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Dos Santos Á, Rollins DE, Hari-Gupta Y, McArthur H, Du M, Ru SYZ, Pidlisna K, Stranger A, Lorgat F, Lambert D, Brown I, Howland K, Aaron J, Wang L, Ellis PJI, Chew TL, Martin-Fernandez M, Pyne ALB, Toseland CP. Autophagy receptor NDP52 alters DNA conformation to modulate RNA polymerase II transcription. Nat Commun 2023; 14:2855. [PMID: 37202403 PMCID: PMC10195817 DOI: 10.1038/s41467-023-38572-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/09/2023] [Indexed: 05/20/2023] Open
Abstract
NDP52 is an autophagy receptor involved in the recognition and degradation of invading pathogens and damaged organelles. Although NDP52 was first identified in the nucleus and is expressed throughout the cell, to date, there is no clear nuclear functions for NDP52. Here, we use a multidisciplinary approach to characterise the biochemical properties and nuclear roles of NDP52. We find that NDP52 clusters with RNA Polymerase II (RNAPII) at transcription initiation sites and that its overexpression promotes the formation of additional transcriptional clusters. We also show that depletion of NDP52 impacts overall gene expression levels in two model mammalian cells, and that transcription inhibition affects the spatial organisation and molecular dynamics of NDP52 in the nucleus. This directly links NDP52 to a role in RNAPII-dependent transcription. Furthermore, we also show that NDP52 binds specifically and with high affinity to double-stranded DNA (dsDNA) and that this interaction leads to changes in DNA structure in vitro. This, together with our proteomics data indicating enrichment for interactions with nucleosome remodelling proteins and DNA structure regulators, suggests a possible function for NDP52 in chromatin regulation. Overall, here we uncover nuclear roles for NDP52 in gene expression and DNA structure regulation.
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Affiliation(s)
- Ália Dos Santos
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2RX, UK
- MRC LMB, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Daniel E Rollins
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, S1 3JD, UK
| | - Yukti Hari-Gupta
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
- MRC LMCB, University College London, Gower Street, London, WC1E 6BT, UK
| | - Hannah McArthur
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Mingxue Du
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, S1 3JD, UK
| | | | - Kseniia Pidlisna
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Ane Stranger
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Faeeza Lorgat
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2RX, UK
| | - Danielle Lambert
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2RX, UK
| | - Ian Brown
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Kevin Howland
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Jesse Aaron
- Advanced Imaging Center, HHMI Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Lin Wang
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, Didcot, Oxford, OX11 0QX, UK
| | - Peter J I Ellis
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Teng-Leong Chew
- Advanced Imaging Center, HHMI Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Marisa Martin-Fernandez
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, Didcot, Oxford, OX11 0QX, UK
| | - Alice L B Pyne
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, S1 3JD, UK
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Binding partners regulate unfolding of myosin VI to activate the molecular motor. Biochem J 2022; 479:1409-1428. [PMID: 35722941 PMCID: PMC9342898 DOI: 10.1042/bcj20220025] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 11/22/2022]
Abstract
Myosin VI is the only minus-end actin motor and it is coupled to various cellular processes ranging from endocytosis to transcription. This multi-potent nature is achieved through alternative isoform splicing and interactions with a network of binding partners. There is a complex interplay between isoforms and binding partners to regulate myosin VI. Here, we have compared the regulation of two myosin VI splice isoforms by two different binding partners. By combining biochemical and single-molecule approaches, we propose that myosin VI regulation follows a generic mechanism, independently of the spliced isoform and the binding partner involved. We describe how myosin VI adopts an autoinhibited backfolded state which is released by binding partners. This unfolding activates the motor, enhances actin binding and can subsequently trigger dimerization. We have further expanded our study by using single-molecule imaging to investigate the impact of binding partners upon myosin VI molecular organization and dynamics.
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