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Collin A, González-Jiménez A, González-Jiménez MDC, Alfonso MJ, Calvo O. The Role of S. cerevisiae Sub1/PC4 in Transcription Elongation Depends on the C-Terminal Region and Is Independent of the ssDNA Binding Domain. Cells 2022; 11:cells11203320. [PMID: 36291192 PMCID: PMC9600219 DOI: 10.3390/cells11203320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/30/2022] Open
Abstract
Saccharomyces cerevisiae Sub1 (ScSub1) has been defined as a transcriptional stimulatory protein due to its homology to the ssDNA binding domain (ssDBD) of human PC4 (hPC4). Recently, PC4/Sub1 orthologues have been elucidated in eukaryotes, prokaryotes, and bacteriophages with functions related to DNA metabolism. Additionally, ScSub1 contains a unique carboxyl–terminal region (CT) of unknown function up to date. Specifically, it has been shown that Sub1 is required for transcription activation, as well as other processes, throughout the transcription cycle. Despite the progress that has been made in understanding the mechanism underlying Sub1′s functions, some questions remain unanswered. As a case in point: whether Sub1’s roles in initiation and elongation are differentially predicated on distinct regions of the protein or how Sub1′s functions are regulated. Here, we uncover some residues that are key for DNA–ScSub1 interaction in vivo, localized in the ssDBD, and required for Sub1 recruitment to promoters. Furthermore, using an array of genetic and molecular techniques, we demonstrate that the CT region is required for transcription elongation by RNA polymerase II (RNAPII). Altogether, our data indicate that Sub1 plays a dual role during transcription—in initiation through the ssDBD and in elongation through the CT region.
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Affiliation(s)
- Alejandro Collin
- Cátedra de Bioquímica y Biología Molecular, Facultad de Ciencias Médicas-INICSA, CONICET-Universidad Nacional de Córdoba, Haya de la Torre s/n, Pabellón Argentina, 2º piso. Ciudad Universitaria, Cordoba CP5000, Argentina
| | - Araceli González-Jiménez
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, C/ Zacarías González, nº2, 37007 Salamanca, Spain
| | | | - Manuel J. Alfonso
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, C/ Zacarías González, nº2, 37007 Salamanca, Spain
| | - Olga Calvo
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, C/ Zacarías González, nº2, 37007 Salamanca, Spain
- Correspondence:
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Garrido-Godino AI, Martín-Expósito M, Gutiérrez-Santiago F, Perez-Fernandez J, Navarro F. Rpb4/7, a key element of RNA pol II to coordinate mRNA synthesis in the nucleus with cytoplasmic functions in Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194846. [PMID: 35905859 DOI: 10.1016/j.bbagrm.2022.194846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/11/2022] [Accepted: 07/17/2022] [Indexed: 06/15/2023]
Affiliation(s)
- A I Garrido-Godino
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
| | - M Martín-Expósito
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
| | - F Gutiérrez-Santiago
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
| | - J Perez-Fernandez
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain.
| | - F Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain; Instituto Universitario de Investigación en Olivar y Aceites de Oliva, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain.
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Liu A, Hou X, Zhang J, Wang W, Dong X, Li J, Zhu X, Xing Q, Huang X, Hu J, Bao Z. Tissue-Specific and Time-Dependent Expressions of PC4s in Bay Scallop ( Argopecten irradians irradians) Reveal Function Allocation in Thermal Response. Genes (Basel) 2022; 13:genes13061057. [PMID: 35741819 PMCID: PMC9223095 DOI: 10.3390/genes13061057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/10/2022] [Accepted: 06/10/2022] [Indexed: 12/10/2022] Open
Abstract
Transcriptional coactivator p15 (PC4) encodes a structurally conserved but functionally diverse protein that plays crucial roles in RNAP-II-mediated transcription, DNA replication and damage repair. Although structures and functions of PC4 have been reported in most vertebrates and some invertebrates, the PC4 genes were less systematically identified and characterized in the bay scallop Argopecten irradians irradians. In this study, five PC4 genes (AiPC4s) were successfully identified in bay scallops via whole-genome scanning through in silico analysis. Protein structure and phylogenetic analyses of AiPC4s were conducted to determine the identities and evolutionary relationships of these genes. Expression levels of AiPC4s were assessed in embryos/larvae at all developmental stages, in healthy adult tissues and in different tissues (mantles, gills, hemocytes and hearts) being processed under 32 °C stress with different time durations (0 h, 6 h, 12 h, 24 h, 3 d, 6 d and 10 d). Spatiotemporal expression profiles of AiPC4s suggested the functional roles of the genes in embryos/larvae at all developmental stages and in healthy adult tissues in bay scallop. Expression regulations (up- and down-) of AiPC4s under high-temperature stress displayed both tissue-specific and time-dependent patterns with function allocations, revealing that AiPC4s performed differentiated functions in response to thermal stress. This work provides clues of molecular function allocation of PC4 in scallops in response to thermal stress and helps in illustrating how marine bivalves resist elevated seawater temperature.
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Affiliation(s)
- Ancheng Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
| | - Xiujiang Hou
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
| | - Junhao Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
| | - Wen Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
| | - Xuecheng Dong
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
| | - Jianshu Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
| | - Xinghai Zhu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
| | - Qiang Xing
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Correspondence: ; Tel.: +86-532-82031969
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China (SOI-OUC), Sanya 572000, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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Zhao T, Vvedenskaya IO, Lai WKM, Basu S, Pugh BF, Nickels BE, Kaplan CD. Ssl2/TFIIH function in transcription start site scanning by RNA polymerase II in Saccharomyces cerevisiae. eLife 2021; 10:e71013. [PMID: 34652274 PMCID: PMC8589449 DOI: 10.7554/elife.71013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/14/2021] [Indexed: 12/31/2022] Open
Abstract
In Saccharomyces cerevisiae, RNA polymerase II (Pol II) selects transcription start sites (TSSs) by a unidirectional scanning process. During scanning, a preinitiation complex (PIC) assembled at an upstream core promoter initiates at select positions within a window ~40-120 bp downstream. Several lines of evidence indicate that Ssl2, the yeast homolog of XPB and an essential and conserved subunit of the general transcription factor (GTF) TFIIH, drives scanning through its DNA-dependent ATPase activity, therefore potentially controlling both scanning rate and scanning extent (processivity). To address questions of how Ssl2 functions in promoter scanning and interacts with other initiation activities, we leveraged distinct initiation-sensitive reporters to identify novel ssl2 alleles. These ssl2 alleles, many of which alter residues conserved from yeast to human, confer either upstream or downstream TSS shifts at the model promoter ADH1 and genome-wide. Specifically, tested ssl2 alleles alter TSS selection by increasing or narrowing the distribution of TSSs used at individual promoters. Genetic interactions of ssl2 alleles with other initiation factors are consistent with ssl2 allele classes functioning through increasing or decreasing scanning processivity but not necessarily scanning rate. These alleles underpin a residue interaction network that likely modulates Ssl2 activity and TFIIH function in promoter scanning. We propose that the outcome of promoter scanning is determined by two functional networks, the first being Pol II activity and factors that modulate it to determine initiation efficiency within a scanning window, and the second being Ssl2/TFIIH and factors that modulate scanning processivity to determine the width of the scanning widow.
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Affiliation(s)
- Tingting Zhao
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - Irina O Vvedenskaya
- Department of Genetics and Waksman Institute, Rutgers UniversityPiscatawayUnited States
| | - William KM Lai
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Shrabani Basu
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - B Franklin Pugh
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Bryce E Nickels
- Department of Genetics and Waksman Institute, Rutgers UniversityPiscatawayUnited States
| | - Craig D Kaplan
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
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5
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González-Jiménez A, Campos A, Navarro F, Clemente-Blanco A, Calvo O. Regulation of Eukaryotic RNAPs Activities by Phosphorylation. Front Mol Biosci 2021; 8:681865. [PMID: 34250017 PMCID: PMC8268151 DOI: 10.3389/fmolb.2021.681865] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/07/2021] [Indexed: 01/11/2023] Open
Abstract
Evolutionarily conserved kinases and phosphatases regulate RNA polymerase II (RNAPII) transcript synthesis by modifying the phosphorylation status of the carboxyl-terminal domain (CTD) of Rpb1, the largest subunit of RNAPII. Proper levels of Rpb1-CTD phosphorylation are required for RNA co-transcriptional processing and to coordinate transcription with other nuclear processes, such as chromatin remodeling and histone modification. Whether other RNAPII subunits are phosphorylated and influences their role in gene expression is still an unanswered question. Much less is known about RNAPI and RNAPIII phosphorylation, whose subunits do not contain functional CTDs. However, diverse studies have reported that several RNAPI and RNAPIII subunits are susceptible to phosphorylation. Some of these phosphorylation sites are distributed within subunits common to all three RNAPs whereas others are only shared between RNAPI and RNAPIII. This suggests that the activities of all RNAPs might be finely modulated by phosphorylation events and raises the idea of a tight coordination between the three RNAPs. Supporting this view, the transcription by all RNAPs is regulated by signaling pathways that sense different environmental cues to adapt a global RNA transcriptional response. This review focuses on how the phosphorylation of RNAPs might regulate their function and we comment on the regulation by phosphorylation of some key transcription factors in the case of RNAPI and RNAPIII. Finally, we discuss the existence of possible common mechanisms that could coordinate their activities.
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Affiliation(s)
- Araceli González-Jiménez
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
| | - Adrián Campos
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Jaén, Spain.,Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Jaén, Jaén, Spain
| | - Andrés Clemente-Blanco
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
| | - Olga Calvo
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
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6
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Chen L, Liao F, Wu J, Wang Z, Jiang Z, Zhang C, Luo P, Ma L, Gong Q, Wang Y, Wang Q, Luo M, Yang Z, Han S, Shi C. Acceleration of ageing via disturbing mTOR-regulated proteostasis by a new ageing-associated gene PC4. Aging Cell 2021; 20:e13370. [PMID: 33957702 PMCID: PMC8208792 DOI: 10.1111/acel.13370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/21/2021] [Accepted: 03/31/2021] [Indexed: 01/08/2023] Open
Abstract
Research on ageing‐associated genes is important for investigating ageing and anti‐ageing strategies. Here, we firstly reported that the human positive cofactor 4 (PC4), a multifunctional and highly conserved nucleoprotein, is accumulated and activated during ageing and causes global accelerated ageing process by disrupting proteostasis. Mechanistically, PC4 interacts with Sin3‐HDAC complex and inhibits its deacetylated activity, leads to hyper‐acetylation of the histones at the promoters of mTOR‐related genes and causes mTOR signalling activation. Accordingly, mTOR activation causes excessive protein synthesis, resulting in impaired proteostasis and accelerated senescence. These results reveal a new biological function of PC4 in vivo, recognizes PC4 as a new ageing‐associated gene and provides a genetically engineered mouse model to simulate natural ageing. More importantly, our findings also indicate that PC4 is involved in histone acetylation and serves as a potential target to improve proteostasis and delay ageing.
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Affiliation(s)
- Long Chen
- Institute of Rocket Force Medicine State Key Laboratory of Trauma, Burns and Combined Injury Third Military Medical University Chongqing China
| | - Fengying Liao
- Institute of Rocket Force Medicine State Key Laboratory of Trauma, Burns and Combined Injury Third Military Medical University Chongqing China
| | - Jie Wu
- Institute of Rocket Force Medicine State Key Laboratory of Trauma, Burns and Combined Injury Third Military Medical University Chongqing China
| | - Ziwen Wang
- Institute of Rocket Force Medicine State Key Laboratory of Trauma, Burns and Combined Injury Third Military Medical University Chongqing China
- Department of Cardiology Geriatric Cardiovascular Disease Research and Treatment Center 252 Hospital of PLA (82nd Group Army Hospital of PLA) Baoding China
| | - Zhongyong Jiang
- Institute of Rocket Force Medicine State Key Laboratory of Trauma, Burns and Combined Injury Third Military Medical University Chongqing China
| | - Chi Zhang
- Institute of Rocket Force Medicine State Key Laboratory of Trauma, Burns and Combined Injury Third Military Medical University Chongqing China
| | - Peng Luo
- Institute of Rocket Force Medicine State Key Laboratory of Trauma, Burns and Combined Injury Third Military Medical University Chongqing China
| | - Le Ma
- Institute of Rocket Force Medicine State Key Laboratory of Trauma, Burns and Combined Injury Third Military Medical University Chongqing China
| | - Qiang Gong
- Department of Hematology Southwest Hospital Third Military Medical University Chongqing China
| | - Yang Wang
- Institute of Rocket Force Medicine State Key Laboratory of Trauma, Burns and Combined Injury Third Military Medical University Chongqing China
| | - Qing Wang
- Institute of Rocket Force Medicine State Key Laboratory of Trauma, Burns and Combined Injury Third Military Medical University Chongqing China
| | - Min Luo
- Institute of Rocket Force Medicine State Key Laboratory of Trauma, Burns and Combined Injury Third Military Medical University Chongqing China
| | - Zeyu Yang
- Breast and Thyroid Surgical Department Chongqing General Hospital University of Chinese Academy of Sciences Chongqing China
| | - Shiqian Han
- Institute of Tropical Medicine Third Military Medical University Chongqing China
| | - Chunmeng Shi
- Institute of Rocket Force Medicine State Key Laboratory of Trauma, Burns and Combined Injury Third Military Medical University Chongqing China
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