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Vergara-Cruces Á, Pramanick I, Pearce D, Vogirala VK, Byrne MJ, Low JKK, Webster MW. Structure of the plant plastid-encoded RNA polymerase. Cell 2024; 187:1145-1159.e21. [PMID: 38428394 DOI: 10.1016/j.cell.2024.01.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/18/2023] [Accepted: 01/24/2024] [Indexed: 03/03/2024]
Abstract
Chloroplast genes encoding photosynthesis-associated proteins are predominantly transcribed by the plastid-encoded RNA polymerase (PEP). PEP is a multi-subunit complex composed of plastid-encoded subunits similar to bacterial RNA polymerases (RNAPs) stably bound to a set of nuclear-encoded PEP-associated proteins (PAPs). PAPs are essential to PEP activity and chloroplast biogenesis, but their roles are poorly defined. Here, we present cryoelectron microscopy (cryo-EM) structures of native 21-subunit PEP and a PEP transcription elongation complex from white mustard (Sinapis alba). We identify that PAPs encase the core polymerase, forming extensive interactions that likely promote complex assembly and stability. During elongation, PAPs interact with DNA downstream of the transcription bubble and with the nascent mRNA. The models reveal details of the superoxide dismutase, lysine methyltransferase, thioredoxin, and amino acid ligase enzymes that are subunits of PEP. Collectively, these data provide a foundation for the mechanistic understanding of chloroplast transcription and its role in plant growth and adaptation.
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Affiliation(s)
- Ángel Vergara-Cruces
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ishika Pramanick
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - David Pearce
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK; School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Vinod K Vogirala
- Electron Bio-Imaging Centre (eBIC), Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Matthew J Byrne
- Electron Bio-Imaging Centre (eBIC), Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2050, Australia
| | - Michael W Webster
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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2
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Bedding MJ, Franck C, Johansen-Leete J, Aggarwal A, Maxwell JWC, Patel K, Hawkins PME, Low JKK, Siddiquee R, Sani HM, Ford DJ, Turville S, Mackay JP, Passioura T, Christie M, Payne RJ. Discovery of High Affinity Cyclic Peptide Ligands for Human ACE2 with SARS-CoV-2 Entry Inhibitory Activity. ACS Chem Biol 2024; 19:141-152. [PMID: 38085789 DOI: 10.1021/acschembio.3c00568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
The development of effective antiviral compounds is essential for mitigating the effects of the COVID-19 pandemic. Entry of SARS-CoV-2 virions into host cells is mediated by the interaction between the viral spike (S) protein and membrane-bound angiotensin-converting enzyme 2 (ACE2) on the surface of epithelial cells. Inhibition of this viral protein-host protein interaction is an attractive avenue for the development of antiviral molecules with numerous spike-binding molecules generated to date. Herein, we describe an alternative approach to inhibit the spike-ACE2 interaction by targeting the spike-binding interface of human ACE2 via mRNA display. Two consecutive display selections were performed to direct cyclic peptide ligand binding toward the spike binding interface of ACE2. Through this process, potent cyclic peptide binders of human ACE2 (with affinities in the picomolar to nanomolar range) were identified, two of which neutralized SARS-CoV-2 entry. This work demonstrates the potential of targeting ACE2 for the generation of anti-SARS-CoV-2 therapeutics as well as broad spectrum antivirals for the treatment of SARS-like betacoronavirus infection.
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Affiliation(s)
- Max J Bedding
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Charlotte Franck
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jason Johansen-Leete
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - Joshua W C Maxwell
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Karishma Patel
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Paige M E Hawkins
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Rezwan Siddiquee
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Hakimeh Moghaddas Sani
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Daniel J Ford
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - Joel P Mackay
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Toby Passioura
- Sydney Analytical Core Research Facility, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Mary Christie
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
- School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
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3
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Low JKK, Patel K, Jones N, Solomon P, Norman A, Maxwell JWC, Pachl P, Matthews JM, Payne RJ, Passioura T, Suga H, Walport LJ, Mackay JP. mRNA display reveals a class of high-affinity bromodomain-binding motifs that are not found in the human proteome. J Biol Chem 2023; 299:105482. [PMID: 37992806 PMCID: PMC10758951 DOI: 10.1016/j.jbc.2023.105482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 11/01/2023] [Accepted: 11/16/2023] [Indexed: 11/24/2023] Open
Abstract
Bromodomains (BDs) regulate gene expression by recognizing protein motifs containing acetyllysine. Although originally characterized as histone-binding proteins, it has since become clear that these domains interact with other acetylated proteins, perhaps most prominently transcription factors. The likely transient nature and low stoichiometry of such modifications, however, has made it challenging to fully define the interactome of any given BD. To begin to address this knowledge gap in an unbiased manner, we carried out mRNA display screens against a BD-the N-terminal BD of BRD3-using peptide libraries that contained either one or two acetyllysine residues. We discovered peptides with very strong consensus sequences and with affinities that are significantly higher than typical BD-peptide interactions. X-ray crystal structures also revealed modes of binding that have not been seen with natural ligands. Intriguingly, however, our sequences are not found in the human proteome, perhaps suggesting that strong binders to BDs might have been selected against during evolution.
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Affiliation(s)
- Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia
| | - Karishma Patel
- School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia
| | - Natasha Jones
- School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia
| | - Paul Solomon
- School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia
| | - Alexander Norman
- School of Chemistry, University of Sydney, New South Wales, Australia
| | | | - Petr Pachl
- School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia
| | - Jacqueline M Matthews
- School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia
| | - Richard J Payne
- School of Chemistry, University of Sydney, New South Wales, Australia
| | - Toby Passioura
- School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia; Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Louise J Walport
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan; Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, United Kingdom; Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom.
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia.
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4
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Bartolec TK, Vázquez-Campos X, Norman A, Luong C, Johnson M, Payne RJ, Wilkins MR, Mackay JP, Low JKK. Cross-linking mass spectrometry discovers, evaluates, and corroborates structures and protein-protein interactions in the human cell. Proc Natl Acad Sci U S A 2023; 120:e2219418120. [PMID: 37071682 PMCID: PMC10151615 DOI: 10.1073/pnas.2219418120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/16/2023] [Indexed: 04/19/2023] Open
Abstract
Significant recent advances in structural biology, particularly in the field of cryoelectron microscopy, have dramatically expanded our ability to create structural models of proteins and protein complexes. However, many proteins remain refractory to these approaches because of their low abundance, low stability, or-in the case of complexes-simply not having yet been analyzed. Here, we demonstrate the power of using cross-linking mass spectrometry (XL-MS) for the high-throughput experimental assessment of the structures of proteins and protein complexes. This included those produced by high-resolution but in vitro experimental data, as well as in silico predictions based on amino acid sequence alone. We present the largest XL-MS dataset to date, describing 28,910 unique residue pairs captured across 4,084 unique human proteins and 2,110 unique protein-protein interactions. We show that models of proteins and their complexes predicted by AlphaFold2, and inspired and corroborated by the XL-MS data, offer opportunities to deeply mine the structural proteome and interactome and reveal mechanisms underlying protein structure and function.
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Affiliation(s)
- Tara K. Bartolec
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Randwick, NSW2052, Australia
| | - Xabier Vázquez-Campos
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Randwick, NSW2052, Australia
| | - Alexander Norman
- School of Chemistry, University of Sydney, Sydney, NSW2006, Australia
| | - Clement Luong
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW2006, Australia
| | - Marcus Johnson
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW2006, Australia
| | - Richard J. Payne
- School of Chemistry, University of Sydney, Sydney, NSW2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW2006, Australia
| | - Marc R. Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Randwick, NSW2052, Australia
| | - Joel P. Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW2006, Australia
| | - Jason K. K. Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW2006, Australia
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5
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Arvindekar SM, Jackman MJ, Low JKK, Landsberg MJ, Mackay JP, Viswanath S. Molecular architecture of nucleosome remodeling and deacetylase sub-complexes by integrative structure determination. Biophys J 2023; 122:472a. [PMID: 36784428 DOI: 10.1016/j.bpj.2022.11.2531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
| | - Matthew J Jackman
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Michael J Landsberg
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
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6
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Loo L, Waller MA, Moreno CL, Cole AJ, Stella AO, Pop OT, Jochum AK, Ali OH, Denes CE, Hamoudi Z, Chung F, Aggarwal A, Low JKK, Patel K, Siddiquee R, Kang T, Mathivanan S, Mackay JP, Jochum W, Flatz L, Hesselson D, Turville S, Neely GG. Fibroblast-expressed LRRC15 is a receptor for SARS-CoV-2 spike and controls antiviral and antifibrotic transcriptional programs. PLoS Biol 2023; 21:e3001967. [PMID: 36757924 PMCID: PMC9910744 DOI: 10.1371/journal.pbio.3001967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/16/2022] [Indexed: 02/10/2023] Open
Abstract
Although ACE2 is the primary receptor for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection, a systematic assessment of host factors that regulate binding to SARS-CoV-2 spike protein has not been described. Here, we use whole-genome CRISPR activation to identify host factors controlling cellular interactions with SARS-CoV-2. Our top hit was a TLR-related cell surface receptor called leucine-rich repeat-containing protein 15 (LRRC15). LRRC15 expression was sufficient to promote SARS-CoV-2 spike binding where they form a cell surface complex. LRRC15 mRNA is expressed in human collagen-producing lung myofibroblasts and LRRC15 protein is induced in severe Coronavirus Disease 2019 (COVID-19) infection where it can be found lining the airways. Mechanistically, LRRC15 does not itself support SARS-CoV-2 infection, but fibroblasts expressing LRRC15 can suppress both pseudotyped and authentic SARS-CoV-2 infection in trans. Moreover, LRRC15 expression in fibroblasts suppresses collagen production and promotes expression of IFIT, OAS, and MX-family antiviral factors. Overall, LRRC15 is a novel SARS-CoV-2 spike-binding receptor that can help control viral load and regulate antiviral and antifibrotic transcriptional programs in the context of COVID-19 infection.
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Affiliation(s)
- Lipin Loo
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Matthew A. Waller
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Cesar L. Moreno
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Alexander J. Cole
- Centenary Institute and Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | | | - Oltin-Tiberiu Pop
- Institute for Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Ann-Kristin Jochum
- Institute for Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
- Institute for Pathology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Omar Hasan Ali
- Institute for Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Christopher E. Denes
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Zina Hamoudi
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Felicity Chung
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Anupriya Aggarwal
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Jason K. K. Low
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Karishma Patel
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Rezwan Siddiquee
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Taeyoung Kang
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Joel P. Mackay
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Wolfram Jochum
- Institute for Pathology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Lukas Flatz
- Institute for Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
- Center for Dermatooncology, Department of Dermatology, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Daniel Hesselson
- Centenary Institute and Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Stuart Turville
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - G. Gregory Neely
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
- * E-mail:
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7
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Abstract
The nucleosome-remodeling and deacetylase (NuRD) complex is an essential transcriptional regulator in all complex animals. All seven core subunits of the complex exist as multiple paralogs, raising the question of whether the complex might utilize paralog switching to achieve cell type-specific functions. We examine the evidence for this idea, making use of published quantitative proteomic data to dissect NuRD composition in 20 different tissues, as well as a large-scale CRISPR knockout screen carried out in >1000 human cancer cell lines. These data, together with recent reports, provide strong support for the idea that distinct permutations of the NuRD complex with tailored functions might regulate tissue-specific gene expression programs.
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Affiliation(s)
- Xavier J Reid
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia.
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8
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Zhong Y, Moghaddas Sani H, Paudel BP, Low JKK, Silva APG, Mueller S, Deshpande C, Panjikar S, Reid XJ, Bedward MJ, van Oijen AM, Mackay JP. The role of auxiliary domains in modulating CHD4 activity suggests mechanistic commonality between enzyme families. Nat Commun 2022; 13:7524. [PMID: 36473839 PMCID: PMC9726900 DOI: 10.1038/s41467-022-35002-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
CHD4 is an essential, widely conserved ATP-dependent translocase that is also a broad tumour dependency. In common with other SF2-family chromatin remodelling enzymes, it alters chromatin accessibility by repositioning histone octamers. Besides the helicase and adjacent tandem chromodomains and PHD domains, CHD4 features 1000 residues of N- and C-terminal sequence with unknown structure and function. We demonstrate that these regions regulate CHD4 activity through different mechanisms. An N-terminal intrinsically disordered region (IDR) promotes remodelling integrity in a manner that depends on the composition but not sequence of the IDR. The C-terminal region harbours an auto-inhibitory region that contacts the helicase domain. Auto-inhibition is relieved by a previously unrecognized C-terminal SANT-SLIDE domain split by ~150 residues of disordered sequence, most likely by binding of this domain to substrate DNA. Our data shed light on CHD4 regulation and reveal strong mechanistic commonality between CHD family members, as well as with ISWI-family remodellers.
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Affiliation(s)
- Yichen Zhong
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Hakimeh Moghaddas Sani
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Bishnu P. Paudel
- grid.1007.60000 0004 0486 528XMolecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522 Australia ,grid.510958.0Illawarra Health and Medical Research Institute, Wollongong, NSW 2522 Australia
| | - Jason K. K. Low
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Ana P. G. Silva
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Stefan Mueller
- grid.1007.60000 0004 0486 528XMolecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522 Australia ,grid.510958.0Illawarra Health and Medical Research Institute, Wollongong, NSW 2522 Australia
| | - Chandrika Deshpande
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Santosh Panjikar
- grid.248753.f0000 0004 0562 0567Australian Synchrotron, Clayton, VIC 3168 Australia ,grid.1002.30000 0004 1936 7857Department of Molecular Biology and Biochemistry, Monash University, Clayton, VIC 3800 Australia
| | - Xavier J. Reid
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Max J. Bedward
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Antoine M. van Oijen
- grid.1007.60000 0004 0486 528XMolecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522 Australia ,grid.510958.0Illawarra Health and Medical Research Institute, Wollongong, NSW 2522 Australia
| | - Joel P. Mackay
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
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9
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Arvindekar S, Jackman MJ, Low JKK, Landsberg MJ, Mackay JP, Viswanath S. Molecular architecture of nucleosome remodeling and deacetylase sub-complexes by integrative structure determination. Protein Sci 2022; 31:e4387. [PMID: 36040254 PMCID: PMC9413472 DOI: 10.1002/pro.4387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/18/2022] [Accepted: 06/19/2022] [Indexed: 11/11/2022]
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex is a chromatin-modifying assembly that regulates gene expression and DNA damage repair. Despite its importance, limited structural information describing the complete NuRD complex is available and a detailed understanding of its mechanism is therefore lacking. Drawing on information from SEC-MALLS, DIA-MS, XLMS, negative-stain EM, X-ray crystallography, NMR spectroscopy, secondary structure predictions, and homology models, we applied Bayesian integrative structure determination to investigate the molecular architecture of three NuRD sub-complexes: MTA1-HDAC1-RBBP4, MTA1N -HDAC1-MBD3GATAD2CC , and MTA1-HDAC1-RBBP4-MBD3-GATAD2A [nucleosome deacetylase (NuDe)]. The integrative structures were corroborated by examining independent crosslinks, cryo-EM maps, biochemical assays, known cancer-associated mutations, and structure predictions from AlphaFold. The robustness of the models was assessed by jack-knifing. Localization of the full-length MBD3, which connects the deacetylase and chromatin remodeling modules in NuRD, has not previously been possible; our models indicate two different locations for MBD3, suggesting a mechanism by which MBD3 in the presence of GATAD2A asymmetrically bridges the two modules in NuRD. Further, our models uncovered three previously unrecognized subunit interfaces in NuDe: HDAC1C -MTA1BAH , MTA1BAH -MBD3MBD , and HDAC160-100 -MBD3MBD . Our approach also allowed us to localize regions of unknown structure, such as HDAC1C and MBD3IDR , thereby resulting in the most complete and robustly cross-validated structural characterization of these NuRD sub-complexes so far.
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Affiliation(s)
- Shreyas Arvindekar
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBangaloreIndia
| | - Matthew J. Jackman
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneQueenslandAustralia
| | - Jason K. K. Low
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
| | - Michael J. Landsberg
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneQueenslandAustralia
| | - Joel P. Mackay
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
| | - Shruthi Viswanath
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBangaloreIndia
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10
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Hodson C, Low JKK, van Twest S, Jones SE, Swuec P, Murphy V, Tsukada K, Fawkes M, Bythell-Douglas R, Davies A, Holien JK, O'Rourke JJ, Parker BL, Glaser A, Parker MW, Mackay JP, Blackford AN, Costa A, Deans AJ. Mechanism of Bloom syndrome complex assembly required for double Holliday junction dissolution and genome stability. Proc Natl Acad Sci U S A 2022; 119:e2109093119. [PMID: 35115399 PMCID: PMC8832983 DOI: 10.1073/pnas.2109093119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 12/17/2021] [Indexed: 12/29/2022] Open
Abstract
The RecQ-like helicase BLM cooperates with topoisomerase IIIα, RMI1, and RMI2 in a heterotetrameric complex (the "Bloom syndrome complex") for dissolution of double Holliday junctions, key intermediates in homologous recombination. Mutations in any component of the Bloom syndrome complex can cause genome instability and a highly cancer-prone disorder called Bloom syndrome. Some heterozygous carriers are also predisposed to breast cancer. To understand how the activities of BLM helicase and topoisomerase IIIα are coupled, we purified the active four-subunit complex. Chemical cross-linking and mass spectrometry revealed a unique architecture that links the helicase and topoisomerase domains. Using biochemical experiments, we demonstrated dimerization mediated by the N terminus of BLM with a 2:2:2:2 stoichiometry within the Bloom syndrome complex. We identified mutations that independently abrogate dimerization or association of BLM with RMI1, and we show that both are dysfunctional for dissolution using in vitro assays and cause genome instability and synthetic lethal interactions with GEN1/MUS81 in cells. Truncated BLM can also inhibit the activity of full-length BLM in mixed dimers, suggesting a putative mechanism of dominant-negative action in carriers of BLM truncation alleles. Our results identify critical molecular determinants of Bloom syndrome complex assembly required for double Holliday junction dissolution and maintenance of genome stability.
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Affiliation(s)
- Charlotte Hodson
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Sylvie van Twest
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Samuel E Jones
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
| | - Paolo Swuec
- Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Vincent Murphy
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Kaima Tsukada
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
- Laboratory for Zero-Carbon Energy, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Matthew Fawkes
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Rohan Bythell-Douglas
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
- Department of Medicine (St. Vincent's), University of Melbourne, Fitzroy, VIC 3065, Australia
| | | | - Jessica K Holien
- Department of Medicine (St. Vincent's), University of Melbourne, Fitzroy, VIC 3065, Australia
- School of Science, RMIT University, Melbourne, VIC 3001, Australia
- Structural Biology Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Julienne J O'Rourke
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Benjamin L Parker
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Astrid Glaser
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Michael W Parker
- Structural Biology Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
- Bio21 Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Andrew N Blackford
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | | | - Andrew J Deans
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia;
- Department of Medicine (St. Vincent's), University of Melbourne, Fitzroy, VIC 3065, Australia
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11
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Abstract
Protein interactions underlie most molecular events in biology. Many methods have been developed to identify protein partners, to measure the affinity with which these biomolecules interact and to characterise the structures of the complexes. Each approach has its own advantages and limitations, and it can be difficult for the newcomer to determine which methodology would best suit their system. This review provides an overview of many of the techniques most widely used to identify protein partners, assess stoichiometry and binding affinity, and determine low-resolution models for complexes. Key methods covered include: yeast two-hybrid analysis, affinity purification mass spectrometry and proximity labelling to identify partners; size-exclusion chromatography, scattering methods, native mass spectrometry and analytical ultracentrifugation to estimate stoichiometry; isothermal titration calorimetry, biosensors and fluorometric methods (including microscale thermophoresis, anisotropy/polarisation, resonance energy transfer, AlphaScreen, and differential scanning fluorimetry) to measure binding affinity; and crosslinking and hydrogen-deuterium exchange mass spectrometry to probe the structure of complexes.
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Affiliation(s)
- Louise J Walport
- The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK.,Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia.
| | - Jacqueline M Matthews
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia.
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia.
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12
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Jindra M, McKinstry WJ, Nebl T, Bittova L, Ren B, Shaw J, Phan T, Lu L, Low JKK, Mackay JP, Sparrow LG, Lovrecz GO, Hill RJ. Purification of an insect juvenile hormone receptor complex enables insights into its post-translational phosphorylation. J Biol Chem 2021; 297:101387. [PMID: 34758356 PMCID: PMC8683598 DOI: 10.1016/j.jbc.2021.101387] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 11/29/2022] Open
Abstract
Juvenile hormone (JH) plays vital roles in insect reproduction, development, and in many aspects of physiology. JH primarily acts at the gene-regulatory level through interaction with an intracellular receptor (JH receptor [JHR]), a ligand-activated complex of transcription factors consisting of the JH-binding protein methoprene-tolerant (MET) and its partner taiman (TAI). Initial studies indicated significance of post-transcriptional phosphorylation, subunit assembly, and nucleocytoplasmic transport of JHR in JH signaling. However, our knowledge of JHR regulation at the protein level remains rudimentary, partly because of the difficulty of obtaining purified and functional JHR proteins. Here, we present a method for high-yield expression and purification of JHR complexes from two insect species, the beetle T. castaneum and the mosquito Aedes aegypti. Recombinant JHR subunits from each species were coexpressed in an insect cell line using a baculovirus system. MET–TAI complexes were purified through affinity chromatography and anion exchange columns to yield proteins capable of binding both the hormonal ligand (JH III) and DNA bearing cognate JH-response elements. We further examined the beetle JHR complex in greater detail. Biochemical analyses and MS confirmed that T. castaneum JHR was a 1:1 heterodimer consisting of MET and Taiman proteins, stabilized by the JHR agonist ligand methoprene. Phosphoproteomics uncovered multiple phosphorylation sites in the MET protein, some of which were induced by methoprene treatment. Finally, we report a functional bipartite nuclear localization signal, straddled by phosphorylated residues, within the disordered C-terminal region of MET. Our present characterization of the recombinant JHR is an initial step toward understanding JHR structure and function.
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Affiliation(s)
- Marek Jindra
- Biology Center, Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic.
| | | | - Thomas Nebl
- CSIRO Manufacturing, CSIRO, Parkville, Victoria, Australia
| | - Lenka Bittova
- Biology Center, Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
| | - Bin Ren
- CSIRO Manufacturing, CSIRO, Parkville, Victoria, Australia
| | - Jan Shaw
- CSIRO Health and Biosecurity, CSIRO, North Ryde, New South Wales, Australia
| | - Tram Phan
- CSIRO Manufacturing, CSIRO, Parkville, Victoria, Australia
| | - Louis Lu
- CSIRO Manufacturing, CSIRO, Parkville, Victoria, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | | | | | - Ronald J Hill
- CSIRO Health and Biosecurity, CSIRO, North Ryde, New South Wales, Australia; School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia.
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13
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Sharifi Tabar M, Giardina C, Feng Y, Francis H, Moghaddas Sani H, Low JKK, Mackay JP, Bailey CG, Rasko JEJ. Unique protein interaction networks define the chromatin remodelling module of the NuRD complex. FEBS J 2021; 289:199-214. [PMID: 34231305 PMCID: PMC9545347 DOI: 10.1111/febs.16112] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/27/2021] [Accepted: 07/06/2021] [Indexed: 01/13/2023]
Abstract
The combination of four proteins and their paralogues including MBD2/3, GATAD2A/B, CDK2AP1 and CHD3/4/5, which we refer to as the MGCC module, form the chromatin remodelling module of the nucleosome remodelling and deacetylase (NuRD) complex. To date, mechanisms by which the MGCC module acquires paralogue-specific function and specificity have not been addressed. Understanding the protein-protein interaction (PPI) network of the MGCC subunits is essential for defining underlying mechanisms of gene regulation. Therefore, using pulldown followed by mass spectrometry analysis (PD-MS), we report a proteome-wide interaction network of the MGCC module in a paralogue-specific manner. Our data also demonstrate that the disordered C-terminal region of CHD3/4/5 is a gateway to incorporate remodelling activity into both ChAHP (CHD4, ADNP, HP1γ) and NuRD complexes in a mutually exclusive manner. We define a short aggregation-prone region (APR) within the C-terminal segment of GATAD2B that is essential for the interaction of CHD4 and CDK2AP1 with the NuRD complex. Finally, we also report an association of CDK2AP1 with the nuclear receptor co-repressor (NCOR) complex. Overall, this study provides insight into the possible mechanisms through which the MGCC module can achieve specificity and diverse biological functions.
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Affiliation(s)
- Mehdi Sharifi Tabar
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia.,Faculty of Medicine & Health, The University of Sydney, NSW, Australia
| | - Caroline Giardina
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia
| | - Yue Feng
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia
| | - Habib Francis
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia
| | | | - Jason K K Low
- School of Life & Environmental Sciences, The University of Sydney, NSW, Australia
| | - Joel P Mackay
- School of Life & Environmental Sciences, The University of Sydney, NSW, Australia
| | - Charles G Bailey
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia.,Faculty of Medicine & Health, The University of Sydney, NSW, Australia.,Cancer & Gene Regulation Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia.,Faculty of Medicine & Health, The University of Sydney, NSW, Australia.,Cell & Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
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14
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Norman A, Franck C, Christie M, Hawkins PME, Patel K, Ashhurst AS, Aggarwal A, Low JKK, Siddiquee R, Ashley CL, Steain M, Triccas JA, Turville S, Mackay JP, Passioura T, Payne RJ. Discovery of Cyclic Peptide Ligands to the SARS-CoV-2 Spike Protein Using mRNA Display. ACS Cent Sci 2021; 7:1001-1008. [PMID: 34230894 PMCID: PMC8189037 DOI: 10.1021/acscentsci.0c01708] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Indexed: 05/03/2023]
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, has led to substantial morbidity, mortality, and disruption globally. Cellular entry of SARS-CoV-2 is mediated by the viral spike protein, and affinity ligands to this surface protein have the potential for applications as antivirals and diagnostic reagents. Here, we describe the affinity selection of cyclic peptide ligands to the SARS-CoV-2 spike protein receptor binding domain (RBD) from three distinct libraries (in excess of a trillion molecules each) by mRNA display. We identified six high affinity molecules with dissociation constants (K D) in the nanomolar range (15-550 nM) to the RBD. The highest affinity ligand could be used as an affinity reagent to detect the spike protein in solution by ELISA, and the cocrystal structure of this molecule bound to the RBD demonstrated that it binds to a cryptic binding site, displacing a β-strand near the C-terminus. Our findings provide key mechanistic insight into the binding of peptide ligands to the SARS-CoV-2 spike RBD, and the ligands discovered in this work may find future use as reagents for diagnostic applications.
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Affiliation(s)
- Alexander Norman
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Charlotte Franck
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
- School
of Life and Environmental Sciences, The
University of Sydney, Sydney, New South Wales 2006, Australia
| | - Mary Christie
- School
of Life and Environmental Sciences, The
University of Sydney, Sydney, New South Wales 2006, Australia
| | - Paige M. E. Hawkins
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Karishma Patel
- School
of Life and Environmental Sciences, The
University of Sydney, Sydney, New South Wales 2006, Australia
| | - Anneliese S. Ashhurst
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
- School
of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - Jason K. K. Low
- School
of Life and Environmental Sciences, The
University of Sydney, Sydney, New South Wales 2006, Australia
| | - Rezwan Siddiquee
- School
of Life and Environmental Sciences, The
University of Sydney, Sydney, New South Wales 2006, Australia
- Sydney Analytical, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Caroline L. Ashley
- School
of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Megan Steain
- School
of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - James A. Triccas
- School
of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - Joel P. Mackay
- School
of Life and Environmental Sciences, The
University of Sydney, Sydney, New South Wales 2006, Australia
| | - Toby Passioura
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- School
of Life and Environmental Sciences, The
University of Sydney, Sydney, New South Wales 2006, Australia
- Sydney Analytical, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Richard J. Payne
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
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15
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Patel K, Solomon PD, Walshe JL, Ford DJ, Wilkinson-White L, Payne RJ, Low JKK, Mackay JP. BET-Family Bromodomains Can Recognize Diacetylated Sequences from Transcription Factors Using a Conserved Mechanism. Biochemistry 2021; 60:648-662. [PMID: 33620209 DOI: 10.1021/acs.biochem.0c00816] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Almost all eukaryotic proteins receive diverse post-translational modifications (PTMs) that modulate protein activity. Many histone PTMs are well characterized, heavily influence gene regulation, and are often predictors of distinct transcriptional programs. Although our understanding of the histone PTM network has matured, much is yet to be understood about the roles of transcription factor (TF) PTMs, which might well represent a similarly complex and dynamic network of functional regulation. Members of the bromodomain and extra-terminal domain (BET) family of proteins recognize acetyllysine residues and relay the signals encoded by these modifications. Here, we have investigated the acetylation dependence of several functionally relevant BET-TF interactions in vitro using surface plasmon resonance, nuclear magnetic resonance, and X-ray crystallography. We show that motifs known to be acetylated in TFs E2F1 and MyoD1 can interact with all bromodomains of BRD2, BRD3, and BRD4. The interactions are dependent on diacetylation of the motifs and show a preference for the first BET bromodomain. Structural mapping of the interactions confirms a conserved mode of binding for the two TFs to the acetyllysine binding pocket of the BET bromodomains, mimicking that of other already established functionally important histone- and TF-BET interactions. We also examined a motif from the TF RelA that is known to be acetylated but were unable to observe any interaction, regardless of the acetylation state of the sequence. Our findings overall advance our understanding of BET-TF interactions and suggest a physical link between the important diacetylated motifs found in E2F1 and MyoD1 and the BET-family proteins.
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Affiliation(s)
- Karishma Patel
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Paul D Solomon
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - James L Walshe
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Daniel J Ford
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | | | - Richard J Payne
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
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16
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Low JKK, Silva APG, Sharifi Tabar M, Torrado M, Webb SR, Parker BL, Sana M, Smits C, Schmidberger JW, Brillault L, Jackman MJ, Williams DC, Blobel GA, Hake SB, Shepherd NE, Landsberg MJ, Mackay JP. The Nucleosome Remodeling and Deacetylase Complex Has an Asymmetric, Dynamic, and Modular Architecture. Cell Rep 2020; 33:108450. [PMID: 33264611 PMCID: PMC8908386 DOI: 10.1016/j.celrep.2020.108450] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/23/2020] [Accepted: 11/09/2020] [Indexed: 12/15/2022] Open
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex is essential for metazoan development but has been refractory to biochemical analysis. We present an integrated analysis of the native mammalian NuRD complex, combining quantitative mass spectrometry, cross-linking, protein biochemistry, and electron microscopy to define the architecture of the complex. NuRD is built from a 2:2:4 (MTA, HDAC, and RBBP) deacetylase module and a 1:1:1 (MBD, GATAD2, and Chromodomain-Helicase-DNA-binding [CHD]) remodeling module, and the complex displays considerable structural dynamics. The enigmatic GATAD2 controls the asymmetry of the complex and directly recruits the CHD remodeler. The MTA-MBD interaction acts as a point of functional switching, with the transcriptional regulator PWWP2A competing with MBD for binding to the MTA-HDAC-RBBP subcomplex. Overall, our data address the long-running controversy over NuRD stoichiometry, provide imaging of the mammalian NuRD complex, and establish the biochemical mechanism by which PWWP2A can regulate NuRD composition. Low et al. examine the architecture of the nucleosome remodeling and deacetylase complex. They define its stoichiometry, use cross-linking mass spectrometry to define subunit locations, and use electron microscopy to reveal large-scale dynamics. They also demonstrate that PWWP2A competes with MBD3 to sequester the HDAC-MTA-RBBP module from NuRD.
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Affiliation(s)
- Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia.
| | - Ana P G Silva
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Mehdi Sharifi Tabar
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Mario Torrado
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Sarah R Webb
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Benjamin L Parker
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Maryam Sana
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | | | | | - Lou Brillault
- School of Chemistry and Molecular Biosciences, University of Queensland, QLD, Australia
| | - Matthew J Jackman
- School of Chemistry and Molecular Biosciences, University of Queensland, QLD, Australia
| | - David C Williams
- Dept of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, NC, USA
| | - Gerd A Blobel
- The Division of Hematology, Children's Hospital of Philadelphia, and the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sandra B Hake
- Institute for Genetics, FB08 Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Nicholas E Shepherd
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Michael J Landsberg
- School of Chemistry and Molecular Biosciences, University of Queensland, QLD, Australia.
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia.
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17
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Patel K, Solomon PD, Walshe JL, Low JKK, Mackay JP. The bromodomains of BET family proteins can recognize diacetylated histone H2A.Z. Protein Sci 2020; 30:464-476. [PMID: 33247496 DOI: 10.1002/pro.4006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/21/2020] [Accepted: 11/24/2020] [Indexed: 02/02/2023]
Abstract
Chemical modifications of histone tails influence genome accessibility and the transcriptional state of eukaryotic cells. Lysine acetylation is one of the most common modifications and acetyllysine-binding bromodomains (BDs) provide a means for acetyllysine marks to be translated into meaningful cellular responses. Here, we have investigated the mechanism underlying the reported association between the Bromodomain and Extra Terminal (BET) family of BD proteins and the essential histone variant H2A.Z. We use NMR spectroscopy to demonstrate a physical interaction between the N-terminal tail of H2A.Z and the BDs of BRD2, BRD3, and BRD4, and show that the interaction is dependent on lysine acetylation in H2A.Z. The BDs preferentially engage a diacetylated H2A.Z-K4acK7ac motif that is reminiscent of sequences found in other biologically important BET BD target proteins, including histones and transcription factors. A H2A.Z-K7acK11ac motif can also bind BET BDs-with a preference for the second BD of each protein. Chemical shift perturbation mapping of the interactions, together with an X-ray crystal structure of BRD2-BD1 bound to H2A.Z-K4acK7ac, shows that H2A.Z binds the canonical AcK binding pocket of the BDs. This mechanism mirrors the conserved binding mode that is unique to the BET BDs, in which two acetylation marks are read simultaneously by a single BD. Our findings provide structural corroboration of biochemical and cell biological data that link H2A.Z and BET-family proteins, suggesting that the function of H2A.Z is enacted through interactions with these chromatin readers.
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Affiliation(s)
- Karishma Patel
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Paul D Solomon
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - James L Walshe
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia.,Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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18
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Xi CR, Di Fazio A, Nadvi NA, Patel K, Xiang MSW, Zhang HE, Deshpande C, Low JKK, Wang XT, Chen Y, McMillan CLD, Isaacs A, Osborne B, Vieira de Ribeiro AJ, McCaughan GW, Mackay JP, Church WB, Gorrell MD. A Novel Purification Procedure for Active Recombinant Human DPP4 and the Inability of DPP4 to Bind SARS-CoV-2. Molecules 2020; 25:molecules25225392. [PMID: 33218025 PMCID: PMC7698748 DOI: 10.3390/molecules25225392] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/09/2020] [Accepted: 11/13/2020] [Indexed: 01/09/2023] Open
Abstract
Proteases catalyse irreversible posttranslational modifications that often alter a biological function of the substrate. The protease dipeptidyl peptidase 4 (DPP4) is a pharmacological target in type 2 diabetes therapy primarily because it inactivates glucagon-like protein-1. DPP4 also has roles in steatosis, insulin resistance, cancers and inflammatory and fibrotic diseases. In addition, DPP4 binds to the spike protein of the MERS virus, causing it to be the human cell surface receptor for that virus. DPP4 has been identified as a potential binding target of SARS-CoV-2 spike protein, so this question requires experimental investigation. Understanding protein structure and function requires reliable protocols for production and purification. We developed such strategies for baculovirus generated soluble recombinant human DPP4 (residues 29–766) produced in insect cells. Purification used differential ammonium sulphate precipitation, hydrophobic interaction chromatography, dye affinity chromatography in series with immobilised metal affinity chromatography, and ion-exchange chromatography. The binding affinities of DPP4 to the SARS-CoV-2 full-length spike protein and its receptor-binding domain (RBD) were measured using surface plasmon resonance and ELISA. This optimised DPP4 purification procedure yielded 1 to 1.8 mg of pure fully active soluble DPP4 protein per litre of insect cell culture with specific activity >30 U/mg, indicative of high purity. No specific binding between DPP4 and CoV-2 spike protein was detected by surface plasmon resonance or ELISA. In summary, a procedure for high purity high yield soluble human DPP4 was achieved and used to show that, unlike MERS, SARS-CoV-2 does not bind human DPP4.
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Affiliation(s)
- Cecy R Xi
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (C.R.X.); (A.D.F.); (N.A.N.); (M.S.W.X.); (H.E.Z.); (X.T.W.); (Y.C.); (B.O.); (A.J.V.d.R.); (G.W.M.)
| | - Arianna Di Fazio
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (C.R.X.); (A.D.F.); (N.A.N.); (M.S.W.X.); (H.E.Z.); (X.T.W.); (Y.C.); (B.O.); (A.J.V.d.R.); (G.W.M.)
| | - Naveed Ahmed Nadvi
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (C.R.X.); (A.D.F.); (N.A.N.); (M.S.W.X.); (H.E.Z.); (X.T.W.); (Y.C.); (B.O.); (A.J.V.d.R.); (G.W.M.)
- Research Portfolio Core Research Facilities, The University of Sydney, Sydney, NSW 2006, Australia
| | - Karishma Patel
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (K.P.); (C.D.); (J.K.K.L.)
| | - Michelle Sui Wen Xiang
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (C.R.X.); (A.D.F.); (N.A.N.); (M.S.W.X.); (H.E.Z.); (X.T.W.); (Y.C.); (B.O.); (A.J.V.d.R.); (G.W.M.)
| | - Hui Emma Zhang
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (C.R.X.); (A.D.F.); (N.A.N.); (M.S.W.X.); (H.E.Z.); (X.T.W.); (Y.C.); (B.O.); (A.J.V.d.R.); (G.W.M.)
| | - Chandrika Deshpande
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (K.P.); (C.D.); (J.K.K.L.)
- Drug Discovery, Sydney Analytical, Core Research Facilities, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Jason K K Low
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (K.P.); (C.D.); (J.K.K.L.)
| | - Xiaonan Trixie Wang
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (C.R.X.); (A.D.F.); (N.A.N.); (M.S.W.X.); (H.E.Z.); (X.T.W.); (Y.C.); (B.O.); (A.J.V.d.R.); (G.W.M.)
| | - Yiqian Chen
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (C.R.X.); (A.D.F.); (N.A.N.); (M.S.W.X.); (H.E.Z.); (X.T.W.); (Y.C.); (B.O.); (A.J.V.d.R.); (G.W.M.)
| | - Christopher L D McMillan
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia; (C.L.D.M.); (A.I.)
| | - Ariel Isaacs
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia; (C.L.D.M.); (A.I.)
| | - Brenna Osborne
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (C.R.X.); (A.D.F.); (N.A.N.); (M.S.W.X.); (H.E.Z.); (X.T.W.); (Y.C.); (B.O.); (A.J.V.d.R.); (G.W.M.)
| | - Ana Júlia Vieira de Ribeiro
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (C.R.X.); (A.D.F.); (N.A.N.); (M.S.W.X.); (H.E.Z.); (X.T.W.); (Y.C.); (B.O.); (A.J.V.d.R.); (G.W.M.)
| | - Geoffrey W McCaughan
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (C.R.X.); (A.D.F.); (N.A.N.); (M.S.W.X.); (H.E.Z.); (X.T.W.); (Y.C.); (B.O.); (A.J.V.d.R.); (G.W.M.)
- AW Morrow GE & Liver Centre, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
| | - Joel P Mackay
- Drug Discovery, Sydney Analytical, Core Research Facilities, The University of Sydney, Sydney, NSW 2006, Australia;
| | - W Bret Church
- Faculty of Medicine and Health, School of Pharmacy, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Mark D Gorrell
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (C.R.X.); (A.D.F.); (N.A.N.); (M.S.W.X.); (H.E.Z.); (X.T.W.); (Y.C.); (B.O.); (A.J.V.d.R.); (G.W.M.)
- Correspondence: ; Tel.: +61-2-9565-6156; Fax: +61-2-9565-6101
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19
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Zhong Y, Paudel BP, Ryan DP, Low JKK, Franck C, Patel K, Bedward MJ, Torrado M, Payne RJ, van Oijen AM, Mackay JP. CHD4 slides nucleosomes by decoupling entry- and exit-side DNA translocation. Nat Commun 2020; 11:1519. [PMID: 32251276 PMCID: PMC7090039 DOI: 10.1038/s41467-020-15183-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 02/21/2020] [Indexed: 11/09/2022] Open
Abstract
Chromatin remodellers hydrolyse ATP to move nucleosomal DNA against histone octamers. The mechanism, however, is only partially resolved, and it is unclear if it is conserved among the four remodeller families. Here we use single-molecule assays to examine the mechanism of action of CHD4, which is part of the least well understood family. We demonstrate that the binding energy for CHD4-nucleosome complex formation-even in the absence of nucleotide-triggers significant conformational changes in DNA at the entry side, effectively priming the system for remodelling. During remodelling, flanking DNA enters the nucleosome in a continuous, gradual manner but exits in concerted 4-6 base-pair steps. This decoupling of entry- and exit-side translocation suggests that ATP-driven movement of entry-side DNA builds up strain inside the nucleosome that is subsequently released at the exit side by DNA expulsion. Based on our work and previous studies, we propose a mechanism for nucleosome sliding.
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Affiliation(s)
- Yichen Zhong
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Bishnu P Paudel
- Molecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia
| | - Daniel P Ryan
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Charlotte Franck
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Karishma Patel
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Max J Bedward
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Mario Torrado
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Antoine M van Oijen
- Molecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, 2522, Australia. .,Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia.
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
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20
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Woodhouse RM, Buchmann G, Hoe M, Harney DJ, Low JKK, Larance M, Boag PR, Ashe A. Chromatin Modifiers SET-25 and SET-32 Are Required for Establishment but Not Long-Term Maintenance of Transgenerational Epigenetic Inheritance. Cell Rep 2019; 25:2259-2272.e5. [PMID: 30463020 DOI: 10.1016/j.celrep.2018.10.085] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 09/25/2018] [Accepted: 10/24/2018] [Indexed: 12/24/2022] Open
Abstract
Some epigenetic modifications are inherited from one generation to the next, providing a potential mechanism for the inheritance of environmentally acquired traits. Transgenerational inheritance of RNAi phenotypes in Caenorhabditis elegans provides an excellent model to study this phenomenon, and although studies have implicated both chromatin modifications and small RNA pathways in heritable silencing, their relative contributions remain unclear. Here, we demonstrate that the putative histone methyltransferases SET-25 and SET-32 are required for establishment of a transgenerational silencing signal but not for long-term maintenance of this signal between subsequent generations, suggesting that transgenerational epigenetic inheritance is a multi-step process with distinct genetic requirements for establishment and maintenance of heritable silencing. Furthermore, small RNA sequencing reveals that the abundance of secondary siRNAs (thought to be the effector molecules of heritable silencing) does not correlate with silencing phenotypes. Together, our results suggest that the current mechanistic models of epigenetic inheritance are incomplete.
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Affiliation(s)
- Rachel M Woodhouse
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia
| | - Gabriele Buchmann
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia
| | - Matthew Hoe
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia
| | - Dylan J Harney
- The University of Sydney, Charles Perkins Centre, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia
| | - Jason K K Low
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia
| | - Mark Larance
- The University of Sydney, Charles Perkins Centre, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia
| | - Peter R Boag
- Monash University, Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Clayton, VIC 3800, Australia
| | - Alyson Ashe
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia; The University of Wollongong, School of Biological Sciences and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
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21
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Sharifi Tabar M, Mackay JP, Low JKK. The stoichiometry and interactome of the Nucleosome Remodeling and Deacetylase (NuRD) complex are conserved across multiple cell lines. FEBS J 2019; 286:2043-2061. [DOI: 10.1111/febs.14800] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/27/2018] [Accepted: 03/01/2019] [Indexed: 12/13/2022]
Affiliation(s)
| | - Joel P. Mackay
- School of Life and Environmental Sciences University of Sydney Australia
| | - Jason K. K. Low
- School of Life and Environmental Sciences University of Sydney Australia
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22
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Lu B, Klingbeil O, Tarumoto Y, Somerville TDD, Huang YH, Wei Y, Wai DC, Low JKK, Milazzo JP, Wu XS, Cao Z, Yan X, Demerdash OE, Huang G, Mackay JP, Kinney JB, Shi J, Vakoc CR. A Transcription Factor Addiction in Leukemia Imposed by the MLL Promoter Sequence. Cancer Cell 2018; 34:970-981.e8. [PMID: 30503706 PMCID: PMC6554023 DOI: 10.1016/j.ccell.2018.10.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 09/07/2018] [Accepted: 10/29/2018] [Indexed: 12/29/2022]
Abstract
The Mixed Lineage Leukemia gene (MLL) is altered in leukemia by chromosomal translocations to produce oncoproteins composed of the MLL N-terminus fused to the C-terminus of a partner protein. Here, we used domain-focused CRISPR screening to identify ZFP64 as an essential transcription factor in MLL-rearranged leukemia. We show that the critical function of ZFP64 in leukemia is to maintain MLL expression via binding to the MLL promoter, which is the most enriched location of ZFP64 occupancy in the human genome. The specificity of ZFP64 for MLL is accounted for by an exceptional density of ZFP64 motifs embedded within the MLL promoter. These findings demonstrate how a sequence anomaly of an oncogene promoter can impose a transcriptional addiction in cancer.
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MESH Headings
- A549 Cells
- Animals
- Cell Line, Tumor
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Gene Expression Regulation, Leukemic
- HEK293 Cells
- High-Throughput Nucleotide Sequencing
- Humans
- K562 Cells
- Leukemia, Biphenotypic, Acute/genetics
- Leukemia, Biphenotypic, Acute/metabolism
- Leukemia, Biphenotypic, Acute/pathology
- Mice, Inbred NOD
- Mice, Knockout
- Mice, SCID
- Myeloid-Lymphoid Leukemia Protein/genetics
- Myeloid-Lymphoid Leukemia Protein/metabolism
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Promoter Regions, Genetic/genetics
- THP-1 Cells
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Translocation, Genetic
- Transplantation, Heterologous
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Affiliation(s)
- Bin Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Olaf Klingbeil
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Yusuke Tarumoto
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Yu-Han Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Yiliang Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Dorothy C Wai
- School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
| | - Joseph P Milazzo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Xiaoli S Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Zhendong Cao
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xiaomei Yan
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | | | - Gang Huang
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
| | - Justin B Kinney
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Junwei Shi
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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23
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Link S, Spitzer RMM, Sana M, Torrado M, Völker-Albert MC, Keilhauer EC, Burgold T, Pünzeler S, Low JKK, Lindström I, Nist A, Regnard C, Stiewe T, Hendrich B, Imhof A, Mann M, Mackay JP, Bartkuhn M, Hake SB. PWWP2A binds distinct chromatin moieties and interacts with an MTA1-specific core NuRD complex. Nat Commun 2018; 9:4300. [PMID: 30327463 PMCID: PMC6191444 DOI: 10.1038/s41467-018-06665-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 09/17/2018] [Indexed: 12/31/2022] Open
Abstract
Chromatin structure and function is regulated by reader proteins recognizing histone modifications and/or histone variants. We recently identified that PWWP2A tightly binds to H2A.Z-containing nucleosomes and is involved in mitotic progression and cranial-facial development. Here, using in vitro assays, we show that distinct domains of PWWP2A mediate binding to free linker DNA as well as H3K36me3 nucleosomes. In vivo, PWWP2A strongly recognizes H2A.Z-containing regulatory regions and weakly binds H3K36me3-containing gene bodies. Further, PWWP2A binds to an MTA1-specific subcomplex of the NuRD complex (M1HR), which consists solely of MTA1, HDAC1, and RBBP4/7, and excludes CHD, GATAD2 and MBD proteins. Depletion of PWWP2A leads to an increase of acetylation levels on H3K27 as well as H2A.Z, presumably by impaired chromatin recruitment of M1HR. Thus, this study identifies PWWP2A as a complex chromatin-binding protein that serves to direct the deacetylase complex M1HR to H2A.Z-containing chromatin, thereby promoting changes in histone acetylation levels.
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Affiliation(s)
- Stephanie Link
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
- Institute for Genetics, Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Ramona M M Spitzer
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
- Institute for Genetics, Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Maryam Sana
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia
| | - Mario Torrado
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia
| | - Moritz C Völker-Albert
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
| | - Eva C Keilhauer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
- Coriolis Pharma, Fraunhoferstr. 18B, 82152, Planegg, Germany
| | - Thomas Burgold
- Wellcome Trust - MRC Stem Cell Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Sebastian Pünzeler
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
- Coparion GmbH & Co. KG, Charles-de-Gaulle-Platz 1d, 50679, Cologne, Germany
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia
| | - Ida Lindström
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia
| | - Andrea Nist
- Genomics Core Facility, Philipps-University Marburg, 35043, Marburg, Germany
| | - Catherine Regnard
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Philipps-University Marburg, 35043, Marburg, Germany
- Institute for Molecular Oncology, Philipps-University Marburg, 35043, Marburg, Germany
| | - Brian Hendrich
- Wellcome Trust - MRC Stem Cell Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Axel Imhof
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
- Center for Integrated Protein Science Munich (CIPSM), 81377, Munich, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
- Center for Integrated Protein Science Munich (CIPSM), 81377, Munich, Germany
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia
| | - Marek Bartkuhn
- Institute for Genetics, Justus-Liebig University Giessen, 35392, Giessen, Germany.
| | - Sandra B Hake
- Institute for Genetics, Justus-Liebig University Giessen, 35392, Giessen, Germany.
- Center for Integrated Protein Science Munich (CIPSM), 81377, Munich, Germany.
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24
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Kielkopf CS, Low JKK, Mok YF, Bhatia S, Palasovski T, Oakley AJ, Whitten AE, Garner B, Brown SHJ. Identification of a novel tetrameric structure for human apolipoprotein-D. J Struct Biol 2018; 203:205-218. [PMID: 29885491 DOI: 10.1016/j.jsb.2018.05.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/18/2018] [Accepted: 05/30/2018] [Indexed: 10/14/2022]
Abstract
Apolipoprotein-D is a 25 kDa glycosylated member of the lipocalin family that folds into an eight-stranded β-barrel with a single adjacent α-helix. Apolipoprotein-D specifically binds a range of small hydrophobic ligands such as progesterone and arachidonic acid and has an antioxidant function that is in part due to the reduction of peroxidised lipids by methionine-93. Therefore, apolipoprotein-D plays multiple roles throughout the body and is protective in Alzheimer's disease, where apolipoprotein-D overexpression reduces the amyloid-β burden in Alzheimer's disease mouse models. Oligomerisation is a common feature of lipocalins that can influence ligand binding. The native structure of apolipoprotein-D, however, has not been conclusively defined. Apolipoprotein-D is generally described as a monomeric protein, although it dimerises when reducing peroxidised lipids. Here, we investigated the native structure of apolipoprotein-D derived from plasma, breast cyst fluid (BCF) and cerebrospinal fluid. In plasma and cerebrospinal fluid, apolipoprotein-D was present in high-molecular weight complexes, potentially in association with lipoproteins. In contrast, apolipoprotein-D in BCF formed distinct oligomeric species. We assessed apolipoprotein-D oligomerisation using native apolipoprotein-D purified from BCF and a suite of complementary methods, including multi-angle laser light scattering, analytical ultracentrifugation and small-angle X-ray scattering. Our analyses showed that apolipoprotein-D predominantly forms a ∼95 to ∼100 kDa tetramer. Small-angle X-ray scattering analysis confirmed these findings and provided a structural model for apolipoprotein-D tetramer. These data indicate apolipoprotein-D rarely exists as a free monomer under physiological conditions and provide insights into novel native structures of apolipoprotein-D and into oligomerisation behaviour in the lipocalin family.
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Affiliation(s)
- Claudia S Kielkopf
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia; School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia; Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia.
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia.
| | - Yee-Foong Mok
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia.
| | - Surabhi Bhatia
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia; School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia.
| | - Tony Palasovski
- Illawarra and Shoalhaven Local Health District (ISLHD), Wollongong, NSW, Australia; Specialist Breast Clinic Sutherland Shire and Wollongong, NSW, Australia; Integrated Specialist Health Care Sutherland Shire, NSW, Australia
| | - Aaron J Oakley
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia; Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia; School of Chemistry, University of Wollongong, Wollongong, NSW, Australia.
| | - Andrew E Whitten
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia.
| | - Brett Garner
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia; School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia; Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia.
| | - Simon H J Brown
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia; School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia; Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia.
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25
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Wai DCC, Szyszka TN, Campbell AE, Kwong C, Wilkinson-White LE, Silva APG, Low JKK, Kwan AH, Gamsjaeger R, Chalmers JD, Patrick WM, Lu B, Vakoc CR, Blobel GA, Mackay JP. The BRD3 ET domain recognizes a short peptide motif through a mechanism that is conserved across chromatin remodelers and transcriptional regulators. J Biol Chem 2018; 293:7160-7175. [PMID: 29567837 DOI: 10.1074/jbc.ra117.000678] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/08/2018] [Indexed: 12/31/2022] Open
Abstract
Members of the bromodomain and extra-terminal domain (BET) family of proteins (bromodomain-containing (BRD) 2, 3, 4, and T) are widely expressed and highly conserved regulators of gene expression in eukaryotes. These proteins have been intimately linked to human disease, and more than a dozen clinical trials are currently underway to test BET-protein inhibitors as modulators of cancer. However, although it is clear that these proteins use their bromodomains to bind both histones and transcription factors bearing acetylated lysine residues, the molecular mechanisms by which BET family proteins regulate gene expression are not well defined. In particular, the functions of the other domains such as the ET domain have been less extensively studied. Here, we examine the properties of the ET domain of BRD3 as a protein/protein interaction module. Using a combination of pulldown and biophysical assays, we demonstrate that BRD3 binds to a range of chromatin-remodeling complexes, including the NuRD, BAF, and INO80 complexes, via a short linear "KIKL" motif in one of the complex subunits. NMR-based structural analysis revealed that, surprisingly, this mode of interaction is shared by the AF9 and ENL transcriptional coregulators that contain an acetyl-lysine-binding YEATS domain and regulate transcriptional elongation. This observation establishes a functional commonality between these two families of cancer-related transcriptional regulators. In summary, our data provide insight into the mechanisms by which BET family proteins might link chromatin acetylation to transcriptional outcomes and uncover an unexpected functional similarity between BET and YEATS family proteins.
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Affiliation(s)
- Dorothy C C Wai
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Taylor N Szyszka
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Amy E Campbell
- Division of Hematology, Children's Hospital of Philadelphia, and the Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Cherry Kwong
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Lorna E Wilkinson-White
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Ana P G Silva
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Ann H Kwan
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Roland Gamsjaeger
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - James D Chalmers
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | - Wayne M Patrick
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | - Bin Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | | | - Gerd A Blobel
- Division of Hematology, Children's Hospital of Philadelphia, and the Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia.
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Torrado M, Low JKK, Silva APG, Schmidberger JW, Sana M, Sharifi Tabar M, Isilak ME, Winning CS, Kwong C, Bedward MJ, Sperlazza MJ, Williams DC, Shepherd NE, Mackay JP. Refinement of the subunit interaction network within the nucleosome remodelling and deacetylase (NuRD) complex. FEBS J 2017; 284:4216-4232. [PMID: 29063705 DOI: 10.1111/febs.14301] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 07/19/2017] [Accepted: 10/18/2017] [Indexed: 01/29/2023]
Abstract
The nucleosome remodelling and deacetylase (NuRD) complex is essential for the development of complex animals. NuRD has roles in regulating gene expression and repairing damaged DNA. The complex comprises at least six proteins with two or more paralogues of each protein routinely identified when the complex is purified from cell extracts. To understand the structure and function of NuRD, a map of direct subunit interactions is needed. Dozens of published studies have attempted to define direct inter-subunit connectivities. We propose that conclusions reported in many such studies are in fact ambiguous for one of several reasons. First, the expression of many NuRD subunits in bacteria is unlikely to lead to folded, active protein. Second, interaction studies carried out in cells that contain endogenous NuRD complex can lead to false positives through bridging of target proteins by endogenous components. Combining existing information on NuRD structure with a protocol designed to minimize false positives, we report a conservative and robust interaction map for the NuRD complex. We also suggest a 3D model of the complex that brings together the existing data on the complex. The issues and strategies discussed herein are also applicable to the analysis of a wide range of multi-subunit complexes. ENZYMES Micrococcal nuclease (MNase), EC 3.1.31.1; histone deacetylase (HDAC), EC 3.5.1.98.
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Affiliation(s)
- Mario Torrado
- School of Life and Environmental Sciences, University of Sydney, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Australia
| | - Ana P G Silva
- School of Life and Environmental Sciences, University of Sydney, Australia
| | | | - Maryam Sana
- School of Life and Environmental Sciences, University of Sydney, Australia
| | | | - Musa E Isilak
- School of Life and Environmental Sciences, University of Sydney, Australia
| | - Courtney S Winning
- School of Life and Environmental Sciences, University of Sydney, Australia
| | - Cherry Kwong
- School of Life and Environmental Sciences, University of Sydney, Australia
| | - Max J Bedward
- School of Life and Environmental Sciences, University of Sydney, Australia
| | - Mary J Sperlazza
- Department of Pathology and Laboratory Medicine, The University of North Carolina - Chapel Hill, NC, USA
| | - David C Williams
- Department of Pathology and Laboratory Medicine, The University of North Carolina - Chapel Hill, NC, USA
| | - Nicholas E Shepherd
- Institute for Molecular Biosciences, The University of Queensland, St Lucia, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Australia
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27
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Schmidberger JW, Sharifi Tabar M, Torrado M, Silva APG, Landsberg MJ, Brillault L, AlQarni S, Zeng YC, Parker BL, Low JKK, Mackay JP. The MTA1 subunit of the nucleosome remodeling and deacetylase complex can recruit two copies of RBBP4/7. Protein Sci 2016; 25:1472-82. [PMID: 27144666 PMCID: PMC4972203 DOI: 10.1002/pro.2943] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 05/02/2016] [Indexed: 11/05/2022]
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex remodels the genome in the context of both gene transcription and DNA damage repair. It is essential for normal development and is distributed across multiple tissues in organisms ranging from mammals to nematode worms. In common with other chromatin-remodeling complexes, however, its molecular mechanism of action is not well understood and only limited structural information is available to show how the complex is assembled. As a step towards understanding the structure of the NuRD complex, we have characterized the interaction between two subunits: the metastasis associated protein MTA1 and the histone-binding protein RBBP4. We show that MTA1 can bind to two molecules of RBBP4 and present negative stain electron microscopy and chemical crosslinking data that allow us to build a low-resolution model of an MTA1-(RBBP4)2 subcomplex. These data build on our understanding of NuRD complex structure and move us closer towards an understanding of the biochemical basis for the activity of this complex.
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Affiliation(s)
| | | | - Mario Torrado
- School of Life and Environmental SciencesUniversity of SydneyNSWAustralia
| | - Ana P. G. Silva
- School of Life and Environmental SciencesUniversity of SydneyNSWAustralia
| | - Michael J. Landsberg
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandQldAustralia
| | - Lou Brillault
- Institute for Molecular Bioscience, University of QueenslandQldAustralia
| | - Saad AlQarni
- School of Life and Environmental SciencesUniversity of SydneyNSWAustralia
| | - Yi Cheng Zeng
- School of Life and Environmental SciencesUniversity of SydneyNSWAustralia
| | - Benjamin L. Parker
- School of Life and Environmental SciencesUniversity of SydneyNSWAustralia
| | - Jason K. K. Low
- School of Life and Environmental SciencesUniversity of SydneyNSWAustralia
| | - Joel P. Mackay
- School of Life and Environmental SciencesUniversity of SydneyNSWAustralia
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Wai DCC, Shihab M, Low JKK, Mackay JP. The zinc fingers of YY1 bind single-stranded RNA with low sequence specificity. Nucleic Acids Res 2016; 44:9153-9165. [PMID: 27369384 PMCID: PMC5100589 DOI: 10.1093/nar/gkw590] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 06/16/2016] [Indexed: 12/22/2022] Open
Abstract
Classical zinc fingers (ZFs) are traditionally considered to act as sequence-specific DNA-binding domains. More recently, classical ZFs have been recognised as potential RNA-binding modules, raising the intriguing possibility that classical-ZF transcription factors are involved in post-transcriptional gene regulation via direct RNA binding. To date, however, only one classical ZF-RNA complex, that involving TFIIIA, has been structurally characterised. Yin Yang-1 (YY1) is a multi-functional transcription factor involved in many regulatory processes, and binds DNA via four classical ZFs. Recent evidence suggests that YY1 also interacts with RNA, but the molecular nature of the interaction remains unknown. In the present work, we directly assess the ability of YY1 to bind RNA using in vitro assays. Systematic Evolution of Ligands by EXponential enrichment (SELEX) was used to identify preferred RNA sequences bound by the YY1 ZFs from a randomised library over multiple rounds of selection. However, a strong motif was not consistently recovered, suggesting that the RNA sequence selectivity of these domains is modest. YY1 ZF residues involved in binding to single-stranded RNA were identified by NMR spectroscopy and found to be largely distinct from the set of residues involved in DNA binding, suggesting that interactions between YY1 and ssRNA constitute a separate mode of nucleic acid binding. Our data are consistent with recent reports that YY1 can bind to RNA in a low-specificity, yet physiologically relevant manner.
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Affiliation(s)
- Dorothy C C Wai
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Manar Shihab
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
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Low JKK, Webb SR, Silva APG, Saathoff H, Ryan DP, Torrado M, Brofelth M, Parker BL, Shepherd NE, Mackay JP. CHD4 Is a Peripheral Component of the Nucleosome Remodeling and Deacetylase Complex. J Biol Chem 2016; 291:15853-66. [PMID: 27235397 DOI: 10.1074/jbc.m115.707018] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Indexed: 01/08/2023] Open
Abstract
Chromatin remodeling enzymes act to dynamically regulate gene accessibility. In many cases, these enzymes function as large multicomponent complexes that in general comprise a central ATP-dependent Snf2 family helicase that is decorated with a variable number of regulatory subunits. The nucleosome remodeling and deacetylase (NuRD) complex, which is essential for normal development in higher organisms, is one such macromolecular machine. The NuRD complex comprises ∼10 subunits, including the histone deacetylases 1 and 2 (HDAC1 and HDAC2), and is defined by the presence of a CHD family remodeling enzyme, most commonly CHD4 (chromodomain helicase DNA-binding protein 4). The existing paradigm holds that CHD4 acts as the central hub upon which the complex is built. We show here that this paradigm does not, in fact, hold and that CHD4 is a peripheral component of the NuRD complex. A complex lacking CHD4 that has HDAC activity can exist as a stable species. The addition of recombinant CHD4 to this nucleosome deacetylase complex reconstitutes a NuRD complex with nucleosome remodeling activity. These data contribute to our understanding of the architecture of the NuRD complex.
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Affiliation(s)
- Jason K K Low
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
| | - Sarah R Webb
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
| | - Ana P G Silva
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
| | - Hinnerk Saathoff
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
| | - Daniel P Ryan
- the Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Mario Torrado
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
| | - Mattias Brofelth
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
| | - Benjamin L Parker
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
| | - Nicholas E Shepherd
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
| | - Joel P Mackay
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
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Low JKK, Im H, Erce MA, Hart-Smith G, Snyder MP, Wilkins MR. Protein substrates of the arginine methyltransferase Hmt1 identified by proteome arrays. Proteomics 2016; 16:465-76. [DOI: 10.1002/pmic.201400564] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 09/27/2015] [Accepted: 11/10/2015] [Indexed: 01/22/2023]
Affiliation(s)
- Jason K. K. Low
- Systems Biology Initiative; School of Biotechnology and Biomolecular Sciences; The University of New South Wales; Sydney Australia
| | - Hogune Im
- Department of Genetics; Stanford University School of Medicine; Palo Alto CA USA
| | - Melissa A. Erce
- Systems Biology Initiative; School of Biotechnology and Biomolecular Sciences; The University of New South Wales; Sydney Australia
| | - Gene Hart-Smith
- Systems Biology Initiative; School of Biotechnology and Biomolecular Sciences; The University of New South Wales; Sydney Australia
| | - Michael P. Snyder
- Department of Genetics; Stanford University School of Medicine; Palo Alto CA USA
| | - Marc R. Wilkins
- Systems Biology Initiative; School of Biotechnology and Biomolecular Sciences; The University of New South Wales; Sydney Australia
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Silva APG, Ryan DP, Galanty Y, Low JKK, Vandevenne M, Jackson SP, Mackay JP. The N-terminal Region of Chromodomain Helicase DNA-binding Protein 4 (CHD4) Is Essential for Activity and Contains a High Mobility Group (HMG) Box-like-domain That Can Bind Poly(ADP-ribose). J Biol Chem 2016; 291:924-38. [PMID: 26565020 PMCID: PMC4705410 DOI: 10.1074/jbc.m115.683227] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/09/2015] [Indexed: 01/11/2023] Open
Abstract
Chromodomain Helicase DNA-binding protein 4 (CHD4) is a chromatin-remodeling enzyme that has been reported to regulate DNA-damage responses through its N-terminal region in a poly(ADP-ribose) polymerase-dependent manner. We have identified and determined the structure of a stable domain (CHD4-N) in this N-terminal region. The-fold consists of a four-α-helix bundle with structural similarity to the high mobility group box, a domain that is well known as a DNA binding module. We show that the CHD4-N domain binds with higher affinity to poly(ADP-ribose) than to DNA. We also show that the N-terminal region of CHD4, although not CHD4-N alone, is essential for full nucleosome remodeling activity and is important for localizing CHD4 to sites of DNA damage. Overall, these data build on our understanding of how CHD4-NuRD acts to regulate gene expression and participates in the DNA-damage response.
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Affiliation(s)
- Ana P G Silva
- From the School of Molecular Bioscience, The University of Sydney, New South Wales 2006, Australia,
| | - Daniel P Ryan
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, and
| | - Yaron Galanty
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Jason K K Low
- From the School of Molecular Bioscience, The University of Sydney, New South Wales 2006, Australia
| | - Marylene Vandevenne
- From the School of Molecular Bioscience, The University of Sydney, New South Wales 2006, Australia
| | - Stephen P Jackson
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Joel P Mackay
- From the School of Molecular Bioscience, The University of Sydney, New South Wales 2006, Australia,
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32
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Saathoff H, Brofelth M, Trinh A, Parker BL, Ryan DP, Low JKK, Webb SR, Silva APG, Mackay JP, Shepherd NE. A peptide affinity reagent for isolating an intact and catalytically active multi-protein complex from mammalian cells. Bioorg Med Chem 2015; 23:960-5. [PMID: 25678017 DOI: 10.1016/j.bmc.2015.01.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 01/14/2015] [Accepted: 01/14/2015] [Indexed: 10/24/2022]
Abstract
We have developed an approach for directly isolating an intact multi-protein chromatin remodeling complex from mammalian cell extracts using synthetic peptide affinity reagent 4. FOG1(1-15), a short peptide sequence known to target subunits of the nucleosome remodeling and deacetylase (NuRD) complex, was joined via a 35-atom hydrophilic linker to the StreptagII peptide. Loading this peptide onto Streptactin beads enabled capture of the intact NuRD complex from MEL cell nuclear extract. Gentle biotin elution yielded the desired intact complex free of significant contaminants and in a form that was catalytically competent in a nucleosome remodeling assay. The efficiency of 4 in isolating the NuRD complex was comparable to other reported methods utilising recombinantly produced GST-FOG1(1-45).
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Affiliation(s)
- Hinnerk Saathoff
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia
| | - Mattias Brofelth
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia
| | - Anne Trinh
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia
| | - Benjamin L Parker
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia
| | - Daniel P Ryan
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 0200, Australia
| | - Jason K K Low
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia
| | - Sarah R Webb
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia
| | - Ana P G Silva
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia
| | - Joel P Mackay
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia
| | - Nicholas E Shepherd
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia.
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Hart-Smith G, Chia SZ, Low JKK, McKay MJ, Molloy MP, Wilkins MR. Stoichiometry of Saccharomyces cerevisiae Lysine Methylation: Insights into Non-histone Protein Lysine Methyltransferase Activity. J Proteome Res 2014; 13:1744-56. [DOI: 10.1021/pr401251k] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Gene Hart-Smith
- NSW
Systems Biology Initiative, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Samantha Z. Chia
- NSW
Systems Biology Initiative, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Jason K. K. Low
- NSW
Systems Biology Initiative, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Matthew J. McKay
- Australian
Proteome Analysis Facility, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Mark P. Molloy
- Australian
Proteome Analysis Facility, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Marc R. Wilkins
- NSW
Systems Biology Initiative, University of New South Wales, Sydney, New South Wales 2052, Australia
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Low JKK, Hart-Smith G, Erce MA, Wilkins MR. The Saccharomyces cerevisiae poly(A)-binding protein is subject to multiple post-translational modifications, including the methylation of glutamic acid. Biochem Biophys Res Commun 2013; 443:543-8. [PMID: 24326073 DOI: 10.1016/j.bbrc.2013.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 12/02/2013] [Indexed: 01/17/2023]
Abstract
Poly(A)-binding protein in mouse and man was recently found to be highly post-translationally modified. Here we analysed an ortholog of this protein, Pab1 from Saccharomyces cerevisiae, to assess the conservation and thus likely importance of these modifications. Pab1 showed the presence of six sites of methylated glutamate, five sites of lysine acetylation, and one phosphorylation of serine. Many modifications on Pab1 showed either complete conservation with those on human or mouse PABPC1, were present on nearby residues and/or were present in the same domain(s). The conservation of methylated glutamate, an unusual modification, was of particular note and suggests a conserved function. Comparison of methylated glutamate sites in human, mouse and yeast poly(A)-binding protein, along with methylation sites catalysed by CheR L-glutamyl protein methyltransferase from Salmonella typhimurium, revealed that the methylation of glutamate preferentially occurs in EE and DE motifs or other small regions of acidic amino acids. The conservation of methylated glutamate in the same protein between mouse, man and yeast suggests the presence of a eukaryotic l-glutamyl protein methyltransferase and that the modification is of functional significance.
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Affiliation(s)
- Jason K K Low
- Systems Biology Laboratory, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Gene Hart-Smith
- Systems Biology Laboratory, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Melissa A Erce
- Systems Biology Laboratory, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Marc R Wilkins
- Systems Biology Laboratory, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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Erce MA, Abeygunawardena D, Low JKK, Hart-Smith G, Wilkins MR. Interactions affected by arginine methylation in the yeast protein-protein interaction network. Mol Cell Proteomics 2013; 12:3184-98. [PMID: 23918811 DOI: 10.1074/mcp.m113.031500] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Protein-protein interactions can be modulated by the methylation of arginine residues. As a means of testing this, we recently described a conditional two-hybrid system, based on the bacterial adenylate cyclase (BACTH) system. Here, we have used this conditional two-hybrid system to explore the effect of arginine methylation in modulating protein-protein interactions in a subset of the Saccharomyces cerevisiae arginine methylproteome network. Interactions between the yeast hub protein Npl3 and yeast proteins Air2, Ded1, Gbp2, Snp1, and Yra1 were first validated in the absence of methylation. The major yeast arginine methyltransferase Hmt1 was subsequently included in the conditional two-hybrid assay, initially to determine the degree of methylation that occurs. Proteins Snp1 and Yra1 were confirmed as Hmt1 substrates, with five and two novel arginine methylation sites mapped by ETD LC-MS/MS on these proteins, respectively. Proteins Ded1 and Gbp2, previously predicted but not confirmed as substrates of Hmt1, were also found to be methylated with five and seven sites mapped respectively. Air2 was found to be a novel substrate of Hmt1 with two sites mapped. Finally, we investigated the interactions of Npl3 with the five interaction partners in the presence of active Hmt1 and in the presence of Hmt1 with a G68R inactivation mutation. We found that the interaction between Npl3 and Air2, and Npl3 and Ded1, were significantly increased in the presence of active Hmt1; the interaction of Npl3 and Snp1 showed a similar degree of increase in interaction but this was not statistically significant. The interactions of Npl3 and Gbp2, along with Npl3 and Yra1, were not significantly increased or decreased by methylation. We conclude that methylarginine may be a widespread means by which the interactions of proteins are modulated.
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Affiliation(s)
- Melissa A Erce
- Systems Biology Laboratory, School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
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Erce MA, Low JKK, Hart-Smith G, Wilkins MR. A conditional two-hybrid (C2H) system for the detection of protein-protein interactions that are mediated by post-translational modification. Proteomics 2013; 13:1059-64. [DOI: 10.1002/pmic.201200477] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 12/10/2012] [Accepted: 01/09/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Melissa A. Erce
- Systems Biology Initiative; School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney Australia
| | - Jason K. K. Low
- Systems Biology Initiative; School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney Australia
| | - Gene Hart-Smith
- Systems Biology Initiative; School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney Australia
| | - Marc R. Wilkins
- Systems Biology Initiative; School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney Australia
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Low JKK, Wilkins MR. Protein arginine methylation in Saccharomyces cerevisiae. FEBS J 2012; 279:4423-43. [PMID: 23094907 DOI: 10.1111/febs.12039] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/10/2012] [Accepted: 10/19/2012] [Indexed: 11/27/2022]
Abstract
Recent research has implicated arginine methylation as a major regulator of cellular processes, including transcription, translation, nucleocytoplasmic transport, signalling, DNA repair, RNA processing and splicing. Arginine methylation is evolutionarily conserved, and it is now thought that it may rival other post-translational modifications such as phosphorylation in terms of its occurrence in the proteome. In addition, multiple recent examples demonstrate an exciting new theme: the interplay between methylation and other post-translational modifications such as phosphorylation. In this review, we summarize our current understanding of arginine methylation and the recent advances made, with a focus on the lower eukaryote Saccharomyces cerevisiae. We cover the types of methylated proteins, their responsible methyltransferases, where and how the effects of arginine methylation are seen in the cell, and, finally, discuss the conservation of the biological function of methylarginines between S. cerevisiae and mammals.
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Affiliation(s)
- Jason K K Low
- Systems Biology Laboratory, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
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Hart-Smith G, Low JKK, Erce MA, Wilkins MR. Enhanced methylarginine characterization by post-translational modification-specific targeted data acquisition and electron-transfer dissociation mass spectrometry. J Am Soc Mass Spectrom 2012; 23:1376-1389. [PMID: 22673836 DOI: 10.1007/s13361-012-0417-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2012] [Revised: 04/27/2012] [Accepted: 05/12/2012] [Indexed: 06/01/2023]
Abstract
When localizing protein post-translational modifications (PTMs) using liquid-chromatography (LC)-tandem mass spectrometry (MS/MS), existing implementations are limited by inefficient selection of PTM-carrying peptides for MS/MS, particularly when PTM site occupancy is sub-stoichiometric. The present contribution describes a method by which peptides carrying specific PTMs of interest-in this study, methylarginines-may be selectively targeted for MS/MS: peptide features are extracted from high mass accuracy single-stage MS data, searched against theoretical PTM-carrying peptide masses, and matching features are subjected to targeted data acquisition LC-MS/MS. Using trypsin digested Saccharomyces cerevisiae Npl3, in which evidence is presented for 18 methylarginine sites-17 of which fall within a glycine-arginine-rich (GAR) domain spanning <120 amino acids-it is shown that this approach outperforms conventional data dependent acquisition (DDA): when applied to a complex protein mixture featuring in vivo methylated Npl3, 95% more (P=0.030) methylarginine-carrying peptides are selected for MS/MS than DDA, leading to an 86% increase (P=0.044) in the number of methylated peptides producing Mascot ion scores ≥20 following electron-transfer dissociation (ETD). Notably, significantly more low abundance arginine methylated peptides (maximum ion intensities <6×10(4) cps) are selected for MS/MS using this approach relative to DDA (50% more in a digest of purified in vitro methylated Npl3). It is also demonstrated that relative to collision-induced dissociation (CID), ETD facilitates a 586% increase (P=0.016) in average Mascot ion scores of methylarginine-carrying peptides. The present PTM-specific targeted data acquisition approach, though described using methylarginine, is applicable to any ionizable PTM of known mass.
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Affiliation(s)
- Gene Hart-Smith
- NSW Systems Biology Initiative, University of New South Wales, Sydney, New South Wales, Australia
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Erce MA, Low JKK, March PE, Wilkins MR, Takayama KM. Identification and functional analysis of RNase E of Vibrio angustum S14 and two-hybrid analysis of its interaction partners. Biochim Biophys Acta 2009; 1794:1107-14. [PMID: 19345289 DOI: 10.1016/j.bbapap.2009.03.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Revised: 03/24/2009] [Accepted: 03/25/2009] [Indexed: 11/18/2022]
Abstract
RNase E is an essential enzyme that catalyses RNA processing. Microdomains which mediate interactions between RNase E and other members of the degradosome have been defined. To further elucidate the role of these microdomains in molecular interactions, we studied RNase E from Vibrio angustum S14. Protein sequence analysis revealed that its C-terminal half is less conserved and structured than its N-terminal half. Within this structural disorder, however, exist five small regions of predicted structural propensity. Four are similar to interaction-mediating microdomains identified in other RNase E proteins; the fifth did not correspond to any known functional motif. The function of the V. angustum S14 enolase-binding microdomain was confirmed using bacterial two-hybrid analysis, demonstrating the conserved function of this microdomain for the first time in a species other than Escherichia coli. Further, PNPase in V. angustum S14 was shown to interact with the last 80 amino acids of the C-terminal region of RNase E. This raises the possibility that PNPase interacts with the small ordered region at residues 1026-1041. The role of RNase E as a hub protein and the implications of microdomain-mediated interactions in relation to specificity and function are discussed.
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Affiliation(s)
- Melissa A Erce
- Systems Biology Laboratory, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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