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Zhang YM, Li B, Wu WQ. Single-molecule insights into repetitive helicases. J Biol Chem 2024:107894. [PMID: 39424144 DOI: 10.1016/j.jbc.2024.107894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Revised: 10/07/2024] [Accepted: 10/09/2024] [Indexed: 10/21/2024] Open
Abstract
Helicases are ubiquitous motors involved in almost all aspects of nucleic acid metabolism; therefore, revealing their unwinding behaviors and mechanisms is fundamentally and medically essential. In recent decades, single-molecule applications have revolutionized our ability to study helicases by avoiding the averaging of bulk assays and bridging the knowledge gap between dynamics and structures. This advancement has updated our understanding of the biochemical properties of helicases, such as their rate, directionality, processivity, and step size, while also uncovering unprecedented mechanistic insights. Among these, repetitive motion, a new feature of helicases, is one of the most remarkable discoveries. However, comprehensive reviews and comparisons are still lacking. Consequently, the present review aims to summarize repetitive helicases, compare the repetitive phenomena, and discuss the underlying molecular mechanisms. This review may provide a systematic understanding of repetitive helicases and help understand their cellular functions.
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Affiliation(s)
- Ya-Mei Zhang
- School of Nursing and Health, School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, Kaifeng Key Laboratory Active Prevention and Nursing of Aizheimer's Disease, Henan University, Kaifeng, 475004, China
| | - Bo Li
- School of Nursing and Health, School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, Kaifeng Key Laboratory Active Prevention and Nursing of Aizheimer's Disease, Henan University, Kaifeng, 475004, China
| | - Wen-Qiang Wu
- School of Nursing and Health, School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, Kaifeng Key Laboratory Active Prevention and Nursing of Aizheimer's Disease, Henan University, Kaifeng, 475004, China.
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Wang M, Li J, Wang Y, Fu H, Qiu H, Li Y, Li M, Lu Y, Fu YV. Single-molecule study reveals Hmo1, not Hho1, promotes chromatin assembly in budding yeast. mBio 2023; 14:e0099323. [PMID: 37432033 PMCID: PMC10470511 DOI: 10.1128/mbio.00993-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 05/25/2023] [Indexed: 07/12/2023] Open
Abstract
Linker histone H1 plays a crucial role in various biological processes, including nucleosome stabilization, high-order chromatin structure organization, gene expression, and epigenetic regulation in eukaryotic cells. Unlike higher eukaryotes, little about the linker histone in Saccharomyces cerevisiae is known. Hho1 and Hmo1 are two long-standing controversial histone H1 candidates in budding yeast. In this study, we directly observed at the single-molecule level that Hmo1, but not Hho1, is involved in chromatin assembly in the yeast nucleoplasmic extracts (YNPE), which can replicate the physiological condition of the yeast nucleus. The presence of Hmo1 facilitates the assembly of nucleosomes on DNA in YNPE, as revealed by single-molecule force spectroscopy. Further single-molecule analysis showed that the lysine-rich C-terminal domain (CTD) of Hmo1 is essential for the function of chromatin compaction, while the second globular domain at the C-terminus of Hho1 impairs its ability. In addition, Hmo1, but not Hho1, forms condensates with double-stranded DNA via reversible phase separation. The phosphorylation fluctuation of Hmo1 coincides with metazoan H1 during the cell cycle. Our data suggest that Hmo1, but not Hho1, possesses some functionality similar to that of linker histone in Saccharomyces cerevisiae, even though some properties of Hmo1 differ from those of a canonical linker histone H1. Our study provides clues for the linker histone H1 in budding yeast and provides insights into the evolution and diversity of histone H1 across eukaryotes. IMPORTANCE There has been a long-standing debate regarding the identity of linker histone H1 in budding yeast. To address this issue, we utilized YNPE, which accurately replicate the physiological conditions in yeast nuclei, in combination with total internal reflection fluorescence microscopy and magnetic tweezers. Our findings demonstrated that Hmo1, rather than Hho1, is responsible for chromatin assembly in budding yeast. Additionally, we found that Hmo1 shares certain characteristics with histone H1, including phase separation and phosphorylation fluctuations throughout the cell cycle. Furthermore, we discovered that the lysine-rich domain of Hho1 is buried by its second globular domain at the C-terminus, resulting in the loss of function that is similar to histone H1. Our study provides compelling evidence to suggest that Hmo1 shares linker histone H1 function in budding yeast and contributes to our understanding of the evolution of linker histone H1 across eukaryotes.
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Affiliation(s)
- Mengxue Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jinghua Li
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Yong Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hang Fu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, China
- School of Physics, University of Chinese Academy of Sciences, Beijing, China
| | - Haoning Qiu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yanying Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- School of Physics, University of Chinese Academy of Sciences, Beijing, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
| | - Ying Lu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- School of Physics, University of Chinese Academy of Sciences, Beijing, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
| | - Yu Vincent Fu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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Foster B, Attwood M, Gibbs-Seymour I. Tools for Decoding Ubiquitin Signaling in DNA Repair. Front Cell Dev Biol 2021; 9:760226. [PMID: 34950659 PMCID: PMC8690248 DOI: 10.3389/fcell.2021.760226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/09/2021] [Indexed: 12/21/2022] Open
Abstract
The maintenance of genome stability requires dedicated DNA repair processes and pathways that are essential for the faithful duplication and propagation of chromosomes. These DNA repair mechanisms counteract the potentially deleterious impact of the frequent genotoxic challenges faced by cells from both exogenous and endogenous agents. Intrinsic to these mechanisms, cells have an arsenal of protein factors that can be utilised to promote repair processes in response to DNA lesions. Orchestration of the protein factors within the various cellular DNA repair pathways is performed, in part, by post-translational modifications, such as phosphorylation, ubiquitin, SUMO and other ubiquitin-like modifiers (UBLs). In this review, we firstly explore recent advances in the tools for identifying factors involved in both DNA repair and ubiquitin signaling pathways. We then expand on this by evaluating the growing repertoire of proteomic, biochemical and structural techniques available to further understand the mechanistic basis by which these complex modifications regulate DNA repair. Together, we provide a snapshot of the range of methods now available to investigate and decode how ubiquitin signaling can promote DNA repair and maintain genome stability in mammalian cells.
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Affiliation(s)
| | | | - Ian Gibbs-Seymour
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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Biochemistry: one molecule at a time. Essays Biochem 2021; 65:1-3. [PMID: 33860798 PMCID: PMC8056033 DOI: 10.1042/ebc20210015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 02/26/2021] [Accepted: 02/26/2021] [Indexed: 12/20/2022]
Abstract
Biological processes are orchestrated by complex networks of molecules. Conventional approaches for studying the action of biomolecules operate on a population level, averaging out any inhomogeneities within the ensemble. Investigating one biological macromolecule at a time allows researchers to directly probe individual behaviours, and thus characterise the intrinsic molecular heterogeneity of the system. Single-molecule methods have unravelled unexpected modes of action for many seemingly well-characterised biomolecules and often proved instrumental in understanding the intricate mechanistic basis of biological processes. This collection of reviews aims to showcase how single-molecule techniques can be used to address important biological questions and to inspire biochemists to ‘zoom in’ to the population and probe individual molecular behaviours, beyond the ensemble average. Furthermore, this issue of Essays in Biochemistry is the very first written and edited entirely by early career researchers, and so it also highlights the strength, diversity and excellence of the younger generation single-molecule scientists who drive this exciting field of research forward.
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