Bautz EK. Nucleic acid-binding regions of the second-largest subunit of Drosophila RNA polymerase II identified by southwestern blotting. FEBS Lett 1994; 344:166-70. [PMID: 8187877 DOI: 10.1016/0014-5793(94)00380-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Analysing overlapping bacterially expressed fragments of the second-largest subunit of Drosophila melanogaster RNA polymerase II in Southwestern DNA binding assays we have identified regions that have the potential to bind nucleic acids non-specifically. A region exhibiting strong DNA binding is located in the N-terminal part of the molecule (amino acids 357-504) and some weak DNA binding is observed for the C-terminal part (amino acids 860-1160). The non-specific DNA binding behavior of these regions is similar to that of the native enzyme. Most of the known mutations responsible for rifampicin resistance map to a region of the Escherichia coli beta subunit corresponding to the N-terminal nucleic acid-binding region, indirectly supporting the notion that this region participates in interaction with the RNA transcript in ternary complexes.
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Affiliation(s)
- R E Kontermann
- Institute of Molecular Genetics, University of Heidelberg, Germany
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11
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Sommer KA, Petersen G, Bautz EK. The gene upstream of DmRP128 codes for a novel GTP-binding protein of Drosophila melanogaster. MOLECULAR & GENERAL GENETICS : MGG 1994; 242:391-8. [PMID: 8121394 DOI: 10.1007/bf00281788] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Upstream of the gene coding for the second-largest subunit of RNA polymerase III (DmRP128) we have found another gene (128up), which is transcribed in the same direction as the RNA polymerase gene. The intergenic distance between the 3' end of 128up mRNA and the 5' end of DmRP128 mRNA is only about 100 bp. Transcripts of 128up are present at a much higher level than DmRP128 RNA in Drosophila Schneider 2 cells, embryos, and adult flies. Two transcription start points, seven nucleotides apart, are found for 128up compared to multiple scattered starts for DmRP128. Sequence analysis of 128up cDNA reveals that the gene codes for a 41 kDa protein with homology to GTP-binding proteins and matching four of the structural sequence motifs characteristic of the superfamily of GTPases. Bacterially expressed 128up protein fused to maltose-binding protein specifically binds GTP. Sequences closely related to the 128up protein are found in species as distant as Halobacterium, yeast or mouse; the murine protein is 80% identical to 128up. This evolutionary conservation is indicative of an important, but as yet unknown, physiological role. In accordance with the sequence conservation, antibodies against 128up specifically cross-react with mouse 3T3 cells and human Hep2 cells where the subcellular localization of the protein is predominantly perinuclear. We propose that 128up is a member of a novel class of GTP-binding proteins.
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Affiliation(s)
- K A Sommer
- Institute of Molecular Genetics, University of Heidelberg, Germany
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12
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Liu Z, Kontermann RE, Schulze RA, Petersen G, Bautz EK. RPII15 codes for the M(r) 15,000 subunit 9 of Drosophila melanogaster RNA polymerase II. FEBS Lett 1993; 335:73-5. [PMID: 8243669 DOI: 10.1016/0014-5793(93)80442-w] [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: 01/29/2023]
Abstract
The RPII15 gene product of Drosophila melanogaster, which has recently been identified by sequence comparison, possesses a high similarity to subunit 9 of yeast RNA polymerase II. Using the polymerase chain reaction the coding region of RPII15 was isolated from genomic DNA of adult flies. Sequence analysis shows four amino acid substitutions in comparison to the previously reported sequence. Antisera were generated against bacterially expressed RPII15 and were used for immunoblotting experiments with RNA polymerase II of Drosophila melanogaster. This analysis identified the M(r) 15,000 subunit 9 as gene product of RPII15.
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Affiliation(s)
- Z Liu
- Institute of Molecular Genetics, University of Heidelberg, Germany
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13
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Mapping mutations in genes encoding the two large subunits of Drosophila RNA polymerase II defines domains essential for basic transcription functions and for proper expression of developmental genes. Mol Cell Biol 1993. [PMID: 8321225 DOI: 10.1128/mcb.13.7.4214] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have mapped a number of mutations at the DNA sequence level in genes encoding the largest (RpII215) and second-largest (RpII140) subunits of Drosophila melanogaster RNA polymerase II. Using polymerase chain reaction (PCR) amplification and single-strand conformation polymorphism (SSCP) analysis, we detected 12 mutations from 14 mutant alleles (86%) as mobility shifts in nondenaturing gel electrophoresis, thus localizing the mutations to the corresponding PCR fragments of about 350 bp. We then determined the mutations at the DNA sequence level by directly subcloning the PCR fragments and sequencing them. The five mapped RpII140 mutations clustered in a C-terminal portion of the second-largest subunit, indicating the functional importance of this region of the subunit. The RpII215 mutations were distributed more broadly, although six of eight clustered in a central region of the subunit. One notable mutation that we localized to this region was the alpha-amanitin-resistant mutation RpII215C4, which also affects RNA chain elongation in vitro. RpII215C4 mapped to a position near the sites of corresponding mutations in mouse and in Caenorhabditis elegans genes, reinforcing the idea that this region is involved in amatoxin binding and transcript elongation. We also mapped mutations in both RpII215 and RpII140 that cause a developmental defect known as the Ubx effect. The clustering of these mutations in each gene suggests that they define functional domains in each subunit whose alteration induces the mutant phenotype.
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14
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Chen Y, Weeks J, Mortin MA, Greenleaf AL. Mapping mutations in genes encoding the two large subunits of Drosophila RNA polymerase II defines domains essential for basic transcription functions and for proper expression of developmental genes. Mol Cell Biol 1993; 13:4214-22. [PMID: 8321225 PMCID: PMC359971 DOI: 10.1128/mcb.13.7.4214-4222.1993] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
We have mapped a number of mutations at the DNA sequence level in genes encoding the largest (RpII215) and second-largest (RpII140) subunits of Drosophila melanogaster RNA polymerase II. Using polymerase chain reaction (PCR) amplification and single-strand conformation polymorphism (SSCP) analysis, we detected 12 mutations from 14 mutant alleles (86%) as mobility shifts in nondenaturing gel electrophoresis, thus localizing the mutations to the corresponding PCR fragments of about 350 bp. We then determined the mutations at the DNA sequence level by directly subcloning the PCR fragments and sequencing them. The five mapped RpII140 mutations clustered in a C-terminal portion of the second-largest subunit, indicating the functional importance of this region of the subunit. The RpII215 mutations were distributed more broadly, although six of eight clustered in a central region of the subunit. One notable mutation that we localized to this region was the alpha-amanitin-resistant mutation RpII215C4, which also affects RNA chain elongation in vitro. RpII215C4 mapped to a position near the sites of corresponding mutations in mouse and in Caenorhabditis elegans genes, reinforcing the idea that this region is involved in amatoxin binding and transcript elongation. We also mapped mutations in both RpII215 and RpII140 that cause a developmental defect known as the Ubx effect. The clustering of these mutations in each gene suggests that they define functional domains in each subunit whose alteration induces the mutant phenotype.
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Affiliation(s)
- Y Chen
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
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Klenk HP, Palm P, Zillig W. DNA-Dependent RNA Polymerases as Phylogenetic Marker Molecules. Syst Appl Microbiol 1993. [DOI: 10.1016/s0723-2020(11)80335-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Kontermann RE, Kobor M, Bautz EK. Identification of a nucleic acid-binding region within the largest subunit of Drosophila melanogaster RNA polymerase II. Protein Sci 1993; 2:223-30. [PMID: 8443600 PMCID: PMC2142351 DOI: 10.1002/pro.5560020211] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The largest and the second-largest subunit of the multisubunit eukaryotic RNA polymerases are involved in interaction with the DNA template and the nascent RNA chain. Using Southwestern DNA-binding techniques and nitrocellulose filter binding assays of bacterially expressed fusion proteins, we have identified a region of the largest, 215-kDa, subunit of Drosophila RNA polymerase II that has the potential to bind nucleic acids nonspecifically. This nucleic acid-binding region is located between amino acid residues 309-384 and is highly conserved within the largest subunits of eukaryotic and bacterial RNA polymerases. A homology to a region of the DNA-binding cleft of Escherichia coli DNA polymerase I involved in binding of the newly synthesized DNA duplex provides indirect evidence that the nucleic acid-binding region of the largest subunit participates in interaction with double-stranded nucleic acids during transcription. The nonspecific DNA-binding behavior of the region is similar to that observed for the native enzyme in nitrocellulose filter binding assays and that of the separated largest subunit in Southwestern assays. A high content of basic amino acid residues is consistent with the electrostatic nature of nonspecific DNA binding by RNA polymerases.
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Affiliation(s)
- R E Kontermann
- Institute of Molecular Genetics, University of Heidelberg, Germany
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Kaufmann J, Florian V, Klein A. TGA cysteine codons and intron sequences in conserved and nonconserved positions are found in macronuclear RNA polymerase genes of Euplotes octocarinatus. Nucleic Acids Res 1992; 20:5985-9. [PMID: 1461731 PMCID: PMC334464 DOI: 10.1093/nar/20.22.5985] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The gene sequences of the second largest subunits of RNA polymerases I and II of Euplotes octocarinatus, RPA2 and RPB2, were determined and compared to the respective known sequences of Saccharomyces cerevisiae. The similarity of the derived polypeptide sequences permitted their assignment to the respective polymerases and allowed the comparison of the zinc binding regions. In frame TGA codons were detected, which are likely to encode conserved cysteinyl residues in the putative zinc-finger region of the RPA2 gene. They were also found in other positions in both the RPA2 and RPB2 genes. The RPB2 gene contains a 30 bp intron close to the 5'-end of its coding region. The 5'-ends of the coding regions of all three genes encoding the largest subunits of the three different polymerases were also analyzed. The zinc finger structures again show the use of TGA codons for conserved cysteinyl residues in two of the genes. An N-terminal intron is located in the RPB1 gene at a conserved position as compared to the respective genes of several other eucarya.
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Affiliation(s)
- J Kaufmann
- Department of Biology, Philipps University, Marburg, Germany
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