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Wang C, Liu Z, Zeng Y, Zhou L, Long Q, Hassan IU, Zhang Y, Qi X, Cai D, Mao B, Lu G, Sun J, Yao Y, Deng Y, Zhao Q, Feng B, Zhou Q, Chan WY, Zhao H. ZSWIM4 regulates embryonic patterning and BMP signaling by promoting nuclear Smad1 degradation. EMBO Rep 2024; 25:646-671. [PMID: 38177922 PMCID: PMC10897318 DOI: 10.1038/s44319-023-00046-w] [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: 02/23/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/06/2024] Open
Abstract
The dorsoventral gradient of BMP signaling plays an essential role in embryonic patterning. Zinc Finger SWIM-Type Containing 4 (zswim4) is expressed in the Spemann-Mangold organizer at the onset of Xenopus gastrulation and is then enriched in the developing neuroectoderm at the mid-gastrula stages. Knockdown or knockout of zswim4 causes ventralization. Overexpression of zswim4 decreases, whereas knockdown of zswim4 increases the expression levels of ventrolateral mesoderm marker genes. Mechanistically, ZSWIM4 attenuates the BMP signal by reducing the protein stability of SMAD1 in the nucleus. Stable isotope labeling by amino acids in cell culture (SILAC) identifies Elongin B (ELOB) and Elongin C (ELOC) as the interaction partners of ZSWIM4. Accordingly, ZSWIM4 forms a complex with the Cul2-RING ubiquitin ligase and ELOB and ELOC, promoting the ubiquitination and degradation of SMAD1 in the nucleus. Our study identifies a novel mechanism that restricts BMP signaling in the nucleus.
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Affiliation(s)
- Chengdong Wang
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ziran Liu
- Qingdao Municipal Center for Disease Control and Prevention, 266033, Qingdao, Shandong, China
| | - Yelin Zeng
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Liangji Zhou
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Qi Long
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Imtiaz Ul Hassan
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yuanliang Zhang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Xufeng Qi
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University, 510632, Guangzhou, Guangdong, China
| | - Dongqing Cai
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University, 510632, Guangzhou, Guangdong, China
| | - Bingyu Mao
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, Yunnan, China
- Kunming Institute of Zoology - The Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Chinese Academy of Sciences, Kunming, China
| | - Gang Lu
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jianmin Sun
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Ningxia Medical University, No. 1160 Shengli Street, 750004, Yinchuan, China
| | - Yonggang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, Yunnan, China
- Kunming Institute of Zoology - The Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Chinese Academy of Sciences, Kunming, China
| | - Yi Deng
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, and Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Qian Zhao
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Bo Feng
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Qin Zhou
- School of Basic Medical Sciences, Harbin Medical University, 150081, Harbin, China
| | - Wai Yee Chan
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Kunming Institute of Zoology - The Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources and Molecular Research of Common Diseases, The Chinese University of Hong Kong, Hong Kong SAR, China
- Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hui Zhao
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
- Kunming Institute of Zoology - The Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources and Molecular Research of Common Diseases, The Chinese University of Hong Kong, Hong Kong SAR, China.
- Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, Hong Kong SAR, China.
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Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P. Structure of the transcribing RNA polymerase II-Elongin complex. Nat Struct Mol Biol 2023; 30:1925-1935. [PMID: 37932450 PMCID: PMC10716050 DOI: 10.1038/s41594-023-01138-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/26/2023] [Indexed: 11/08/2023]
Abstract
Elongin is a heterotrimeric elongation factor for RNA polymerase (Pol) II transcription that is conserved among metazoa. Here, we report three cryo-EM structures of human Elongin bound to transcribing Pol II. The structures show that Elongin subunit ELOA binds the RPB2 side of Pol II and anchors the ELOB-ELOC subunit heterodimer. ELOA contains a 'latch' that binds between the end of the Pol II bridge helix and funnel helices, thereby inducing a conformational change near the polymerase active center. The latch is required for the elongation-stimulatory activity of Elongin, but not for Pol II binding, indicating that Elongin functions by allosterically regulating the conformational mobility of the polymerase active center. Elongin binding to Pol II is incompatible with association of the super elongation complex, PAF1 complex and RTF1, which also contain an elongation-stimulatory latch element.
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Affiliation(s)
- Ying Chen
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Goran Kokic
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Christian Dienemann
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Olexandr Dybkov
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- University Medical Center Göttingen, Institute of Clinical Chemistry, Bioanalytics Group, Göttingen, Germany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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Morgan MA, Mohammad Parast S, Iwanaszko M, Aoi Y, Yoo D, Dumar ZJ, Howard BC, Helmin KA, Liu Q, Thakur WR, Zeidner JM, Singer BD, Eichler EE, Shilatifard A. ELOA3: A primate-specific RNA polymerase II elongation factor encoded by a tandem repeat gene cluster. SCIENCE ADVANCES 2023; 9:eadj1261. [PMID: 37992162 PMCID: PMC10664989 DOI: 10.1126/sciadv.adj1261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/19/2023] [Indexed: 11/24/2023]
Abstract
The biological role of the repetitive DNA sequences in the human genome remains an outstanding question. Recent long-read human genome assemblies have allowed us to identify a function for one of these repetitive regions. We have uncovered a tandem array of conserved primate-specific retrogenes encoding the protein Elongin A3 (ELOA3), a homolog of the RNA polymerase II (RNAPII) elongation factor Elongin A (ELOA). Our genomic analysis shows that the ELOA3 gene cluster is conserved among primates and the number of ELOA3 gene repeats is variable in the human population and across primate species. Moreover, the gene cluster has undergone concerted evolution and homogenization within primates. Our biochemical studies show that ELOA3 functions as a promoter-associated RNAPII pause-release elongation factor with distinct biochemical and functional features from its ancestral homolog, ELOA. We propose that the ELOA3 gene cluster has evolved to fulfil a transcriptional regulatory function unique to the primate lineage that can be targeted to regulate cellular hyperproliferation.
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Affiliation(s)
- Marc A. J. Morgan
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Saeid Mohammad Parast
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Marta Iwanaszko
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yuki Aoi
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - DongAhn Yoo
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA 98195, USA
| | - Zachary J. Dumar
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Benjamin C. Howard
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kathryn A. Helmin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Qianli Liu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - William R. Thakur
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jacob M. Zeidner
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Benjamin D. Singer
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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Stampone E, Bencivenga D, Capellupo MC, Roberti D, Tartaglione I, Perrotta S, Della Ragione F, Borriello A. Genome editing and cancer therapy: handling the hypoxia-responsive pathway as a promising strategy. Cell Mol Life Sci 2023; 80:220. [PMID: 37477829 PMCID: PMC10361942 DOI: 10.1007/s00018-023-04852-2] [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: 05/02/2023] [Revised: 06/14/2023] [Accepted: 06/29/2023] [Indexed: 07/22/2023]
Abstract
The precise characterization of oxygen-sensing pathways and the identification of pO2-regulated gene expression are both issues of critical importance. The O2-sensing system plays crucial roles in almost all the pivotal human processes, including the stem cell specification, the growth and development of tissues (such as embryogenesis), the modulation of intermediate metabolism (including the shift of the glucose metabolism from oxidative to anaerobic ATP production and vice versa), and the control of blood pressure. The solid cancer microenvironment is characterized by low oxygen levels and by the consequent activation of the hypoxia response that, in turn, allows a complex adaptive response characterized mainly by neoangiogenesis and metabolic reprogramming. Recently, incredible advances in molecular genetic methodologies allowed the genome editing with high efficiency and, above all, the precise identification of target cells/tissues. These new possibilities and the knowledge of the mechanisms of adaptation to hypoxia suggest the effective development of new therapeutic approaches based on the manipulation, targeting, and exploitation of the oxygen-sensor system molecular mechanisms.
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Affiliation(s)
- Emanuela Stampone
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via Luigi De Crecchio, 7, 80138, Naples, Italy
| | - Debora Bencivenga
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via Luigi De Crecchio, 7, 80138, Naples, Italy
| | - Maria Chiara Capellupo
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via Luigi De Crecchio, 7, 80138, Naples, Italy
| | - Domenico Roberti
- Department of the Woman, the Child and of the General and Specialty Surgery, University of Campania "L. Vanvitelli", Via Luigi De Crecchio, 2, 80138, Naples, Italy
| | - Immacolata Tartaglione
- Department of the Woman, the Child and of the General and Specialty Surgery, University of Campania "L. Vanvitelli", Via Luigi De Crecchio, 2, 80138, Naples, Italy
| | - Silverio Perrotta
- Department of the Woman, the Child and of the General and Specialty Surgery, University of Campania "L. Vanvitelli", Via Luigi De Crecchio, 2, 80138, Naples, Italy
| | - Fulvio Della Ragione
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via Luigi De Crecchio, 7, 80138, Naples, Italy.
| | - Adriana Borriello
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via Luigi De Crecchio, 7, 80138, Naples, Italy.
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Pal S, Biswas D. Promoter-proximal regulation of gene transcription: Key factors involved and emerging role of general transcription factors in assisting productive elongation. Gene 2023:147571. [PMID: 37331491 DOI: 10.1016/j.gene.2023.147571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 06/20/2023]
Abstract
The pausing of RNA polymerase II (Pol II) at the promoter-proximal sites is a key rate-limiting step in gene expression. Cells have dedicated a specific set of proteins that sequentially establish pause and then release the Pol II from promoter-proximal sites. A well-controlled pausing and subsequent release of Pol II is crucial for thefine tuning of expression of genes including signal-responsive and developmentally-regulated ones. The release of paused Pol II broadly involves its transition from initiation to elongation. In this review article, we will discuss the phenomenon of Pol II pausing, the underlying mechanism, and also the role of different known factors, with an emphasis on general transcription factors, involved in this overall regulation. We will further discuss some recent findings suggesting a possible role (underexplored) of initiation factors in assisting the transition of transcriptionally-engaged paused Pol II into productive elongation.
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Affiliation(s)
- Sujay Pal
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata - 32, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Debabrata Biswas
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata - 32, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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6
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Guo F, Islam MA, Lv C, Jin X, Sun L, Zhao K, Lu J, Yan R, Zhang W, Shi Y, Li N, Sun D. Insights into the Bioinformatics and Transcriptional Analysis of the Elongator Complexes ( ELPs) Gene Family of Wheat: TaELPs Contribute to Wheat Abiotic Stress Tolerance and Leaf Senescence. PLANTS (BASEL, SWITZERLAND) 2023; 12:952. [PMID: 36840300 PMCID: PMC9961319 DOI: 10.3390/plants12040952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Elongator complexes (ELPs) are the protein complexes that promote transcription through histone acetylation in eukaryotic cells and interact with elongating RNA polymerase II (RNAPII). ELPs' role in plant growth and development, signal transduction, and response to biotic and abiotic stresses have been confirmed in model plants. However, the functions of the wheat ELP genes are not well documented. The present study identified 18 members of the ELPs from the wheat genome with a homology search. Further, bioinformatics and transcription patterns in response to different stress conditions were analyzed to dissect their potential regulatory mechanisms in wheat. Gene duplication analysis showed that 18 pairs of ELP paralogous genes were derived from segmental duplication, which was divided into six clades by protein phylogenetic and cluster analysis. The orthologous analysis of wheat TaELP genes showed that TaELP genes may have evolved from orthologous genes of other plant species or closely related plants. Moreover, a variety of cis-acting regulatory elements (CAREs) related to growth and development, hormone response, and biotic and abiotic stresses were identified in the TaELPs' promoter regions. The qRT-PCR analysis showed that the transcription of TaELPs was induced under hormone, salt, and drought stress and during leaf senescence. The TaELP2 gene was silenced with BSMV-VIGS, and TaELP2 was preliminarily verified to be involved in the regulation of wheat leaf senescence. Overall, TaELP genes might be regulated by hormone signaling pathways and response to abiotic stress and leaf senescence, which could be investigated further as potential candidate genes for wheat abiotic stress tolerance and yield improvement.
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Affiliation(s)
- Feng Guo
- State Key Laboratory of Sustainable Dryland Agriculture, College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Md Ashraful Islam
- State Key Laboratory of Sustainable Dryland Agriculture, College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
- Department of Biological Sciences, University of North Texas, Denton, TX 76201, USA
| | - Chenxu Lv
- State Key Laboratory of Sustainable Dryland Agriculture, College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Xiujuan Jin
- State Key Laboratory of Sustainable Dryland Agriculture, College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Lili Sun
- State Key Laboratory of Sustainable Dryland Agriculture, College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Kai Zhao
- State Key Laboratory of Sustainable Dryland Agriculture, College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Juan Lu
- State Key Laboratory of Sustainable Dryland Agriculture, College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Rongyue Yan
- State Key Laboratory of Sustainable Dryland Agriculture, College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Wenjun Zhang
- State Key Laboratory of Sustainable Dryland Agriculture, College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Yugang Shi
- State Key Laboratory of Sustainable Dryland Agriculture, College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Ning Li
- State Key Laboratory of Sustainable Dryland Agriculture, College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Daizhen Sun
- State Key Laboratory of Sustainable Dryland Agriculture, College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
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Liu X, Liu X. PRC2, Chromatin Regulation, and Human Disease: Insights From Molecular Structure and Function. Front Oncol 2022; 12:894585. [PMID: 35800061 PMCID: PMC9255955 DOI: 10.3389/fonc.2022.894585] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/17/2022] [Indexed: 01/25/2023] Open
Abstract
Polycomb repressive complex 2 (PRC2) is a multisubunit histone-modifying enzyme complex that mediates methylation of histone H3 lysine 27 (H3K27). Trimethylated H3K27 (H3K27me3) is an epigenetic hallmark of gene silencing. PRC2 plays a crucial role in a plethora of fundamental biological processes, and PRC2 dysregulation has been repeatedly implicated in cancers and developmental disorders. Here, we review the current knowledge on mechanisms of cellular regulation of PRC2 function, particularly regarding H3K27 methylation and chromatin targeting. PRC2-related disease mechanisms are also discussed. The mode of action of PRC2 in gene regulation is summarized, which includes competition between H3K27 methylation and acetylation, crosstalk with transcription machinery, and formation of high-order chromatin structure. Recent progress in the structural biology of PRC2 is highlighted from the aspects of complex assembly, enzyme catalysis, and chromatin recruitment, which together provide valuable insights into PRC2 function in close-to-atomic detail. Future studies on the molecular function and structure of PRC2 in the context of native chromatin and in the presence of other regulators like RNAs will continue to deepen our understanding of the stability and plasticity of developmental transcriptional programs broadly impacted by PRC2.
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HIF-1α Hydroxyprolines Modulate Oxygen-Dependent Protein Stability Via Single VHL Interface With Comparable Effect on Ubiquitination Rate. J Mol Biol 2021; 433:167244. [PMID: 34537235 DOI: 10.1016/j.jmb.2021.167244] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 09/01/2021] [Accepted: 09/08/2021] [Indexed: 12/19/2022]
Abstract
The basic molecular mechanism underlying mammalian oxygen-dependent regulation of hypoxia-inducible factor (HIF) via the von Hippel-Lindau E3 ubiquitin ligase is well established. The principal step in this critical cellular process is the hydroxylation of either or both of the two conserved proline residues P402 and P564 within the oxygen-dependent degradation domain (ODD) of HIF-1α subunit via prolyl hydroxylases, which is necessary for binding VHL. However, the significance of the two prolines has remained unclear considering that only one hydroxyproline is sufficient for the recruitment of VHL. Here, we show using biophysical analyses that both hydroxyprolines bind to the same interface on VHL with similar affinity; VHL binding affinity to HIF-1α ODD remains relatively unchanged regardless of whether the ODD contains one or two hydroxyprolines; ODD with two hydroxyprolines can accommodate two VHLs; and the rate of in vitro ubiquitination of ODD with one hydroxyproline via VHL E3 ligase is comparable to the rate observed with ODD containing two hydroxyprolines. However, the two hydroxyprolines show distinct contributions to the intracellular stability of HIF-1α ODD. These results demonstrate for the first time that the graduated HIF-1α stability profile observed over a range of oxygen tension is not attributed to the binding of or ubiquitination via VHL per se, but is likely due to the preceding events such as the efficacy of oxygen-dependent prolyl hydroxylase-mediated hydroxylation of HIF-1α.
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Hu L, Zhang W, Xiang Z, Wang Y, Zeng C, Wang X, Tan C, Zhang Y, Li F, Xiao Y, Zhou L, Li J, Wu C, Xiang Y, Xiang L, Zhang X, Wang X, Yang W, Chen M, Ran Q, Li Z, Chen L. EloA promotes HEL polyploidization upon PMA stimulation through enhanced ERK1/2 activity. Platelets 2021; 33:755-763. [PMID: 34697988 DOI: 10.1080/09537104.2021.1988548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Megakaryocytes (MKs) are the unique non-pathological cells that undergo polyploidization in mammals. The polyploid formation is critical for understanding the MK biology, and transcriptional regulation is involved in the differentiation and maturation of MKs. However, little is known about the functions of transcriptional elongation factors in the MK polyploidization. In this study, we investigated the role of transcription elongation factor EloA in the polyploidy formation during the MK differentiation. We found that EloA was highly expressed in the erythroleukemia cell lines HEL and K562. Knockdown of EloA in HEL cell line was shown to impair the phorbol myristate acetate (PMA) induced polyploidization process, which was used extensively to model megakaryocytic differentiation. Selective over-expression of EloA mutants with Pol II elongation activity partially restored the polyploidization. RNA-sequencing revealed that knockdown of EloA decelerated the transcription of genes enriched in the ERK1/2 cascade pathway. The phosphorylation activity of ERK1/2 decreased upon the EloA inhibition, and the polyploidization process of HEL was hindered when ERK1/2 phosphorylation was inhibited by PD0325901 or SCH772984. This study evidenced a positive role of EloA in HEL polyploidization upon PMA stimulation through enhanced ERK1/2 activity.
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Affiliation(s)
- Lanyue Hu
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, the Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Weiwei Zhang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, the Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Zheng Xiang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, the Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Yali Wang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, the Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Cheng Zeng
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, the Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Xiaojie Wang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, the Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Chengning Tan
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, the Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Yichi Zhang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, the Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Fengjie Li
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, the Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Yanni Xiao
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, the Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Luping Zhou
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, the Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Jiuxuan Li
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, the Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Chun Wu
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, the Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Yang Xiang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, the Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Lixin Xiang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, the Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Xiaomei Zhang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, the Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Xueying Wang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, the Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Wuchen Yang
- Department of Hematology, The Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Maoshan Chen
- Australian Centre for Blood Diseases (Acbd), Clinical Central School, Monash University, Melbourne, Australia
| | - Qian Ran
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, the Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Zhongjun Li
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, the Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Li Chen
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, the Second Affiliated Hospital, Army Medical University, Chongqing, China
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10
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Elongin functions as a loading factor for Mediator at ATF6α-regulated ER stress response genes. Proc Natl Acad Sci U S A 2021; 118:2108751118. [PMID: 34544872 DOI: 10.1073/pnas.2108751118] [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] [Accepted: 08/05/2021] [Indexed: 12/11/2022] Open
Abstract
The bZIP transcription factor ATF6α is a master regulator of endoplasmic reticulum (ER) stress response genes. In this report, we identify the multifunctional RNA polymerase II transcription factor Elongin as a cofactor for ATF6α-dependent transcription activation. Biochemical studies reveal that Elongin functions at least in part by facilitating ATF6α-dependent loading of Mediator at the promoters and enhancers of ER stress response genes. Depletion of Elongin from cells leads to impaired transcription of ER stress response genes and to defects in the recruitment of Mediator and its CDK8 kinase subunit. Taken together, these findings bring to light a role for Elongin as a loading factor for Mediator during the ER stress response.
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11
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Weems JC, Slaughter BD, Unruh JR, Weaver KJ, Miller BD, Delventhal KM, Conaway JW, Conaway RC. A role for the Cockayne Syndrome B (CSB)-Elongin ubiquitin ligase complex in signal-dependent RNA polymerase II transcription. J Biol Chem 2021; 297:100862. [PMID: 34116057 PMCID: PMC8294581 DOI: 10.1016/j.jbc.2021.100862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/27/2021] [Accepted: 06/07/2021] [Indexed: 11/19/2022] Open
Abstract
The Elongin complex was originally identified as an RNA polymerase II (RNAPII) elongation factor and subsequently as the substrate recognition component of a Cullin-RING E3 ubiquitin ligase. More recent evidence indicates that the Elongin ubiquitin ligase assembles with the Cockayne syndrome B helicase (CSB) in response to DNA damage and can target stalled polymerases for ubiquitylation and removal from the genome. In this report, we present evidence that the CSB-Elongin ubiquitin ligase pathway has roles beyond the DNA damage response in the activation of RNAPII-mediated transcription. We observed that assembly of the CSB-Elongin ubiquitin ligase is induced not just by DNA damage, but also by a variety of signals that activate RNAPII-mediated transcription, including endoplasmic reticulum (ER) stress, amino acid starvation, retinoic acid, glucocorticoids, and doxycycline treatment of cells carrying several copies of a doxycycline-inducible reporter. Using glucocorticoid receptor (GR)-regulated genes as a model, we showed that glucocorticoid-induced transcription is accompanied by rapid recruitment of CSB and the Elongin ubiquitin ligase to target genes in a step that depends upon the presence of transcribing RNAPII on those genes. Consistent with the idea that the CSB-Elongin pathway plays a direct role in GR-regulated transcription, mouse cells lacking the Elongin subunit Elongin A exhibit delays in both RNAPII accumulation on and dismissal from target genes following glucocorticoid addition and withdrawal, respectively. Taken together, our findings bring to light a new role for the CSB-Elongin pathway in RNAPII-mediated transcription.
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Affiliation(s)
- Juston C Weems
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | | | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Kyle J Weaver
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Brandon D Miller
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Kym M Delventhal
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Joan W Conaway
- Stowers Institute for Medical Research, Kansas City, Missouri, USA; Department of Biochemistry & Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA.
| | - Ronald C Conaway
- Stowers Institute for Medical Research, Kansas City, Missouri, USA; Department of Biochemistry & Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA.
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12
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Barba-Aliaga M, Alepuz P, Pérez-Ortín JE. Eukaryotic RNA Polymerases: The Many Ways to Transcribe a Gene. Front Mol Biosci 2021; 8:663209. [PMID: 33968992 PMCID: PMC8097091 DOI: 10.3389/fmolb.2021.663209] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/09/2021] [Indexed: 01/04/2023] Open
Abstract
In eukaryotic cells, three nuclear RNA polymerases (RNA pols) carry out the transcription from DNA to RNA, and they all seem to have evolved from a single enzyme present in the common ancestor with archaea. The multiplicity of eukaryotic RNA pols allows each one to remain specialized in the synthesis of a subset of transcripts, which are different in the function, length, cell abundance, diversity, and promoter organization of the corresponding genes. We hypothesize that this specialization of RNA pols has conditioned the evolution of the regulatory mechanisms used to transcribe each gene subset to cope with environmental changes. We herein present the example of the homeostatic regulation of transcript levels versus changes in cell volume. We propose that the diversity and instability of messenger RNAs, transcribed by RNA polymerase II, have conditioned the appearance of regulatory mechanisms based on different gene promoter strength and mRNA stability. However, for the regulation of ribosomal RNA levels, which are very stable and transcribed mainly by RNA polymerase I from only one promoter, different mechanisms act based on gene copy variation, and a much simpler regulation of the synthesis rate.
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Affiliation(s)
- Marina Barba-Aliaga
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, València, Spain.,Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, València, Spain
| | - Paula Alepuz
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, València, Spain.,Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, València, Spain
| | - José E Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, València, Spain.,Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, València, Spain
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13
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Ardehali MB, Damle M, Perea-Resa C, Blower MD, Kingston RE. Elongin A associates with actively transcribed genes and modulates enhancer RNA levels with limited impact on transcription elongation rate in vivo. J Biol Chem 2020; 296:100202. [PMID: 33334895 PMCID: PMC7948453 DOI: 10.1074/jbc.ra120.015877] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/06/2020] [Accepted: 12/16/2020] [Indexed: 01/08/2023] Open
Abstract
Elongin A (EloA) is an essential transcription factor that stimulates the rate of RNA polymerase II (Pol II) transcription elongation in vitro. However, its role as a transcription factor in vivo has remained underexplored. Here we show that in mouse embryonic stem cells, EloA localizes to both thousands of Pol II transcribed genes with preference for transcription start site and promoter regions and a large number of active enhancers across the genome. EloA deletion results in accumulation of transcripts from a subset of enhancers and their adjacent genes. Notably, EloA does not substantially enhance the elongation rate of Pol II in vivo. We also show that EloA localizes to the nucleoli and associates with RNA polymerase I transcribed ribosomal RNA gene, Rn45s. EloA is a highly disordered protein, which we demonstrate forms phase-separated condensates in vitro, and truncation mutations in the intrinsically disordered regions (IDR) of EloA interfere with its targeting and localization to the nucleoli. We conclude that EloA broadly associates with transcribed regions, tunes RNA Pol II transcription levels via impacts on enhancer RNA synthesis, and interacts with the rRNA producing/processing machinery in the nucleolus. Our work opens new avenues for further investigation of the role of this functionally multifaceted transcription factor in enhancer and ribosomal RNA biology.
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Affiliation(s)
- M Behfar Ardehali
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Manashree Damle
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Carlos Perea-Resa
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael D Blower
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.
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14
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Cramer P. Eukaryotic Transcription Turns 50. Cell 2020; 179:808-812. [PMID: 31675494 DOI: 10.1016/j.cell.2019.09.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 12/15/2022]
Abstract
This year we celebrate the 50th anniversary of the discovery of the three eukaryotic RNA polymerases. Ever since this seminal event in 1969, researchers have investigated the intricate mechanisms of gene transcription with great dedication. The transcription field continues to influence developmental, stem cell, and cancer biology.
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Affiliation(s)
- Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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15
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Liu X, Zurlo G, Zhang Q. The Roles of Cullin-2 E3 Ubiquitin Ligase Complex in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1217:173-186. [PMID: 31898228 DOI: 10.1007/978-981-15-1025-0_11] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Posttranslational protein modifications play an important role in regulating protein stability and cellular function. There are at least eight Cullin family members. Among them, Cullin-2 forms a functional E3 ligase complex with elongin B, elongin C, RING-box protein 1 (RBX1, also called ROC1), as well as the substrate recognition subunit (SRS) to promote the substrate ubiquitination and degradation. In this book chapter, we will review Cullin-2 E3 ligase complexes that include various SRS proteins, including von Hippel Lindau (pVHL), leucine-rich repeat protein-1 (LRR-1), preferentially expressed antigen of melanoma (PRAME), sex-determining protein FEM-1 and early embryogenesis protein ZYG-11. We will focus on the VHL signaling pathway in clear cell renal cell carcinoma (ccRCC), which may reveal various therapeutic avenues in treating this lethal cancer.
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Affiliation(s)
- Xijuan Liu
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Giada Zurlo
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA.,Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Qing Zhang
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA. .,Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA. .,Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA. .,Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA.
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16
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The hunt for RNA polymerase II elongation factors: a historical perspective. Nat Struct Mol Biol 2019; 26:771-776. [PMID: 31439940 DOI: 10.1038/s41594-019-0283-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 07/18/2019] [Indexed: 02/07/2023]
Abstract
The discovery of the three eukaryotic nuclear RNA polymerases paved the way for serious biochemical investigations of eukaryotic transcription and the identification of eukaryotic transcription factors. Here we describe this adventure from our vantage point, with a focus on the hunt for factors that regulate elongation by RNA polymerase II.
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17
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Jang SM, Redon CE, Aladjem MI. Chromatin-Bound Cullin-Ring Ligases: Regulatory Roles in DNA Replication and Potential Targeting for Cancer Therapy. Front Mol Biosci 2018; 5:19. [PMID: 29594129 PMCID: PMC5859106 DOI: 10.3389/fmolb.2018.00019] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/12/2018] [Indexed: 12/14/2022] Open
Abstract
Cullin-RING (Really Interesting New Gene) E3 ubiquitin ligases (CRLs), the largest family of E3 ubiquitin ligases, are functional multi-subunit complexes including substrate receptors, adaptors, cullin scaffolds, and RING-box proteins. CRLs are responsible for ubiquitination of ~20% of cellular proteins and are involved in diverse biological processes including cell cycle progression, genome stability, and oncogenesis. Not surprisingly, cullins are deregulated in many diseases and instances of cancer. Recent studies have highlighted the importance of CRL-mediated ubiquitination in the regulation of DNA replication/repair, including specific roles in chromatin assembly and disassembly of the replication machinery. The development of novel therapeutics targeting the CRLs that regulate the replication machinery and chromatin in cancer is now an attractive therapeutic strategy. In this review, we summarize the structure and assembly of CRLs and outline their cellular functions and their diverse roles in cancer, emphasizing the regulatory functions of nuclear CRLs in modulating the DNA replication machinery. Finally, we discuss the current strategies for targeting CRLs against cancer in the clinic.
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Affiliation(s)
| | | | - Mirit I. Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
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18
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Weems JC, Slaughter BD, Unruh JR, Boeing S, Hall SM, McLaird MB, Yasukawa T, Aso T, Svejstrup JQ, Conaway JW, Conaway RC. Cockayne syndrome B protein regulates recruitment of the Elongin A ubiquitin ligase to sites of DNA damage. J Biol Chem 2017; 292:6431-6437. [PMID: 28292928 PMCID: PMC5399097 DOI: 10.1074/jbc.c117.777946] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 02/27/2017] [Indexed: 01/05/2023] Open
Abstract
Elongin A performs dual functions as the transcriptionally active subunit of RNA polymerase II (Pol II) elongation factor Elongin and as the substrate recognition subunit of a Cullin-RING E3 ubiquitin ligase that ubiquitylates Pol II in response to DNA damage. Assembly of the Elongin A ubiquitin ligase and its recruitment to sites of DNA damage is a tightly regulated process induced by DNA-damaging agents and α-amanitin, a drug that induces Pol II stalling. In this study, we demonstrate (i) that Elongin A and the ubiquitin ligase subunit CUL5 associate in cells with the Cockayne syndrome B (CSB) protein and (ii) that this interaction is also induced by DNA-damaging agents and α-amanitin. In addition, we present evidence that the CSB protein promotes stable recruitment of the Elongin A ubiquitin ligase to sites of DNA damage. Our findings are consistent with the model that the Elongin A ubiquitin ligase and the CSB protein function together in a common pathway in response to Pol II stalling and DNA damage.
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Affiliation(s)
- Juston C Weems
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Brian D Slaughter
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Jay R Unruh
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Stefan Boeing
- the Mechanisms of Transcription Laboratory, The Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, United Kingdom
| | - Shawn M Hall
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Merry B McLaird
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Takashi Yasukawa
- the Department of Functional Genomics, Kochi Medical School, Kohasu, Oko-cho, Nankoku, Kochi 783-8505, Japan
| | - Teijiro Aso
- the Department of Functional Genomics, Kochi Medical School, Kohasu, Oko-cho, Nankoku, Kochi 783-8505, Japan
| | - Jesper Q Svejstrup
- the Mechanisms of Transcription Laboratory, The Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, United Kingdom
| | - Joan W Conaway
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110,
- the Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, and
| | - Ronald C Conaway
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110,
- the Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, and
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19
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Hwang W, Artan M, Seo M, Lee D, Nam HG, Lee SV. Inhibition of elongin C promotes longevity and protein homeostasis via HIF-1 in C. elegans. Aging Cell 2015; 14:995-1002. [PMID: 26361075 PMCID: PMC4693473 DOI: 10.1111/acel.12390] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2015] [Indexed: 01/17/2023] Open
Abstract
The transcription factor hypoxia‐inducible factor 1 (HIF‐1) is crucial for responses to low oxygen and promotes longevity in Caenorhabditis elegans. We previously performed a genomewide RNA interference screen and identified many genes that act as potential negative regulators of HIF‐1. Here, we functionally characterized these genes and found several novel genes that affected lifespan. The worm ortholog of elongin C, elc‐1, encodes a subunit of E3 ligase and transcription elongation factor. We found that knockdown of elc‐1 prolonged lifespan and delayed paralysis caused by impaired protein homeostasis. We further showed that elc‐1 RNA interference increased lifespan and protein homeostasis by upregulating HIF‐1. The roles of elongin C and HIF‐1 are well conserved in eukaryotes. Thus, our study may provide insights into the aging regulatory pathway consisting of elongin C and HIF‐1 in complex metazoans.
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Affiliation(s)
- Wooseon Hwang
- Department of Life SciencesPohang University of Science and TechnologyPohangGyeongbuk37673South Korea
| | - Murat Artan
- Information Technology Convergence EngineeringPohang University of Science and TechnologyPohangGyeongbuk37673South Korea
| | - Mihwa Seo
- School of Interdisciplinary Bioscience and BioengineeringPohang University of Science and TechnologyPohangGyeongbuk37673South Korea
- Center for Plant Aging ResearchInstitute for Basic ScienceDaegu42988South Korea
| | - Dongyeop Lee
- Department of Life SciencesPohang University of Science and TechnologyPohangGyeongbuk37673South Korea
| | - Hong Gil Nam
- Center for Plant Aging ResearchInstitute for Basic ScienceDaegu42988South Korea
- Department of New BiologyDGISTDaegu42988South Korea
| | - Seung‐Jae V. Lee
- Department of Life SciencesPohang University of Science and TechnologyPohangGyeongbuk37673South Korea
- Information Technology Convergence EngineeringPohang University of Science and TechnologyPohangGyeongbuk37673South Korea
- School of Interdisciplinary Bioscience and BioengineeringPohang University of Science and TechnologyPohangGyeongbuk37673South Korea
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20
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Zhai Y, Deng Y, Cheng G, Peng L, Zheng Y, Yang Y, Xu J. Sugarcane Elongin C is involved in infection by sugarcane mosaic disease pathogens. Biochem Biophys Res Commun 2015; 466:312-8. [PMID: 26362180 DOI: 10.1016/j.bbrc.2015.09.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 09/03/2015] [Indexed: 11/18/2022]
Abstract
Sugarcane (Saccharum sp. hybrid) provides the main source of sugar for humans. Sugarcane mosaic disease (SMD) is a major threat to sugarcane production. Currently, control of SMD is mainly dependent on breeding resistant cultivars through hybridization, which is time-consuming. Understanding the mechanism of viral infection may facilitate novel strategies to breed cultivars resistant to SMD and to control the disease. In this study, a wide interaction was detected between the viral VPg protein and host proteins. Several genes were screened from sugarcane cDNA library that could interact with Sugarcane streak mosaic virus VPg, including SceIF4E1 and ScELC. ScELC was predicted to be a cytoplasmic protein, but subcellular localization analysis showed it was distributed both in cytoplasmic and nuclear, and interactions were also detected between ScELC and VPg of SCMV or SrMV that reveal ScELC was widely used in the SMD pathogen infection process. ScELC and VPgs interacted in the nucleus, and may function to enhance the viral transcription rate. ScELC also interacted with SceIF4E2 both in the cytoplasm and nucleus, but not with SceIF4E1 and SceIF4E3. These results suggest that ScELC may be essential for the function of SceIF4E2, an isomer of eIF4E.
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Affiliation(s)
- Yushan Zhai
- Key Laboratory of Sugarcane Biology and Genetic Breeding, MOA, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, Fujian 350002, PR China
| | - Yuqing Deng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, MOA, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, Fujian 350002, PR China
| | - Guangyuan Cheng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, MOA, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, Fujian 350002, PR China
| | - Lei Peng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, MOA, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, Fujian 350002, PR China
| | - Yanru Zheng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, MOA, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, Fujian 350002, PR China
| | - Yongqing Yang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, MOA, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, Fujian 350002, PR China.
| | - Jingsheng Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, MOA, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, Fujian 350002, PR China.
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21
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Targeting Cullin-RING E3 ubiquitin ligases for drug discovery: structure, assembly and small-molecule modulation. Biochem J 2015; 467:365-86. [PMID: 25886174 PMCID: PMC4403949 DOI: 10.1042/bj20141450] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In the last decade, the ubiquitin–proteasome system has emerged as a valid target for the development of novel therapeutics. E3 ubiquitin ligases are particularly attractive targets because they confer substrate specificity on the ubiquitin system. CRLs [Cullin–RING (really interesting new gene) E3 ubiquitin ligases] draw particular attention, being the largest family of E3s. The CRLs assemble into functional multisubunit complexes using a repertoire of substrate receptors, adaptors, Cullin scaffolds and RING-box proteins. Drug discovery targeting CRLs is growing in importance due to mounting evidence pointing to significant roles of these enzymes in diverse biological processes and human diseases, including cancer, where CRLs and their substrates often function as tumour suppressors or oncogenes. In the present review, we provide an account of the assembly and structure of CRL complexes, and outline the current state of the field in terms of available knowledge of small-molecule inhibitors and modulators of CRL activity. A comprehensive overview of the reported crystal structures of CRL subunits, components and full-size complexes, alone or with bound small molecules and substrate peptides, is included. This information is providing increasing opportunities to aid the rational structure-based design of chemical probes and potential small-molecule therapeutics targeting CRLs.
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22
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Weems JC, Slaughter BD, Unruh JR, Hall SM, McLaird MB, Gilmore JM, Washburn MP, Florens L, Yasukawa T, Aso T, Conaway JW, Conaway RC. Assembly of the Elongin A Ubiquitin Ligase Is Regulated by Genotoxic and Other Stresses. J Biol Chem 2015; 290:15030-41. [PMID: 25878247 DOI: 10.1074/jbc.m114.632794] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Indexed: 11/06/2022] Open
Abstract
Elongin A performs dual functions in cells as a component of RNA polymerase II (Pol II) transcription elongation factor Elongin and as the substrate recognition subunit of a Cullin-RING E3 ubiquitin ligase that has been shown to target Pol II stalled at sites of DNA damage. Here we investigate the mechanism(s) governing conversion of the Elongin complex from its elongation factor to its ubiquitin ligase form. We report the discovery that assembly of the Elongin A ubiquitin ligase is a tightly regulated process. In unstressed cells, Elongin A is predominately present as part of Pol II elongation factor Elongin. Assembly of Elongin A into the ubiquitin ligase is strongly induced by genotoxic stress; by transcriptional stresses that lead to accumulation of stalled Pol II; and by other stimuli, including endoplasmic reticulum and nutrient stress and retinoic acid signaling, that activate Elongin A-dependent transcription. Taken together, our findings shed new light on mechanisms that control the Elongin A ubiquitin ligase and suggest that it may play a role in Elongin A-dependent transcription.
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Affiliation(s)
- Juston C Weems
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Brian D Slaughter
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Jay R Unruh
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Shawn M Hall
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Merry B McLaird
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Joshua M Gilmore
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Michael P Washburn
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110, the Departments of Pathology and Laboratory Medicine and
| | - Laurence Florens
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Takashi Yasukawa
- the Department of Functional Genomics, Kochi Medical School, Kohasu, Oko-cho, Nankoku, Kochi 783-8505, Japan
| | - Teijiro Aso
- the Department of Functional Genomics, Kochi Medical School, Kohasu, Oko-cho, Nankoku, Kochi 783-8505, Japan
| | - Joan W Conaway
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110, Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, and
| | - Ronald C Conaway
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110, Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, and
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23
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Zhu M, Chen Y, Ding XS, Webb SL, Zhou T, Nelson RS, Fan Z. Maize Elongin C interacts with the viral genome-linked protein, VPg, of Sugarcane mosaic virus and facilitates virus infection. THE NEW PHYTOLOGIST 2014; 203:1291-1304. [PMID: 24954157 PMCID: PMC4143955 DOI: 10.1111/nph.12890] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 05/08/2014] [Indexed: 05/18/2023]
Abstract
The viral genome-linked protein, VPg, of potyviruses is involved in viral genome replication and translation. To determine host proteins that interact with Sugarcane mosaic virus (SCMV) VPg, a yeast two-hybrid screen was used and a maize (Zea mays) Elongin C (ZmElc) protein was identified. ZmELC transcript was observed in all maize organs, but most highly in leaves and pistil extracts, and ZmElc was present in the cytoplasm and nucleus of maize cells in the presence or absence of SCMV. ZmELC expression was increased in maize tissue at 4 and 6 d post SCMV inoculation. When ZmELC was transiently overexpressed in maize protoplasts the accumulation of SCMV RNA was approximately doubled compared with the amount of virus in control protoplasts. Silencing ZmELC expression using a Brome mosaic virus-based gene silencing vector (virus-induced gene silencing) did not influence maize plant growth and development, but did decrease RNA accumulation of two isolates of SCMV and host transcript encoding ZmeIF4E during SCMV infection. Interestingly, Maize chlorotic mottle virus, from outside the Potyviridae, was increased in accumulation after silencing ZmELC expression. Our results describe both the location of ZmElc expression in maize and a new activity associated with an Elc: support of potyvirus accumulation.
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Affiliation(s)
- Min Zhu
- State Key Laboratory of Agro-biotechnology and Key Laboratory for Plant Pathology – Ministry of Agriculture, China Agricultural UniversityBeijing, 100193, China
| | - Yuting Chen
- State Key Laboratory of Agro-biotechnology and Key Laboratory for Plant Pathology – Ministry of Agriculture, China Agricultural UniversityBeijing, 100193, China
| | - Xin Shun Ding
- Plant Biology Division, The Samuel Roberts Noble Foundation, Inc.2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Stephen L Webb
- Department of Computing Services, The Samuel Roberts Noble Foundation Inc.2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Tao Zhou
- State Key Laboratory of Agro-biotechnology and Key Laboratory for Plant Pathology – Ministry of Agriculture, China Agricultural UniversityBeijing, 100193, China
| | - Richard S Nelson
- Plant Biology Division, The Samuel Roberts Noble Foundation, Inc.2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Zaifeng Fan
- State Key Laboratory of Agro-biotechnology and Key Laboratory for Plant Pathology – Ministry of Agriculture, China Agricultural UniversityBeijing, 100193, China
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Rougeot J, Renard M, Randsholt NB, Peronnet F, Mouchel-Vielh E. The elongin complex antagonizes the chromatin factor Corto for vein versus intervein cell identity in Drosophila wings. PLoS One 2013; 8:e77592. [PMID: 24204884 PMCID: PMC3804554 DOI: 10.1371/journal.pone.0077592] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 09/10/2013] [Indexed: 01/08/2023] Open
Abstract
Drosophila wings mainly consist of two cell types, vein and intervein cells. Acquisition of either fate depends on specific expression of genes that are controlled by several signaling pathways. The nuclear mechanisms that translate signaling into regulation of gene expression are not completely understood, but they involve chromatin factors from the Trithorax (TrxG) and Enhancers of Trithorax and Polycomb (ETP) families. One of these is the ETP Corto that participates in intervein fate through interaction with the Drosophila EGF Receptor--MAP kinase ERK pathway. Precise mechanisms and molecular targets of Corto in this process are not known. We show here that Corto interacts with the Elongin transcription elongation complex. This complex, that consists of three subunits (Elongin A, B, C), increases RNA polymerase II elongation rate in vitro by suppressing transient pausing. Analysis of phenotypes induced by EloA, B, or C deregulation as well as genetic interactions suggest that the Elongin complex might participate in vein vs intervein specification, and antagonizes corto as well as several TrxG genes in this process. Chromatin immunoprecipitation experiments indicate that Elongin C and Corto bind the vein-promoting gene rhomboid in wing imaginal discs. We propose that Corto and the Elongin complex participate together in vein vs intervein fate, possibly through tissue-specific transcriptional regulation of rhomboid.
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Affiliation(s)
- Julien Rougeot
- Université Pierre et Marie Curie-Paris 6, UMR7622, Paris, France ; Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Paris, France
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Wang X, Wang X, Zhang H, Lv M, Zuo T, Wu H, Wang J, Liu D, Wang C, Zhang J, Li X, Wu J, Yu B, Kong W, Yu X. Interactions between HIV-1 Vif and human ElonginB-ElonginC are important for CBF-β binding to Vif. Retrovirology 2013; 10:94. [PMID: 23988114 PMCID: PMC3765967 DOI: 10.1186/1742-4690-10-94] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 08/26/2013] [Indexed: 01/18/2023] Open
Abstract
Background The HIV-1 accessory factor Vif is necessary for efficient viral infection in non-permissive cells. Vif antagonizes the antiviral activity of human cytidine deaminase APOBEC3 proteins that confer the non-permissive phenotype by tethering them (APOBEC3DE/3F/3G) to the Vif-CBF-β-ElonginB-ElonginC-Cullin5-Rbx (Vif-CBF-β-EloB-EloC-Cul5-Rbx) E3 complex to induce their proteasomal degradation. EloB and EloC were initially reported as positive regulatory subunits of the Elongin (SIII) complex. Thereafter, EloB and EloC were found to be components of Cul-E3 complexes, contributing to proteasomal degradation of specific substrates. CBF-β is a newly identified key regulator of Vif function, and more information is needed to further clarify its regulatory mechanism. Here, we comprehensively investigated the functions of EloB (together with EloC) in the Vif-CBF-β-Cul5 E3 ligase complex. Results The results revealed that: (1) EloB (and EloC) positively affected the recruitment of CBF-β to Vif. Both knockdown of endogenous EloB and over-expression of its mutant with a 34-residue deletion in the COOH-terminal tail (EloBΔC34/EBΔC34) impaired the Vif-CBF-β interaction. (2) Introduction of both the Vif SLQ → AAA mutant (VifΔSLQ, which dramatically impairs Vif-EloB-EloC binding) and the Vif PPL → AAA mutant (VifΔPPL, which is thought to reduce Vif-EloB binding) could reduce CBF-β binding. (3) EloB-EloC but not CBF-β could greatly enhance the folding of full-length Vif in Escherichia coli. (4) The over-expression of EloB or the N-terminal ubiquitin-like (UbL) domain of EloB could significantly improve the stability of Vif/VifΔSLQ/VifΔPPL through the region between residues 9 and 14. Conclusion Our results indicate that the Vif interaction with EloB-EloC may contribute to recruitment of CBF-β to Vif, demonstrating that the EloB C-teminus may play a role in improving Vif function and that the over-expression of EloB results in Vif stabilization.
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Affiliation(s)
- Xiaodan Wang
- National Engineering Laboratory for AIDS Vaccine, College of Life Science, Jilin University, Changchun, Jilin Province, People's Republic of China.
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Discovery of structural alterations in solid tumor oligodendroglioma by single molecule analysis. BMC Genomics 2013; 14:505. [PMID: 23885787 PMCID: PMC3727977 DOI: 10.1186/1471-2164-14-505] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 07/23/2013] [Indexed: 12/31/2022] Open
Abstract
Background Solid tumors present a panoply of genomic alterations, from single base changes to the gain or loss of entire chromosomes. Although aberrations at the two extremes of this spectrum are readily defined, comprehensive discernment of the complex and disperse mutational spectrum of cancer genomes remains a significant challenge for current genome analysis platforms. In this context, high throughput, single molecule platforms like Optical Mapping offer a unique perspective. Results Using measurements from large ensembles of individual DNA molecules, we have discovered genomic structural alterations in the solid tumor oligodendroglioma. Over a thousand structural variants were identified in each tumor sample, without any prior hypotheses, and often in genomic regions deemed intractable by other technologies. These findings were then validated by comprehensive comparisons to variants reported in external and internal databases, and by selected experimental corroborations. Alterations range in size from under 5 kb to hundreds of kilobases, and comprise insertions, deletions, inversions and compound events. Candidate mutations were scored at sub-genic resolution and unambiguously reveal structural details at aberrant loci. Conclusions The Optical Mapping system provides a rich description of the complex genomes of solid tumors, including sequence level aberrations, structural alterations and copy number variants that power generation of functional hypotheses for oligodendroglioma genetics.
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Kawauchi J, Inoue M, Fukuda M, Uchida Y, Yasukawa T, Conaway RC, Conaway JW, Aso T, Kitajima S. Transcriptional properties of mammalian elongin A and its role in stress response. J Biol Chem 2013; 288:24302-15. [PMID: 23828199 DOI: 10.1074/jbc.m113.496703] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Elongin A was shown previously to be capable of potently activating the rate of RNA polymerase II (RNAPII) transcription elongation in vitro by suppressing transient pausing by the enzyme at many sites along DNA templates. The role of Elongin A in RNAPII transcription in mammalian cells, however, has not been clearly established. In this report, we investigate the function of Elongin A in RNAPII transcription. We present evidence that Elongin A associates with the IIO form of RNAPII at sites of newly transcribed RNA and is relocated to dotlike domains distinct from those containing RNAPII when cells are treated with the kinase inhibitor 5,6-dichloro-1-β-d-ribofuranosylbenzimidazole. Significantly, Elongin A is required for maximal induction of transcription of the stress response genes ATF3 and p21 in response to several stimuli. Evidence from structure-function studies argues that Elongin A transcription elongation activity, but not its ubiquitination activity, is most important for its function in induction of transcription of ATF3 and p21. Taken together, our data provide new insights into the function of Elongin A in RNAPII transcription and bring to light a previously unrecognized role for Elongin A in the regulation of stress response genes.
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Affiliation(s)
- Junya Kawauchi
- Department of Biochemical Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
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Zhang WN, Wang L, Wang Q, Luo X, Fang DF, Chen Y, Pan X, Man JH, Xia Q, Jin BF, Li WH, Li T, Liang B, Chen L, Gong WL, Yu M, Li AL, Zhou T, Li HY. CUEDC2 (CUE domain-containing 2) and SOCS3 (suppressors of cytokine signaling 3) cooperate to negatively regulate Janus kinase 1/signal transducers and activators of transcription 3 signaling. J Biol Chem 2011; 287:382-392. [PMID: 22084247 DOI: 10.1074/jbc.m111.276832] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Janus kinase 1/signal transducers and activators of transcription 3 (JAK1/STAT3) pathway is one of the recognized oncogenic signaling pathways that frequently overactivated in a variety of human tumors. Despite rapid progress in elucidating the molecular mechanisms of activation of JAK/STAT pathway, the processes that regulate JAK/STAT deactivation need to be further clarified. Here we demonstrate that CUE domain-containing 2 (CUEDC2) inhibits cytokine-induced phosphorylation of JAK1 and STAT3 and the subsequent STAT3 transcriptional activity. Further analysis by a yeast two-hybrid assay showed that CUEDC2 could engage in a specific interaction with a key JAK/STAT inhibitor, SOCS3 (suppressors of cytokine signaling 3). The interaction between CUEDC2 and SOCS3 is required for the inhibitory effect of CUEDC2 on JAK1 and STAT3 activity. Additionally, we found CUEDC2 functions collaboratively with SOCS3 to inhibit JAK1/STAT3 signaling by increasing SOCS3 stability via enhancing its association with Elongin C. Therefore, our findings revealed a new biological activity for CUEDC2 as the regulator of JAK1/STAT3 signaling and paved the way to a better understanding of the mechanisms by which SOCS3 has been linked to suppression of the JAK/STAT pathway.
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Affiliation(s)
- Wei-Na Zhang
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Li Wang
- Beijing Institute of Biotechnology, Beijing 100071, China
| | - Qiong Wang
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xue Luo
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Di-Feng Fang
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Yuan Chen
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Xin Pan
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Jiang-Hong Man
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Qing Xia
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Bao-Feng Jin
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Wei-Hua Li
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Tao Li
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Bing Liang
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Liang Chen
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Wei-Li Gong
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Ming Yu
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Ai-Ling Li
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Tao Zhou
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China.
| | - Hui-Yan Li
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China.
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Baxter SS, Carlson LA, Mayer AMS, Hall ML, Fay MJ. Granulocytic differentiation of HL-60 promyelocytic leukemia cells is associated with increased expression of Cul5. In Vitro Cell Dev Biol Anim 2009; 45:264-74. [PMID: 19118439 DOI: 10.1007/s11626-008-9163-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Accepted: 12/03/2008] [Indexed: 12/25/2022]
Abstract
The human HL-60 promyelocytic leukemia cell line has been widely used as a model for studying granulocytic differentiation. All-trans retinoic acid (ATRA) treatment of HL-60 cells promotes granulocytic differentiation and is effective as differentiation therapy for patients with acute promyelocytic leukemia. The identification of genes that are transcriptionally regulated by ATRA has provided insight into granulocytic differentiation and differentiation therapy. The Asb-2 (ankyrin repeat SOCS box 2) gene has previously been identified as a transcriptional target in ATRA-treated HL-60 cells. The ASB-2 protein forms an E3 ubiquitin ligase complex with the proteins, Cul5, regulator of cullin 2 (ROC2), and elongin B and C. The purpose of this study was to determine if there is increased expression of Cul5 during granulocytic differentiation of HL-60 cells. To induce granulocytic differentiation, HL-60 cells were treated for 5 d with ATRA and differentiation was confirmed by examining superoxide anion production, nuclear morphology, and changes in the expression of CD11b, CD13, and CD15. Quantitative real-time RT-PCR was used to measure Cul5 mRNA expression and also the expression of other components of the E3 ubiquitin ligase (ASB-2, ROC2, elongin B and C). Granulocytic differentiation of HL-60 cells was associated with a 1.6-, 1.7-, and 23-fold statistically significant (P <or= 0.05) increase in mRNA expression for Cul5, ROC2, and ASB-2, respectively. No significant change was found in elongin B and C mRNA expression. Using Western blot analysis, the expression of Cul5 protein was increased 6.5-fold with granulocytic differentiation of the HL-60 cells. Increased expression of multiple components of the Cul5-containing E3 ubiquitin ligase complex with ATRA treatment of HL-60 cells indicates that this complex may play an important role in granulocytic differentiation.
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Affiliation(s)
- Shaneen S Baxter
- Department of Pharmacology, Chicago College of Osteopathic Medicine, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA
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LeJeune D, Chen X, Ruggiero C, Berryhill S, Ding B, Li S. Yeast Elc1 plays an important role in global genomic repair but not in transcription coupled repair. DNA Repair (Amst) 2009; 8:40-50. [DOI: 10.1016/j.dnarep.2008.08.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Revised: 08/28/2008] [Accepted: 08/28/2008] [Indexed: 11/16/2022]
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Mammalian Elongin A complex mediates DNA-damage-induced ubiquitylation and degradation of Rpb1. EMBO J 2008; 27:3256-66. [PMID: 19037258 DOI: 10.1038/emboj.2008.249] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Accepted: 11/05/2008] [Indexed: 01/21/2023] Open
Abstract
The Elongin complex stimulates the rate of transcription elongation by RNA polymerase II (pol II) by suppressing transient pausing of the pol II at many sites along the DNA. Elongin is composed of a transcriptionally active A subunit and two small regulatory B and C subunits, which can form an isolable Elongin BC subcomplex. Here, we have shown that both the ubiquitylation and proteasomal degradation of the largest subunit of pol II (Rpb1) following UV-irradiation are significantly suppressed in Elongin A-deficient cells; however, in both cases suppression is rescued by transfection of wild-type Elongin A. Moreover, we have demonstrated that the Elongin A-Elongin BC complex is capable of assembling with the Cul5/Rbx2 module, and that this hetero-pentamer complex efficiently ubiquitylates Rpb1 in vitro. Mechanistic studies indicate that colocalization of Elongin A and Cul5 in cells and the interaction of Elongin A with the Ser5-phosphorylated form of Rpb1 are strongly enhanced following UV-irradiation. Taken together, our results suggest that mammalian Elongin A is directly involved in ubiquitylation and degradation of Rpb1 following DNA damage.
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Piessevaux J, De Ceuninck L, Catteeuw D, Peelman F, Tavernier J. Elongin B/C recruitment regulates substrate binding by CIS. J Biol Chem 2008; 283:21334-46. [PMID: 18508766 DOI: 10.1074/jbc.m803742200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
SOCS proteins play a major role in the regulation of cytokine signaling. They are recruited to activated receptors and can suppress signaling by different mechanisms including targeting of the receptor complex for proteasomal degradation. The activity of SOCS proteins is regulated at different levels including transcriptional control and posttranslational modification. We describe here a novel regulatory mechanism for CIS, one of the members of this protein family. A CIS mutant deficient in recruitment of the Elongin B/C complex completely failed to suppress STAT5 activation. This deficiency was not caused by altered turnover of CIS but by loss of cytokine receptor interaction. Intriguingly, no such effect was seen for binding to MyD88. The interaction between CIS and the Elongin B/C complex, which depends on the levels of uncomplexed Elongin B/C, was easily disrupted. This regulatory mechanism may be unique for CIS, as similar mutations in SOCS1, -2, -3, -6, and -7 had no functional impact. Our findings indicate that the SOCS box not only plays a role in the formation of E3 ligase complexes but, at least for CIS, can also regulate the binding modus of SOCS box-containing proteins.
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Affiliation(s)
- Julie Piessevaux
- Department of Medical Protein Research, Flanders Institute for Biotechnology (VIB), Ghent University, A. Baertsoenkaai 3, Ghent, Belgium
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33
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Microarray gene expression profiling of mouse brain mRNA in a model of lithium treatment. Psychiatr Genet 2008; 18:64-72. [DOI: 10.1097/ypg.0b013e3282fb0051] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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34
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Kinoshita K, Goryo K, Takada M, Tomokuni Y, Aso T, Okuda H, Shuin T, Fukumura H, Sogawa K. Ternary complex formation of pVHL, elongin B and elongin C visualized in living cells by a fluorescence resonance energy transfer-fluorescence lifetime imaging microscopy technique. FEBS J 2007; 274:5567-75. [DOI: 10.1111/j.1742-4658.2007.06075.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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35
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Ribar B, Prakash L, Prakash S. ELA1 and CUL3 are required along with ELC1 for RNA polymerase II polyubiquitylation and degradation in DNA-damaged yeast cells. Mol Cell Biol 2007; 27:3211-6. [PMID: 17296727 PMCID: PMC1899920 DOI: 10.1128/mcb.00091-07] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Treatment of yeast and human cells with DNA-damaging agents elicits lysine 48-linked polyubiquitylation of Rpb1, the largest subunit of RNA polymerase II (Pol II), which targets Pol II for proteasomal degradation. However, the ubiquitin ligase (E3) responsible for Pol II polyubiquitylation has not been identified in humans or the yeast Saccharomyces cerevisiae. Here we show that elongin A (Ela1) and cullin 3 (Cul3) are required for Pol II polyubiquitylation and degradation in yeast cells, and on the basis of these and other observations, we propose that an E3 comprised of elongin C (Elc1), Ela1, Cul3, and the RING finger protein Roc1 (Rbx1) mediates this process in yeast cells. This study provides, in addition to the identification of the E3 required for Pol II polyubiquitylation and degradation in yeast cells, the first evidence for a specific function in yeast for a member of the elongin C/BC-box protein/cullin family of ligases. Also, these observations raise the distinct possibility that the elongin C-containing ubiquitin ligase, the von Hippel-Lindau tumor suppressor complex, promotes Pol II polyubiquitylation and degradation in human cells.
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Affiliation(s)
- Balazs Ribar
- University of Texas Medical Branch at Galveston, 301 University Blvd., Galveston, TX 77555-1061, USA
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36
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Miyata K, Yasukawa T, Fukuda M, Takeuchi T, Yamazaki K, Sakumi K, Tamamori-Adachi M, Ohnishi Y, Ohtsuki Y, Nakabeppu Y, Kitajima S, Onishi S, Aso T. Induction of apoptosis and cellular senescence in mice lacking transcription elongation factor, Elongin A. Cell Death Differ 2006; 14:716-26. [PMID: 17170753 DOI: 10.1038/sj.cdd.4402067] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Elongin A is a transcription elongation factor that increases the overall rate of mRNA chain elongation by RNA polymerase II. To gain more insight into the physiological functions of Elongin A, we generated Elongin A-deficient mice. Elongin A homozygous mutant (Elongin A(-/-)) embryos demonstrated a severely retarded development and died at between days 10.5 and 12.5 of gestation, most likely due to extensive apoptosis. Moreover, mouse embryonic fibroblasts (MEFs) derived from Elongin A(-/-) embryos exhibited not only increased apoptosis but also senescence-like growth defects accompanied by the activation of p38 MAPK and p53. Knockdown of Elongin A in MEFs by RNA interference also dramatically induced the senescent phenotype. A study using inhibitors of p38 MAPK and p53 and the generation of Elongin A-deficient mice with p53-null background suggests that both the p38 MAPK and p53 pathways are responsible for the induction of senescence-like phenotypes, whereas additional signaling pathways appear to be involved in the mediation of apoptosis in Elongin A(-/-) cells. Taken together, our results suggest that Elongin A is required for the transcription of genes essential for early embryonic development and downregulation of its activity is tightly associated with cellular senescence.
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Affiliation(s)
- K Miyata
- Department of Functional Genomics, Kochi Medical School, Kohasu, Oko-cho, Nankoku, Kochi, Japan
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Yasukawa T, Sugimura K, Fukuda M, Yamazaki K, Kitajima S, Okumura K, Aso T. Functional characterization of a mammalian transcription factor, Elongin A. Biochem Biophys Res Commun 2006; 352:237-43. [PMID: 17112477 DOI: 10.1016/j.bbrc.2006.11.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Accepted: 11/06/2006] [Indexed: 11/17/2022]
Abstract
Elongin A is the transcriptionally active subunit of the Elongin complex that strongly stimulates the rate of elongation by RNA polymerase II (pol II) by suppressing the transient pausing of the polymerase at many sites along the DNA template. We have recently shown that Elongin A-deficient mice are embryonic lethal, and mouse embryonic fibroblasts (MEFs) derived from Elongin A(-/-) embryos display not only increased apoptosis but also senescence-like phenotypes accompanied by the activation of p53. To further understand the function of Elongin A in vivo, we have carried out the structure-function analysis of Elongin A and identified sequences critical to its nuclear localization and direct interaction with pol II. Moreover, we have analyzed the replication fork movement in wild-type and Elongin A(-/-) MEFs, and shown the possibility that the genomic instability observed in Elongin A(-/-) MEFs might be caused by the replication fork collapse due to Elongin A deficiency.
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Affiliation(s)
- Takashi Yasukawa
- Department of Functional Genomics, Kochi Medical School, Kohasu, Oko-cho, Nankoku, Kochi 783-8505, Japan
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Ribar B, Prakash L, Prakash S. Requirement of ELC1 for RNA polymerase II polyubiquitylation and degradation in response to DNA damage in Saccharomyces cerevisiae. Mol Cell Biol 2006; 26:3999-4005. [PMID: 16705154 PMCID: PMC1489084 DOI: 10.1128/mcb.00293-06] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Treatment of Saccharomyces cerevisiae and human cells with DNA-damaging agents such as UV light or 4-nitroquinoline-1-oxide induces polyubiquitylation of the largest RNA polymerase II (Pol II) subunit, Rpb1, which results in rapid Pol II degradation by the proteasome. Here we identify a novel role for the yeast Elc1 protein in mediating Pol II polyubiquitylation and degradation in DNA-damaged yeast cells and propose the involvement of a ubiquitin ligase, of which Elc1 is a component, in this process. In addition, we present genetic evidence for a possible involvement of Elc1 in Rad7-Rad16-dependent nucleotide excision repair (NER) of lesions from the nontranscribed regions of the genome and suggest a role for Elc1 in increasing the proficiency of repair of nontranscribed DNA, where as a component of the Rad7-Rad16-Elc1 ubiquitin ligase, it would promote the efficient turnover of the NER ensemble from the lesion site in a Rad23-19S proteasomal complex-dependent reaction.
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Affiliation(s)
- Balazs Ribar
- Sealy Center for Molecular Science, University of Texas Medical Branch at Galveston, Galveston, TX 77555-1061, USA
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39
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Kamura T, Maenaka K, Kotoshiba S, Matsumoto M, Kohda D, Conaway RC, Conaway JW, Nakayama KI. VHL-box and SOCS-box domains determine binding specificity for Cul2-Rbx1 and Cul5-Rbx2 modules of ubiquitin ligases. Genes Dev 2005; 18:3055-65. [PMID: 15601820 PMCID: PMC535916 DOI: 10.1101/gad.1252404] [Citation(s) in RCA: 371] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ECS (Elongin B/C-Cul2/Cul5-SOCS-box protein) complex is a member of a family of ubiquitin ligases that share a Cullin-Rbx module. SOCS-box proteins recruit substrates to the ECS complex and are linked to Cullin-Rbx via Elongin B/C. VHL has been implicated as a SOCS-box protein, but lacks a C-terminal sequence (downstream of the BC box) of the SOCS box. We now show that VHL specifically interacts with endogenous Cul2-Rbx1 in mammalian cells, whereas SOCS-box proteins associate with Cul5-Rbx2. We also identify LRR-1 and FEM1B as proteins that share a region of homology with VHL (the VHL box, including the BC box and downstream residues) and associate with Cul2-Rbx1. ECS complexes can thus be classified into two distinct protein assemblies, that is, those that contain a subunit with a VHL box (composed of the BC box and a downstream Cul2 box) that interacts with Cul2-Rbx1, and those that contain a subunit with a SOCS box (BC box and downstream Cul5 box) that interacts with Cul5-Rbx2. Domain-swapping analyses showed that the specificity of interaction of VHL-box and SOCS-box proteins with Cullin-Rbx modules is determined by the Cul2 and Cul5 boxes, respectively. Finally, RNAi-mediated knockdown of the Cul2-Rbx1 inhibited the VHL-mediated degradation of HIF-2alpha, whereas knockdown of Cul5-Rbx2 did not affect it. These data suggest that the functions of the Cul2-Rbx1 and Cul5-Rbx2 modules are distinct.
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Affiliation(s)
- Takumi Kamura
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
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40
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Gerber M, Tenney K, Conaway JW, Conaway RC, Eissenberg JC, Shilatifard A. Regulation of Heat Shock Gene Expression by RNA Polymerase II Elongation Factor, Elongin A. J Biol Chem 2005; 280:4017-20. [PMID: 15611125 DOI: 10.1074/jbc.c400487200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The elongation stage of transcription by RNA polymerase II (Pol II) has emerged as an essential regulated step. Elongin A (EloA) is the largest subunit of the Elongin complex that can increase the catalytic rate of mRNA synthesis by Pol II. We recently demonstrated that the Elongin A homologue in Drosophila, dEloA, is essential and has properties consistent with those of a Pol II elongation factor in vivo. The goal of this study was to test whether dEloA is required for heat shock gene transcription, since heat shock gene expression is thought to be controlled at the level of Pol II elongation. Here, we demonstrate that dEloA is rapidly recruited to heat shock loci with Pol II in response to heat shock. Furthermore, through the use of RNA interference in vivo, we show that dEloA is required for the proper expression of one of these genes, HSP70, and that its requirement for heat shock gene expression is exerted after the initiation of transcription at heat shock loci. Our data represent the first demonstration of an essential role for an RNA polymerase II elongation factor in the regulation of heat shock gene expression in an animal model.
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Affiliation(s)
- Mark Gerber
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University Health Sciences Center, Saint Louis, Missouri 63104, USA
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41
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Sims RJ, Belotserkovskaya R, Reinberg D. Elongation by RNA polymerase II: the short and long of it. Genes Dev 2004; 18:2437-68. [PMID: 15489290 DOI: 10.1101/gad.1235904] [Citation(s) in RCA: 533] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Appreciable advances into the process of transcript elongation by RNA polymerase II (RNAP II) have identified this stage as a dynamic and highly regulated step of the transcription cycle. Here, we discuss the many factors that regulate the elongation stage of transcription. Our discussion includes the classical elongation factors that modulate the activity of RNAP II, and the more recently identified factors that facilitate elongation on chromatin templates. Additionally, we discuss the factors that associate with RNAP II, but do not modulate its catalytic activity. Elongation is highlighted as a central process that coordinates multiple stages in mRNA biogenesis and maturation.
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Affiliation(s)
- Robert J Sims
- Howard Hughes Medical Institute, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
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42
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Heuzé ML, Guibal FC, Banks CA, Conaway JW, Conaway RC, Cayre YE, Benecke A, Lutz PG. ASB2 is an Elongin BC-interacting protein that can assemble with Cullin 5 and Rbx1 to reconstitute an E3 ubiquitin ligase complex. J Biol Chem 2004; 280:5468-74. [PMID: 15590664 DOI: 10.1074/jbc.m413040200] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The ankyrin repeat-containing protein with a suppressor of cytokine signaling box-2 (ASB2) gene was identified as a retinoic acid-response gene and a target of the promyelocytic leukemia-retinoic acid receptor-alpha oncogenic protein characteristic of acute promyelocytic leukemia. Expression of ASB2 in myeloid leukemia cells inhibits growth and promotes commitment, recapitulating an early step known to be critical for differentiation. Here we show that ASB2, by interacting with the Elongin BC complex, can assemble with Cullin5.Rbx1 to form an E3 ubiquitin ligase complex that stimulates polyubiquitination by the E2 ubiquitin-conjugating enzyme Ubc5. This is a first indication that a member of the ASB protein family, ASB2, is a subunit of an ECS (Elongin C-Cullin-SOCS box)-type E3 ubiquitin ligase complex. Altogether, our results strongly suggest that ASB2 targets specific proteins to destruction by the proteasome in leukemia cells that have been induced to differentiate.
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Affiliation(s)
- Mélina L Heuzé
- INSERM, U417, Hôpital Robert Debré, 48 Boulevard Serurier, F-75935 Paris Cedex 19, France
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43
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Gerber M, Eissenberg JC, Kong S, Tenney K, Conaway JW, Conaway RC, Shilatifard A. In vivo requirement of the RNA polymerase II elongation factor elongin A for proper gene expression and development. Mol Cell Biol 2004; 24:9911-9. [PMID: 15509793 PMCID: PMC525478 DOI: 10.1128/mcb.24.22.9911-9919.2004] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A number of transcription factors that increase the catalytic rate of mRNA synthesis by RNA polymerase II (Pol II) have been purified from higher eukaryotes. Among these are the ELL family, DSIF, and the heterotrimeric elongin complex. Elongin A, the largest subunit of the elongin complex, is the transcriptionally active subunit, while the smaller elongin B and C subunits appear to act as regulatory subunits. While much is known about the in vitro properties of elongin A and other members of this class of elongation factors, the physiological role(s) of these proteins remain largely unclear. To elucidate in vivo functions of elongin A, we have characterized its Drosophila homologue (dEloA). dEloA associates with transcriptionally active puff sites within Drosophila polytene chromosomes and exhibits many of the expected biochemical and cytological properties consistent with a Pol II-associated elongation factor. RNA interference-mediated depletion of dEloA demonstrated that elongin A is an essential factor that is required for proper metamorphosis. Consistent with this observation, dEloA expression peaks during the larval stages of development, suggesting that this factor may be important for proper regulation of developmental events during these stages. The discovery of the role of elongin A in an in vivo model system defines the novel contribution played by RNA polymerase II elongation machinery in regulation of gene expression that is required for proper development.
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Affiliation(s)
- Mark Gerber
- Edward A. Doisy Department of Biochemistry and Molecular Biology, St. Louis University Health Sciences Center, 1402 South Grand Blvd., St. Louis, MO 63104, USA
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44
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Li Z, Metze D, Nashan D, Müller-Tidow C, Serve HL, Poremba C, Luger TA, Böhm M. Expression of SOCS-1, suppressor of cytokine signalling-1, in human melanoma. J Invest Dermatol 2004; 123:737-45. [PMID: 15373779 DOI: 10.1111/j.0022-202x.2004.23408.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Cytokine resistance is a well-established feature of melanoma cell progression and represents also a major obstacle in immunotherapy of patients with metastatic melanoma. To check whether suppressors of cytokine signalling (SOCS) play a role in cytokine resistance and tumor progression of melanoma, we investigated the expression and regulation of SOCS-1, an established negative regulator of interleukin-6 (IL-6) and interferon (IFN) signalling. In vitro SOCS-1 transcripts were detectable by RT-PCR in 8 out of 8 human melanoma cell lines derived from different tumor stages. Normal human melanocytes also expressed SOCS-1 mRNA in the presence or absence of artificial growth factors. Both IL-6 and alpha-IFN induced rapid and transient SOCS-1 mRNA expression in WM35 and WM9 melanoma cells. At the protein level, SOCS-1 was undetectable in normal human melanocytes whereas uniformly expressed in all tested melanoma cell lines. The aberrant SOCS-1 protein expression in melanoma cells was recapitalized in situ as shown by immunohistochemical analysis. SOCS-1 immunoreactivity was closely related to tumor invasion (Clark level), tumor thickness according to Breslow, and stage of the disease. In contrast, melanocytes in normal skin or melanocytic nevi lacked SOCS-1 protein expression. Our findings show that melanoma cells express a member of the SOCS family, SOCS-1, in vitro and in situ. SOCS-1 is a progression marker of human melanoma and may downregulate biological responses by endogenous and/or therapeutically administered cytokines.
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Affiliation(s)
- Zhuo Li
- Department of Dermatology and Ludwig Boltzmann Institute for Cell Biology and Immunobiology of the Skin, University of Münster, Münster, Germany
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45
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Hanada T, Kinjyo I, Inagaki-Ohara K, Yoshimura A. Negative regulation of cytokine signaling by CIS/SOCS family proteins and their roles in inflammatory diseases. Rev Physiol Biochem Pharmacol 2004; 149:72-86. [PMID: 12687406 DOI: 10.1007/s10254-003-0015-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Immune and inflammatory systems are controlled by multiple cytokines, including interleukins (ILs) and interferons. These cytokines exert their biological functions through Janus tyrosine kinases (JAKs) and STAT transcription factors. The CIS (cytokine-inducible SH2 protein) and SOCS (suppressors of cytokine signaling) are a family of intracellular proteins, several of which have emerged as key physiological regulators of cytokine responses, including those that regulate the inflammatory systems. In this review, we focused on the molecular mechanism of the action of CIS/SOCS family proteins and their roles in inflammatory diseases. Furthermore, we illustrate several approaches for treating inflammatory diseases by modulating extracellular and intracellular signaling pathways.
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Affiliation(s)
- T Hanada
- Division of Molecular and Cellular Immunology, Medical Institute of Bioregulation, Kyushu University, Maidashi, 812-8582 Higashi-ku, Fukuoka, Japan
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46
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Shilatifard A. Transcriptional elongation control by RNA polymerase II: a new frontier. ACTA ACUST UNITED AC 2004; 1677:79-86. [PMID: 15020049 DOI: 10.1016/j.bbaexp.2003.11.013] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2003] [Revised: 11/18/2003] [Accepted: 11/18/2003] [Indexed: 01/22/2023]
Abstract
The transcription elongation complex, once thought to be composed of merely the DNA template, RNA polymerase II and the nascent RNA transcript, is now burgeoning as a unit as multifaceted and complicated as the transcription initiation complex. Studies concentrated in defining the elongation stage of transcription during the past recent years have resulted in the discovery of a diverse collection of transcription elongation factors that are either directly involved in the regulation of the rate of the elongating RNA polymerase II or can modulate messenger RNA (mRNA) processing and transport. Such studies have demonstrated that the elongation stage of transcription is highly regulated and has opened a new era of studies defining the molecular role of such transcription elongation factors in cellular development, differentiation and disease progression. Recent studies on the role of RNA polymerase II elongation factors in regulating of the overall rate of transcription both in vitro and in vivo, histone modification by methylation and organismal development will be reviewed here.
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Affiliation(s)
- Ali Shilatifard
- Department of Biochemistry and the Cancer Center, Saint Louis University School of Medicine, 1402 South Grand Blvd, St. Louis, MO 63104, USA.
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47
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Kong SE, Shilatifard A, Conaway RC, Conaway JW. Preparation and assay of RNA polymerase II elongation factors elongin and ELL. Methods Enzymol 2004; 371:276-83. [PMID: 14712707 DOI: 10.1016/s0076-6879(03)71020-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Affiliation(s)
- Stephanie E Kong
- Stowers Institute Medical Research, 1000 E. 50th Street, Kansas City, Missouri 64110, USA
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48
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Abstract
Synthesis of eukaryotic mRNA by RNA polymerase II is an elaborate biochemical process that requires the concerted action of a large set of transcription factors. RNA polymerase II transcription proceeds through multiple stages designated preinitiation, initiation, and elongation. Historically, studies of the elongation stage of eukaryotic mRNA synthesis have lagged behind studies of the preinitiation and initiation stages; however, in recent years, efforts to elucidate the mechanisms governing elongation have led to the discovery of a diverse collection of transcription factors that directly regulate the activity of elongating RNA polymerase II. Moreover, these studies have revealed unanticipated roles for the RNA polymerase II elongation complex in such processes as DNA repair and recombination and the proper processing and nucleocytoplasmic transport of mRNA. Below we describe these recent advances, which highlight the important role of the RNA polymerase II elongation complex in regulation of eukaryotic gene expression.
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Affiliation(s)
- Ali Shilatifard
- Edward A. Doisey Department of Biochemistry, St. Louis University School of Medicine, St. Louis, Missouri 63104, USA.
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49
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Tamura K, Miyata K, Sugahara K, Onishi S, Shuin T, Aso T. Identification of EloA-BP1, a novel Elongin A binding protein with an exonuclease homology domain. Biochem Biophys Res Commun 2003; 309:189-95. [PMID: 12943681 DOI: 10.1016/s0006-291x(03)01556-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Elongin complex stimulates the rate of transcription elongation by RNA polymerase II by suppressing the transient pausing of the polymerase at many sites along the DNA template. Elongin is composed of a transcriptionally active A subunit, and two positive regulatory B and C subunits. Although the NH(2)-terminal approximately 120 amino acid region of Elongin A is dispensable for its transcriptional activity in vitro, it shares significant sequence similarity with the NH(2)-terminus of other class of transcription factors SII and CRSP70, suggesting that the NH(2)-terminus mediates interactions important for the regulation of transcription in vivo. To identify proteins that can bind to these conserved sequences, a human B cell cDNA library was screened using the NH(2)-terminus of Elongin A as bait in a yeast two-hybrid system. Here, we report on the cloning and characterization of a novel human exonuclease domain-containing protein, Elongin A-binding protein 1 (EloA-BP1). EloA-BP1 is composed of 1221 amino acids and its mRNA is ubiquitously expressed. Double immunofluorescence labeling in COS7 cells suggested that EloA-BP1 and Elongin A are colocalized to the cell nucleus. By using an in vitro binding assay, we show that EloA-BP1 is capable of binding not only the NH(2)-terminal approximately 120 amino acid region of Elongin A, but also that of SII. Although the purified EloA-BP1 had no detectable effect on the rate of transcription elongation in vitro, it may play some role in the regulation of elongation in vivo.
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Affiliation(s)
- Kenji Tamura
- Department of Functional Genomics, Faculty of Medicine, Kochi Medical School, Kohasu, Oko-cho, Nankoku, Kochi, Japan
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50
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Gerber M, Shilatifard A. Transcriptional elongation by RNA polymerase II and histone methylation. J Biol Chem 2003; 278:26303-6. [PMID: 12764140 DOI: 10.1074/jbc.r300014200] [Citation(s) in RCA: 143] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
mRNA synthesis in eukaryotic organisms is a key biological process that is regulated at multiple levels. From the covalent modifications of chromatin by a number of chromatin remodeling complexes during the initiation and activation steps of transcription to the processing of mRNA transcripts, a very large consortium of proteins and multiprotein complexes is critical for gene expression by RNA polymerase II. The list of proteins essential for the successful synthesis of mRNA continues to grow at a rapid pace. Recent advances in this area of research have been focused on transcription through chromatin. In this article, we will review the recent literature linking the key biochemical process of transcriptional elongation by RNA polymerase II to histone methylation by COMPASS, Dot1p, and Set2 methyltransferases.
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Affiliation(s)
- Mark Gerber
- Department of Biochemistry and the St. Louis University Cancer Center, St. Louis University School of Medicine, St. Louis, Missouri 63104, USA
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