1
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Rajendra KC, Cheng R, Zhou S, Lizarazo S, Smith D, Van Bortle K. Evidence of RNA polymerase III recruitment and transcription at protein-coding gene promoters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.08.598009. [PMID: 38895345 PMCID: PMC11185800 DOI: 10.1101/2024.06.08.598009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
RNA polymerase (Pol) I, II, and III are most commonly described as having distinct roles in synthesizing ribosomal RNA (rRNA), messenger RNA (mRNA), and specific small noncoding (nc)RNAs, respectively. This delineation of transcriptional responsibilities is not definitive, however, as evidenced by instances of Pol II recruitment to genes conventionally transcribed by Pol III, including the co-transcription of RPPH1 - the catalytic RNA component of RNase P. A comprehensive understanding of the interplay between RNA polymerase complexes remains lacking, however, due to limited comparative analyses for all three enzymes. To address this gap, we applied a uniform framework for quantifying global Pol I, II, and III occupancies that integrates currently available human RNA polymerase ChIP-seq datasets. Occupancy maps are combined with a comprehensive multi-class promoter set that includes protein-coding genes, noncoding genes, and repetitive elements. While our genomic survey appropriately identifies recruitment of Pol I, II, and III to canonical target genes, we unexpectedly discover widespread recruitment of the Pol III machinery to promoters of specific protein-coding genes, supported by colocalization patterns observed for several Pol III-specific subunits. We show that Pol III-occupied Pol II promoters are enriched for small, nascent RNA reads terminating in a run of 4 Ts, a unique hallmark of Pol III transcription termination and evidence of active Pol III activity at these sites. Pol III disruption differentially modulates the expression of Pol III-occupied coding genes, which are functionally enriched for ribosomal proteins and genes broadly linked to unfavorable outcomes in cancer. Our map also identifies additional, currently unannotated genomic elements occupied by Pol III with clear signatures of nascent RNA species that are sensitive to disruption of La (SSB) - a Pol III-related RNA chaperone protein. These findings reshape our current understanding of the interplay between Pols II and III and identify potentially novel small ncRNAs with broad implications for gene regulatory paradigms and RNA biology.
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Affiliation(s)
- K C Rajendra
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Ruiying Cheng
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Sihang Zhou
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Simon Lizarazo
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Duncan Smith
- Department of Biology, New York University, New York, NY
| | - Kevin Van Bortle
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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2
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Serrano A, Moret M, Fernández-Parras I, Bombarely A, Luque F, Navarro F. RNA Polymerases IV and V Are Involved in Olive Fruit Development. Genes (Basel) 2023; 15:1. [PMID: 38275583 PMCID: PMC10815247 DOI: 10.3390/genes15010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Transcription is carried out in most eukaryotes by three multimeric complexes (RNA polymerases I, II and III). However, plants contain two additional RNA polymerases (IV and V), which have evolved from RNA polymerase II. RNA polymerases II, IV and V contain both common and specific subunits that may specialise some of their functions. In this study, we conducted a search for the genes that putatively code for the specific subunits of RNA polymerases IV and V, as well as those corresponding to RNA polymerase II in olive trees. Based on the homology with the genes of Arabidopsis thaliana, we identified 13 genes that putatively code for the specific subunits of polymerases IV and V, and 16 genes that code for the corresponding specific subunits of polymerase II in olives. The transcriptomic analysis by RNA-Seq revealed that the expression of the RNA polymerases IV and V genes was induced during the initial stages of fruit development. Given that RNA polymerases IV and V are involved in the transcription of long non-coding RNAs, we investigated their expression and observed relevant changes in the expression of this type of RNAs. Particularly, the expression of the intergenic and intronic long non-coding RNAs tended to increase in the early steps of fruit development, suggesting their potential role in this process. The positive correlation between the expression of RNA polymerases IV and V subunits and the expression of non-coding RNAs supports the hypothesis that RNA polymerases IV and V may play a role in fruit development through the synthesis of this type of RNAs.
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Affiliation(s)
- Alicia Serrano
- Instituto Universitario de Investigación en Olivar y Aceites de Oliva, Universidad de Jaén, 23071 Jaén, Spain; (A.S.); (M.M.); (I.F.-P.)
| | - Martín Moret
- Instituto Universitario de Investigación en Olivar y Aceites de Oliva, Universidad de Jaén, 23071 Jaén, Spain; (A.S.); (M.M.); (I.F.-P.)
| | - Isabel Fernández-Parras
- Instituto Universitario de Investigación en Olivar y Aceites de Oliva, Universidad de Jaén, 23071 Jaén, Spain; (A.S.); (M.M.); (I.F.-P.)
| | - Aureliano Bombarely
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC and Universitat Politécnica de Valencia, 46011 Valencia, Spain;
| | - Francisco Luque
- Instituto Universitario de Investigación en Olivar y Aceites de Oliva, Universidad de Jaén, 23071 Jaén, Spain; (A.S.); (M.M.); (I.F.-P.)
| | - Francisco Navarro
- Departamento de Biología Experimental, Universidad de Jaén, 23071 Jaén, Spain
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3
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Zhang Y, Pang Y, Zhang K, Song X, Gao J, Zhang S, Deng W. RNA polymerase I subunit RPA43 activates rRNA expression and cell proliferation but inhibits cell migration. Biochim Biophys Acta Gen Subj 2023:130411. [PMID: 37343605 DOI: 10.1016/j.bbagen.2023.130411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/21/2023] [Accepted: 06/13/2023] [Indexed: 06/23/2023]
Abstract
The products synthesized by RNA polymerase I (Pol I) play fundamental roles in several cellular processes, including ribosomal biogenesis, protein synthesis, cell metabolism, and growth. Deregulation of Pol I products can cause various diseases such as ribosomopathies, leukaemia, and solid tumours. However, the detailed mechanism of Pol I-directed transcription remains elusive, and the roles of Pol I subunits in rRNA synthesis and cellular activities still need clarification. In this study, we found that RPA43 expression levels positively correlate with Pol I product accumulation and cell proliferation, indicating that RPA43 activates these processes. Unexpectedly, RPA43 depletion promoted HeLa cell migration, suggesting that RPA43 functions as a negative regulator in cell migration. Mechanistically, RPA43 positively modulates the recruitment of Pol I transcription machinery factors to the rDNA promoter by activating the transcription of the genes encoding Pol I transcription machinery factors. RPA43 inhibits cell migration by dampening the expression of c-JUN and Integrin. Collectively, we found that RPA43 plays opposite roles in cell proliferation and migration except for driving Pol I-dependent transcription. These findings provide novel insights into the regulatory mechanism of Pol I-mediated transcription and cell proliferation and a potential pathway to developing anti-cancer drugs using RPA43 as a target.
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Affiliation(s)
- Yue Zhang
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei province 430065, China
| | - Yaoyu Pang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7GE, UK
| | - Kewei Zhang
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei province 430065, China
| | - Xiaoye Song
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei province 430065, China
| | - Junwei Gao
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei province 430065, China
| | - Shuting Zhang
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei province 430065, China
| | - Wensheng Deng
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei province 430065, China.
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4
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Ma L, Wang L, Gao M, Zhang X, Zhao X, Xie D, Zhang J, Wang Z, Hou L, Zeng F. Rtr1 is required for Rpb1-Rpb2 assembly of RNAPII and prevents their cytoplasmic clump formation. FASEB J 2022; 36:e22585. [PMID: 36190433 DOI: 10.1096/fj.202200698rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 09/03/2022] [Accepted: 09/20/2022] [Indexed: 11/11/2022]
Abstract
RNA polymerase II (RNAPII) is an essential machinery for catalyzing mRNA synthesis and controlling cell fate in eukaryotes. Although the structure and function of RNAPII have been relatively defined, the molecular mechanism of its assembly process is not clear. The identification and functional analysis of assembly factors will provide new understanding to transcription regulation. In this study, we identify that RTR1, a known transcription regulator, is a new multicopy genetic suppressor of mutants of assembly factors Gpn3, Gpn2, and Rba50. We demonstrate that Rtr1 is directly required to assemble the two largest subunits of RNAPII by coordinating with Gpn3 and Npa3. Deletion of RTR1 leads to cytoplasmic clumping of RNAPII subunit and multiple copies of RTR1 can inhibit the formation of cytoplasmic clump of RNAPII subunit in gpn3-9 mutant, indicating a new layer function of Rtr1 in checking proper assembly of RNAPII. In addition, we find that disrupted activity of Rtr1 phosphatase does not trigger the formation of cytoplasmic clump of RNAPII subunit in a catalytically inactive mutant of RTR1. Based on these results, we conclude that Rtr1 cooperates with Gpn3 and Npa3 to assemble RNAPII core.
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Affiliation(s)
- Lujie Ma
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China.,College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Le Wang
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Mengdi Gao
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Xinjie Zhang
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Xiangdong Zhao
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Debao Xie
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Jing Zhang
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Zhen Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China.,College of Science & Technology, Hebei Agricultural University, Cangzhou, China
| | - Lifeng Hou
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Fanli Zeng
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China.,College of Life Sciences, Hebei Agricultural University, Baoding, China
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5
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Actin dynamics in protein homeostasis. Biosci Rep 2022; 42:231720. [PMID: 36043949 PMCID: PMC9469105 DOI: 10.1042/bsr20210848] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
Cell homeostasis is maintained in all organisms by the constant adjustment of cell constituents and organisation to account for environmental context. Fine-tuning of the optimal balance of proteins for the conditions, or protein homeostasis, is critical to maintaining cell homeostasis. Actin, a major constituent of the cytoskeleton, forms many different structures which are acutely sensitive to the cell environment. Furthermore, actin structures interact with and are critically important for the function and regulation of multiple factors involved with mRNA and protein production and degradation, and protein regulation. Altogether, actin is a key, if often overlooked, regulator of protein homeostasis across eukaryotes. In this review, we highlight these roles and how they are altered following cell stress, from mRNA transcription to protein degradation.
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6
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Boguta M. Assembly of RNA polymerase III complex involves a putative co-translational mechanism. Gene 2022; 824:146394. [PMID: 35278633 DOI: 10.1016/j.gene.2022.146394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 02/28/2022] [Accepted: 03/04/2022] [Indexed: 11/04/2022]
Abstract
Detailed knowledge of structures of yeast RNA polymerases (RNAPs) contrasts with the limited information that is available on the control of their assembly. RNAP enzymes are large heteromeric complexes that function in the nucleus, but they are assembled in the cytoplasm and imported to the nucleus with help from specific auxiliary factors. Here, I review a recent study that suggests that the formation of an early-stage assembly intermediate of the RNAP III complex occurs through a co-translational mechanism. According to our hypothesis, RNAP III assembly might be seeded while the Rpb10 subunit of the enzyme core is being synthesized by cytoplasmic ribosome machinery. The co-translational assembly of RNAP III is mediated by Rbs1 protein which binds to 3'-untranslated regions in mRNA in a way that depends on the R3H domain in the Rbs1 sequence.
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Affiliation(s)
- Magdalena Boguta
- Laboratory of tRNA Transcription, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland.
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7
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Npa3-Gpn3 cooperate to assemble RNA polymerase II and prevent clump of its subunits in the cytoplasm. Int J Biol Macromol 2022; 206:837-848. [PMID: 35314265 DOI: 10.1016/j.ijbiomac.2022.03.081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/11/2022] [Accepted: 03/13/2022] [Indexed: 01/16/2023]
Abstract
RNA polymerase II (RNAPII) is an essential machinery in eukaryotes that catalyzes mRNA synthesis and controls cell fate. Although the structure and function of RNAPII are relatively well defined, the molecular mechanism of its assembly process is poorly understood. Three members of GPN-loop GTPase family Npa3/Gpn1, Gpn2, and Gpn3 participate in the biogenesis of RNAPII with non-redundant roles. In this study, we demonstrate that Gpn3 and Npa3 directly participate in the assembly of the two largest subunits during biogenesis of RNAPII. When Gpn3 is defective, assembly of RNAPII is disrupted, leading to cytoplasmic foci of RNAPII subunits. Long-term assembly factor defects will lead to the accumulation of different kind of newly synthesized RNAPII subunits in the cytoplasm to form foci, and this can be prevented by recovery of the defective assembly factor. Cytoplasmic foci of RNAPII subunits in mutants of these assembly factors reveals a new cellular rescue response named the 'RNAPII assembly stress response'.
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8
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Xie D, Zhao X, Ma L, Wang L, Li P, Cheng H, Li Z, Zeng P, Zhang J, Zeng F. Rba50 and Gpn2 recruit the second largest subunits for the assembly of RNA polymerase II and III. Int J Biol Macromol 2022; 204:565-575. [PMID: 35176321 DOI: 10.1016/j.ijbiomac.2022.02.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 11/18/2022]
Abstract
Although remarkable progress has been made toward understanding the structures of eukaryotic RNA polymerases, the pathways and factors that facilitate their assembly remain unresolved. Essential proteins Rba50 and Gpn2 are required for Rpb3 subcomplex assembly, but whether they participate in subsequent assembly steps is unknown. Herein, we performed comprehensive genetic screens to explore Rba50 function. We identified two unique extragenic rba50-3-suppressing mutations that map to genes encoding the Rba50-interacting protein Gpn2, and Rpb2, the second largest subunit of RNAPII. Both gpn2-R347S and rpb2-V1171G variants bypass Rpb1 cytoplasmic arrest and temperature-sensitive growth defects of the rba50-3 mutant. GPN2 and RPB2 were also identified as novel multicopy suppressors of the rba50-3 mutant. Rapid depletion of Rba50 affected Rpb3-Rpb2 association during RNAPII assembly. Importantly, we demonstrated that Gpn2 facilitates the association of Rba50 and Rpb2. Our results imply that Rba50-Gpn2 interaction is essential for Rpb2 recruitment during RNAPII assembly following Rpb3 subcomplex assembly. Furthermore, the Rba50-Gpn2 complex appears to play a similar role in the assembly of RNAPIII. We therefore propose a model in which Rba50 interacts with Gpn2 and thereby promotes loading of the second largest subunit of RNAP II and III onto the previously assembled subcomplex.
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Affiliation(s)
- Debao Xie
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei 071001, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Xiangdong Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei 071001, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Lujie Ma
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei 071001, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Le Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei 071001, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Pan Li
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei 071001, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Hongqian Cheng
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei 071001, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Zhaoying Li
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei 071001, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Pei Zeng
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei 071001, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Jing Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei 071001, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Fanli Zeng
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei 071001, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001, China.
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9
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Garrido-Godino AI, Cuevas-Bermúdez A, Gutiérrez-Santiago F, Mota-Trujillo MDC, Navarro F. The Association of Rpb4 with RNA Polymerase II Depends on CTD Ser5P Phosphatase Rtr1 and Influences mRNA Decay in Saccharomyces cerevisiae. Int J Mol Sci 2022; 23:ijms23042002. [PMID: 35216121 PMCID: PMC8875030 DOI: 10.3390/ijms23042002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 02/04/2023] Open
Abstract
Rtr1 is an RNA polymerase II (RNA pol II) CTD-phosphatase that influences gene expression during the transition from transcription initiation to elongation and during transcription termination. Rtr1 interacts with the RNA pol II and this interaction depends on the phosphorylation state of the CTD of Rpb1, which may influence dissociation of the heterodimer Rpb4/7 during transcription. In addition, Rtr1 was proposed as an RNA pol II import factor in RNA pol II biogenesis and participates in mRNA decay by autoregulating the turnover of its own mRNA. Our work shows that Rtr1 acts in RNA pol II assembly by mediating the Rpb4/7 association with the rest of the enzyme. RTR1 deletion alters RNA pol II assembly and increases the amount of RNA pol II associated with the chromatin that lacks Rpb4, decreasing Rpb4-mRNA imprinting and, consequently, increasing mRNA stability. Thus, Rtr1 interplays RNA pol II biogenesis and mRNA decay regulation. Our data also indicate that Rtr1 mediates mRNA decay regulation more broadly than previously proposed by cooperating with Rpb4. Interestingly, our data include new layers in the mechanisms of gene regulation and in the crosstalk between mRNA synthesis and decay by demonstrating how the association of Rpb4/7 to the RNA pol II influences mRNA decay.
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Affiliation(s)
- Ana I. Garrido-Godino
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain; (A.I.G.-G.); (A.C.-B.); (F.G.-S.); (M.d.C.M.-T.)
| | - Abel Cuevas-Bermúdez
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain; (A.I.G.-G.); (A.C.-B.); (F.G.-S.); (M.d.C.M.-T.)
| | - Francisco Gutiérrez-Santiago
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain; (A.I.G.-G.); (A.C.-B.); (F.G.-S.); (M.d.C.M.-T.)
| | - Maria del Carmen Mota-Trujillo
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain; (A.I.G.-G.); (A.C.-B.); (F.G.-S.); (M.d.C.M.-T.)
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain; (A.I.G.-G.); (A.C.-B.); (F.G.-S.); (M.d.C.M.-T.)
- Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
- Correspondence: ; Tel.: +34-953-212-771; Fax: +34-953-211-875
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10
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Rudzińska I, Płonka M, Armatowska A, Turowski TW, Boguta M. Rbs1 protein, involved in RNA polymerase III complex assembly in the yeast Saccharomyces cerevisiae, induces a Gcn4 response and forms aggregates when overproduced. Gene 2022; 809:146034. [PMID: 34688816 DOI: 10.1016/j.gene.2021.146034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/26/2021] [Accepted: 10/19/2021] [Indexed: 11/24/2022]
Abstract
We previously reported the function of Rbs1 protein in RNA polymerase III complex assembly via interactions with both, proteins and mRNAs. Rbs1 is a poly(A)-binding protein. The R3H domain in Rbs1 is required for mRNA interactions. The present study utilized the results of a genome-wide analysis of RNA binding by Rbs1 to show a direct interaction between Rbs1 with the 5'-untranslated region (5'-UTR) in PCL5 mRNA. By examining Pcl5 protein levels, we found that Rbs1 overproduction inhibited the translation of PCL5 mRNA. Pcl5 is a cyclin that is associated with Pho85 kinase, which is involved in the degradation of Gcn4 transcription factor. Consequently, lower levels of Pcl5 that resulted from Rbs1 overproduction increased the Gcn4 response. The functional R3H domain in Rbs1 was required for the downregulation of Pcl5 translation and increase in the Gcn4 response, thus validating a regulatory mechanism that relies on the interaction between Rbs1 and the 5'-UTR in PCL5 mRNA. Rbs1 protein was further characterized by microscopy, which identified single Rbs1 assemblies in part of the cell population. The presence of Rbs1 aggregates was confirmed by the fractionation of cellular extracts. Altogether, our results suggest a more general role of Rbs1 in regulating cellular metabolism beyond the assembly of RNA polymerase III.
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Affiliation(s)
- Izabela Rudzińska
- Laboratory of tRNA Transcription, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Marta Płonka
- Laboratory of tRNA Transcription, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Alicja Armatowska
- Laboratory of tRNA Transcription, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Tomasz W Turowski
- Laboratory of Transcription Mechanisms, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Magdalena Boguta
- Laboratory of tRNA Transcription, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland.
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11
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Kessler AC, Maraia RJ. The nuclear and cytoplasmic activities of RNA polymerase III, and an evolving transcriptome for surveillance. Nucleic Acids Res 2021; 49:12017-12034. [PMID: 34850129 PMCID: PMC8643620 DOI: 10.1093/nar/gkab1145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 12/23/2022] Open
Abstract
A 1969 report that described biochemical and activity properties of the three eukaryotic RNA polymerases revealed Pol III as highly distinguishable, even before its transcripts were identified. Now known to be the most complex, Pol III contains several stably-associated subunits referred to as built-in transcription factors (BITFs) that enable highly efficient RNA synthesis by a unique termination-associated recycling process. In vertebrates, subunit RPC7(α/β) can be of two forms, encoded by POLR3G or POLR3GL, with differential activity. Here we review promoter-dependent transcription by Pol III as an evolutionary perspective of eukaryotic tRNA expression. Pol III also provides nonconventional functions reportedly by promoter-independent transcription, one of which is RNA synthesis from DNA 3'-ends during repair. Another is synthesis of 5'ppp-RNA signaling molecules from cytoplasmic viral DNA in a pathway of interferon activation that is dysfunctional in immunocompromised patients with mutations in Pol III subunits. These unconventional functions are also reviewed, including evidence that link them to the BITF subunits. We also review data on a fraction of the human Pol III transcriptome that evolved to include vault RNAs and snaRs with activities related to differentiation, and in innate immune and tumor surveillance. The Pol III of higher eukaryotes does considerably more than housekeeping.
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Affiliation(s)
- Alan C Kessler
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892 USA
| | - Richard J Maraia
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892 USA
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12
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Reprogramming mRNA Expression in Response to Defect in RNA Polymerase III Assembly in the Yeast Saccharomyces cerevisiae. Int J Mol Sci 2021; 22:ijms22147298. [PMID: 34298922 PMCID: PMC8306304 DOI: 10.3390/ijms22147298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/25/2021] [Accepted: 07/03/2021] [Indexed: 12/18/2022] Open
Abstract
The coordinated transcription of the genome is the fundamental mechanism in molecular biology. Transcription in eukaryotes is carried out by three main RNA polymerases: Pol I, II, and III. One basic problem is how a decrease in tRNA levels, by downregulating Pol III efficiency, influences the expression pattern of protein-coding genes. The purpose of this study was to determine the mRNA levels in the yeast mutant rpc128-1007 and its overdose suppressors, RBS1 and PRT1. The rpc128-1007 mutant prevents assembly of the Pol III complex and functionally mimics similar mutations in human Pol III, which cause hypomyelinating leukodystrophies. We applied RNAseq followed by the hierarchical clustering of our complete RNA-seq transcriptome and functional analysis of genes from the clusters. mRNA upregulation in rpc128-1007 cells was generally stronger than downregulation. The observed induction of mRNA expression was mostly indirect and resulted from the derepression of general transcription factor Gcn4, differently modulated by suppressor genes. rpc128-1007 mutation, regardless of the presence of suppressors, also resulted in a weak increase in the expression of ribosome biogenesis genes. mRNA genes that were downregulated by the reduction of Pol III assembly comprise the proteasome complex. In summary, our results provide the regulatory links affected by Pol III assembly that contribute differently to cellular fitness.
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