1
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Collin A, González-Jiménez A, González-Jiménez MDC, Alfonso MJ, Calvo O. The Role of S. cerevisiae Sub1/PC4 in Transcription Elongation Depends on the C-Terminal Region and Is Independent of the ssDNA Binding Domain. Cells 2022; 11:cells11203320. [PMID: 36291192 PMCID: PMC9600219 DOI: 10.3390/cells11203320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/30/2022] Open
Abstract
Saccharomyces cerevisiae Sub1 (ScSub1) has been defined as a transcriptional stimulatory protein due to its homology to the ssDNA binding domain (ssDBD) of human PC4 (hPC4). Recently, PC4/Sub1 orthologues have been elucidated in eukaryotes, prokaryotes, and bacteriophages with functions related to DNA metabolism. Additionally, ScSub1 contains a unique carboxyl–terminal region (CT) of unknown function up to date. Specifically, it has been shown that Sub1 is required for transcription activation, as well as other processes, throughout the transcription cycle. Despite the progress that has been made in understanding the mechanism underlying Sub1′s functions, some questions remain unanswered. As a case in point: whether Sub1’s roles in initiation and elongation are differentially predicated on distinct regions of the protein or how Sub1′s functions are regulated. Here, we uncover some residues that are key for DNA–ScSub1 interaction in vivo, localized in the ssDBD, and required for Sub1 recruitment to promoters. Furthermore, using an array of genetic and molecular techniques, we demonstrate that the CT region is required for transcription elongation by RNA polymerase II (RNAPII). Altogether, our data indicate that Sub1 plays a dual role during transcription—in initiation through the ssDBD and in elongation through the CT region.
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Affiliation(s)
- Alejandro Collin
- Cátedra de Bioquímica y Biología Molecular, Facultad de Ciencias Médicas-INICSA, CONICET-Universidad Nacional de Córdoba, Haya de la Torre s/n, Pabellón Argentina, 2º piso. Ciudad Universitaria, Cordoba CP5000, Argentina
| | - Araceli González-Jiménez
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, C/ Zacarías González, nº2, 37007 Salamanca, Spain
| | | | - Manuel J. Alfonso
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, C/ Zacarías González, nº2, 37007 Salamanca, Spain
| | - Olga Calvo
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, C/ Zacarías González, nº2, 37007 Salamanca, Spain
- Correspondence:
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2
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Hou Y, Gan T, Fang T, Zhao Y, Luo Q, Liu X, Qi L, Zhang Y, Jia F, Han J, Li S, Wang S, Wang F. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3070-3082. [PMID: 35258624 PMCID: PMC8989551 DOI: 10.1093/nar/gkac151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/16/2022] [Accepted: 02/20/2022] [Indexed: 11/23/2022] Open
Abstract
Pyridostatin (PDS) is a well-known G-quadruplex (G4) inducer and stabilizer, yet its target genes have remained unclear. Herein, applying MS proteomics strategy, we revealed PDS significantly downregulated 22 proteins but upregulated 16 proteins in HeLa cancer cells, of which the genes both contain a number of G4 potential sequences, implying that PDS regulation on gene expression is far more complicated than inducing/stabilizing G4 structures. The PDS-downregulated proteins consequently upregulated 6 proteins to activate cyclin and cell cycle regulation, suggesting that PDS itself is not a potential anticancer agent, at least toward HeLa cancer cells. Importantly, SUB1, which encodes human positive cofactor and DNA lesion sensor PC4, was downregulated by 4.76-fold. Further studies demonstrated that the downregulation of PC4 dramatically promoted the cytotoxicity of trans-[PtCl2(NH3)(thiazole)] (trans-PtTz) toward HeLa cells to a similar level of cisplatin, contributable to retarding the repair of 1,3-trans-PtTz crosslinked DNA lesion mediated by PC4. These findings not only provide new insights into better understanding on the biological functions of PDS but also implicate a strategy for the rational design of novel multi-targeting platinum anticancer drugs via conjugation of PDS as a ligand to the coordination scaffold of transplatin for battling drug resistance to cisplatin.
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Affiliation(s)
- Yinzhu Hou
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Analytical Chemistry for Living Biosystems; National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, No. 2 Zhongguancun North First Street, Haidian District, 100190 Beijing, P.R. China
- College of Chemical Science, University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, 100049 Beijing, P.R. China
| | - Tieliang Gan
- College of Chemical Science, University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, 100049 Beijing, P.R. China
| | - Tiantian Fang
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Analytical Chemistry for Living Biosystems; National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, No. 2 Zhongguancun North First Street, Haidian District, 100190 Beijing, P.R. China
| | - Yao Zhao
- Correspondence may also be addressed to Yao Zhao. Tel: +86 010 62529069;
| | - Qun Luo
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Analytical Chemistry for Living Biosystems; National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, No. 2 Zhongguancun North First Street, Haidian District, 100190 Beijing, P.R. China
- College of Chemical Science, University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, 100049 Beijing, P.R. China
| | - Xingkai Liu
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Analytical Chemistry for Living Biosystems; National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, No. 2 Zhongguancun North First Street, Haidian District, 100190 Beijing, P.R. China
- College of Chemical Science, University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, 100049 Beijing, P.R. China
| | - Luyu Qi
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Analytical Chemistry for Living Biosystems; National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, No. 2 Zhongguancun North First Street, Haidian District, 100190 Beijing, P.R. China
- College of Chemical Science, University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, 100049 Beijing, P.R. China
| | - Yanyan Zhang
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Analytical Chemistry for Living Biosystems; National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, No. 2 Zhongguancun North First Street, Haidian District, 100190 Beijing, P.R. China
| | - Feifei Jia
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Analytical Chemistry for Living Biosystems; National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, No. 2 Zhongguancun North First Street, Haidian District, 100190 Beijing, P.R. China
| | - Juanjuan Han
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Analytical Chemistry for Living Biosystems; National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, No. 2 Zhongguancun North First Street, Haidian District, 100190 Beijing, P.R. China
| | - Shumu Li
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Analytical Chemistry for Living Biosystems; National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, No. 2 Zhongguancun North First Street, Haidian District, 100190 Beijing, P.R. China
| | - Shijun Wang
- Correspondence may also be addressed to Shijun Wang. Tel: +86 0531 89628750;
| | - Fuyi Wang
- To whom correspondence should be addressed. Tel: +86 010 62529069;
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3
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Crooke ST, Liang XH, Baker BF, Crooke RM. Antisense technology: A review. J Biol Chem 2021; 296:100416. [PMID: 33600796 PMCID: PMC8005817 DOI: 10.1016/j.jbc.2021.100416] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/15/2022] Open
Abstract
Antisense technology is beginning to deliver on the broad promise of the technology. Ten RNA-targeted drugs including eight single-strand antisense drugs (ASOs) and two double-strand ASOs (siRNAs) have now been approved for commercial use, and the ASOs in phase 2/3 trials are innovative, delivered by multiple routes of administration and focused on both rare and common diseases. In fact, two ASOs are used in cardiovascular outcome studies and several others in very large trials. Interest in the technology continues to grow, and the field has been subject to a significant number of reviews. In this review, we focus on the molecular events that result in the effects observed and use recent clinical results involving several different ASOs to exemplify specific molecular mechanisms and specific issues. We conclude with the prospective on the technology.
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Affiliation(s)
- Stanley T Crooke
- Core Antisense Research, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA.
| | - Xue-Hai Liang
- Core Antisense Research, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA
| | - Brenda F Baker
- Development Communication, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA
| | - Rosanne M Crooke
- Antisense Drug Discovery, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA
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4
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Crooke ST, Vickers TA, Liang XH. Phosphorothioate modified oligonucleotide-protein interactions. Nucleic Acids Res 2020; 48:5235-5253. [PMID: 32356888 PMCID: PMC7261153 DOI: 10.1093/nar/gkaa299] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/08/2020] [Accepted: 04/17/2020] [Indexed: 12/18/2022] Open
Abstract
Antisense oligonucleotides (ASOs) interact with target RNAs via hybridization to modulate gene expression through different mechanisms. ASO therapeutics are chemically modified and include phosphorothioate (PS) backbone modifications and different ribose and base modifications to improve pharmacological properties. Modified PS ASOs display better binding affinity to the target RNAs and increased binding to proteins. Moreover, PS ASO protein interactions can affect many aspects of their performance, including distribution and tissue delivery, cellular uptake, intracellular trafficking, potency and toxicity. In this review, we summarize recent progress in understanding PS ASO protein interactions, highlighting the proteins with which PS ASOs interact, the influence of PS ASO protein interactions on ASO performance, and the structure activity relationships of PS ASO modification and protein interactions. A detailed understanding of these interactions can aid in the design of safer and more potent ASO drugs, as illustrated by recent findings that altering ASO chemical modifications dramatically improves therapeutic index.
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5
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Janowski R, Niessing D. The large family of PC4-like domains - similar folds and functions throughout all kingdoms of life. RNA Biol 2020; 17:1228-1238. [PMID: 32476604 PMCID: PMC7549692 DOI: 10.1080/15476286.2020.1761639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RNA- and DNA-binding domains are essential building blocks for specific regulation of gene expression. While a number of canonical nucleic acid binding domains share sequence and structural conservation, others are less obviously linked by evolutionary traits. In this review, we describe a protein fold of about 150 aa in length, bearing a conserved β-β-β-β-α-linker-β-β-β-β-α topology and similar nucleic acid binding properties but no apparent sequence conservation. The same overall fold can also be achieved by dimerization of two proteins, each bearing a β-β-β-β-α topology. These proteins include but are not limited to the transcription factors PC4 and P24 from humans and plants, respectively, the human RNA-transport factor Pur-α (also termed PURA), as well as the ssDNA-binding SP_0782 protein from Streptococcus pneumonia and the bacteriophage coat proteins PP7 and MS2. Besides their common overall topology, these proteins share common nucleic acids binding surfaces and thus functional similarity. We conclude that these PC4-like domains include proteins from all kingdoms of life and are much more abundant than previously known.
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Affiliation(s)
- Robert Janowski
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health , Neuherberg, Germany
| | - Dierk Niessing
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health , Neuherberg, Germany.,Institute of Pharmaceutical Biotechnology, Ulm University , Ulm, Germany
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6
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Vickers TA, Migawa MT, Seth PP, Crooke ST. Interaction of ASOs with PC4 Is Highly Influenced by the Cellular Environment and ASO Chemistry. J Am Chem Soc 2020; 142:9661-9674. [PMID: 32374993 DOI: 10.1021/jacs.0c01808] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The activity of PS-ASOs is strongly influenced by association with both inter- and intracellular proteins. The sequence, chemical nature, and structure of the ASO can have profound influences on the interaction of PS-ASOs with specific proteins. A more thorough understanding of how these pharmacological agents interact with various proteins and how chemical modifications, sequence, and structure influence interactions with proteins is needed to inform future ASO design efforts. To better understand the chemistry of PS-ASO interactions, we have focused on human positive cofactor 4 (PC4). Although several studies have investigated the in vitro binding properties of PC4 with endogenous nucleic acids, little is known about the chemistry of interaction of PS-ASOs with this protein. Here we examine in detail the impact of ASO backbone chemistry, 2'-modifications, and buffer environment on the binding affinity of PC4. In addition, using site-directed mutagenesis, we identify those amino acids that are specifically required for ASO binding interactions, and by substitution of abasic nucleotides we identify the positions on the ASO that most strongly influence affinity for PC4. Finally, to confirm that the interactions observed in vitro are biologically relevant, we use a recently developed complementation reporter system to evaluate the kinetics and subcellular localization of the interaction of ASO and PC4 in live cells.
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Affiliation(s)
- Timothy A Vickers
- Department of Core Antisense Research, IONIS Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Michael T Migawa
- Department of Medicinal ChemistryIONIS Pharmaceuticals, Inc.2855 Gazelle CourtCarlsbadCalifornia92010United States
| | - Punit P Seth
- Department of Medicinal ChemistryIONIS Pharmaceuticals, Inc.2855 Gazelle CourtCarlsbadCalifornia92010United States
| | - Stanley T Crooke
- Department of Core Antisense Research, IONIS Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
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7
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Hyjek-Składanowska M, Vickers TA, Napiórkowska A, Anderson BA, Tanowitz M, Crooke ST, Liang XH, Seth PP, Nowotny M. Origins of the Increased Affinity of Phosphorothioate-Modified Therapeutic Nucleic Acids for Proteins. J Am Chem Soc 2020; 142:7456-7468. [PMID: 32202774 DOI: 10.1021/jacs.9b13524] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The phosphorothioate backbone modification (PS) is one of the most widely used chemical modifications for enhancing the drug-like properties of nucleic acid-based drugs, including antisense oligonucleotides (ASOs). PS-modified nucleic acid therapeutics show improved metabolic stability from nuclease-mediated degradation and exhibit enhanced interactions with plasma, cell-surface, and intracellular proteins, which facilitates their tissue distribution and cellular uptake in animals. However, little is known about the structural basis of the interactions of PS nucleic acids with proteins. Here, we report a crystal structure of the DNA-binding domain of a model ASO-binding protein PC4, in complex with a full PS 2'-OMe DNA gapmer ASO. To our knowledge this is the first structure of a complex between a protein and fully PS nucleic acid. Each PC4 dimer comprises two DNA-binding interfaces. In the structure one interface binds the 5'-terminal 2'-OMe PS flank of the ASO, while the other interface binds the regular PS DNA central part in the opposite polarity. As a result, the ASO forms a hairpin-like structure. ASO binding also induces the formation of a dimer of dimers of PC4, which is stabilized by base pairing between homologous regions of the ASOs bound by each dimer of PC4. The protein interacts with the PS nucleic acid through a network of electrostatic and hydrophobic interactions, which provides insights into the origins for the enhanced affinity of PS for proteins. The importance of these contacts was further confirmed in a NanoBRET binding assay using a Nano luciferase tagged PC4 acting as the BRET donor, to a fluorescently conjugated ASO acting as the BRET acceptor. Overall, our results provide insights into the molecular forces that govern the interactions of PS ASOs with cellular proteins and provide a potential model for how these interactions can template protein-protein interactions causative of cellular toxicity.
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Affiliation(s)
- Malwina Hyjek-Składanowska
- Structural Biology Center, International Institute of Molecular and Cell Biology, 4 Trojdena St., 02-109 Warsaw, Poland.,Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland
| | - Timothy A Vickers
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Agnieszka Napiórkowska
- Structural Biology Center, International Institute of Molecular and Cell Biology, 4 Trojdena St., 02-109 Warsaw, Poland.,Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland
| | - Brooke A Anderson
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Michael Tanowitz
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Stanley T Crooke
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Xue-Hai Liang
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Punit P Seth
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Marcin Nowotny
- Structural Biology Center, International Institute of Molecular and Cell Biology, 4 Trojdena St., 02-109 Warsaw, Poland.,Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland
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8
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Boon M, De Zitter E, De Smet J, Wagemans J, Voet M, Pennemann FL, Schalck T, Kuznedelov K, Severinov K, Van Meervelt L, De Maeyer M, Lavigne R. 'Drc', a structurally novel ssDNA-binding transcription regulator of N4-related bacterial viruses. Nucleic Acids Res 2020; 48:445-459. [PMID: 31724707 PMCID: PMC7145618 DOI: 10.1093/nar/gkz1048] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/16/2019] [Accepted: 10/23/2019] [Indexed: 12/22/2022] Open
Abstract
Bacterial viruses encode a vast number of ORFan genes that lack similarity to any other known proteins. Here, we present a 2.20 Å crystal structure of N4-related Pseudomonas virus LUZ7 ORFan gp14, and elucidate its function. We demonstrate that gp14, termed here as Drc (ssDNA-binding RNA Polymerase Cofactor), preferentially binds single-stranded DNA, yet contains a structural fold distinct from other ssDNA-binding proteins (SSBs). By comparison with other SSB folds and creation of truncation and amino acid substitution mutants, we provide the first evidence for the binding mechanism of this unique fold. From a biological perspective, Drc interacts with the phage-encoded RNA Polymerase complex (RNAPII), implying a functional role as an SSB required for the transition from early to middle gene transcription during phage infection. Similar to the coliphage N4 gp2 protein, Drc likely binds locally unwound middle promoters and recruits the phage RNA polymerase. However, unlike gp2, Drc does not seem to need an additional cofactor for promoter melting. A comparison among N4-related phage genera highlights the evolutionary diversity of SSB proteins in an otherwise conserved transcription regulation mechanism.
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Affiliation(s)
- Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Elke De Zitter
- Department of Chemistry, Biomolecular Architecture, KU Leuven, Leuven 3001, Belgium
| | - Jeroen De Smet
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Jeroen Wagemans
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Marleen Voet
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Friederike L Pennemann
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Thomas Schalck
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | | | | | - Luc Van Meervelt
- Department of Chemistry, Biomolecular Architecture, KU Leuven, Leuven 3001, Belgium
| | - Marc De Maeyer
- Department of Chemistry, Laboratory of Biomolecular Modelling and Design, KU Leuven, Leuven 3001, Belgium
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
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9
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Gong Y, Li S, Li Y, Zhu J, Yang Y, Liu M. Mutation of leucine 20 causes a change of local conformation indirectly impairing the DNA binding of SP_0782 from Streptococcus pneumoniae. Biochem Biophys Res Commun 2020; 524:103-108. [PMID: 31980174 DOI: 10.1016/j.bbrc.2020.01.057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 01/11/2020] [Indexed: 12/24/2022]
Abstract
SP_0782 from Streptococcus pneumoniae is a dimeric PC4-like protein binding single-stranded DNA (ssDNA), and is potentially involved in maintenance of genome stability and natural transformation. SP_0782 binds with different lengths of ssDNA in various patterns through accommodating nucleotides differently in its two DNA-binding regions (DBRs). Here, we report the characterization of a novel site, leucine 20 (L20), which is not located in the DBRs but impairs the DNA binding when mutated to alanine (L20A). The L20A mutation markedly reduced the DNA-binding affinity of SP_0782 for ssDNA dT19G1, and affected the formation of high-order SP_0782:dT19G1 complexes. The side chain of L20 shows interactions with several residues at the backside of the DBRs in apo SP_0782 structure, and the L20A mutation led to a change of circular dichroism (CD) spectrum and broad chemical shift perturbations (CSPs) in NMR spectrum compared with the wild type. The most affected residues in NMR spectrum included F39 and R49 located in DBR2, as well as K60 in DBR1, which was suggested to be important for cooperative binding of ssDNA by the two subunits in SP_0782 dimer. Thus, the L20A mutation caused a local conformational change of SP_0782, which exerted an indirect effect on the DNA-binding interface and therefore impaired the affinity for ssDNA dT19G1. Interestingly, this L20 site is conserved in bacterial but not eukaryotic PC4-like proteins, suggesting an evolutionary divergence. This study provides an insight into the structure-function relationship of SP_0782, and an amino-acid site probably targeted for inhibiting bacteria selectively.
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Affiliation(s)
- Yixuan Gong
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuangli Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China.
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China.
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China
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10
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Li S, Lu G, Fang X, Ramelot TA, Kennedy MA, Zhou X, Gong P, Zhang X, Liu M, Zhu J, Yang Y. Structural insight into the length-dependent binding of ssDNA by SP_0782 from Streptococcus pneumoniae, reveals a divergence in the DNA-binding interface of PC4-like proteins. Nucleic Acids Res 2020; 48:432-444. [PMID: 31713614 PMCID: PMC7145681 DOI: 10.1093/nar/gkz1045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/30/2019] [Accepted: 11/07/2019] [Indexed: 12/13/2022] Open
Abstract
SP_0782 from Streptococcus pneumoniae is a dimeric protein that potentially binds with single-stranded DNA (ssDNA) in a manner similar to human PC4, the prototype of PC4-like proteins, which plays roles in transcription and maintenance of genome stability. In a previous NMR study, SP_0782 exhibited an ssDNA-binding property different from YdbC, a prokaryotic PC4-like protein from Lactococcus lactis, but the underlying mechanism remains unclear. Here, we show that although SP_0782 adopts an overall fold similar to those of PC4 and YdbC, the ssDNA length occupied by SP_0782 is shorter than those occupied by PC4 and YdbC. SP_0782 exhibits varied binding patterns for different lengths of ssDNA, and tends to form large complexes with ssDNA in a potential high-density binding manner. The structures of SP_0782 complexed with different ssDNAs reveal that the varied binding patterns are associated with distinct capture of nucleotides in two major DNA-binding regions of SP_0782. Moreover, a comparison of known structures of PC4-like proteins complexed with ssDNA reveals a divergence in the binding interface between prokaryotic and eukaryotic PC4-like proteins. This study provides insights into the ssDNA-binding mechanism of PC4-like proteins, and benefits further study regarding the biological function of SP_0782, probably in DNA protection and natural transformation.
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MESH Headings
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Binding Sites
- Crystallography, X-Ray
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- DNA-Binding Proteins/chemistry
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Humans
- Kinetics
- Lactococcus lactis/genetics
- Lactococcus lactis/metabolism
- Models, Molecular
- Nucleic Acid Conformation
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Folding
- Protein Interaction Domains and Motifs
- Streptococcus pneumoniae/genetics
- Streptococcus pneumoniae/metabolism
- Thermodynamics
- Transcription Factors/chemistry
- Transcription Factors/genetics
- Transcription Factors/metabolism
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Affiliation(s)
- Shuangli Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoliang Lu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiang Fang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Theresa A Ramelot
- Department of Chemistry and Biochemistry, and the Northeast Structural Genomics Consortium, Miami University, Oxford, OH 45056, USA
| | - Michael A Kennedy
- Department of Chemistry and Biochemistry, and the Northeast Structural Genomics Consortium, Miami University, Oxford, OH 45056, USA
| | - Xin Zhou
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
| | - Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xu Zhang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
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11
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Roychowdhury A, Joret C, Bourgeois G, Heurgué-Hamard V, Lafontaine DLJ, Graille M. The DEAH-box RNA helicase Dhr1 contains a remarkable carboxyl terminal domain essential for small ribosomal subunit biogenesis. Nucleic Acids Res 2019; 47:7548-7563. [PMID: 31188444 PMCID: PMC6698733 DOI: 10.1093/nar/gkz529] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/28/2019] [Accepted: 06/03/2019] [Indexed: 01/02/2023] Open
Abstract
Ribosome biogenesis is an essential process in all living cells, which entails countless highly sequential and dynamic structural reorganization events. These include formation of dozens RNA helices through Watson-Crick base-pairing within ribosomal RNAs (rRNAs) and between rRNAs and small nucleolar RNAs (snoRNAs), transient association of hundreds of proteinaceous assembly factors to nascent precursor (pre-)ribosomes, and stable assembly of ribosomal proteins. Unsurprisingly, the largest group of ribosome assembly factors are energy-consuming proteins (NTPases) including 25 RNA helicases in budding yeast. Among these, the DEAH-box Dhr1 is essential to displace the box C/D snoRNA U3 from the pre-rRNAs where it is bound in order to prevent premature formation of the central pseudoknot, a dramatic irreversible long-range interaction essential to the overall folding of the small ribosomal subunit. Here, we report the crystal structure of the Dhr1 helicase module, revealing the presence of a remarkable carboxyl-terminal domain essential for Dhr1 function in ribosome biogenesis in vivo and important for its interaction with its coactivator Utp14 in vitro. Furthermore, we report the functional consequences on ribosome biogenesis of DHX37 (human Dhr1) mutations found in patients suffering from microcephaly and other neurological diseases.
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Affiliation(s)
| | - Clément Joret
- RNA Molecular Biology, ULB Cancer Research Center (U-CRC), Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles (ULB), B-6041 Charleroi-Gosselies, Belgium
| | | | | | - Denis L J Lafontaine
- RNA Molecular Biology, ULB Cancer Research Center (U-CRC), Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles (ULB), B-6041 Charleroi-Gosselies, Belgium
| | - Marc Graille
- BIOC, CNRS, Ecole polytechnique, IP Paris, F-91128 Palaiseau, France
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12
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Zhao Y, Zhang Y, Huang J, Wang S, Yi L, Zhang X, Xu M, Fang X, Liu J. The effect of phosphate ion on the ssDNA binding mode of MoSub1, a Sub1/PC4 homolog from rice blast fungus. Proteins 2018; 87:257-264. [PMID: 30561148 DOI: 10.1002/prot.25647] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/21/2018] [Accepted: 12/12/2018] [Indexed: 11/09/2022]
Abstract
MoSub1 is an ortholog of yeast single stranded DNA binding protein Sub1 or human PC4 from rice blast fungus. All of them share a similar DNA binding region and may have similar biological roles. The well-studied Sub1/PC4 has been reported to play multiple roles in DNA metabolic processes, such as transcription and DNA repair and their DNA binding capacity is significantly affected by phosphorylation. Here, we determined the crystal structure of MoSub1 complexed with ssDNA in a phosphate solution. The crystal structure of the MoSub1-ssDNA complex was solved to a resolution of 2.04 Å. A phosphate ion at the interface of the protein-DNA interaction of the complex bridged the lys84 of the protein and two nucleotides. The DNA was bound in novel mode (L mode) in the MoSub1 complex in the presence of phosphate ions, while DNA bound in the straight mode in the absence of the phosphate ion and in U mode in the same binding motif of the PC4-ssDNA complex. The crystal structure of the complex and a small-angle X-ray scattering analysis revealed that the phosphate ion at the protein-DNA interface affected the DNA binding mode of MoSub1 to oligo-DNA and provided a new structural clue for studying its functions.
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Affiliation(s)
- Yanxiang Zhao
- Department of Plant Pathology, and MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing, China.,College of Plant Health and Medicine, and Key Lab of Integrated Crop Disease and Pest Management of Shandong Province, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Yikan Zhang
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jinguang Huang
- Department of Plant Pathology, and MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing, China.,College of Plant Health and Medicine, and Key Lab of Integrated Crop Disease and Pest Management of Shandong Province, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Shanshan Wang
- Department of Plant Pathology, and MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing, China
| | - Long Yi
- Department of Plant Pathology, and MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing, China.,Nanxiong Tobacco Research Institute of Guangdong, Nanxiong, Guangdong, China
| | - Xin Zhang
- Department of Plant Pathology, and MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing, China
| | - Min Xu
- Department of Plant Pathology, and MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing, China
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Junfeng Liu
- Department of Plant Pathology, and MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing, China
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13
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Sub1/PC4, a multifaceted factor: from transcription to genome stability. Curr Genet 2017; 63:1023-1035. [DOI: 10.1007/s00294-017-0715-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 05/24/2017] [Accepted: 05/26/2017] [Indexed: 10/19/2022]
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14
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Griffin WC, Gao J, Byrd AK, Chib S, Raney KD. A biochemical and biophysical model of G-quadruplex DNA recognition by positive coactivator of transcription 4. J Biol Chem 2017; 292:9567-9582. [PMID: 28416612 DOI: 10.1074/jbc.m117.776211] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/14/2017] [Indexed: 12/22/2022] Open
Abstract
DNA sequences that are guanine-rich have received considerable attention because of their potential to fold into a secondary, four-stranded DNA structure termed G-quadruplex (G4), which has been implicated in genomic instability and some human diseases. We have previously identified positive coactivator of transcription (PC4), a single-stranded DNA (ssDNA)-binding protein, as a novel G4 interactor. Here, to expand on these previous observations, we biochemically and biophysically characterized the interaction between PC4 and G4DNA. PC4 can bind alternative G4DNA topologies with a low nanomolar Kd value of ∼2 nm, similar to that observed for ssDNA. In consideration of the different structural features between G4DNA and ssDNA, these binding data indicated that PC4 can interact with G4DNA in a manner distinct from ssDNA. The stoichiometry of the PC4-G4 complex was 1:1 for PC4 dimer:G4 substrate. PC4 did not enhance the rate of folding of G4DNA, and formation of the PC4-G4DNA complex did not result in unfolding of the G4DNA structure. We assembled a G4DNA structure flanked by duplex DNA. We find that PC4 can interact with this G4DNA, as well as the complementary C-rich strand. Molecular docking simulations and DNA footprinting experiments suggest a model where a PC4 dimer accommodates the DNA with one monomer on the G4 strand and the second monomer bound to the C-rich strand. Collectively, these data provide a novel mode of PC4 binding to a DNA secondary structure that remains within the framework of the model for binding to ssDNA. Additionally, consideration of the PC4-G4DNA interaction could provide insight into the biological functions of PC4, which remain incompletely understood.
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Affiliation(s)
- Wezley C Griffin
- From the Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7101
| | - Jun Gao
- From the Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7101
| | - Alicia K Byrd
- From the Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7101
| | - Shubeena Chib
- From the Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7101
| | - Kevin D Raney
- From the Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7101
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15
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Li S, Ramelot TA, Kennedy MA, Liu M, Yang Y. Chemical shift assignments of the homodimer protein SP_0782 (7-79) from Streptococcus pneumoniae. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:341-344. [PMID: 27386853 DOI: 10.1007/s12104-016-9697-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 07/02/2016] [Indexed: 06/06/2023]
Abstract
The protein SP_0782 from Streptococcus pneumonia is a small homodimeric protein that belongs to a protein family containing representative members with single-stranded DNA (ssDNA) binding functions. The ssDNA binding of the homolog YdbC from Lactococcus lactis was previously characterized when bound to a 20-mer of pyridine-rich ssDNA, sharing an overall similar structural fold with the human transcription coactivator PC4. We report that SP_0782 exhibits distinct differences in ssDNA binding properties from YdbC as revealed by NMR titration experiments. Unlike the binding of the ssDNA dT19G1 to PC4 and YdbC, SP_0782 resulted in aggregation. In addition, SP_0782 exhibits favorable binding to shorter ssDNA such as dT6. The reason is unclear, and the SP_0782 structure-function relationship remains to be elucidated. Here, we report the complete (1)H, (13)C, and (15)N backbone and side chain NMR assignments of SP_0782, residues 7-79.
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Affiliation(s)
- Shuangli Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Theresa A Ramelot
- Department of Chemistry and Biochemistry, and the Northeast Structural Genomics Consortium, Miami University, Oxford, OH, 45056, USA
| | - Michael A Kennedy
- Department of Chemistry and Biochemistry, and the Northeast Structural Genomics Consortium, Miami University, Oxford, OH, 45056, USA
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China.
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16
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Abstract
SMYD3 is a member of the SET and MYND-domain family of methyl-transferases, the increased expression of which correlates with poor prognosis in various types of cancer. In liver and colon tumors, SMYD3 is localized in the nucleus, where it interacts with RNA Pol II and H3K4me3 and functions as a selective transcriptional amplifier of oncogenes and genes that control cell proliferation and metastatic spread. Smyd3 expression has a high discriminative power for the characterization of liver tumors and positively correlates with poor prognosis. In lung and pancreatic cancer, SMYD3 acts in the cytoplasm, potentiating oncogenic Ras/ERK signaling through the methylation of the MAP3K2 kinase and the subsequent release from its inhibitor. A clinico-pathological analysis of lung cancer patients uncovers prognostic significance of SMYD3 only for first progression survival. However, stratification of patients according to their smoking history significantly expands the prognostic value of SMYD3 to overall survival and other features, suggesting that smoking-related effects saturate the clinical analysis and mask the function of SMYD3 as an oncogenic potentiator.
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17
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Structural analysis and knock-out of a Burkholderia pseudomallei homolog of the eukaryotic transcription coactivator PC4. Gene 2016; 577:140-7. [DOI: 10.1016/j.gene.2015.11.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 11/20/2015] [Accepted: 11/21/2015] [Indexed: 10/22/2022]
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18
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Gao J, Zybailov BL, Byrd AK, Griffin WC, Chib S, Mackintosh SG, Tackett AJ, Raney KD. Yeast transcription co-activator Sub1 and its human homolog PC4 preferentially bind to G-quadruplex DNA. Chem Commun (Camb) 2015; 51:7242-4. [PMID: 25813861 DOI: 10.1039/c5cc00742a] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Using a G-quadruplex bait, we identified the transcription co-activator Sub1 as a G-quadruplex binding protein by quantitative LC-MS/MS and demonstrated in vivo G-quadruplex binding by ChIP. In vitro, Sub1, and its human homolog PC4, bind preferentially to G-quadruplexes. This provides a possible mechanism by which G-quadruplexes can influence gene transcription.
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Affiliation(s)
- Jun Gao
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Slot 516, Little Rock, AR 72205, USA.
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19
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The Sub1 nuclear protein protects DNA from oxidative damage. Mol Cell Biochem 2015; 412:165-71. [PMID: 26708217 DOI: 10.1007/s11010-015-2621-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 12/08/2015] [Indexed: 10/22/2022]
Abstract
Reactive oxygen species are a by-product of aerobic metabolism that can damage lipid, proteins, and nucleic acids. Oxidative damage to DNA is especially critical, because it can lead to cell death or mutagenesis. Previously we reported that the yeast sub1 deletion mutant is sensitive to hydrogen peroxide treatment and that the human SUB1 can complement the sensitivity of the yeast sub1 mutant. In this study, we find that Sub1 protects DNA from oxidative damage in vivo and in vitro. We demonstrate that transcription of SUB1 mRNA is induced by oxidative stress and that the sub1Δ mutant has an increased number of chromosomal DNA strand breaks after peroxide treatment. We further demonstrate that purified Sub1 protein can protect DNA from oxidative damage in vitro, using the metal ion catalyzed oxidation assay.
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20
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Kim JM, Kim K, Schmidt T, Punj V, Tucker H, Rice JC, Ulmer TS, An W. Cooperation between SMYD3 and PC4 drives a distinct transcriptional program in cancer cells. Nucleic Acids Res 2015; 43:8868-83. [PMID: 26350217 PMCID: PMC4605318 DOI: 10.1093/nar/gkv874] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 08/19/2015] [Indexed: 01/17/2023] Open
Abstract
SET and MYND domain containing protein 3 (SMYD3) is a histone methyltransferase, which has been implicated in cell growth and cancer pathogenesis. Increasing evidence suggests that SMYD3 can influence distinct oncogenic processes by acting as a gene-specific transcriptional regulator. However, the mechanistic aspects of SMYD3 transactivation and whether SMYD3 acts in concert with other transcription modulators remain unclear. Here, we show that SMYD3 interacts with the human positive coactivator 4 (PC4) and that such interaction potentiates a group of genes whose expression is linked to cell proliferation and invasion. SMYD3 cooperates functionally with PC4, because PC4 depletion results in the loss of SMYD3-mediated H3K4me3 and target gene expression. Individual depletion of SMYD3 and PC4 diminishes the recruitment of both SMYD3 and PC4, indicating that SMYD3 and PC4 localize at target genes in a mutually dependent manner. Artificial tethering of a SMYD3 mutant incapable of binding to its cognate elements and interacting with PC4 to target genes is sufficient for achieving an active transcriptional state in SMYD3-deficient cells. These observations suggest that PC4 contributes to SMYD3-mediated transactivation primarily by stabilizing SMYD3 occupancy at target genes. Together, these studies define expanded roles for SMYD3 and PC4 in gene regulation and provide an unprecedented documentation of their cooperative functions in stimulating oncogenic transcription.
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Affiliation(s)
- Jin-Man Kim
- Department of Biochemistry and Molecular Biology, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Kyunghwan Kim
- Department of Biochemistry and Molecular Biology, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA Department of Biology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Thomas Schmidt
- Department of Biochemistry and Molecular Biology, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90033, USA
| | - Vasu Punj
- Department of Medicine, Norris Comprehensive Cancer Center, 1450 Biggy Street, Los Angeles, CA 90033, USA
| | - Haley Tucker
- University of Texas at Austin, Institute for Cellular and Molecular Biology, Austin, TX 78712, USA
| | - Judd C Rice
- Department of Biochemistry and Molecular Biology, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Tobias S Ulmer
- Department of Biochemistry and Molecular Biology, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90033, USA
| | - Woojin An
- Department of Biochemistry and Molecular Biology, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
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21
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PC4 promotes genome stability and DNA repair through binding of ssDNA at DNA damage sites. Oncogene 2015; 35:761-70. [DOI: 10.1038/onc.2015.135] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/18/2015] [Accepted: 03/23/2015] [Indexed: 01/07/2023]
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22
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Abstract
ssDNA binding proteins (SSBs) protect ssDNA from chemical and enzymatic assault that can derail DNA processing machinery. Complexes between SSBs and ssDNA are often highly stable, but predicting their structures is challenging, mostly because of the inherent flexibility of ssDNA and the geometric and energetic complexity of the interfaces that it forms. Here, we report a newly developed coarse-grained model to predict the structure of SSB-ssDNA complexes. The model is successfully applied to predict the binding modes of six SSBs with ssDNA strands of lengths of 6-65 nt. In addition to charge-charge interactions (which are often central to governing protein interactions with nucleic acids by means of electrostatic complementarity), an essential energetic term to predict SSB-ssDNA complexes is the interactions between aromatic residues and DNA bases. For some systems, flexibility is required from not only the ssDNA but also, the SSB to allow it to undergo conformational changes and the penetration of the ssDNA into its binding pocket. The association mechanisms can be quite varied, and in several cases, they involve the ssDNA sliding along the protein surface. The binding mechanism suggests that coarse-grained models are appropriate to study the motion of SSBs along ssDNA, which is expected to be central to the function carried out by the SSBs.
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23
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Huang J, Zhao Y, Liu H, Huang D, Cheng X, Zhao W, Taylor IA, Liu J, Peng YL. Substitution of tryptophan 89 with tyrosine switches the DNA binding mode of PC4. Sci Rep 2015; 5:8789. [PMID: 25739870 PMCID: PMC4350104 DOI: 10.1038/srep08789] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/04/2015] [Indexed: 11/17/2022] Open
Abstract
PC4, a well-known general transcription cofactor, has multiple functions in transcription and DNA repair. Residue W89, is engaged in stacking interactions with DNA in PC4, but substituted by tyrosine in some PC4 orthologous proteins. In order to understand the consequences and reveal the molecular details of this substitution we have determined the crystal structures of the PC4 orthologue MoSub1 and a PC4 W89Y mutant in complex with DNA. In the structure of MoSub1-DNA complex, Y74 interacts directly with a single nucleotide of oligo DNA. By comparison, the equivalent residue, W89 in wild type PC4 interacts with two nucleotides and the base of the second nucleotide has distinct orientation relative to that of the first one. A hydrophobic patch around W89 that favours interaction with two nucleotides is not formed in the PC4 W89Y mutant. Therefore, the change of the surface hydrophobicity around residue 89 results in a difference between the modes of DNA interaction. These results indicate that the conserved Y74 in MoSub1 or W89 in PC4, are not only key residues in making specific interactions with DNA but also required to determine the DNA binding mode of PC4 proteins.
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Affiliation(s)
- Jinguang Huang
- 1] State key Laboratory of Agrobiotechnology, China Agricultural University, No2 Yunamingyuanxilu, Beijing. 100193, China [2] MOA Key Laboratory of Plant Pathology, China Agricultural University, No2 Yunamingyuanxilu, Beijing. 100193, China [3] College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao, Shandong. 266109, China
| | - Yanxiang Zhao
- MOA Key Laboratory of Plant Pathology, China Agricultural University, No2 Yunamingyuanxilu, Beijing. 100193, China
| | - Huaian Liu
- MOA Key Laboratory of Plant Pathology, China Agricultural University, No2 Yunamingyuanxilu, Beijing. 100193, China
| | - Dan Huang
- MOA Key Laboratory of Plant Pathology, China Agricultural University, No2 Yunamingyuanxilu, Beijing. 100193, China
| | - Xiankun Cheng
- MOA Key Laboratory of Plant Pathology, China Agricultural University, No2 Yunamingyuanxilu, Beijing. 100193, China
| | - Wensheng Zhao
- 1] State key Laboratory of Agrobiotechnology, China Agricultural University, No2 Yunamingyuanxilu, Beijing. 100193, China [2] MOA Key Laboratory of Plant Pathology, China Agricultural University, No2 Yunamingyuanxilu, Beijing. 100193, China
| | - Ian A Taylor
- Molecular Structure, MRC-NIMR, The Ridgeway, London, NW7 1AA, United Kingdom
| | - Junfeng Liu
- MOA Key Laboratory of Plant Pathology, China Agricultural University, No2 Yunamingyuanxilu, Beijing. 100193, China
| | - You-Liang Peng
- 1] State key Laboratory of Agrobiotechnology, China Agricultural University, No2 Yunamingyuanxilu, Beijing. 100193, China [2] MOA Key Laboratory of Plant Pathology, China Agricultural University, No2 Yunamingyuanxilu, Beijing. 100193, China
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24
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Akimoto Y, Yamamoto S, Iida S, Hirose Y, Tanaka A, Hanaoka F, Ohkuma Y. Transcription cofactor PC4 plays essential roles in collaboration with the small subunit of general transcription factor TFIIE. Genes Cells 2014; 19:879-90. [PMID: 25308091 DOI: 10.1111/gtc.12187] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 09/01/2014] [Indexed: 11/27/2022]
Abstract
In eukaryotes, positive cofactor 4 (PC4) stimulates activator-dependent transcription by facilitating transcription initiation and the transition from initiation to elongation. It also forms homodimers and binds to single-stranded DNA and various transcriptional activators, including the general transcription factor TFIIH. In this study, we further investigated PC4 from Homo sapiens and the nematode Caenorhabditis elegans (hPC4 and cePC4, respectively). hPC4 strongly stimulated transcription on a linearized template, whereas it alleviated transcription on a supercoiled template. Transcriptional stimulation by PC4 was also alleviated by increasing the amount of TFIID. GST pull-down studies with general transcription factors indicated that both hPC4 and cePC4 bind strongly to TFIIB, TFIIEβ, TFIIFα, TFIIFβ and TFIIH XPB subunits and weakly to TBP and TFIIH p62. However, only hPC4 bound to CDK7. The effect of each PC4 on transcription was studied in combination with TFIIEβ. hPC4 stimulated both basal and activated transcription, whereas cePC4 primarily stimulated activated transcription, especially in the presence of TFIIEβ from C. elegans. Finally, hPC4 bound to the C-terminal region of hTFIIEβ adjacent to the basic region. These results indicate that PC4 plays essential roles in the transition step from transcription initiation to elongation by binding to melted DNA in collaboration with TFIIEβ.
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Affiliation(s)
- Yusuke Akimoto
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
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25
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Wang W, Ding J, Zhang Y, Hu Y, Wang DC. Structural insights into the unique single-stranded DNA-binding mode of Helicobacter pylori DprA. Nucleic Acids Res 2013; 42:3478-91. [PMID: 24369431 PMCID: PMC3950713 DOI: 10.1093/nar/gkt1334] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Natural transformation (NT) in bacteria is a complex process, including binding, uptake, transport and recombination of exogenous DNA into the chromosome, consequently generating genetic diversity and driving evolution. DNA processing protein A (DprA), which is distributed among virtually all bacterial species, is involved in binding to the internalized single-stranded DNA (ssDNA) and promoting the loading of RecA on ssDNA during NTs. Here we present the structures of DNA_processg_A (DprA) domain of the Helicobacter pylori DprA (HpDprA) and its complex with an ssDNA at 2.20 and 1.80 Å resolutions, respectively. The complex structure revealed for the first time how the conserved DprA domain binds to ssDNA. Based on structural comparisons and binding assays, a unique ssDNA-binding mode is proposed: the dimer of HpDprA binds to ssDNA through two small, positively charged binding pockets of the DprA domains with classical Rossmann folds and the key residue Arg52 is re-oriented to ‘open’ the pocket in order to accommodate one of the bases of ssDNA, thus enabling HpDprA to grasp substrate with high affinity. This mode is consistent with the oligomeric composition of the complex as shown by electrophoretic mobility-shift assays and static light scattering measurements, but differs from the direct polymeric complex of Streptococcus pneumoniae DprA–ssDNA.
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Affiliation(s)
- Wei Wang
- The National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
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Werten S. Identification of the ssDNA-binding protein of bacteriophage T5: Implications for T5 replication. BACTERIOPHAGE 2013; 3:e27304. [PMID: 24482743 DOI: 10.4161/bact.27304] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 11/21/2013] [Indexed: 11/19/2022]
Abstract
In a recent study, we identified and characterized the long-elusive replicative single-stranded DNA-binding protein of bacteriophage T5, which we showed is related to the eukaryotic transcription coactivator PC4. Here, we provide an extended discussion of these data, report several additional observations and consider implications for the recombination-dependent replication mechanism of the T5 genus, which is still poorly understood.
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Affiliation(s)
- Sebastiaan Werten
- Institute for Biochemistry; University of Greifswald; Greifswald, Germany
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27
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Steigemann B, Schulz A, Werten S. Bacteriophage T5 Encodes a Homolog of the Eukaryotic Transcription Coactivator PC4 Implicated in Recombination-Dependent DNA Replication. J Mol Biol 2013; 425:4125-33. [DOI: 10.1016/j.jmb.2013.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 08/24/2013] [Accepted: 09/02/2013] [Indexed: 11/30/2022]
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28
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Feklistov A, Darst SA. Crystallographic analysis of an RNA polymerase σ-subunit fragment complexed with -10 promoter element ssDNA: quadruplex formation as a possible tool for engineering crystal contacts in protein-ssDNA complexes. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:950-5. [PMID: 23989139 PMCID: PMC3758139 DOI: 10.1107/s1744309113020368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 07/23/2013] [Indexed: 11/10/2022]
Abstract
Structural studies of -10 promoter element recognition by domain 2 of the RNA polymerase σ subunit [Feklistov & Darst (2011), Cell, 147, 1257-1269] reveal an unusual crystal-packing arrangement dominated by G-quartets. The 3'-terminal GGG motif of the oligonucleotide used in crystallization participates in G-quadruplex formation with GGG motifs from symmetry-related complexes. Stacking between neighboring G-quadruplexes results in the formation of pseudo-continuous four-stranded columns running throughout the length of the crystal (G-columns). Here, a new crystal form is presented with a different arrangement of G-columns and it is proposed that the fortuitous finding of G-quartet packing could be useful in engineering crystal contacts in protein-ssDNA complexes.
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Affiliation(s)
- Andrey Feklistov
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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29
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Rossi P, Barbieri CM, Aramini JM, Bini E, Lee HW, Janjua H, Xiao R, Acton TB, Montelione GT. Structures of apo- and ssDNA-bound YdbC from Lactococcus lactis uncover the function of protein domain family DUF2128 and expand the single-stranded DNA-binding domain proteome. Nucleic Acids Res 2013; 41:2756-68. [PMID: 23303792 PMCID: PMC3575825 DOI: 10.1093/nar/gks1348] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Single-stranded DNA (ssDNA) binding proteins are important in basal metabolic pathways for gene transcription, recombination, DNA repair and replication in all domains of life. Their main cellular role is to stabilize melted duplex DNA and protect genomic DNA from degradation. We have uncovered the molecular function of protein domain family domain of unknown function DUF2128 (PF09901) as a novel ssDNA binding domain. This bacterial domain strongly associates into a dimer and presents a highly positively charged surface that is consistent with its function in non-specific ssDNA binding. Lactococcus lactis YdbC is a representative of DUF2128. The solution NMR structures of the 20 kDa apo-YdbC dimer and YdbC:dT19G1 complex were determined. The ssDNA-binding energetics to YdbC were characterized by isothermal titration calorimetry. YdbC shows comparable nanomolar affinities for pyrimidine and mixed oligonucleotides, and the affinity is sufficiently strong to disrupt duplex DNA. In addition, YdbC binds with lower affinity to ssRNA, making it a versatile nucleic acid-binding domain. The DUF2128 family is related to the eukaryotic nuclear protein positive cofactor 4 (PC4) family and to the PUR family both by fold similarity and molecular function.
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Affiliation(s)
- Paolo Rossi
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and the Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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30
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Acker J, Conesa C, Lefebvre O. Yeast RNA polymerase III transcription factors and effectors. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:283-95. [PMID: 23063749 DOI: 10.1016/j.bbagrm.2012.10.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 09/27/2012] [Accepted: 10/03/2012] [Indexed: 12/19/2022]
Abstract
Recent data indicate that the well-defined transcription machinery of RNA polymerase III (Pol III) is probably more complex than commonly thought. In this review, we describe the yeast basal transcription factors of Pol III and their involvements in the transcription cycle. We also present a list of proteins detected on genes transcribed by Pol III (class III genes) that might participate in the transcription process. Surprisingly, several of these proteins are involved in RNA polymerase II transcription. Defining the role of these potential new effectors in Pol III transcription in vivo will be the challenge of the next few years. This article is part of a Special Issue entitled: Transcription by Odd Pols.
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Affiliation(s)
- Joël Acker
- CEA, iBiTecS, Gif Sur Yvette, F-91191, France
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31
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Huang J, Zhao Y, Huang D, Liu H, Justin N, Zhao W, Liu J, Peng Y. Structural features of the single-stranded DNA-binding protein MoSub1 from Magnaporthe oryzae. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1071-6. [PMID: 22948907 DOI: 10.1107/s0907444912019932] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 05/03/2012] [Indexed: 11/10/2022]
Abstract
The well studied general transcription cofactor Sub1/PC4 has multiple functions in transcription. It plays both a negative and a positive role in transcription initiation and is involved in elongation and downstream transcription processes and as a transcription reinitiation factor. MoSub1, a Sub1/PC4 orthologue from rice blast fungus, binds the single-stranded DNA dT(12) tightly with an affinity of 186 nM. The crystal structure of MoSub1 has been solved to 1.79 Å resolution. The structure of the protein shows high similiarity to the structure of PC4 and it has a similar dimer interface and DNA-binding region to PC4, indicating that MoSub1 could bind DNA using the same motif as other proteins of the Sub1/PC4 family. There are two novel features in the MoSub1 structure: a region N-terminal to the DNA-binding domain and a C-terminal extension. The region N-terminal to the DNA-binding domain of MoSub1 turns back towards the DNA-binding site and may interact directly with DNA or the DNA-binding site. The C-terminal extension region, which is absent in PC4, may not be capable of interacting with DNA and is one possible reason for the differences between Sub1 and PC4.
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Affiliation(s)
- Jinguang Huang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, People's Republic of China
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32
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Das D, Folkers GE, van Dijk M, Jaspers NGJ, Hoeijmakers JHJ, Kaptein R, Boelens R. The structure of the XPF-ssDNA complex underscores the distinct roles of the XPF and ERCC1 helix- hairpin-helix domains in ss/ds DNA recognition. Structure 2012; 20:667-75. [PMID: 22483113 DOI: 10.1016/j.str.2012.02.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 01/22/2012] [Accepted: 02/17/2012] [Indexed: 11/26/2022]
Abstract
Human XPF/ERCC1 is a structure-specific DNA endonuclease that nicks the damaged DNA strand at the 5' end during nucleotide excision repair. We determined the structure of the complex of the C-terminal domain of XPF with 10 nt ssDNA. A positively charged region within the second helix of the first HhH motif contacts the ssDNA phosphate backbone. One guanine base is flipped out of register and positioned in a pocket contacting residues from both HhH motifs of XPF. Comparison to other HhH-containing proteins indicates a one-residue deletion in the second HhH motif of XPF that has altered the hairpin conformation, thereby permitting ssDNA interactions. Previous nuclear magnetic resonance studies showed that ERCC1 in the XPF-ERCC1 heterodimer can bind dsDNA. Combining the two observations gives a model that underscores the asymmetry of the human XPF/ERCC1 heterodimer in binding at an ss/ds DNA junction.
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Affiliation(s)
- Devashish Das
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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33
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Debnath S, Chatterjee S, Arif M, Kundu TK, Roy S. Peptide-protein interactions suggest that acetylation of lysines 381 and 382 of p53 is important for positive coactivator 4-p53 interaction. J Biol Chem 2011; 286:25076-87. [PMID: 21586571 DOI: 10.1074/jbc.m110.205328] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human transcriptional positive coactivator 4 (PC4) activates several p53-dependent genes. It has been demonstrated that this is a consequence of direct interaction with p53. Previously, we have concluded that PC4 interacts mainly with the C-terminal negative regulatory domain of p53 through its DNA binding C-terminal half. NMR chemical shift perturbation studies with peptide fragments indicated that amino acids 380-386 of p53 are crucial for interaction with PC4. This was verified by fluorescence anisotropy and sedimentation velocity studies. A peptide consisting of p53-(380-386) sequence, when attached to a cell penetration tag and nuclear localization signal, localizes to the nucleus and inhibits luciferase gene expression from a transfected plasmid carrying a Luc gene under a p53-dependent promoter. Acetylation of lysine 382/381 enhanced the binding of this peptide to PC4 by about an order of magnitude. NMR and mutagenesis studies indicated that serine 73 of PC4 is an important residue for recognition of p53. Intermolecular nuclear Overhauser effect placed aspartate 76 in the vicinity of lysine 381, indicating that the region around residues 73-76 of PC4 is important for p53 recognition. We conclude that the 380-386 region of p53 interacts with the region around residues 73-76 of PC4, and acetylation of lysine 382/381 of p53 may play an important role in modulating p53-PC4 interaction and as a consequence PC4 mediated activation of p53 target genes.
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Affiliation(s)
- Subrata Debnath
- Division of Structural Biology and Bioinformatics, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research (India), 4, Raja S. C. Mullick Road, Kolkata 700032, India
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34
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Genome-wide location analysis reveals a role for Sub1 in RNA polymerase III transcription. Proc Natl Acad Sci U S A 2009; 106:14265-70. [PMID: 19706510 DOI: 10.1073/pnas.0900162106] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human PC4 and the yeast ortholog Sub1 have multiple functions in RNA polymerase II transcription. Genome-wide mapping revealed that Sub1 is present on Pol III-transcribed genes. Sub1 was found to interact with components of the Pol III transcription system and to stimulate the initiation and reinitiation steps in a system reconstituted with all recombinant factors. Sub1 was required for optimal Pol III gene transcription in exponentially growing cells.
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35
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Rajagopalan S, Andreeva A, Teufel DP, Freund SM, Fersht AR. Interaction between the transactivation domain of p53 and PC4 exemplifies acidic activation domains as single-stranded DNA mimics. J Biol Chem 2009; 284:21728-37. [PMID: 19525231 PMCID: PMC2755895 DOI: 10.1074/jbc.m109.006429] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 06/11/2009] [Indexed: 12/03/2022] Open
Abstract
The tumor suppressor p53 regulates cell cycle arrest and apoptosis by transactivating several genes that are critical for these processes. The transcriptional activity of p53 is often regulated by post-translational modifications and its interactions with various transcriptional coactivators. Here we report a physical interaction between the N-terminal transactivation domain (TAD) of p53 and the C-terminal DNA-binding domain of positive cofactor 4 (PC4(CTD)). Using NMR spectroscopy, we showed that residues 35-57 (TAD2) interact with PC4. (15)N,(1)H HSQC and fluorescence competition experiments indicated that TAD binds to the DNA-binding site of PC4. Hepta-phosphorylation of the TAD peptide increased its binding affinity. Computer modeling of the p53N-PC4 complex revealed several important interactions that are reminiscent of those in the single-stranded DNA-PC4 complex. The ubiquitous nature of the acidic transactivation domain of p53 in mediating interactions with several transcription cofactors is also manifested as a DNA mimetic.
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Affiliation(s)
| | - Antonina Andreeva
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
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36
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Mortusewicz O, Roth W, Li N, Cardoso MC, Meisterernst M, Leonhardt H. Recruitment of RNA polymerase II cofactor PC4 to DNA damage sites. ACTA ACUST UNITED AC 2008; 183:769-76. [PMID: 19047459 PMCID: PMC2592824 DOI: 10.1083/jcb.200808097] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The multifunctional nuclear protein positive cofactor 4 (PC4) is involved in various cellular processes including transcription, replication, and chromatin organization. Recently, PC4 has been identified as a suppressor of oxidative mutagenesis in Escherichia coli and Saccharomyces cerevisiae. To investigate a potential role of PC4 in mammalian DNA repair, we used a combination of live cell microscopy, microirradiation, and fluorescence recovery after photobleaching analysis. We found a clear accumulation of endogenous PC4 at DNA damage sites introduced by either chemical agents or laser microirradiation. Using fluorescent fusion proteins and specific mutants, we demonstrated that the rapid recruitment of PC4 to laser-induced DNA damage sites is independent of poly(ADP-ribosyl)ation and γH2AX but depends on its single strand binding capacity. Furthermore, PC4 showed a high turnover at DNA damages sites compared with the repair factors replication protein A and proliferating cell nuclear antigen. We propose that PC4 plays a role in the early response to DNA damage by recognizing single-stranded DNA and may thus initiate or facilitate the subsequent steps of DNA repair.
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Affiliation(s)
- Oliver Mortusewicz
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
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37
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Batta K, Kundu TK. Activation of p53 function by human transcriptional coactivator PC4: role of protein-protein interaction, DNA bending, and posttranslational modifications. Mol Cell Biol 2007; 27:7603-14. [PMID: 17785449 PMCID: PMC2169069 DOI: 10.1128/mcb.01064-07] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Tumor suppressor p53 controls cell cycle checkpoints and apoptosis via the transactivation of several genes that are involved in these processes. The functions of p53 are regulated by a wide variety of proteins, which interact with it either directly or indirectly. The multifunctional human transcriptional coactivator PC4 interacts with p53 in vivo and in vitro and regulates its function. Here we report the molecular mechanisms of the PC4-mediated activation of p53 function. PC4 interacts with the DNA binding and C-terminal domains of p53 through its DNA binding domain, which is essential for the stimulation of p53 DNA binding. Remarkably, ligation-mediated circularization assays reveal that PC4 induces significant bending in the DNA double helix. Deletion mutants defective in DNA bending are found to be impaired in activating p53-mediated DNA binding and apoptosis. Furthermore, acetylation of PC4 enhances, while phosphorylation abolishes, its ability to bend DNA, activate p53 DNA binding, and, thereby, regulate p53 functions. In conclusion, PC4 activates p53 recruitment to p53-responsive promoters (Bax and p21) in vivo through its interaction with p53 and by providing bent substrate for p53 recruitment. These results elucidate the general molecular mechanisms of activation of p53 function, mediated by its coactivators.
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Affiliation(s)
- Kiran Batta
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, P.O. Bangalore-560064, India
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