1
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Gantner BN, Palma FR, Kayzuka C, Lacchini R, Foltz DR, Backman V, Kelleher N, Shilatifard A, Bonini MG. Histone oxidation as a new mechanism of metabolic control over gene expression. Trends Genet 2024:S0168-9525(24)00134-3. [PMID: 38910033 DOI: 10.1016/j.tig.2024.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/30/2024] [Accepted: 05/30/2024] [Indexed: 06/25/2024]
Abstract
The emergence of aerobic respiration created unprecedented bioenergetic advantages, while imposing the need to protect critical genetic information from reactive byproducts of oxidative metabolism (i.e., reactive oxygen species, ROS). The evolution of histone proteins fulfilled the need to shield DNA from these potentially damaging toxins, while providing the means to compact and structure massive eukaryotic genomes. To date, several metabolism-linked histone post-translational modifications (PTMs) have been shown to regulate chromatin structure and gene expression. However, whether and how PTMs enacted by metabolically produced ROS regulate adaptive chromatin remodeling remain relatively unexplored. Here, we review novel mechanistic insights into the interactions of ROS with histones and their consequences for the control of gene expression regulation, cellular plasticity, and behavior.
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Affiliation(s)
- Benjamin N Gantner
- Department of Medicine, Division of Endocrinology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Flavio R Palma
- Division of Hematology Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Cezar Kayzuka
- Division of Hematology Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Department of Pharmacology, Ribeirao Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil; Department of Psychiatric Nursing and Human Sciences, Ribeirao Preto College of Nursing, University of Sao Paulo, Sao Paulo, Brazil
| | - Riccardo Lacchini
- Department of Psychiatric Nursing and Human Sciences, Ribeirao Preto College of Nursing, University of Sao Paulo, Sao Paulo, Brazil
| | - Daniel R Foltz
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Vadim Backman
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Department of Bioengineering, McCormick School of Engineering, Northwestern University, Chicago, IL, USA
| | - Neil Kelleher
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Chemistry of Life Processes Institute, Northwestern University, Chicago, IL, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Marcelo G Bonini
- Division of Hematology Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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2
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Cochran K, Yin M, Mantripragada A, Schreiber J, Marinov GK, Kundaje A. Dissecting the cis-regulatory syntax of transcription initiation with deep learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596138. [PMID: 38853896 PMCID: PMC11160661 DOI: 10.1101/2024.05.28.596138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Despite extensive characterization of mammalian Pol II transcription, the DNA sequence determinants of transcription initiation at a third of human promoters and most enhancers remain poorly understood. Hence, we trained and interpreted a neural network called ProCapNet that accurately models base-resolution initiation profiles from PRO-cap experiments using local DNA sequence. ProCapNet learns sequence motifs with distinct effects on initiation rates and TSS positioning and uncovers context-specific cryptic initiator elements intertwined within other TF motifs. ProCapNet annotates predictive motifs in nearly all actively transcribed regulatory elements across multiple cell-lines, revealing a shared cis-regulatory logic across promoters and enhancers mediated by a highly epistatic sequence syntax of cooperative and competitive motif interactions. ProCapNet models of RAMPAGE profiles measuring steady-state RNA abundance at TSSs distill initiation signals on par with models trained directly on PRO-cap profiles. ProCapNet learns a largely cell-type-agnostic cis-regulatory code of initiation complementing sequence drivers of cell-type-specific chromatin state critical for accurate prediction of cell-type-specific transcription initiation.
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Affiliation(s)
- Kelly Cochran
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | | | | | - Jacob Schreiber
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
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3
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Cai YD, Chow GK, Hidalgo S, Liu X, Jackson KC, Vasquez CD, Gao ZY, Lam VH, Tabuloc CA, Zheng H, Zhao C, Chiu JC. Alternative splicing of clock transcript mediates the response of circadian clocks to temperature changes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593646. [PMID: 38766142 PMCID: PMC11100826 DOI: 10.1101/2024.05.10.593646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Circadian clocks respond to temperature changes over the calendar year, allowing organisms to adjust their daily biological rhythms to optimize health and fitness. In Drosophila, seasonal adaptations and temperature compensation are regulated by temperature-sensitive alternative splicing (AS) of period (per) and timeless (tim) genes that encode key transcriptional repressors of clock gene expression. Although clock (clk) gene encodes the critical activator of clock gene expression, AS of its transcripts and its potential role in temperature regulation of clock function have not been explored. We therefore sought to investigate whether clk exhibits AS in response to temperature and the functional changes of the differentially spliced transcripts. We observed that clk transcripts indeed undergo temperature-sensitive AS. Specifically, cold temperature leads to the production of an alternative clk transcript, hereinafter termed clk-cold, which encodes a CLK isoform with an in-frame deletion of four amino acids proximal to the DNA binding domain. Notably, serine 13 (S13), which we found to be a CK1α-dependent phosphorylation site, is among the four amino acids deleted in CLK-cold protein. Using a combination of transgenic fly, tissue culture, and in vitro experiments, we demonstrated that upon phosphorylation at CLK(S13), CLK-DNA interaction is reduced, thus decreasing CLK occupancy at clock gene promoters. This is in agreement with our findings that CLK occupancy at clock genes and transcriptional output are elevated at cold temperature, which can be explained by the higher amounts of CLK-cold isoforms that lack S13 residue. This study provides new insights into the complex collaboration between AS and phospho-regulation in shaping temperature responses of the circadian clock.
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Affiliation(s)
- Yao D. Cai
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Gary K. Chow
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Sergio Hidalgo
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Xianhui Liu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Kiya C. Jackson
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Cameron D. Vasquez
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Zita Y. Gao
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Vu H. Lam
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Christine A. Tabuloc
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Haiyan Zheng
- Biological Mass Spectrometry Facility, Robert Wood Johnson Medical School and Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Caifeng Zhao
- Biological Mass Spectrometry Facility, Robert Wood Johnson Medical School and Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Joanna C. Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
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4
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Kumari P, Sarovar Bhavesh N. Birth and death view of DNA, RNA, and proteins. Gene 2023; 883:147672. [PMID: 37506987 DOI: 10.1016/j.gene.2023.147672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/26/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
The potential of cells to guide their genome and configure genes to express at a given time and in response to specific stimuli is pivotal to regulate cellular processes such as tissue differentiation, organogenesis, organismal development, homeostasis, and disease. In this review, we focus on the diverse mechanisms involved in DNA replication and its degradation, mRNA synthesis, and associated regulation such as RNA capping, splicing, tailing, and export. mRNA turnover including Decapping, deadenylation, RNA interference, and Nonsense mediated mRNA decay followed by protein translation, post-translational modification, and protein turnover. We highlight recent advances in understanding the complex series of molecular mechanisms responsible for the remarkable cellular regulatory mechanisms.
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Affiliation(s)
- Pooja Kumari
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, Jharkhand 834001, India.
| | - Neel Sarovar Bhavesh
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India.
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5
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Xie L, Liu S, Zhang Y, Tian W, Xu D, Li J, Luo X, Li L, Bian Y, Li F, Hao Y, He Z, Xia X, Song X, Cao S. Efficient proteome-wide identification of transcription factors targeting Glu-1: A case study for functional validation of TaB3-2A1 in wheat. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1952-1965. [PMID: 37381172 PMCID: PMC10502752 DOI: 10.1111/pbi.14103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/13/2023] [Accepted: 06/05/2023] [Indexed: 06/30/2023]
Abstract
High-molecular-weight glutenin subunits (HMW-GS), a major component of seed storage proteins (SSP) in wheat, largely determine processing quality. HMW-GS encoded by GLU-1 loci are mainly controlled at the transcriptional level by interactions between cis-elements and transcription factors (TFs). We previously identified a conserved cis-regulatory module CCRM1-1 as the most essential cis-element for Glu-1 endosperm-specific high expression. However, the TFs targeting CCRM1-1 remained unknown. Here, we built the first DNA pull-down plus liquid chromatography-mass spectrometry platform in wheat and identified 31 TFs interacting with CCRM1-1. TaB3-2A1 as proof of concept was confirmed to bind to CCRM1-1 by yeast one hybrid and electrophoretic mobility shift assays. Transactivation experiments demonstrated that TaB3-2A1 repressed CCRM1-1-driven transcription activity. TaB3-2A1 overexpression significantly reduced HMW-GS and other SSP, but enhanced starch content. Transcriptome analyses confirmed that enhanced expression of TaB3-2A1 down-regulated SSP genes and up-regulated starch synthesis-related genes, such as TaAGPL3, TaAGPS2, TaGBSSI, TaSUS1 and TaSUS5, suggesting that it is an integrator modulating the balance of carbon and nitrogen metabolism. TaB3-2A1 also had significant effects on agronomic traits, including heading date, plant height and grain weight. We identified two major haplotypes of TaB3-2A1 and found that TaB3-2A1-Hap1 conferred lower seed protein content, but higher starch content, plant height and grain weight than TaB3-2A1-Hap2 and was subjected to positive selection in a panel of elite wheat cultivars. These findings provide a high-efficiency tool to detect TFs binding to targeted promoters, considerable gene resources for dissecting regulatory mechanisms underlying Glu-1 expression, and a useful gene for wheat improvement.
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Affiliation(s)
- Lina Xie
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
- College of AgronomyNorthwest A&F UniversityYanglingShaanxi ProvinceChina
| | - Siyang Liu
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Yong Zhang
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Wenfei Tian
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
- International Maize and Wheat Improvement Center (CIMMYT) China OfficeChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Dengan Xu
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Jihu Li
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Xumei Luo
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Lingli Li
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Yingjie Bian
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Faji Li
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Yuanfeng Hao
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
- International Maize and Wheat Improvement Center (CIMMYT) China OfficeChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Xiyue Song
- College of AgronomyNorthwest A&F UniversityYanglingShaanxi ProvinceChina
| | - Shuanghe Cao
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
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6
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Zhang X, Yang L, Gan Q, Jiang S, Liang D, Gao J, Meng Y. BmTBP upregulates the transcription of BmSuc1 in silkworm (Bombyx mori) by binding to BmTfΙΙA-S. INSECT SCIENCE 2023; 30:1405-1419. [PMID: 36585848 DOI: 10.1111/1744-7917.13168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/06/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
The BmSuc1 gene, which encodes a novel animal-type β-fructofuranosidase (EC 3.2.1.26), was first cloned and identified in silkworm (Bombyx mori). As an essential sucrase, the activity of BmSUC1 is unaffected by alkaloidal sugar mimics in mulberry leaves. This enzyme may also directly regulate the degree of sucrose hydrolysis in the silkworm midgut. In addition, BmSUC1 is involved in the synthesis of sericin 1 in the silk gland tissue. However, the mechanism underlying the regulation of BmSuc1 transcription remains unclear. In this study, we analyzed the BmSuc1 promoter activity using a dual-luciferase reporter assay and identified 4 regions that are critical for transcriptional activation. The gene encoding a predicted transcription factor (TATA-box-binding protein; BmTBP) capable of binding to the core promoter regions was cloned. A quantitative real-time polymerase chain reaction analysis indicated the gene was highly expressed in the midgut. Downregulating BmTBP expression via RNA interference decreased the expression of BmSuc1 at the transcript and protein levels. An electrophoretic mobility shift analysis and chromatin immunoprecipitation indicated that BmTBP can bind to the TATA-box cis-regulatory element in the BmSuc1 promoter. Furthermore, a bioinformatics-based analysis and a far-western blot revealed the interaction between BmTBP and another transcription factor (BmTfIIA-S). The luciferase reporter gene assay results confirmed that the BmTBP-BmTfIIA-S complex increases the BmSuc1 promoter activity. Considered together, these findings suggest that BmTBP regulates BmSuc1 expression through its interaction with BmTfIIA-S.
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Affiliation(s)
- Xinwei Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- Department of Pathology, Henan Provincial People's Hospital, Zhengzhou, China
| | - Liangli Yang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- Anhui International Joint Research and Development Center of Sericulture Resources Utilization, Hefei, China
| | - Quan Gan
- Anhui Academy of Agricultural Sciences, Hefei, China
| | - Song Jiang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- Anhui International Joint Research and Development Center of Sericulture Resources Utilization, Hefei, China
| | - Dan Liang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- Anhui International Joint Research and Development Center of Sericulture Resources Utilization, Hefei, China
| | - Junshan Gao
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yan Meng
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- Anhui International Joint Research and Development Center of Sericulture Resources Utilization, Hefei, China
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7
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Fournier M, Leclerc P, Leray A, Champelovier D, Agbazahou F, Dahmani F, Bidaux G, Furlan A, Héliot L. Combined SPT and FCS methods reveal a mechanism of RNAP II oversampling in cell nuclei. Sci Rep 2023; 13:14633. [PMID: 37669988 PMCID: PMC10480184 DOI: 10.1038/s41598-023-38668-8] [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: 01/05/2023] [Accepted: 07/12/2023] [Indexed: 09/07/2023] Open
Abstract
Gene expression orchestration is a key question in fundamental and applied research. Different models for transcription regulation were proposed, yet the dynamic regulation of RNA polymerase II (RNAP II) activity remains a matter of debate. To improve our knowledge of this topic, we investigated RNAP II motility in eukaryotic cells by combining single particle tracking (SPT) and fluorescence correlation spectroscopy (FCS) techniques, to take advantage of their different sensitivities in order to analyze together slow and fast molecular movements. Thanks to calibrated samples, we developed a benchmark for quantitative analysis of molecular dynamics, to eliminate the main potential instrumental biases. We applied this workflow to study the diffusion of RPB1, the catalytic subunit of RNAP II. By a cross-analysis of FCS and SPT, we could highlight different RPB1 motility states and identifyed a stationary state, a slow diffusion state, and two different modes of subdiffusion. Interestingly, our analysis also unveiled the oversampling by RPB1 of nuclear subdomains. Based on these data, we propose a novel model of spatio-temporal transcription regulation. Altogether, our results highlight the importance of combining microscopy approaches at different time scales to get a full insight into the real complexity of molecular kinetics in cells.
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Affiliation(s)
- Marie Fournier
- Univ. Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France
| | - Pierre Leclerc
- Univ. Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France
| | - Aymeric Leray
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS, Université de Bourgogne Franche Comte, Dijon, France
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France
| | - Dorian Champelovier
- Univ. Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France
| | - Florence Agbazahou
- Univ. Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France
| | - Fatima Dahmani
- Univ. Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France
| | - Gabriel Bidaux
- INSERM UMR 1060, CarMeN Laboratory, IHU OPERA, Hôpital Louis Pradel, Hospices Civils de Lyon, Univ Lyon1, Lyon, France
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France
| | - Alessandro Furlan
- Univ. Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France.
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 -CANTHER -Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille, 59000, France.
- Unité Tumorigenèse et Résistance aux Traitements, Centre Oscar Lambret, 59000, Lille, France.
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France.
| | - Laurent Héliot
- Univ. Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France.
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France.
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Lamas-Maceiras M, Vizoso-Vázquez Á, Barreiro-Alonso A, Cámara-Quílez M, Cerdán ME. Thanksgiving to Yeast, the HMGB Proteins History from Yeast to Cancer. Microorganisms 2023; 11:microorganisms11040993. [PMID: 37110415 PMCID: PMC10142021 DOI: 10.3390/microorganisms11040993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Yeasts have been a part of human life since ancient times in the fermentation of many natural products used for food. In addition, in the 20th century, they became powerful tools to elucidate the functions of eukaryotic cells as soon as the techniques of molecular biology developed. Our molecular understandings of metabolism, cellular transport, DNA repair, gene expression and regulation, and the cell division cycle have all been obtained through biochemistry and genetic analysis using different yeasts. In this review, we summarize the role that yeasts have had in biological discoveries, the use of yeasts as biological tools, as well as past and on-going research projects on HMGB proteins along the way from yeast to cancer.
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Affiliation(s)
- Mónica Lamas-Maceiras
- Centro Interdisciplinar de Química y Biología (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
- Facultad de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
| | - Ángel Vizoso-Vázquez
- Centro Interdisciplinar de Química y Biología (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
- Facultad de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
| | - Aida Barreiro-Alonso
- Centro Interdisciplinar de Química y Biología (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
- Facultad de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
| | - María Cámara-Quílez
- Centro Interdisciplinar de Química y Biología (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
- Facultad de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
| | - María Esperanza Cerdán
- Centro Interdisciplinar de Química y Biología (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
- Facultad de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
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9
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Dutagaci B, Duan B, Qiu C, Kaplan CD, Feig M. Characterization of RNA polymerase II trigger loop mutations using molecular dynamics simulations and machine learning. PLoS Comput Biol 2023; 19:e1010999. [PMID: 36947548 PMCID: PMC10069792 DOI: 10.1371/journal.pcbi.1010999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 04/03/2023] [Accepted: 03/06/2023] [Indexed: 03/23/2023] Open
Abstract
Catalysis and fidelity of multisubunit RNA polymerases rely on a highly conserved active site domain called the trigger loop (TL), which achieves roles in transcription through conformational changes and interaction with NTP substrates. The mutations of TL residues cause distinct effects on catalysis including hypo- and hyperactivity and altered fidelity. We applied molecular dynamics simulation (MD) and machine learning (ML) techniques to characterize TL mutations in the Saccharomyces cerevisiae RNA Polymerase II (Pol II) system. We did so to determine relationships between individual mutations and phenotypes and to associate phenotypes with MD simulated structural alterations. Using fitness values of mutants under various stress conditions, we modeled phenotypes along a spectrum of continual values. We found that ML could predict the phenotypes with 0.68 R2 correlation from amino acid sequences alone. It was more difficult to incorporate MD data to improve predictions from machine learning, presumably because MD data is too noisy and possibly incomplete to directly infer functional phenotypes. However, a variational auto-encoder model based on the MD data allowed the clustering of mutants with different phenotypes based on structural details. Overall, we found that a subset of loss-of-function (LOF) and lethal mutations tended to increase distances of TL residues to the NTP substrate, while another subset of LOF and lethal substitutions tended to confer an increase in distances between TL and bridge helix (BH). In contrast, some of the gain-of-function (GOF) mutants appear to cause disruption of hydrophobic contacts among TL and nearby helices.
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Affiliation(s)
- Bercem Dutagaci
- Department of Molecular and Cell Biology, University of California Merced, Merced, California, United States of America
| | - Bingbing Duan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Chenxi Qiu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Craig D. Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
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10
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Gorbea Colón JJ, Palao L, Chen SF, Kim HJ, Snyder L, Chang YW, Tsai KL, Murakami K. Structural basis of a transcription pre-initiation complex on a divergent promoter. Mol Cell 2023; 83:574-588.e11. [PMID: 36731470 PMCID: PMC10162435 DOI: 10.1016/j.molcel.2023.01.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 11/28/2022] [Accepted: 01/06/2023] [Indexed: 02/04/2023]
Abstract
Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single direction, it is unknown how divergent transcription arises. Here, the Saccharomyces cerevisiae Mediator complexed with a PIC (Med-PIC) was assembled on a divergent promoter and analyzed by cryoelectron microscopy. The structure reveals two distinct Med-PICs forming a dimer through the Mediator tail module, induced by a homodimeric activator protein localized near the dimerization interface. The tail dimer is associated with ∼80-bp upstream DNA, such that two flanking core promoter regions are positioned and oriented in a suitable form for PIC assembly in opposite directions. Also, cryoelectron tomography visualized the progress of the PIC assembly on the two core promoter regions, providing direct evidence for the role of the Med-PIC dimer in divergent transcription.
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Affiliation(s)
- Jose J Gorbea Colón
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leon Palao
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shin-Fu Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Hee Jong Kim
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Laura Snyder
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Kuang-Lei Tsai
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Kenji Murakami
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Center for Genome Integrity, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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11
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Carter ZI, Jacobs RQ, Schneider DA, Lucius AL. Transient-State Kinetic Analysis of the RNA Polymerase II Nucleotide Incorporation Mechanism. Biochemistry 2023; 62:95-108. [PMID: 36525636 PMCID: PMC10069233 DOI: 10.1021/acs.biochem.2c00608] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Eukaryotic RNA polymerase II (Pol II) is an essential enzyme that lies at the core of eukaryotic biology. Due to its pivotal role in gene expression, Pol II has been subjected to a substantial number of investigations. We aim to further our understanding of Pol II nucleotide incorporation by utilizing transient-state kinetic techniques to examine Pol II single nucleotide addition on the millisecond time scale. We analyzed Saccharomyces cerevisiae Pol II incorporation of ATP or an ATP analog, Sp-ATP-α-S. Here we have measured the rate constants governing individual steps of the Pol II transcription cycle in the presence of ATP or Sp-ATP-α-S. These results suggest that Pol II catalyzes nucleotide incorporation by binding the next cognate nucleotide and immediately catalyzes bond formation and bond formation is either followed by a conformational change or pyrophosphate release. By comparing our previously published RNA polymerase I (Pol I) and Pol I lacking the A12 subunit (Pol I ΔA12) results that we collected under the same conditions with the identical technique, we show that Pol II and Pol I ΔA12 exhibit similar nucleotide addition mechanisms. This observation indicates that removal of the A12 subunit from Pol I results in a Pol II like enzyme. Taken together, these data further our collective understanding of Pol II's nucleotide incorporation mechanism and the evolutionary divergence of RNA polymerases across the three domains of life.
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Affiliation(s)
- Zachariah I Carter
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama35233, United States
| | - Ruth Q Jacobs
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama35233, United States
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama35233, United States
| | - Aaron L Lucius
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama35233, United States
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12
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Graczyk A, Radzikowska-Cieciura E, Kaczmarek R, Pawlowska R, Chworos A. Modified Nucleotides for Chemical and Enzymatic Synthesis of Therapeutic RNA. Curr Med Chem 2023; 30:1320-1347. [PMID: 36239720 DOI: 10.2174/0929867330666221014111403] [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: 03/02/2022] [Revised: 04/22/2022] [Accepted: 05/16/2022] [Indexed: 11/22/2022]
Abstract
In recent years, RNA has emerged as a medium with a broad spectrum of therapeutic potential, however, for years, a group of short RNA fragments was studied and considered therapeutic molecules. In nature, RNA plays both functions, with coding and non-coding potential. For RNA, like any other therapeutic, to be used clinically, certain barriers must be crossed. Among them, there are biocompatibility, relatively low toxicity, bioavailability, increased stability, target efficiency and low off-target effects. In the case of RNA, most of these obstacles can be overcome by incorporating modified nucleotides into its structure. This may be achieved by both, in vitro and in vivo biosynthetic methods, as well as chemical synthesis. Some advantages and disadvantages of each approach are summarized here. The wide range of nucleotide analogues has been tested for their utility as monomers for RNA synthesis. Many of them have been successfully implemented, and a lot of pre-clinical and clinical studies involving modified RNA have been carried out. Some of these medications have already been introduced into clinics. After the huge success of RNA-based vaccines that were introduced into widespread use in 2020, and the introduction to the market of some RNA-based drugs, RNA therapeutics containing modified nucleotides appear to be the future of medicine.
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Affiliation(s)
- Anna Graczyk
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Ewa Radzikowska-Cieciura
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Renata Kaczmarek
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Roza Pawlowska
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Arkadiusz Chworos
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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13
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Li R, Wang M, Gong P. Crystal structure of a pre-chemistry viral RNA-dependent RNA polymerase suggests participation of two basic residues in catalysis. Nucleic Acids Res 2022; 50:12389-12399. [PMID: 36477355 PMCID: PMC9757066 DOI: 10.1093/nar/gkac1133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 10/19/2022] [Accepted: 11/10/2022] [Indexed: 12/13/2022] Open
Abstract
The nucleic acid polymerase-catalyzed nucleotidyl transfer reaction associated with polymerase active site closure is a key step in the nucleotide addition cycle (NAC). Two proton transfer events can occur in such a nucleotidyl transfer: deprotonation of the priming nucleotide 3'-hydroxyl nucleophile and protonation of the pyrophosphate (PPi) leaving group. In viral RNA-dependent RNA polymerases (RdRPs), whether and how active site residues participate in this two-proton transfer reaction remained to be clarified. Here we report a 2.5 Å resolution crystal structure of enterovirus 71 (EV71) RdRP in a catalytically closed pre-chemistry conformation, with a proposed proton donor candidate K360 in close contact with the NTP γ-phosphate. Enzymology data reveal that K360 mutations not only reduce RdRP catalytic efficiency but also alter pH dependency profiles in both elongation and pre-elongation synthesis modes. Interestingly, mutations at R174, an RdRP-invariant residue in motif F, had similar effects with additional impact on the Michaelis constant of NTP (KM,NTP). However, direct participation in protonation was not evident for K360 or R174. Our data suggest that both K360 and R174 participate in nucleotidyl transfer, while their possible roles in acid-base or positional catalysis are discussed in comparison with other classes of nucleic acid polymerases.
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Affiliation(s)
| | | | - Peng Gong
- To whom correspondence should be addressed.
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14
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Nawaz K, Cziesielski MJ, Mariappan KG, Cui G, Aranda M. Histone modifications and DNA methylation act cooperatively in regulating symbiosis genes in the sea anemone Aiptasia. BMC Biol 2022; 20:265. [DOI: 10.1186/s12915-022-01469-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
Abstract
Background
The symbiotic relationship between cnidarians and dinoflagellates is one of the most widespread endosymbiosis in our oceans and provides the ecological basis of coral reef ecosystems. Although many studies have been undertaken to unravel the molecular mechanisms underlying these symbioses, we still know little about the epigenetic mechanisms that control the transcriptional responses to symbiosis.
Results
Here, we used the model organism Exaiptasia diaphana to study the genome-wide patterns and putative functions of the histone modifications H3K27ac, H3K4me3, H3K9ac, H3K36me3, and H3K27me3 in symbiosis. While we find that their functions are generally conserved, we observed that colocalization of more than one modification and or DNA methylation correlated with significantly higher gene expression, suggesting a cooperative action of histone modifications and DNA methylation in promoting gene expression. Analysis of symbiosis genes revealed that activating histone modifications predominantly associated with symbiosis-induced genes involved in glucose metabolism, nitrogen transport, amino acid biosynthesis, and organism growth while symbiosis-suppressed genes were involved in catabolic processes.
Conclusions
Our results provide new insights into the mechanisms of prominent histone modifications and their interaction with DNA methylation in regulating symbiosis in cnidarians.
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15
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Basu A, Bobrovnikov DG, Cieza B, Arcon JP, Qureshi Z, Orozco M, Ha T. Deciphering the mechanical code of the genome and epigenome. Nat Struct Mol Biol 2022; 29:1178-1187. [PMID: 36471057 PMCID: PMC10142808 DOI: 10.1038/s41594-022-00877-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/18/2022] [Indexed: 12/12/2022]
Abstract
Diverse DNA-deforming processes are impacted by the local mechanical and structural properties of DNA, which in turn depend on local sequence and epigenetic modifications. Deciphering this mechanical code (that is, this dependence) has been challenging due to the lack of high-throughput experimental methods. Here we present a comprehensive characterization of the mechanical code. Utilizing high-throughput measurements of DNA bendability via loop-seq, we quantitatively established how the occurrence and spatial distribution of dinucleotides, tetranucleotides and methylated CpG impact DNA bendability. We used our measurements to develop a physical model for the sequence and methylation dependence of DNA bendability. We validated the model by performing loop-seq on mouse genomic sequences around transcription start sites and CTCF-binding sites. We applied our model to test the predictions of all-atom molecular dynamics simulations and to demonstrate that sequence and epigenetic modifications can mechanically encode regulatory information in diverse contexts.
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Affiliation(s)
- Aakash Basu
- Department of Biosciences, Durham University, Durham, UK. .,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Dmitriy G Bobrovnikov
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Basilio Cieza
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Juan Pablo Arcon
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Zan Qureshi
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Biochemistry and Biomedicine, Universitat de Barcelona, Barcelona, Spain
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA. .,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA. .,Howard Hughes Medical Institute, Baltimore, MD, USA.
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16
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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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17
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Shrestha HK, Fichman Y, Engle NL, Tschaplinski TJ, Mittler R, Dixon RA, Hettich RL, Barros J, Abraham PE. Multi-omic characterization of bifunctional peroxidase 4-coumarate 3-hydroxylase knockdown in Brachypodium distachyon provides insights into lignin modification-associated pleiotropic effects. FRONTIERS IN PLANT SCIENCE 2022; 13:908649. [PMID: 36247563 PMCID: PMC9554711 DOI: 10.3389/fpls.2022.908649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
A bifunctional peroxidase enzyme, 4-coumarate 3-hydroxylase (C3H/APX), provides a parallel route to the shikimate shunt pathway for the conversion of 4-coumarate to caffeate in the early steps of lignin biosynthesis. Knockdown of C3H/APX (C3H/APX-KD) expression has been shown to reduce the lignin content in Brachypodium distachyon. However, like many other lignin-modified plants, C3H/APX-KDs show unpredictable pleiotropic phenotypes, including stunted growth, delayed senescence, and reduced seed yield. A system-wide level understanding of altered biological processes in lignin-modified plants can help pinpoint the lignin-modification associated growth defects to benefit future studies aiming to negate the yield penalty. Here, a multi-omic approach was used to characterize molecular changes resulting from C3H/APX-KD associated lignin modification and negative growth phenotype in Brachypodium distachyon. Our findings demonstrate that C3H/APX knockdown in Brachypodium stems substantially alters the abundance of enzymes implicated in the phenylpropanoid biosynthetic pathway and disrupt cellular redox homeostasis. Moreover, it elicits plant defense responses associated with intracellular kinases and phytohormone-based signaling to facilitate growth-defense trade-offs. A deeper understanding along with potential targets to mitigate the pleiotropic phenotypes identified in this study could aid to increase the economic feasibility of lignocellulosic biofuel production.
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Affiliation(s)
- Him K. Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, United States
| | - Yosef Fichman
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | - Nancy L. Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | | | - Ron Mittler
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | - Richard A. Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
| | - Robert L. Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jaime Barros
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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18
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Zhou P, Li D, Luo F, Wan X. NCOA2 coordinates with the transcriptional KAT2B-NF-κB partner to trigger inflammation response in acute kidney injury. Gene X 2022; 832:146583. [PMID: 35597525 DOI: 10.1016/j.gene.2022.146583] [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: 01/14/2022] [Revised: 04/15/2022] [Accepted: 05/16/2022] [Indexed: 11/04/2022] Open
Abstract
Dysregulation of multiple genes is an important risk factor for acute kidney injury (AKI). Numerous genes, such as proinflammatory cytokines, intracellular cell adhesion molecules (ICAMs), and nitric oxide synthases (NOSs), are implicated in AKI pathogenesis. However, the molecular mechanisms involved in the dysregulation of these genes are still obscure. Herein, we discovered that two subunits of NF-κB (p50 and p65) couple with lysine acetyltransferase 2B (KAT2B) and nuclear receptor coactivator 2 (NOCA2) to assemble a transcriptional complex in a LPS-induced mouse model of AKI. The NCOA2-KAT2B-NF-κB complex bound to the promoters of some NF-κB target genes, such as interleukin 1 beta (IL-1B), IL-6, tumor necrosis factor alpha (TNFA), ICAM1, vascular cell adhesion molecule 1 (VCAM1), cluster of differentiation 38 (CD38), CD40, CD80, and NOS2, and transactivated their expression. In vitro knockdown of components of the NCOA2-KAT2B-NF-κB complex or blockage of KAT2B by its inhibitors (5-chloro-2-(4-nitrophenyl)-3(2H)-isothiazolone [CNIT] and garcinol) significantly decreased the expression of these NF-κB target genes following LPS treatment. The administration of CNIT and garcinol significantly improved the in vivo outcomes of the AKI mice. Our findings reveal the underlying mechanism of NF-κB target upregulation in the pathogenesis of LPS-induced AKI and identify a new therapeutic strategy for AKI that involves targeting the NCOA2-KAT2B-NF-κB complex.
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Affiliation(s)
- Ping Zhou
- Department of Nephrology, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang 330006, Jiangxi, China
| | - Dongdong Li
- Department of Respiratory Medicine, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang 330006, Jiangxi, China
| | - Fuli Luo
- Department of Diagnosis and Treatment of Chronic Kidney Diseases, Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang 330096, Jiangxi, China
| | - Xiaoxiao Wan
- Department of Nephrology, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang 330006, Jiangxi, China.
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19
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Nuclear mRNA Export and Aging. Int J Mol Sci 2022; 23:ijms23105451. [PMID: 35628261 PMCID: PMC9142925 DOI: 10.3390/ijms23105451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 02/04/2023] Open
Abstract
The relationship between transcription and aging is one that has been studied intensively and experimentally with diverse attempts. However, the impact of the nuclear mRNA export on the aging process following its transcription is still poorly understood, although the nuclear events after transcription are coupled closely with the transcription pathway because the essential factors required for mRNA transport, namely TREX, TREX-2, and nuclear pore complex (NPC), physically and functionally interact with various transcription factors, including the activator/repressor and pre-mRNA processing factors. Dysregulation of the mediating factors for mRNA export from the nucleus generally leads to the aberrant accumulation of nuclear mRNA and further impairment in the vegetative growth and normal lifespan and the pathogenesis of neurodegenerative diseases. The optimal stoichiometry and density of NPC are destroyed during the process of cellular aging, and their damage triggers a defect of function in the nuclear permeability barrier. This review describes recent findings regarding the role of the nuclear mRNA export in cellular aging and age-related neurodegenerative disorders.
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20
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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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21
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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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22
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Yang C, Fujiwara R, Kim HJ, Basnet P, Zhu Y, Colón JJG, Steimle S, Garcia BA, Kaplan CD, Murakami K. Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II. Mol Cell 2022; 82:660-676.e9. [PMID: 35051353 PMCID: PMC8818039 DOI: 10.1016/j.molcel.2021.12.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 11/04/2021] [Accepted: 12/15/2021] [Indexed: 02/05/2023]
Abstract
Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous to capture pol II in the initiating state. Here, we report multiple structures of initiation complexes converted de novo from a 33-subunit yeast pre-initiation complex (PIC) through catalytic activities and subsequently stalled at different template positions. We determine that PICs in the initially transcribing complex (ITC) can synthesize a transcript of ∼26 nucleotides before transitioning to an elongation complex (EC) as determined by the loss of general transcription factors (GTFs). Unexpectedly, transition to an EC was greatly accelerated when an ITC encountered a downstream EC stalled at promoter proximal regions and resulted in a collided head-to-end dimeric EC complex. Our structural analysis reveals a dynamic state of TFIIH, the largest of GTFs, in PIC/ITC with distinct functional consequences at multiple steps on the pathway to elongation.
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Affiliation(s)
- Chun Yang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, U.S.A
| | - Rina Fujiwara
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, U.S.A.,Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Hee Jong Kim
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, U.S.A.,Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA,Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Pratik Basnet
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Yunye Zhu
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Jose J. Gorbea Colón
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, U.S.A.,Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Stefan Steimle
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, U.S.A
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, U.S.A.,Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Craig D. Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Kenji Murakami
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, U.S.A.,Lead contact,Correspondence to:
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23
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Zhang X, Hu Y, Liu G, Liu M, Li Z, Zhao J, Song X, Zhong Y, Qu Y, Wang L, Qin Y. The complex Tup1-Cyc8 bridges transcription factor ClrB and putative histone methyltransferase LaeA to activate the expression of cellulolytic genes. Mol Microbiol 2022; 117:1002-1022. [PMID: 35072962 DOI: 10.1111/mmi.14885] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 11/28/2022]
Abstract
The degradation of lignocellulosic biomass by cellulolytic enzymes is involved in the global carbon cycle. The hydrolysis of lignocellulosic biomass into fermentable sugars is potential as excellent industrial resource to produce a variety of chemical products. The production of cellulolytic enzymes is regulated mainly at the transcriptional level in filamentous fungi. Transcription factor ClrB and the putative histone methyltransferase LaeA, are both necessary for the expression of cellulolytic genes. However, the mechanism by which transcription factors and methyltransferase coordinately regulate cellulolytic genes is still unknown. Here, we reveal a transcriptional regulatory mechanism involving Penicillium oxalicum transcription factor ClrB (PoClrB), complex Tup1-Cyc8, and putative histone methyltransferase LaeA (PoLaeA). As the transcription factor, PoClrB binds the targeted promoters of cellulolytic genes, recruits PoTup1-Cyc8 complex via direct interaction with PoTup1. PoTup1 interacts with PoCyc8 to form the coactivator complex PoTup1-Cyc8. Then, PoTup1 recruits putative histone methyltransferase PoLaeA to modify the chromatin structure of the upstream region of cellulolytic genes, thereby facilitating the binding of transcription machinery to activating the corresponding cellulolytic gene expression. Our results contribute to a better understanding of complex transcriptional regulation mechanisms of cellulolytic genes and will be valuable for lignocellulosic biorefining.
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Affiliation(s)
- Xiujun Zhang
- National Glycoengineering Research Center, Shandong University, Qingdao, China.,State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China.,School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Yueyan Hu
- National Glycoengineering Research Center, Shandong University, Qingdao, China.,State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Guodong Liu
- National Glycoengineering Research Center, Shandong University, Qingdao, China.,State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Meng Liu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Zhonghai Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China.,State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Jian Zhao
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Xin Song
- National Glycoengineering Research Center, Shandong University, Qingdao, China.,State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yaohua Zhong
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yinbo Qu
- National Glycoengineering Research Center, Shandong University, Qingdao, China.,State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yuqi Qin
- National Glycoengineering Research Center, Shandong University, Qingdao, China.,State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
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24
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Gong P. Within and Beyond the Nucleotide Addition Cycle of Viral RNA-dependent RNA Polymerases. Front Mol Biosci 2022; 8:822218. [PMID: 35083282 PMCID: PMC8784604 DOI: 10.3389/fmolb.2021.822218] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/21/2021] [Indexed: 11/13/2022] Open
Abstract
Nucleotide addition cycle (NAC) is a fundamental process utilized by nucleic acid polymerases when carrying out nucleic acid biosynthesis. An induced-fit mechanism is usually taken by these polymerases upon NTP/dNTP substrate binding, leading to active site closure and formation of a phosphodiester bond. In viral RNA-dependent RNA polymerases, the post-chemistry translocation is stringently controlled by a structurally conserved motif, resulting in asymmetric movement of the template-product duplex. This perspective focuses on viral RdRP NAC and related mechanisms that have not been structurally clarified to date. Firstly, RdRP movement along the template strand in the absence of catalytic events may be relevant to catalytic complex dissociation or proofreading. Secondly, pyrophosphate or non-cognate NTP-mediated cleavage of the product strand 3′-nucleotide can also play a role in reactivating paused or arrested catalytic complexes. Furthermore, non-cognate NTP substrates, including NTP analog inhibitors, can not only alter NAC when being misincorporated, but also impact on subsequent NACs. Complications and challenges related to these topics are also discussed.
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Affiliation(s)
- Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, China
- *Correspondence: Peng Gong,
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25
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Ke F, Yu XD, Wang ZH, Gui JF, Zhang QY. Replication and transcription machinery for ranaviruses: components, correlation, and functional architecture. Cell Biosci 2022; 12:6. [PMID: 34991685 PMCID: PMC8734342 DOI: 10.1186/s13578-021-00742-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ranaviruses (family Iridoviridae) are promiscuous pathogens that can infect across species barriers in poikilotherms and can replicate in amphibian and fish cells and even in cultured mammalian cells. However, as nucleocytoplasmic large DNA viruses (NCLDVs), their replication and transcription mechanisms remain largely unknown. Here, we screened and uncovered the replication and transcription machinery of two ranaviruses, Andrias davidianus ranavirus (ADRV) and Rana grylio virus (RGV), by a combination of methods, including the isolation of proteins on nascent DNA, recombinant virus-based affinity, and NanoLuc complementation assay. RESULTS The ranavirus replication and transcription machinery was deeply dissected and identified as a complicated apparatus containing at least 30 viral and 6 host proteins. The viral proteins ADRV-47L/RGV-63R (DNA polymerase, vDPOL), ADRV-23L/RGV-91R (proliferating cell nuclear antigen, vPCNA), ADRV-85L/RGV-27R (single-stranded DNA binding protein, vSSB), ADRV-88L/RGV-24R (vhelicase/primase), etc., constitute the core replisome. Specifically, the core of the transcription complex, the viral RNA polymerase, contain the host RNAPII subunits Rpb3, Rpb6, and Rpb11, which was a first report in NCLDVs. Furthermore, correlations and interactions among these factors in the machinery were described. Significantly, the replisome core protein vDPOL (ADRV-47L) can interact with numerous viral and host proteins and could act as a linker and regulation center in viral DNA replication and transcription. Thus, these results depicted an architecture for ranavirus replication and transcription. CONCLUSIONS Up to 36 components from ranavirus and their host were found to form viral replisomes and transcription complexes using a series of precise methods, which further constructed an architecture for ranavirus replication and transcription in which vDPOL was a key central factor and various components correlated and cooperated. Therefore, it provides a cornerstone for further understanding the mechanisms of the replication and transcription of ranaviruses which can ensure the efficient production of progeny virus and adaptation to cross-species infection.
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Affiliation(s)
- Fei Ke
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Wuhan, 430072, China.,The Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xue-Dong Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zi-Hao Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Wuhan, 430072, China.,The Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi-Ya Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Wuhan, 430072, China. .,The Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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26
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Merkl PE, Schächner C, Pilsl M, Schwank K, Hergert K, Längst G, Milkereit P, Griesenbeck J, Tschochner H. Analysis of Yeast RNAP I Transcription of Nucleosomal Templates In Vitro. Methods Mol Biol 2022; 2533:39-59. [PMID: 35796981 PMCID: PMC9761914 DOI: 10.1007/978-1-0716-2501-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Nuclear eukaryotic RNA polymerases (RNAPs) transcribe a chromatin template in vivo. Since the basic unit of chromatin, the nucleosome, renders the DNA largely inaccessible, RNAPs have to overcome the nucleosomal barrier for efficient RNA synthesis. Gaining mechanistical insights in the transcription of chromatin templates will be essential to understand the complex process of eukaryotic gene expression. In this article we describe the use of defined in vitro transcription systems for comparative analysis of highly purified RNAPs I-III from S. cerevisiae (hereafter called yeast) transcribing in vitro reconstituted nucleosomal templates. We also provide a protocol to study promoter-dependent RNAP I transcription of purified native 35S ribosomal RNA (rRNA) gene chromatin.
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Affiliation(s)
- Philipp E Merkl
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
- TUM ForTe, Technische Universität München, Munich, Germany
| | - Christopher Schächner
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Michael Pilsl
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Katrin Schwank
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Kristin Hergert
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Gernot Längst
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Philipp Milkereit
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany.
| | - Joachim Griesenbeck
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany.
| | - Herbert Tschochner
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
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27
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Baptista B, Carapito R, Laroui N, Pichon C, Sousa F. mRNA, a Revolution in Biomedicine. Pharmaceutics 2021; 13:2090. [PMID: 34959371 PMCID: PMC8707022 DOI: 10.3390/pharmaceutics13122090] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 12/23/2022] Open
Abstract
The perspective of using messenger RNA (mRNA) as a therapeutic molecule first faced some uncertainties due to concerns about its instability and the feasibility of large-scale production. Today, given technological advances and deeper biomolecular knowledge, these issues have started to be addressed and some strategies are being exploited to overcome the limitations. Thus, the potential of mRNA has become increasingly recognized for the development of new innovative therapeutics, envisioning its application in immunotherapy, regenerative medicine, vaccination, and gene editing. Nonetheless, to fully potentiate mRNA therapeutic application, its efficient production, stabilization and delivery into the target cells are required. In recent years, intensive research has been carried out in this field in order to bring new and effective solutions towards the stabilization and delivery of mRNA. Presently, the therapeutic potential of mRNA is undoubtedly recognized, which was greatly reinforced by the results achieved in the battle against the COVID-19 pandemic, but there are still some issues that need to be improved, which are critically discussed in this review.
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Affiliation(s)
- Bruno Baptista
- CICS-UBI—Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (B.B.); (R.C.)
| | - Rita Carapito
- CICS-UBI—Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (B.B.); (R.C.)
| | - Nabila Laroui
- Centre de Biophysique Moléculaire (CBM), UPR 4301 CNRS, University of Orléans, 45071 Orléans, France;
| | - Chantal Pichon
- Centre de Biophysique Moléculaire (CBM), UPR 4301 CNRS, University of Orléans, 45071 Orléans, France;
| | - Fani Sousa
- CICS-UBI—Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (B.B.); (R.C.)
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28
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Dixit G, Prabhu A. The pleiotropic peroxisome proliferator activated receptors: Regulation and therapeutics. Exp Mol Pathol 2021; 124:104723. [PMID: 34822814 DOI: 10.1016/j.yexmp.2021.104723] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/02/2021] [Accepted: 11/15/2021] [Indexed: 02/07/2023]
Abstract
The Peroxisome proliferator-activated receptors (PPARs) are key regulators of metabolic events in our body. Owing to their implication in maintenance of homeostasis, both PPAR agonists and antagonists assume therapeutic significance. Understanding the molecular mechanisms of each of the PPAR isotypes in the healthy body and during disease is crucial to exploiting their full therapeutic potential. This article is an attempt to present a rational analysis of the multifaceted therapeutic effects and underlying mechanisms of isotype-specific PPAR agonists, dual PPAR agonists, pan PPAR agonists as well as PPAR antagonists. A holistic understanding of the mechanistic dimensions of these key metabolic regulators will guide future efforts to identify novel molecules in the realm of metabolic, inflammatory and immunotherapeutic diseases.
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Affiliation(s)
- Gargi Dixit
- Department of Pharmaceutical Chemistry & Quality Assurance, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai, India
| | - Arati Prabhu
- Department of Pharmaceutical Chemistry & Quality Assurance, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai, India.
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29
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Abstract
Chloroplasts, the sites of photosynthesis and sources of reducing power, are at the core of the success story that sets apart autotrophic plants from most other living organisms. Along with their fellow organelles (e.g., amylo-, chromo-, etio-, and leucoplasts), they form a group of intracellular biosynthetic machines collectively known as plastids. These plant cell constituents have their own genome (plastome), their own (70S) ribosomes, and complete enzymatic equipment covering the full range from DNA replication via transcription and RNA processive modification to translation. Plastid RNA synthesis (gene transcription) involves the collaborative activity of two distinct types of RNA polymerases that differ in their phylogenetic origin as well as their architecture and mode of function. The existence of multiple plastid RNA polymerases is reflected by distinctive sets of regulatory DNA elements and protein factors. This complexity of the plastid transcription apparatus thus provides ample room for regulatory effects at many levels within and beyond transcription. Research in this field offers insight into the various ways in which plastid genes, both singly and groupwise, can be regulated according to the needs of the entire cell. Furthermore, it opens up strategies that allow to alter these processes in order to optimize the expression of desired gene products.
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Affiliation(s)
- Jennifer Ortelt
- Department of Biology and Biotechnology, University of Bochum, Bochum, Germany
| | - Gerhard Link
- Department of Biology and Biotechnology, University of Bochum, Bochum, Germany.
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30
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de Vries L, Guevara-Rozo S, Cho M, Liu LY, Renneckar S, Mansfield SD. Tailoring renewable materials via plant biotechnology. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:167. [PMID: 34353358 PMCID: PMC8344217 DOI: 10.1186/s13068-021-02010-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/06/2021] [Indexed: 05/03/2023]
Abstract
Plants inherently display a rich diversity in cell wall chemistry, as they synthesize an array of polysaccharides along with lignin, a polyphenolic that can vary dramatically in subunit composition and interunit linkage complexity. These same cell wall chemical constituents play essential roles in our society, having been isolated by a variety of evolving industrial processes and employed in the production of an array of commodity products to which humans are reliant. However, these polymers are inherently synthesized and intricately packaged into complex structures that facilitate plant survival and adaptation to local biogeoclimatic regions and stresses, not for ease of deconstruction and commercial product development. Herein, we describe evolving techniques and strategies for altering the metabolic pathways related to plant cell wall biosynthesis, and highlight the resulting impact on chemistry, architecture, and polymer interactions. Furthermore, this review illustrates how these unique targeted cell wall modifications could significantly extend the number, diversity, and value of products generated in existing and emerging biorefineries. These modifications can further target the ability for processing of engineered wood into advanced high performance materials. In doing so, we attempt to illuminate the complex connection on how polymer chemistry and structure can be tailored to advance renewable material applications, using all the chemical constituents of plant-derived biopolymers, including pectins, hemicelluloses, cellulose, and lignins.
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Affiliation(s)
- Lisanne de Vries
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- US Department of Energy (DOE) Great Lakes Bioenergy Research Center, the Wisconsin Energy Institute, University of Wisconsin - Madison, Madison, WI , 53726, USA
| | - Sydne Guevara-Rozo
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - MiJung Cho
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Li-Yang Liu
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Scott Renneckar
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Shawn D Mansfield
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- US Department of Energy (DOE) Great Lakes Bioenergy Research Center, the Wisconsin Energy Institute, University of Wisconsin - Madison, Madison, WI , 53726, USA.
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31
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Gong P. Structural basis of viral RNA-dependent RNA polymerase nucleotide addition cycle in picornaviruses. Enzymes 2021; 49:215-233. [PMID: 34696833 DOI: 10.1016/bs.enz.2021.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
RNA-dependent RNA polymerases (RdRPs) encoded by RNA viruses represent a unique class of processive nucleic acid polymerases, carrying out DNA-independent replication/transcription processes. Although viral RdRPs have versatile global structures, they do share a structurally highly conserved active site comprising catalytic motifs A-G. In spite of different initiation modes, the nucleotide addition cycle (NAC) in the RdRP elongation phase probably follows consistent mechanisms. In this chapter, representative structures of picornavirus RdRP elongation complexes are used to illustrate RdRP NAC mechanisms. In the pre-chemistry part of the NAC, RdRPs utilize a unique palm domain-based active site closure that can be further decomposed into two sequential steps. In the post-chemistry part of the NAC, the translocation process is stringently controlled by the RdRP-specific motif G, resulting in asymmetric movements of the template-product RNA. Future efforts to elucidate regulation/intervention mechanisms by mismatched NTPs or nucleotide analog antivirals are necessary to achieve comprehensive understandings of viral RdRP NAC.
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Affiliation(s)
- Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China; Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, China.
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32
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The transrepression and transactivation roles of CtBPs in the pathogenesis of different diseases. J Mol Med (Berl) 2021; 99:1335-1347. [PMID: 34196767 DOI: 10.1007/s00109-021-02107-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/31/2021] [Accepted: 06/25/2021] [Indexed: 02/06/2023]
Abstract
Gene transcription is strictly controlled by transcriptional complexes, which are assemblies of transcription factors, transcriptional regulators, and co-regulators. Mammalian genomes encode two C-terminal-binding proteins (CtBPs), CtBP1 and CtBP2, which are both well-known transcriptional corepressors of oncogenic processes. Their overexpression in tumors is associated with malignant behavior, such as uncontrolled cell proliferation, migration, and invasion, as well as with an increase in the epithelial-mesenchymal transition. CtBPs coordinate with other transcriptional regulators, such as histone deacetylases (HDACs) and histone acetyltransferases (p300 and CBP [CREBP-binding protein]) that contain the PXDLS motif, and with transcription factors to assemble transcriptional complexes that dock onto the promoters of genes to initiate gene transcription. Emerging evidence suggests that CtBPs function as both corepressors and coactivators in different biological processes ranging from apoptosis to inflammation and osteogenesis. Therapeutic targeting of CtBPs or the interactions required to form transcriptional complexes has also shown promising effects in preventing disease progression. This review summarizes the most recent progress in the study of CtBP functions and therapeutic inhibitors in different biological processes. This knowledge may enable a better understanding of the complexity of the roles of CtBPs, while providing new insights into therapeutic strategies that target CtBPs.
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33
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Schnell AP, Kohrt S, Thoma-Kress AK. Latency Reversing Agents: Kick and Kill of HTLV-1? Int J Mol Sci 2021; 22:ijms22115545. [PMID: 34073995 PMCID: PMC8197370 DOI: 10.3390/ijms22115545] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 12/14/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1), the cause of adult T-cell leukemia/lymphoma (ATLL), is a retrovirus, which integrates into the host genome and persistently infects CD4+ T-cells. Virus propagation is stimulated by (1) clonal expansion of infected cells and (2) de novo infection. Viral gene expression is induced by the transactivator protein Tax, which recruits host factors like positive transcription elongation factor b (P-TEFb) to the viral promoter. Since HTLV-1 gene expression is repressed in vivo by viral, cellular, and epigenetic mechanisms in late phases of infection, HTLV-1 avoids an efficient CD8+ cytotoxic T-cell (CTL) response directed against the immunodominant viral Tax antigen. Hence, therapeutic strategies using latency reversing agents (LRAs) sought to transiently activate viral gene expression and antigen presentation of Tax to enhance CTL responses towards HTLV-1, and thus, to expose the latent HTLV-1 reservoir to immune destruction. Here, we review strategies that aimed at enhancing Tax expression and Tax-specific CTL responses to interfere with HTLV-1 latency. Further, we provide an overview of LRAs including (1) histone deacetylase inhibitors (HDACi) and (2) activators of P-TEFb, that have mainly been studied in context of human immunodeficiency virus (HIV), but which may also be powerful in the context of HTLV-1.
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34
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Structural Insights into the Respiratory Syncytial Virus RNA Synthesis Complexes. Viruses 2021; 13:v13050834. [PMID: 34063087 PMCID: PMC8147935 DOI: 10.3390/v13050834] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/30/2021] [Accepted: 05/02/2021] [Indexed: 12/13/2022] Open
Abstract
RNA synthesis in respiratory syncytial virus (RSV), a negative-sense (-) nonsegmented RNA virus, consists of viral gene transcription and genome replication. Gene transcription includes the positive-sense (+) viral mRNA synthesis, 5'-RNA capping and methylation, and 3' end polyadenylation. Genome replication includes (+) RNA antigenome and (-) RNA genome synthesis. RSV executes the viral RNA synthesis using an RNA synthesis ribonucleoprotein (RNP) complex, comprising four proteins, the nucleoprotein (N), the large protein (L), the phosphoprotein (P), and the M2-1 protein. We provide an overview of the RSV RNA synthesis and the structural insights into the RSV gene transcription and genome replication process. We propose a model of how the essential four proteins coordinate their activities in different RNA synthesis processes.
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Selinski J, Scheibe R. Central Metabolism in Mammals and Plants as a Hub for Controlling Cell Fate. Antioxid Redox Signal 2021; 34:1025-1047. [PMID: 32620064 PMCID: PMC8060724 DOI: 10.1089/ars.2020.8121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/15/2020] [Accepted: 06/23/2020] [Indexed: 02/06/2023]
Abstract
Significance: The importance of oxidoreductases in energy metabolism together with the occurrence of enzymes of central metabolism in the nucleus gave rise to the active research field aiming to understand moonlighting enzymes that undergo post-translational modifications (PTMs) before carrying out new tasks. Recent Advances: Cytosolic enzymes were shown to induce gene transcription after PTM and concomitant translocation to the nucleus. Changed properties of the oxidized forms of cytosolic glyceraldehyde 3-phosphate dehydrogenase, and also malate dehydrogenases and others, are the basis for a hypothesis suggesting moonlighting functions that directly link energy metabolism to adaptive responses required for maintenance of redox-homeostasis in all eukaryotes. Critical Issues: Small molecules, such as metabolic intermediates, coenzymes, or reduced glutathione, were shown to fine-tune the redox switches, interlinking redox state, metabolism, and induction of new functions via nuclear gene expression. The cytosol with its metabolic enzymes connecting energy fluxes between the various cell compartments can be seen as a hub for redox signaling, integrating the different signals for graded and directed responses in stressful situations. Future Directions: Enzymes of central metabolism were shown to interact with p53 or the assumed plant homologue suppressor of gamma response 1 (SOG1), an NAM, ATAF, and CUC transcription factor involved in the stress response upon ultraviolet exposure. Metabolic enzymes serve as sensors for imbalances, their inhibition leading to changed energy metabolism, and the adoption of transcriptional coactivator activities. Depending on the intensity of the impact, rerouting of energy metabolism, proliferation, DNA repair, cell cycle arrest, immune responses, or cell death will be induced. Antioxid. Redox Signal. 34, 1025-1047.
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Affiliation(s)
- Jennifer Selinski
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Renate Scheibe
- Department of Plant Physiology, Faculty of Biology/Chemistry, Osnabrueck University, Osnabrueck, Germany
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Zhang J, Yue W, Zhou Y, Liao M, Chen X, Hua J. Super enhancers-Functional cores under the 3D genome. Cell Prolif 2021; 54:e12970. [PMID: 33336467 PMCID: PMC7848964 DOI: 10.1111/cpr.12970] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/28/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022] Open
Abstract
Complex biochemical reactions take place in the nucleus all the time. Transcription machines must follow the rules. The chromatin state, especially the three-dimensional structure of the genome, plays an important role in gene regulation and expression. The super enhancers are important for defining cell identity in mammalian developmental processes and human diseases. It has been shown that the major components of transcriptional activation complexes are recruited by super enhancer to form phase-separated condensates. We summarize the current knowledge about super enhancer in the 3D genome. Furthermore, a new related transcriptional regulation model from super enhancer is outlined to explain its role in the mammalian cell progress.
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Affiliation(s)
- Juqing Zhang
- College of Veterinary MedicineShaanxi Centre of Stem Cells Engineering & TechnologyNorthwest A&F UniversityYanglingChina
| | - Wei Yue
- College of Veterinary MedicineShaanxi Centre of Stem Cells Engineering & TechnologyNorthwest A&F UniversityYanglingChina
| | - Yaqi Zhou
- College of Life ScienceNorthwest A&F UniversityYanglingChina
| | - Mingzhi Liao
- College of Life ScienceNorthwest A&F UniversityYanglingChina
| | - Xingqi Chen
- Department of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| | - Jinlian Hua
- College of Veterinary MedicineShaanxi Centre of Stem Cells Engineering & TechnologyNorthwest A&F UniversityYanglingChina
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Imashimizu M, Tanaka M, Hoshina H. Gre factors prevent thermal and mechanical stresses induced by terahertz irradiation during transcription. Genes Cells 2020; 26:56-64. [PMID: 33247986 DOI: 10.1111/gtc.12822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/18/2020] [Accepted: 11/21/2020] [Indexed: 11/29/2022]
Abstract
During transcription in cells, the transcription complex consisting of RNA polymerase, DNA and nascent RNA is exposed to fluctuating temperature and pressure. However, little is known about the mechanism of transcriptional homeostasis under fluctuating physical parameters. In this study, we generated these fluctuating parameters using pulsed local heating and acoustic waves in the reaction system of transcription by Escherichia coli RNA polymerase, using a terahertz free-electron laser. We demonstrated that transcription processes, including abortive initiation and elongation pausing, and the fidelity of elongation are significantly affected by the laser-based local perturbations. We also found that all these functional alternations in the transcription process are almost completely mitigated by the presence of Gre proteins. It is well known that Gre proteins enhance RNA cleavage of polymerase by binding to the pore structure termed secondary channel. Recently, the chaperone activities have also been proposed for Gre proteins, yet the details directly associated with transcription are largely unknown. Our finding indicates that Gre proteins are necessary for maintaining transcriptional homeostasis under thermal and mechanical stresses.
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Affiliation(s)
- Masahiko Imashimizu
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Masahito Tanaka
- Research Institute for Measurement and Analytical Instrumentation, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Hiromichi Hoshina
- Terahertz Sensing and Imaging Team, Center for Advanced Photonics, RIKEN, Sendai, Miyagi, Japan
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Chen L, Bellone RR, Wang Y, Singer-Berk M, Sugasawa K, Ford JM, Artandi SE. A novel DDB2 mutation causes defective recognition of UV-induced DNA damages and prevalent equine squamous cell carcinoma. DNA Repair (Amst) 2020; 97:103022. [PMID: 33276309 DOI: 10.1016/j.dnarep.2020.103022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/22/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023]
Abstract
Squamous cell carcinoma (SCC) occurs frequently in the human Xeroderma Pigmentosum (XP) syndrome and is characterized by deficient UV-damage repair. SCC is the most common equine ocular cancer and the only associated genetic risk factor is a UV-damage repair protein. Specifically, a missense mutation in horse DDB2 (T338M) was strongly associated with both limbal SCC and third eyelid SCC in three breeds of horses (Halflinger, Belgian, and Rocky Mountain Horses) and was hypothesized to impair binding to UV-damaged DNA. Here, we investigate DDB2-T338M mutant's capacity to recognize UV lesions in vitro and in vivo, together with human XP mutants DDB2-R273H and -K244E. We show that the recombinant DDB2-T338M assembles with DDB1, but fails to show any detectable binding to DNA substrates with or without UV lesions, due to a potential structural disruption of the rigid DNA recognition β-loop. Consistently, we demonstrate that the cellular DDB2-T338M is defective in its recruitment to focally radiated DNA damages, and in its access to chromatin. Thus, we provide direct functional evidence indicating the DDB2-T338M recapitulates molecular defects of human XP mutants, and is the causal loss-of-function allele that gives rise to equine ocular SCCs. Our findings shed new light on the mechanism of DNA recognition by UV-DDB and on the initiation of ocular malignancy.
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Affiliation(s)
- Lu Chen
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Rebecca R Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA; Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA
| | - Yan Wang
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Moriel Singer-Berk
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA; Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA
| | - Kaoru Sugasawa
- Biosignal Research Center, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - James M Ford
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Steven E Artandi
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
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Signaling Mechanism of Transcriptional Bursting: A Technical Resolution-Independent Study. BIOLOGY 2020; 9:biology9100339. [PMID: 33086528 PMCID: PMC7603168 DOI: 10.3390/biology9100339] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 01/22/2023]
Abstract
Simple Summary Following changing cellular signals, various genes adjust their activities and initiate transcripts with the right rates. The precision of such a transcriptional response has a fundamental role in the survival and development of lives. Quite unexpectedly, gene transcription has been uncovered to occur in sporadic bursts, rather than in a continuous manner. This has raised a provoking issue of how the bursting transmits regulatory signals, and it remains controversial whether the burst size, frequency, or both, take the role of signal transmission. Here, this study showed that only the burst frequency was subject to modulation by activators that carry the regulatory signals. A higher activator concentration led to a larger frequency, whereas the size remains unchanged. When very high, the burst cluster emerged, which may be mistaken as a large burst. This work thus supports the conclusion that transcription regulation is in a “digital” way. Abstract Gene transcription has been uncovered to occur in sporadic bursts. However, due to technical difficulties in differentiating individual transcription initiation events, it remains debated as to whether the burst size, frequency, or both are subject to modulation by transcriptional activators. Here, to bypass technical constraints, we addressed this issue by introducing two independent theoretical methods including analytical research based on the classic two-model and information entropy research based on the architecture of transcription apparatus. Both methods connect the signaling mechanism of transcriptional bursting to the characteristics of transcriptional uncertainty (i.e., the differences in transcriptional levels of the same genes that are equally activated). By comparing the theoretical predictions with abundant experimental data collected from published papers, the results exclusively support frequency modulation. To further validate this conclusion, we showed that the data that appeared to support size modulation essentially supported frequency modulation taking into account the existence of burst clusters. This work provides a unified scheme that reconciles the debate on burst signaling.
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Liu X, Xie D, Hua Y, Zeng P, Ma L, Zeng F. Npa3 interacts with Gpn3 and assembly factor Rba50 for RNA polymerase II biogenesis. FASEB J 2020; 34:15547-15558. [PMID: 32985767 DOI: 10.1096/fj.202001523r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/01/2020] [Accepted: 09/15/2020] [Indexed: 12/12/2022]
Abstract
RNA polymerase II is one of the most vital macromolecular complexes in eukaryotes and the assembly of such complete enzyme requires many factors. Three members of GPN-loop GTPase family Npa3/Gpn1, Gpn2, and Gpn3 participate in the biogenesis of RNA polymerase II with nonredundant roles. We show here that rapid degradation of each GPN protein in yeast leads to cytoplasmic accumulation of Rpb1 and defects in the assembly of RNA polymerase II, suggesting conserved functions of GPN paralogs for RNA polymerase II biogenesis as in humans. Taking advantage of a multicopy genetic screening, we identified GPN3 and assembly factor RBA50 among others as strong suppressors of npa3ts mutants. We further demonstrated that Npa3 interacts with Gpn3 and Rba50, similarly human Gpn1 physically interacts with Gpn3 and RPAP1 (human analog of Rba50). Moreover, a mutual dependency of protein levels of Npa3 and Gpn3 was also clearly presented in yeast using an auxin-inducible degron (AID) system. Interestingly, Rpb2, the second largest subunit of RNA polymerase II was determined to be the subunit that interacts with both Gpn1 and Rba50, indicating a close association of Npa3 and Rba50 in Rpb2 subcomplex assembly. Based on these results, we conclude that Npa3 interacts with Gpn3 and Rba50, for RNA polymerase II biogenesis. We therefore propose that multiple factors may coordinate through conserved regulatory mechanisms in the assembly of RNA polymerase complex.
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Affiliation(s)
- Xueqin Liu
- College of Life Sciences, Hebei Agricultural University, Baoding, China.,State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
| | - Debao Xie
- College of Life Sciences, Hebei Agricultural University, Baoding, China.,State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
| | - Yu Hua
- Peking-Tsinghua Center for Life Sciences, The National Laboratory of Protein and Plant Gene Research, The College of Life Sciences, Peking University, Beijing, China
| | - Pei Zeng
- College of Life Sciences, Hebei Agricultural University, Baoding, China.,State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
| | - Lujie Ma
- College of Life Sciences, Hebei Agricultural University, Baoding, China.,State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
| | - Fanli Zeng
- College of Life Sciences, Hebei Agricultural University, Baoding, China.,State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China.,Peking-Tsinghua Center for Life Sciences, The National Laboratory of Protein and Plant Gene Research, The College of Life Sciences, Peking University, Beijing, China
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RNA polymerase II subunit D is essential for zebrafish development. Sci Rep 2020; 10:13213. [PMID: 32764610 PMCID: PMC7413394 DOI: 10.1038/s41598-020-70110-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/20/2020] [Indexed: 11/09/2022] Open
Abstract
DNA-directed RNA polymerase II (pol II) is composed of ten core and two dissociable subunits. The dissociable subcomplex is a heterodimer of Rpb4/Polr2d and Rpb7/Polr2g, which are encoded by RPB4/polr2d and RPB7/polr2g genes, respectively. Functional studies of Rpb4/Polr2d in yeast have revealed that Rpb4 plays a role primarily in pol II-mediated RNA synthesis and partly in various mRNA regulations including pre-mRNA splicing, nuclear export of mRNAs and decay of mRNAs. Although Rpb4 is evolutionally highly conserved from yeast to human, it is dispensable for survival in budding yeast S. cerevisiae, whereas it was indispensable for survival in fission yeast S. pombe, slime molds and fruit fly. To elucidate whether Rpb4/Polr2d is necessary for development and survival of vertebrate animals, we generated polr2d-deficient zebrafish. The polr2d mutant embryos exhibited progressive delay of somitogenesis at the onset of 11 h postfertilization (hpf). Mutant embryos then showed increased cell death at 15 hpf, displayed hypoplasia such as small eye and cardiac edema by 48 hpf and prematurely died by 60 hpf. In accordance with these developmental defects, our RT-qPCR revealed that expression of housekeeping and zygotic genes was diminished in mutants. Collectively, we conclude that Rpb4/Polr2d is indispensable for vertebrate development.
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Summanwar A, Basu U, Rahman H, Kav NNV. Non-coding RNAs as emerging targets for crop improvement. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 297:110521. [PMID: 32563460 DOI: 10.1016/j.plantsci.2020.110521] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 04/30/2020] [Accepted: 05/03/2020] [Indexed: 05/23/2023]
Abstract
Food security is affected by climate change, population growth, as well as abiotic and biotic stresses. Conventional and molecular marker assisted breeding and genetic engineering techniques have been employed extensively for improving resistance to biotic stress in crop plants. Advances in next-generation sequencing technologies have permitted the exploration and identification of parts of the genome that extend beyond the regions with protein coding potential. These non-coding regions of the genome are transcribed to generate many types of non-coding RNAs (ncRNAs). These ncRNAs are involved in the regulation of growth, development, and response to stresses at transcriptional and translational levels. ncRNAs, including long ncRNAs (lncRNAs), small RNAs and circular RNAs have been recognized as important regulators of gene expression in plants and have been suggested to play important roles in plant immunity and adaptation to abiotic and biotic stresses. In this article, we have reviewed the current state of knowledge with respect to lncRNAs and their mechanism(s) of action as well as their regulatory functions, specifically within the context of biotic stresses. Additionally, we have provided insights into how our increased knowledge about lncRNAs may be used to improve crop tolerance to these devastating biotic stresses.
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Affiliation(s)
- Aarohi Summanwar
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada
| | - Urmila Basu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada
| | - Habibur Rahman
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada.
| | - Nat N V Kav
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada.
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Abstract
Chromatin is a highly dynamic structure that closely relates with gene expression in eukaryotes. ATP-dependent chromatin remodelling, histone post-translational modification and DNA methylation are the main ways that mediate such plasticity. The histone variant H2A.Z is frequently encountered in eukaryotes, and can be deposited or removed from nucleosomes by chromatin remodelling complex SWR1 or INO80, respectively, leading to altered chromatin state. H2A.Z has been found to be involved in a diverse range of biological processes, including genome stability, DNA repair and transcriptional regulation. Due to their formidable production of secondary metabolites, filamentous fungi play outstanding roles in pharmaceutical production, food safety and agriculture. During the last few years, chromatin structural changes were proven to be a key factor associated with secondary metabolism in fungi. However, studies on the function of H2A.Z are scarce. Here, we summarize current knowledge of H2A.Z functions with a focus on filamentous fungi. We propose that H2A.Z is a potential target involved in the regulation of secondary metabolite biosynthesis by fungi.
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Peil K, Jürgens H, Luige J, Kristjuhan K, Kristjuhan A. Taf14 is required for the stabilization of transcription pre-initiation complex in Saccharomyces cerevisiae. Epigenetics Chromatin 2020; 13:24. [PMID: 32460824 PMCID: PMC7254723 DOI: 10.1186/s13072-020-00347-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/21/2020] [Indexed: 12/19/2022] Open
Abstract
Background The YEATS domain is a highly conserved protein structure that interacts with acetylated and crotonylated lysine residues in N-terminal tails of histones. The budding yeast genome encodes three YEATS domain proteins (Taf14, Yaf9, and Sas5) that are all the subunits of different complexes involved in histone acetylation, gene transcription, and chromatin remodeling. As the strains deficient in all these three genes are inviable, it has been proposed that the YEATS domain is essential in yeast. In this study we investigate in more detail the requirement of YEATS domain proteins for yeast survival and the possible roles of Taf14 YEATS domain in the regulation of gene transcription. Results We found that YEATS domains are not essential for the survival of Saccharomyces cerevisiae cells. Although the full deletion of all YEATS proteins is lethal in yeast, we show that the viability of cells can be restored by the expression of the YEATS-less version of Taf14 protein. We also explore the in vivo functions of Taf14 protein and show that the primary role of its YEATS domain is to stabilize the transcription pre-initiation complex (PIC). Our results indicate that Taf14-mediated interactions become crucial for PIC formation in rpb9Δ cells, where the recruitment of TFIIF to the PIC is hampered. Although H3 K9 residue has been identified as the interaction site of the Taf14 YEATS domain in vitro, we found that it is not the only interaction target in vivo. Conclusions Lethality of YEATS-deficient cells can be rescued by the expression of truncated Taf14 protein lacking the entire YEATS domain, indicating that the YEATS domains are not required for cell survival. The YEATS domain of Taf14 participates in PIC stabilization and acetylated/crotonylated H3K9 is not the critical target of the Taf14 YEATS domain in vivo.
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Affiliation(s)
- Kadri Peil
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia
| | - Henel Jürgens
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia
| | - Johanna Luige
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia.,Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Kersti Kristjuhan
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia
| | - Arnold Kristjuhan
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia.
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Molecular determinants underlying functional innovations of TBP and their impact on transcription initiation. Nat Commun 2020; 11:2384. [PMID: 32404905 PMCID: PMC7221094 DOI: 10.1038/s41467-020-16182-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/13/2020] [Indexed: 02/07/2023] Open
Abstract
TATA-box binding protein (TBP) is required for every single transcription event in archaea and eukaryotes. It binds DNA and harbors two repeats with an internal structural symmetry that show sequence asymmetry. At various times in evolution, TBP has acquired multiple interaction partners and different organisms have evolved TBP paralogs with additional protein regions. Together, these observations raise questions of what molecular determinants (i.e. key residues) led to the ability of TBP to acquire new interactions, resulting in an increasingly complex transcriptional system in eukaryotes. We present a comprehensive study of the evolutionary history of TBP and its interaction partners across all domains of life, including viruses. Our analysis reveals the molecular determinants and suggests a unified and multi-stage evolutionary model for the functional innovations of TBP. These findings highlight how concerted chemical changes on a conserved structural scaffold allow for the emergence of complexity in a fundamental biological process. The TATA-box binding protein (TBP) is required for transcription initiation in archaea and eukaryotes. Here the authors delineate how TBP’s function has evolved new functional features through context-dependent interactions with various protein partners.
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Song C, Peng Z, Lin X, Luo H, Song M, Jin L, Xiao X, Ji H. Study on Interaction Between TATA-Box Binding Protein (TBP), TATA-Box and Multiprotein Bridging Factor 1(MBF1) in Beauveria bassiana by Graphene-Based Electrochemical Biosensors. Front Chem 2020; 8:278. [PMID: 32351940 PMCID: PMC7174728 DOI: 10.3389/fchem.2020.00278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/23/2020] [Indexed: 11/13/2022] Open
Abstract
The regulation of transcription level is an important step in gene expression process. Beauveria bassiana is a broad-spectrum insecticidal fungi widely used in the biologic control of arthropod. The regulation of its transcription level is a multilevel complex process. Multiprotein bridging factor 1(MBF1) is a transcriptional co-activator that bridges sequence-specific activators and the TATA-box binding protein(TBP), Little is known about the interaction between MBF1, TBP, and TBP binding to DNA(TATA-sequences)in filamentous fungi of Beauveria bassiana, The binding of TBP to TATA-box and TBP to MBF1 was investigated via electrochemical biosensor. Graphene oxide has an electronic mobility that is unattainable for any metal, so it will be highly sensitive as a test electrode. Hence, we developed a simple, sensitive and specific sensor based on an TBP probe and graphene oxide that successfully detected the interaction of TBP and TATA-box or MBF1. From the electrochemical impedance spectroscopy (EIS), we find that the radius will increase when adding TATA-box or MBF1 buffer to the modified TBP protein electrode. When adding no TATA-box or no MBF1, the radius is relatively unchanged. The interaction between TBP and TATA-box or MBF1 was proved based on the results. These data confirmed the specificity of the interactions, (1) our developed graphene-based electrochemical biosensor can be used for monitoring the interaction between TBP and TATA-box or MBF1, (2) TBP can bind to TATA-box, (3) TBP can bind to MBF1, and (4) TBP mediates the interactions of MBF1 to DNA. Therefore, this work provided a label-free, low-cost and simple detection method for the complex process of eukaryotic gene transcription regulation.
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Affiliation(s)
- Chi Song
- Department of Life Science and Technology, Changshu Institute of Technology, Changshu, China
| | - Zhijia Peng
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing, China
| | - Xiaogang Lin
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing, China
| | - Haoyue Luo
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing, China
| | - Min Song
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing, China
| | - Lifeng Jin
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing, China
| | - Xiangyue Xiao
- Department of Life Science and Technology, Changshu Institute of Technology, Changshu, China
| | - Hong Ji
- Department of Life Science and Technology, Changshu Institute of Technology, Changshu, China
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The Important Function of Mediator Complex in Controlling the Developmental Transitions in Plants. Int J Mol Sci 2020; 21:ijms21082733. [PMID: 32326439 PMCID: PMC7215822 DOI: 10.3390/ijms21082733] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/09/2020] [Accepted: 04/11/2020] [Indexed: 12/24/2022] Open
Abstract
Developmental transitions in plants are tightly associated with changes in the transcriptional regulation of gene expression. One of the most important regulations is conferred by cofactors of RNA polymerase II including the mediator complex, a large complex with a modular organization. The mediator complex recruits transcription factors to bind to the specific sites of genes including protein-coding genes and non-coding RNA genes to promote or repress the transcription initiation and elongation using a protein-protein interaction module. Mediator complex subunits have been isolated and identified in plants and the function of most mediator subunits in whole life cycle plants have been revealed. Studies have shown that the Mediator complex is indispensable for the regulation of plant developmental transitions by recruiting age-, flowering-, or hormone-related transcription factors. Here, we first overviewed the Mediator subunits in plants, and then we summarized the specific Mediator subunits involved in developmental transitions, including vegetative phase change and floral transition. Finally, we proposed the future directions to further explore their roles in plants. The link between Mediator subunits and developmental transitions implies the necessity to explore targets of this complex as a potential application in developing high quality crop varieties.
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P-TEFb as A Promising Therapeutic Target. Molecules 2020; 25:molecules25040838. [PMID: 32075058 PMCID: PMC7070488 DOI: 10.3390/molecules25040838] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 01/19/2023] Open
Abstract
The positive transcription elongation factor b (P-TEFb) was first identified as a general factor that stimulates transcription elongation by RNA polymerase II (RNAPII), but soon afterwards it turned out to be an essential cellular co-factor of human immunodeficiency virus (HIV) transcription mediated by viral Tat proteins. Studies on the mechanisms of Tat-dependent HIV transcription have led to radical advances in our knowledge regarding the mechanism of eukaryotic transcription, including the discoveries that P-TEFb-mediated elongation control of cellular transcription is a main regulatory step of gene expression in eukaryotes, and deregulation of P-TEFb activity plays critical roles in many human diseases and conditions in addition to HIV/AIDS. P-TEFb is now recognized as an attractive and promising therapeutic target for inflammation/autoimmune diseases, cardiac hypertrophy, cancer, infectious diseases, etc. In this review article, I will summarize our knowledge about basic P-TEFb functions, the regulatory mechanism of P-TEFb-dependent transcription, P-TEFb’s involvement in biological processes and diseases, and current approaches to manipulating P-TEFb functions for the treatment of these diseases.
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Li K, Zhao B, Wei D, Wang W, Cui Y, Qian L, Liu G. miR‑146a improves hepatic lipid and glucose metabolism by targeting MED1. Int J Mol Med 2019; 45:543-555. [PMID: 31894315 PMCID: PMC6984781 DOI: 10.3892/ijmm.2019.4443] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/19/2019] [Indexed: 12/12/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is one of the most common chronic liver diseases worldwide. Increasing evidence has shown that microRNAs (miRNAs) play a vital role in the progression of NAFLD. The aim of the present study was to examine the expression level and roles of miR-146a in fatty liver of high-fat diet (HFD) and ob/ob mice and fatty acid-treated hepatic cells using RT-qPCR and western blot analysis. The results showed that the expression of miR-146a was significantly decreased in the livers of high-fat diet (HFD) and ob/ob mice and free fatty acid-stimulated cells by RT-qPCR. Overexpression of hepatic miR-146a improved glucose and insulin tolerance as well as lipid accumulation in the liver by promoting the oxidative metabolism of fatty acids. In addition, the overexpression of miR-146a increased the amount of mitochondria and promoted mitochondrial respiration in hepatocytes. Similarly, inhibition of miR-146a expression levels significantly reduced mitochondrial numbers in AML12 cells as well as the expression of mitochondrial respiration related genes. Additionally, MED1 was a direct target of miR-146a and restoring MED1 abolished the metabolic effects of miR-146a on lipid metabolism and mitochondrial function. Therefore, results of the present study identified a novel function of miR-146a in glucose and lipid metabolism in targeting MED1, suggesting that miR-146a serves as a potential therapeutic target for metabolic syndrome disease.
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Affiliation(s)
- Kun Li
- Department of Biomedical and Health Science, School of Life and Health Science, Anhui Science and Technology University, Fengyang, Anhui 233100, P.R. China
| | - Bao Zhao
- Department of Otorhinolaryngology Head and Neck Surgery, First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Diandian Wei
- Department of Biomedical and Health Science, School of Life and Health Science, Anhui Science and Technology University, Fengyang, Anhui 233100, P.R. China
| | - Wenrui Wang
- Department of Biotechnology, School of Life Science and Technology, Bengbu Medical College, Bengbu, Anhui 233030, P.R. China
| | - Yixuan Cui
- Department of Otorhinolaryngology Head and Neck Surgery, First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Lisheng Qian
- Department of Biomedical and Health Science, School of Life and Health Science, Anhui Science and Technology University, Fengyang, Anhui 233100, P.R. China
| | - Guodong Liu
- Department of Biomedical and Health Science, School of Life and Health Science, Anhui Science and Technology University, Fengyang, Anhui 233100, P.R. China
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Babbitt GA, Fokoue EP, Evans JR, Diller KI, Adams LE. DROIDS 3.0-Detecting Genetic and Drug Class Variant Impact on Conserved Protein Binding Dynamics. Biophys J 2019; 118:541-551. [PMID: 31928763 PMCID: PMC7002913 DOI: 10.1016/j.bpj.2019.12.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 01/07/2023] Open
Abstract
The application of statistical methods to comparatively framed questions about the molecular dynamics (MD) of proteins can potentially enable investigations of biomolecular function beyond the current sequence and structural methods in bioinformatics. However, the chaotic behavior in single MD trajectories requires statistical inference that is derived from large ensembles of simulations representing the comparative functional states of a protein under investigation. Meaningful interpretation of such complex forms of big data poses serious challenges to users of MD. Here, we announce Detecting Relative Outlier Impacts from Molecular Dynamic Simulation (DROIDS) 3.0, a method and software package for comparative protein dynamics that includes maxDemon 1.0, a multimethod machine learning application that trains on large ensemble comparisons of concerted protein motions in opposing functional states generated by DROIDS and deploys learned classifications of these states onto newly generated MD simulations. Local canonical correlations in learning patterns generated from independent, yet identically prepared, MD validation runs are used to identify regions of functionally conserved protein dynamics. The subsequent impacts of genetic and/or drug class variants on conserved dynamics can also be analyzed by deploying the classifiers on variant MD simulations and quantifying how often these altered protein systems display opposing functional states. Here, we present several case studies of complex changes in functional protein dynamics caused by temperature, genetic mutation, and binding interactions with nucleic acids and small molecules. We demonstrate that our machine learning algorithm can properly identify regions of functionally conserved dynamics in ubiquitin and TATA-binding protein (TBP). We quantify the impact of genetic variation in TBP and drug class variation targeting the ATP-binding region of Hsp90 on conserved dynamics. We identify regions of conserved dynamics in Hsp90 that connect the ATP binding pocket to other functional regions. We also demonstrate that dynamic impacts of various Hsp90 inhibitors rank accordingly with how closely they mimic natural ATP binding.
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Affiliation(s)
- Gregory A Babbitt
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York.
| | - Ernest P Fokoue
- School of Mathematical Sciences, Rochester Institute of Technology, Rochester, New York
| | - Joshua R Evans
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Kyle I Diller
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York; Golisano College for Computing and Information Science, Rochester, New York
| | - Lily E Adams
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
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