1
|
Qian J, Wang B, Artsimovitch I, Dunlap D, Finzi L. Force and the α-C-terminal domains bias RNA polymerase recycling. Nat Commun 2024; 15:7520. [PMID: 39214958 PMCID: PMC11364550 DOI: 10.1038/s41467-024-51603-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 08/13/2024] [Indexed: 09/04/2024] Open
Abstract
After an RNA polymerase reaches a terminator, instead of dissociating from the template, it may diffuse along the DNA and recommence RNA synthesis from the previous or a different promoter. Magnetic tweezers were used to monitor such secondary transcription and determine the effects of low forces assisting or opposing translocation, protein roadblocks, and transcription factors. Remarkably, up to 50% of Escherichia coli (E. coli) RNA polymerases diffused along the DNA after termination. Force biased the direction of diffusion (sliding) and the velocity increased rapidly with force up to 0.7 pN and much more slowly thereafter. Sigma factor 70 (σ70) likely remained associated with the DNA promoting sliding and enabling re-initiation from promoters in either orientation. However, deletions of the α-C-terminal domains severely limited the ability of RNAP to turn around between successive rounds of transcription. The addition of elongation factor NusG, which competes with σ70 for binding to RNAP, limited additional rounds of transcription. Surprisingly, sliding RNA polymerases blocked by a DNA-bound lac repressor could slowly re-initiate transcription and were not affected by NusG, suggesting a σ-independent pathway. Low forces effectively biased promoter selection suggesting a prominent role for topological entanglements that affect RNA polymerase translocation.
Collapse
Affiliation(s)
- Jin Qian
- Physics Department, Emory University, Atlanta, GA, USA
| | - Bing Wang
- The Center for RNA Biology and Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Irina Artsimovitch
- The Center for RNA Biology and Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - David Dunlap
- Department of Physics & Astronomy, Clemson University, Clemson, SC, USA
| | - Laura Finzi
- Department of Physics & Astronomy, Clemson University, Clemson, SC, USA.
| |
Collapse
|
2
|
Kuo HC, Prupes J, Chou CW, Finkelstein IJ. Massively parallel profiling of RNA-targeting CRISPR-Cas13d. Nat Commun 2024; 15:498. [PMID: 38216559 PMCID: PMC10786891 DOI: 10.1038/s41467-024-44738-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 01/02/2024] [Indexed: 01/14/2024] Open
Abstract
CRISPR-Cas13d cleaves RNA and is used in vivo and for diagnostics. However, a systematic understanding of its RNA binding and cleavage specificity is lacking. Here, we describe an RNA Chip-Hybridized Association-Mapping Platform (RNA-CHAMP) for measuring the binding affinity for > 10,000 RNAs containing structural perturbations and other alterations relative to the CRISPR RNA (crRNA). Deep profiling of Cas13d reveals that it does not require a protospacer flanking sequence but is exquisitely sensitive to secondary structure within the target RNA. Cas13d binding is penalized by mismatches in the distal crRNA-target RNA region, while alterations in the proximal region inhibit nuclease activity. A biophysical model built from these data reveals that target recognition initiates in the distal end of the target RNA. Using this model, we design crRNAs that can differentiate between SARS-CoV-2 variants by modulating nuclease activation. This work describes the key determinants of RNA targeting by a type VI CRISPR enzyme.
Collapse
Affiliation(s)
- Hung-Che Kuo
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA.
| | - Joshua Prupes
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA.
| |
Collapse
|
3
|
Kim S, Kim Y, Lee JY. Real-time single-molecule visualization using DNA curtains reveals the molecular mechanisms underlying DNA repair pathways. DNA Repair (Amst) 2024; 133:103612. [PMID: 38128155 DOI: 10.1016/j.dnarep.2023.103612] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/06/2023] [Accepted: 12/10/2023] [Indexed: 12/23/2023]
Abstract
The demand for direct observation of biomolecular interactions provides new insights into the molecular mechanisms underlying many biological processes. Single-molecule imaging techniques enable real-time visualization of individual biomolecules, providing direct observations of protein machines. Various single-molecule imaging techniques have been developed and have contributed to breakthroughs in biological research. One such technique is the DNA curtain, a novel, high-throughput, single-molecule platform that integrates lipid fluidity, nano-fabrication, microfluidics, and fluorescence imaging. Many DNA metabolic reactions, such as replication, transcription, and chromatin dynamics, have been studied using DNA curtains. In particular, the DNA curtain platform has been intensively applied in investigating the molecular details of DNA repair processes. This article reviews DNA curtain techniques and their applications for imaging DNA repair proteins.
Collapse
Affiliation(s)
- Subin Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Youngseo Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Ja Yil Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea.
| |
Collapse
|
4
|
Zalejski J, Sun J, Sharma A. Unravelling the Mystery inside Cells by Using Single-Molecule Fluorescence Imaging. J Imaging 2023; 9:192. [PMID: 37754956 PMCID: PMC10532472 DOI: 10.3390/jimaging9090192] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/01/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023] Open
Abstract
Live-cell imaging is a powerful technique to study the dynamics and mechanics of various biological molecules like proteins, organelles, DNA, and RNA. With the rapid evolution of optical microscopy, our understanding of how these molecules are implicated in the cells' most critical physiological roles deepens. In this review, we focus on how spatiotemporal nanoscale live-cell imaging at the single molecule level allows for profound contributions towards new discoveries in life science. This review will start by summarizing how single-molecule tracking has been used to analyze membrane dynamics, receptor-ligand interactions, protein-protein interactions, inner- and extra-cellular transport, gene expression/transcription, and whole organelle tracking. We then move on to how current authors are trying to improve single-molecule tracking and overcome current limitations by offering new ways of labeling proteins of interest, multi-channel/color detection, improvements in time-lapse imaging, and new methods and programs to analyze the colocalization and movement of targets. We later discuss how single-molecule tracking can be a beneficial tool used for medical diagnosis. Finally, we wrap up with the limitations and future perspectives of single-molecule tracking and total internal reflection microscopy.
Collapse
Affiliation(s)
| | | | - Ashutosh Sharma
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA; (J.Z.); (J.S.)
| |
Collapse
|
5
|
Kuo HC, Prupes J, Chou CW, Finkelstein IJ. Massively Parallel Profiling of RNA-targeting CRISPR-Cas13d. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.27.534188. [PMID: 37034598 PMCID: PMC10081190 DOI: 10.1101/2023.03.27.534188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Type VI CRISPR enzymes cleave target RNAs and are widely used for gene regulation, RNA tracking, and diagnostics. However, a systematic understanding of their RNA binding specificity and cleavage activation is lacking. Here, we describe RNA chip-hybridized association-mapping platform (RNA-CHAMP), a massively parallel platform that repurposes next-generation DNA sequencing chips to measure the binding affinity for over 10,000 RNA targets containing structural perturbations, mismatches, insertions, and deletions relative to the CRISPR RNA (crRNA). Deep profiling of Cas13d, a compact and widely used RNA nuclease, reveals that it does not require a protospacer flanking sequence (PFS) but is exquisitely sensitive to secondary structure within the target RNA. Cas13d binding is strongly penalized by mismatches, insertions, and deletions in the distal crRNA-target RNA regions, while alterations in the proximal region inhibit nuclease activity without affecting binding. A biophysical model built from these data reveals that target recognition begins at the distal end of unstructured target RNAs and proceeds to the proximal end. Using this model, we designed a series of partially mismatched guide RNAs that modulate nuclease activity to detect single nucleotide polymorphisms (SNPs) in circulating SARS-CoV-2 variants. This work describes the key determinants of RNA targeting by a type VI CRISPR enzyme to improve CRISPR diagnostics and in vivo RNA editing. More broadly, RNA-CHAMP provides a quantitative platform for systematically measuring protein-RNA interactions.
Collapse
Affiliation(s)
- Hung-Che Kuo
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Joshua Prupes
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Ilya J. Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, USA
| |
Collapse
|
6
|
Kang Y, An S, Min D, Lee JY. Single-molecule fluorescence imaging techniques reveal molecular mechanisms underlying deoxyribonucleic acid damage repair. Front Bioeng Biotechnol 2022; 10:973314. [PMID: 36185427 PMCID: PMC9520083 DOI: 10.3389/fbioe.2022.973314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Advances in single-molecule techniques have uncovered numerous biological secrets that cannot be disclosed by traditional methods. Among a variety of single-molecule methods, single-molecule fluorescence imaging techniques enable real-time visualization of biomolecular interactions and have allowed the accumulation of convincing evidence. These techniques have been broadly utilized for studying DNA metabolic events such as replication, transcription, and DNA repair, which are fundamental biological reactions. In particular, DNA repair has received much attention because it maintains genomic integrity and is associated with diverse human diseases. In this review, we introduce representative single-molecule fluorescence imaging techniques and survey how each technique has been employed for investigating the detailed mechanisms underlying DNA repair pathways. In addition, we briefly show how live-cell imaging at the single-molecule level contributes to understanding DNA repair processes inside cells.
Collapse
Affiliation(s)
- Yujin Kang
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Soyeong An
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Duyoung Min
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Ja Yil Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea
- Center for Genomic Integrity, Institute of Basic Sciences, Ulsan, South Korea
- *Correspondence: Ja Yil Lee,
| |
Collapse
|
7
|
Lu D, Chen B. Coordinated motion of molecular motors on DNA chains with branch topology. ACTA MECHANICA SINICA = LI XUE XUE BAO 2022; 38:621225. [PMID: 35601132 PMCID: PMC9109741 DOI: 10.1007/s10409-021-09045-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/25/2021] [Indexed: 06/15/2023]
Abstract
To understand the macroscopic mechanical behaviors of responsive DNA hydrogels integrated with DNA motors, we constructed a state map for the translocation process of a single FtsKC on a single DNA chain at the molecular level and then investigated the movement of single or multiple FtsKC motors on DNA chains with varied branch topologies. Our studies indicate that multiple FtsKC motors can have coordinated motion, which is mainly due to the force-responsive behavior of individual FtsKC motors. We further suggest the potential application of motors of FtsKC, together with DNA chains of specific branch topology, to serve as strain sensors in hydrogels.
Collapse
Affiliation(s)
- Di Lu
- Department of Engineering Mechanics, Zhejiang University, Hangzhou, 310058 China
| | - Bin Chen
- Department of Engineering Mechanics, Zhejiang University, Hangzhou, 310058 China
- Key Laboratory of Soft Machines and Smart Devices of Zhejiang Province, Hangzhou, 310027 China
| |
Collapse
|
8
|
Bi L, Qin Z, Hou XM, Modesti M, Sun B. Simultaneous Mechanical and Fluorescence Detection of Helicase-Catalyzed DNA Unwinding. Methods Mol Biol 2022; 2478:329-347. [PMID: 36063326 DOI: 10.1007/978-1-0716-2229-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Helicases are ubiquitous molecular motor proteins that utilize the energy derived from the hydrolysis of nucleoside triphosphates (NTPs) to transiently convert the duplex form of nucleic acids to single-stranded intermediates for many biological processes. These enzymes play vital roles in nearly all aspects of nucleic acid metabolism, such as DNA repair and RNA splicing. Understanding helicase's functional roles requires methods to dissect the mechanisms of motor proteins at the molecular level. In the past three decades, there has been a large increase in the application of single-molecule approaches to investigate helicases. These techniques, such as optical tweezers and single-molecule fluorescence, offer capabilities to monitor helicase motions with unprecedented spatiotemporal resolution, to apply quantitative forces to probe the chemo-mechanical activities of these motors and to resolve helicase heterogeneity at the single-molecule level. In this chapter, we describe a single-molecule method that combines optical tweezers with confocal fluorescence microscopy to study helicase-catalyzed DNA unwinding. Using Bloom syndrome protein (BLM), a multifunctional helicase that maintains genome stability, as an example, we show that this method allows for the simultaneous detection of displacement, force and fluorescence signals of a single DNA molecule during unwinding in real time, leading to the discovery of a distinct bidirectional unwinding mode of BLM that is activated by a single-stranded DNA binding protein called replication protein A (RPA). We provide detailed instructions on how to prepare two DNA templates to be used in the assays, purify the BLM and RPA proteins, perform single-molecule experiments, and acquire and analyse the data.
Collapse
Affiliation(s)
- Lulu Bi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhenheng Qin
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Mauro Modesti
- Cancer Research Center of Marseille, Marseille, France
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| |
Collapse
|
9
|
Kamagata K. Single-Molecule Microscopy Meets Molecular Dynamics Simulations for Characterizing the Molecular Action of Proteins on DNA and in Liquid Condensates. Front Mol Biosci 2021; 8:795367. [PMID: 34869607 PMCID: PMC8639857 DOI: 10.3389/fmolb.2021.795367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/03/2021] [Indexed: 11/13/2022] Open
Abstract
DNA-binding proteins trigger various cellular functions and determine cellular fate. Before performing functions such as transcription, DNA repair, and DNA recombination, DNA-binding proteins need to search for and bind to their target sites in genomic DNA. Under evolutionary pressure, DNA-binding proteins have gained accurate and rapid target search and binding strategies that combine three-dimensional search in solution, one-dimensional sliding along DNA, hopping and jumping on DNA, and intersegmental transfer between two DNA molecules. These mechanisms can be achieved by the unique structural and dynamic properties of these proteins. Single-molecule fluorescence microscopy and molecular dynamics simulations have characterized the molecular actions of DNA-binding proteins in detail. Furthermore, these methodologies have begun to characterize liquid condensates induced by liquid-liquid phase separation, e.g., molecular principles of uptake and dynamics in droplets. This review discusses the molecular action of DNA-binding proteins on DNA and in liquid condensate based on the latest studies that mainly focused on the model protein p53.
Collapse
Affiliation(s)
- Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
| |
Collapse
|
10
|
Kamagata K, Ouchi K, Tan C, Mano E, Mandali S, Wu Y, Takada S, Takahashi S, Johnson RC. The HMGB chromatin protein Nhp6A can bypass obstacles when traveling on DNA. Nucleic Acids Res 2020; 48:10820-10831. [PMID: 32997109 PMCID: PMC7641734 DOI: 10.1093/nar/gkaa799] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/13/2020] [Accepted: 09/15/2020] [Indexed: 12/16/2022] Open
Abstract
DNA binding proteins rapidly locate their specific DNA targets through a combination of 3D and 1D diffusion mechanisms, with the 1D search involving bidirectional sliding along DNA. However, even in nucleosome-free regions, chromosomes are highly decorated with associated proteins that may block sliding. Here we investigate the ability of the abundant chromatin-associated HMGB protein Nhp6A from Saccharomyces cerevisiae to travel along DNA in the presence of other architectural DNA binding proteins using single-molecule fluorescence microscopy. We observed that 1D diffusion by Nhp6A molecules is retarded by increasing densities of the bacterial proteins Fis and HU and by Nhp6A, indicating these structurally diverse proteins impede Nhp6A mobility on DNA. However, the average travel distances were larger than the average distances between neighboring proteins, implying Nhp6A is able to bypass each of these obstacles. Together with molecular dynamics simulations, our analyses suggest two binding modes: mobile molecules that can bypass barriers as they seek out DNA targets, and near stationary molecules that are associated with neighboring proteins or preferred DNA structures. The ability of mobile Nhp6A molecules to bypass different obstacles on DNA suggests they do not block 1D searches by other DNA binding proteins.
Collapse
Affiliation(s)
- Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Department of Chemistry, Faculty of Science, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Kana Ouchi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Cheng Tan
- Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Eriko Mano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Sridhar Mandali
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1737 USA
| | - Yining Wu
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Department of Chemistry, Faculty of Science, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Satoshi Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Department of Chemistry, Faculty of Science, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Reid C Johnson
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1737 USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|
11
|
Kang Y, Cheon NY, Cha J, Kim A, Kim HI, Lee L, Kim KO, Jo K, Lee JY. High-throughput single-molecule imaging system using nanofabricated trenches and fluorescent DNA-binding proteins. Biotechnol Bioeng 2020; 117:1640-1648. [PMID: 32162675 DOI: 10.1002/bit.27331] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/02/2020] [Accepted: 03/11/2020] [Indexed: 12/18/2022]
Abstract
DNA curtain is a high-throughput system, integrating a lipid bilayer, fluorescence imaging, and microfluidics to probe protein-DNA interactions in real-time and has provided in-depth understanding of DNA metabolism. Especially, the microfluidic platform of a DNA curtain is highly suitable for a biochip. In the DNA curtain, DNA molecules are aligned along chromium nanobarriers, which are fabricated on a slide surface, and visualized using an intercalating dye, YOYO-1. Although the chromium barriers confer precise geometric alignment of DNA, reuse of the slides is limited by wear of the barriers during cleaning. YOYO-1 is rapidly photobleached and causes photocleavage of DNA under continuous laser illumination, restricting DNA observation to a brief time window. To address these challenges, we developed a new nanopatterned slide, upon which carved nanotrenches serve as diffusion barriers. The nanotrenches were robust under harsh cleaning conditions, facilitating the maintenance of surface cleanliness that is essential to slide reuse. We also stained DNA with a fluorescent protein with a DNA-binding motif, fluorescent protein-DNA binding peptide (FP-DBP). FP-DBP was slowly photobleached and did not cause DNA photocleavage. This new DNA curtain system enables a more stable and repeatable investigation of real-time protein-DNA interactions and will serve as a good platform for lab-on-a-chip.
Collapse
Affiliation(s)
- Yujin Kang
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Na Young Cheon
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Jongjin Cha
- Department of Physics and Astronomy, Seoul National University, Seoul, Republic of Korea
| | - Ayoung Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Hyung-Il Kim
- UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Luda Lee
- UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Kang O Kim
- UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul, Republic of Korea
| | - Ja Yil Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea.,Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
| |
Collapse
|
12
|
Kang W, Ha KS, Uhm H, Park K, Lee JY, Hohng S, Kang C. Transcription reinitiation by recycling RNA polymerase that diffuses on DNA after releasing terminated RNA. Nat Commun 2020; 11:450. [PMID: 31974350 PMCID: PMC6978380 DOI: 10.1038/s41467-019-14200-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 12/10/2019] [Indexed: 11/24/2022] Open
Abstract
Despite extensive studies on transcription mechanisms, it is unknown how termination complexes are disassembled, especially in what order the essential components dissociate. Our single-molecule fluorescence study unveils that RNA transcript release precedes RNA polymerase (RNAP) dissociation from the DNA template much more often than their concurrent dissociations in intrinsic termination of bacterial transcription. As termination is defined by the release of product RNA from the transcription complex, the subsequent retention of RNAP on DNA constitutes a previously unidentified stage, termed here as recycling. During the recycling stage, post-terminational RNAPs one-dimensionally diffuse on DNA in downward and upward directions, and can initiate transcription again at the original and nearby promoters in the case of retaining a sigma factor. The efficiency of this event, termed here as reinitiation, increases with supplement of a sigma factor. In summary, after releasing RNA product at intrinsic termination, recycling RNAP diffuses on the DNA template for reinitiation most of the time. Bacterial transcription is terminated when RNA polymerases encounter terminator sequences. Using a single-molecule fluorescence assay, here the authors show that the release of transcript RNA precedes RNA polymerase dissociation and that the remaining RNA polymerase can reinitiate at nearby promoters.
Collapse
Affiliation(s)
- Wooyoung Kang
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kook Sun Ha
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,Department of Life Science, University of Suwon, Gyeonggi-do, 18323, Republic of Korea
| | - Heesoo Uhm
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National University, Seoul, 08826, Republic of Korea.,Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Kyuhyong Park
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ja Yil Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Sungchul Hohng
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Changwon Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
| |
Collapse
|
13
|
Cho C, Jang J, Kang Y, Watanabe H, Uchihashi T, Kim SJ, Kato K, Lee JY, Song JJ. Structural basis of nucleosome assembly by the Abo1 AAA+ ATPase histone chaperone. Nat Commun 2019; 10:5764. [PMID: 31848341 PMCID: PMC6917787 DOI: 10.1038/s41467-019-13743-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 11/20/2019] [Indexed: 11/10/2022] Open
Abstract
The fundamental unit of chromatin, the nucleosome, is an intricate structure that requires histone chaperones for assembly. ATAD2 AAA+ ATPases are a family of histone chaperones that regulate nucleosome density and chromatin dynamics. Here, we demonstrate that the fission yeast ATAD2 homolog, Abo1, deposits histone H3-H4 onto DNA in an ATP-hydrolysis-dependent manner by in vitro reconstitution and single-tethered DNA curtain assays. We present cryo-EM structures of an ATAD2 family ATPase to atomic resolution in three different nucleotide states, revealing unique structural features required for histone loading on DNA, and directly visualize the transitions of Abo1 from an asymmetric spiral (ATP-state) to a symmetric ring (ADP- and apo-states) using high-speed atomic force microscopy (HS-AFM). Furthermore, we find that the acidic pore of ATP-Abo1 binds a peptide substrate which is suggestive of a histone tail. Based on these results, we propose a model whereby Abo1 facilitates H3-H4 loading by utilizing ATP.
Collapse
Affiliation(s)
- Carol Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea.
| | - Juwon Jang
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Yujin Kang
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Hiroki Watanabe
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan
| | - Takayuki Uchihashi
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.,Department of Physics, Nagoya University, Nagoya, Japan
| | - Seung Joong Kim
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Koichi Kato
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Ja Yil Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea.
| | - Ji-Joon Song
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea.
| |
Collapse
|
14
|
Cheon NY, Kim HS, Yeo JE, Schärer OD, Lee JY. Single-molecule visualization reveals the damage search mechanism for the human NER protein XPC-RAD23B. Nucleic Acids Res 2019; 47:8337-8347. [PMID: 31372632 PMCID: PMC6895271 DOI: 10.1093/nar/gkz629] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/05/2019] [Accepted: 07/12/2019] [Indexed: 11/14/2022] Open
Abstract
DNA repair is critical for maintaining genomic integrity. Finding DNA lesions initiates the entire repair process. In human nucleotide excision repair (NER), XPC-RAD23B recognizes DNA lesions and recruits downstream factors. Although previous studies revealed the molecular features of damage identification by the yeast orthologs Rad4-Rad23, the dynamic mechanisms by which human XPC-RAD23B recognizes DNA defects have remained elusive. Here, we directly visualized the motion of XPC-RAD23B on undamaged and lesion-containing DNA using high-throughput single-molecule imaging. We observed three types of one-dimensional motion of XPC-RAD23B along DNA: diffusive, immobile and constrained. We found that consecutive AT-tracks led to increase in proteins with constrained motion. The diffusion coefficient dramatically increased according to ionic strength, suggesting that XPC-RAD23B diffuses along DNA via hopping, allowing XPC-RAD23B to bypass protein obstacles during the search for DNA damage. We also examined how XPC-RAD23B identifies cyclobutane pyrimidine dimers (CPDs) during diffusion. XPC-RAD23B makes futile attempts to bind to CPDs, consistent with low CPD recognition efficiency. Moreover, XPC-RAD23B binds CPDs in biphasic states, stable for lesion recognition and transient for lesion interrogation. Taken together, our results provide new insight into how XPC-RAD23B searches for DNA lesions in billions of base pairs in human genome.
Collapse
Affiliation(s)
- Na Young Cheon
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Hyun-Suk Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Jung-Eun Yeo
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Orlando D Schärer
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.,Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Ja Yil Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.,Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| |
Collapse
|
15
|
Mohapatra S, Lin CT, Feng XA, Basu A, Ha T. Single-Molecule Analysis and Engineering of DNA Motors. Chem Rev 2019; 120:36-78. [DOI: 10.1021/acs.chemrev.9b00361] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | | | | | | | - Taekjip Ha
- Howard Hughes Medical Institute, Baltimore, Maryland 21205, United States
| |
Collapse
|
16
|
Two-step chromosome segregation in the stalked budding bacterium Hyphomonas neptunium. Nat Commun 2019; 10:3290. [PMID: 31337764 PMCID: PMC6650430 DOI: 10.1038/s41467-019-11242-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/28/2019] [Indexed: 12/11/2022] Open
Abstract
Chromosome segregation typically occurs after replication has finished in eukaryotes but during replication in bacteria. Here, we show that the alphaproteobacterium Hyphomonas neptunium, which proliferates by bud formation at the tip of a stalk-like cellular extension, segregates its chromosomes in a unique two-step process. First, the two sister origin regions are targeted to opposite poles of the mother cell, driven by the ParABS partitioning system. Subsequently, once the bulk of chromosomal DNA has been replicated and the bud exceeds a certain threshold size, the cell initiates a second segregation step during which it transfers the stalk-proximal origin region through the stalk into the nascent bud compartment. Thus, while chromosome replication and segregation usually proceed concurrently in bacteria, the two processes are largely uncoupled in H. neptunium, reminiscent of eukaryotic mitosis. These results indicate that stalked budding bacteria have evolved specific mechanisms to adjust chromosome segregation to their unusual life cycle.
Collapse
|
17
|
Xue H, Zhan Z, Zhang K, Fu YV. Visualizing the Interaction Between the Qdot-labeled Protein and Site-specifically Modified λ DNA at the Single Molecule Level. J Vis Exp 2018:57967. [PMID: 30080193 PMCID: PMC6126486 DOI: 10.3791/57967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The fluorescence microscopy has made great contributions in dissecting the mechanisms of complex biological processes at the single molecule level. In single molecule assays for studying DNA-protein interactions, there are two important factors for consideration: the DNA substrate with enough length for easy observation and labeling a protein with a suitable fluorescent probe. 48.5 kb λ DNA is a good candidate for the DNA substrate. Quantum dots (Qdots), as a class of fluorescent probes, allow long-time observation (minutes to hours) and high-quality image acquisition. In this paper, we present a protocol to study DNA-protein interactions at the single-molecule level, which includes preparing a site-specifically modified λ DNA and labeling a target protein with streptavidin-coated Qdots. For a proof of concept, we choose ORC (origin recognition complex) in budding yeast as a protein of interest and visualize its interaction with an ARS (autonomously replicating sequence) using TIRFM. Compared with other fluorescent probes, Qdots have obvious advantages in single molecule studies due to its high stability against photobleaching, but it should be noted that this property limits its application in quantitative assays.
Collapse
Affiliation(s)
- Huijun Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences; Savaid Medical School, University of Chinese Academy of Sciences
| | - Zhengyan Zhan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences
| | - Kaining Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences; Savaid Medical School, University of Chinese Academy of Sciences
| | - Yu Vincent Fu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences; Savaid Medical School, University of Chinese Academy of Sciences;
| |
Collapse
|
18
|
LeGresley SE, Briggs K, Fischer CJ. Molecular motor translocation kinetics: Application of Monte Carlo computer simulations to determine microscopic kinetic parameters. Biosystems 2018; 168:8-25. [PMID: 29733888 DOI: 10.1016/j.biosystems.2018.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/30/2018] [Accepted: 05/02/2018] [Indexed: 10/17/2022]
Abstract
Methods for studying the translocation of motor proteins along a filament (e.g., nucleic acid and polypeptide) typically monitor the total production of ADP, the arrival/departure of the motor protein at/from a particular location (often one end of the filament), or the dissociation of the motor protein from the filament. The associated kinetic time courses are often analyzed using a simple sequential uniform n-step mechanism to estimate the macroscopic kinetic parameters (e.g., translocation rate and processivity) and the microscopic kinetic parameters (e.g., kinetic step-size and the rate constant for the rate-limiting step). These sequential uniform n-step mechanisms assume repetition of uniform and irreversible rate-limiting steps of forward motion along the filament. In order to determine how the presence of non-uniform motion (e.g., backward motion, random pauses, or jumping) affects the estimates of parameters obtained from such analyses, we evaluated computer simulated translocation time courses containing non-uniform motion using a simple sequential uniform n-step model. By comparing the kinetic parameters estimated from the analysis of the data generated by these simulations with the input parameters of the simulations, we were able to determine which of the kinetic parameters were likely to be over/under estimated due to non-uniform motion of the motor protein.
Collapse
Affiliation(s)
- Sarah E LeGresley
- Department of Physics and Astronomy, University of Kansas, 1251 Wescoe Hall Dr., 1082 Malott Hall, Lawrence, KS 66045, USA
| | - Koan Briggs
- Department of Physics and Astronomy, University of Kansas, 1251 Wescoe Hall Dr., 1082 Malott Hall, Lawrence, KS 66045, USA
| | - Christopher J Fischer
- Department of Physics and Astronomy, University of Kansas, 1251 Wescoe Hall Dr., 1082 Malott Hall, Lawrence, KS 66045, USA.
| |
Collapse
|
19
|
Liu N, Chistol G, Cui Y, Bustamante C. Mechanochemical coupling and bi-phasic force-velocity dependence in the ultra-fast ring ATPase SpoIIIE. eLife 2018; 7:32354. [PMID: 29504934 PMCID: PMC5858925 DOI: 10.7554/elife.32354] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 03/03/2018] [Indexed: 11/22/2022] Open
Abstract
Multi-subunit ring-shaped ATPases are molecular motors that harness chemical free energy to perform vital mechanical tasks such as polypeptide translocation, DNA unwinding, and chromosome segregation. Previously we reported the intersubunit coordination and stepping behavior of the hexameric ring-shaped ATPase SpoIIIE (Liu et al., 2015). Here we use optical tweezers to characterize the motor’s mechanochemistry. Analysis of the motor response to external force at various nucleotide concentrations identifies phosphate release as the likely force-generating step. Analysis of SpoIIIE pausing indicates that pauses are off-pathway events. Characterization of SpoIIIE slipping behavior reveals that individual motor subunits engage DNA upon ATP binding. Furthermore, we find that SpoIIIE’s velocity exhibits an intriguing bi-phasic dependence on force. We hypothesize that this behavior is an adaptation of ultra-fast motors tasked with translocating DNA from which they must also remove DNA-bound protein roadblocks. Based on these results, we formulate a comprehensive mechanochemical model for SpoIIIE.
Collapse
Affiliation(s)
- Ninning Liu
- Jason L. Choy Laboratory of Single Molecule Biophysics, University of California, Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Gheorghe Chistol
- Jason L. Choy Laboratory of Single Molecule Biophysics, University of California, Berkeley, Berkeley, United States.,Department of Physics, University of California, Berkeley, Berkeley, United States
| | - Yuanbo Cui
- Jason L. Choy Laboratory of Single Molecule Biophysics, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
| | - Carlos Bustamante
- Jason L. Choy Laboratory of Single Molecule Biophysics, University of California, Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Department of Physics, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Department of Chemistry and Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Kavli Energy NanoSciences Institute at the University of California, Berkeley and the Lawrence Berkeley National Laboratory, Berkeley, United States
| |
Collapse
|
20
|
De Tullio L, Kaniecki K, Greene EC. Single-Stranded DNA Curtains for Studying the Srs2 Helicase Using Total Internal Reflection Fluorescence Microscopy. Methods Enzymol 2018; 600:407-437. [PMID: 29458768 DOI: 10.1016/bs.mie.2017.12.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Helicases are crucial participants in many types of DNA repair reactions, including homologous recombination. The properties of these enzymes can be assayed by traditional bulk biochemical analysis; however, these types of assays cannot directly access some types of information. In particular, bulk biochemical assays cannot readily access information that may be obscured in population averages. Single-molecule assays offer the potential advantage of being able to visualize the molecules in question in real time, thus providing direct access to questions relating to translocation velocity, processivity, and insights into how helicases may behave on different types of substrates. Here, we describe the use of single-stranded DNA (ssDNA) curtains as an assay for directly viewing the behavior of the Saccharomyces cerevisiae Srs2 helicase on single molecules of ssDNA. When used with total internal reflection fluorescence microscopy, these methods can be used to track the binding and movements of individual helicase complexes, and allow new insights into helicase behaviors at the single-molecule level.
Collapse
|
21
|
Berghuis BA, Raducanu VS, Elshenawy MM, Jergic S, Depken M, Dixon NE, Hamdan SM, Dekker NH. What is all this fuss about Tus? Comparison of recent findings from biophysical and biochemical experiments. Crit Rev Biochem Mol Biol 2017; 53:49-63. [DOI: 10.1080/10409238.2017.1394264] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Bojk A. Berghuis
- Department of Bionanoscience, Kavli institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Vlad-Stefan Raducanu
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Mohamed M. Elshenawy
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Slobodan Jergic
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
| | - Martin Depken
- Department of Bionanoscience, Kavli institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Nicholas E. Dixon
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
| | - Samir M. Hamdan
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Nynke H. Dekker
- Department of Bionanoscience, Kavli institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| |
Collapse
|
22
|
Division-induced DNA double strand breaks in the chromosome terminus region of Escherichia coli lacking RecBCD DNA repair enzyme. PLoS Genet 2017; 13:e1006895. [PMID: 28968392 PMCID: PMC5638614 DOI: 10.1371/journal.pgen.1006895] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 10/12/2017] [Accepted: 06/23/2017] [Indexed: 12/27/2022] Open
Abstract
Marker frequency analysis of the Escherichia coli recB mutant chromosome has revealed a deficit of DNA in a specific zone of the terminus, centred on the dif/TerC region. Using fluorescence microscopy of a marked chromosomal site, we show that the dif region is lost after replication completion, at the time of cell division, in one daughter cell only, and that the phenomenon is transmitted to progeny. Analysis by marker frequency and microscopy shows that the position of DNA loss is not defined by the replication fork merging point since it still occurs in the dif/TerC region when the replication fork trap is displaced in strains harbouring ectopic Ter sites. Terminus DNA loss in the recB mutant is also independent of dimer resolution by XerCD at dif and of Topo IV action close to dif. It occurs in the terminus region, at the point of inversion of the GC skew, which is also the point of convergence of specific sequence motifs like KOPS and Chi sites, regardless of whether the convergence of GC skew is at dif (wild-type) or a newly created sequence. In the absence of FtsK-driven DNA translocation, terminus DNA loss is less precisely targeted to the KOPS convergence sequence, but occurs at a similar frequency and follows the same pattern as in FtsK+ cells. Importantly, using ftsIts, ftsAts division mutants and cephalexin treated cells, we show that DNA loss of the dif region in the recB mutant is decreased by the inactivation of cell division. We propose that it results from septum-induced chromosome breakage, and largely contributes to the low viability of the recB mutant. RecBCD protein complex is an important player of DSB repair in bacteria and bacteria that cannot repair DNA double-stranded breaks (DSB) have a low viability. Whole genome sequencing analyses showed a deficit in specific sequences of the chromosome terminus region in recB mutant cells, suggesting terminus DNA degradation during growth. We studied here the phenomenon of terminus DNA loss by whole genome sequencing and microscopy analyses of exponentially growing bacteria. We tested all processes known to take place in the chromosome terminus region for a putative role in DNA loss: replication fork termination, dimer resolution, resolution of catenated chromosomes, and translocation of the chromosome arms in daughter cells during septum formation. None of the mutations that affect these processes prevents the phenomenon. However, we observed that terminus DNA loss is abolished in cells that cannot divide. We propose that in cells defective for RecBCD-mediated DSB repair the terminus region of the chromosome remains in the way of the growing septum during cell division, then septum closure triggers chromosome breakage and, in turn, DNA degradation.
Collapse
|
23
|
Kim Y, de la Torre A, Leal AA, Finkelstein IJ. Efficient modification of λ-DNA substrates for single-molecule studies. Sci Rep 2017; 7:2071. [PMID: 28522818 PMCID: PMC5437064 DOI: 10.1038/s41598-017-01984-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 04/05/2017] [Indexed: 01/15/2023] Open
Abstract
Single-molecule studies of protein-nucleic acid interactions frequently require site-specific modification of long DNA substrates. The bacteriophage λ is a convenient source of high quality long (48.5 kb) DNA. However, introducing specific sequences, tertiary structures, and chemical modifications into λ-DNA remains technically challenging. Most current approaches rely on multi-step ligations with low yields and incomplete products. Here, we describe a molecular toolkit for rapid preparation of modified λ-DNA. A set of PCR cassettes facilitates the introduction of recombinant DNA sequences into the λ-phage genome with 90-100% yield. Extrahelical structures and chemical modifications can be inserted at user-defined sites via an improved nicking enzyme-based strategy. As a proof-of-principle, we explore the interactions of S. cerevisiae Proliferating Cell Nuclear Antigen (yPCNA) with modified DNA sequences and structures incorporated within λ-DNA. Our results demonstrate that S. cerevisiae Replication Factor C (yRFC) can load yPCNA onto 5'-ssDNA flaps, (CAG)13 triplet repeats, and homoduplex DNA. However, yPCNA remains trapped on the (CAG)13 structure, confirming a proposed mechanism for triplet repeat expansion. We anticipate that this molecular toolbox will be broadly useful for other studies that require site-specific modification of long DNA substrates.
Collapse
Affiliation(s)
- Yoori Kim
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Armando de la Torre
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Andrew A Leal
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, 78712, USA.
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, 78712, USA.
| |
Collapse
|
24
|
Cuculis L, Schroeder CM. A Single-Molecule View of Genome Editing Proteins: Biophysical Mechanisms for TALEs and CRISPR/Cas9. Annu Rev Chem Biomol Eng 2017; 8:577-597. [PMID: 28489428 DOI: 10.1146/annurev-chembioeng-060816-101603] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Exciting new advances in genome engineering have unlocked the potential to radically alter the treatment of human disease. In this review, we discuss the application of single-molecule techniques to uncover the mechanisms behind two premier classes of genome editing proteins: transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated system (Cas). These technologies have facilitated a striking number of gene editing applications in a variety of organisms; however, we are only beginning to understand the molecular mechanisms governing the DNA editing properties of these systems. Here, we discuss the DNA search and recognition process for TALEs and Cas9 that have been revealed by recent single-molecule experiments.
Collapse
Affiliation(s)
- Luke Cuculis
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801;
| | - Charles M Schroeder
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; .,Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| |
Collapse
|
25
|
Castillo F, Benmohamed A, Szatmari G. Xer Site Specific Recombination: Double and Single Recombinase Systems. Front Microbiol 2017; 8:453. [PMID: 28373867 PMCID: PMC5357621 DOI: 10.3389/fmicb.2017.00453] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/03/2017] [Indexed: 12/20/2022] Open
Abstract
The separation and segregation of newly replicated bacterial chromosomes can be constrained by the formation of circular chromosome dimers caused by crossing over during homologous recombination events. In Escherichia coli and most bacteria, dimers are resolved to monomers by site-specific recombination, a process performed by two Chromosomally Encoded tyrosine Recombinases (XerC and XerD). XerCD recombinases act at a 28 bp recombination site dif, which is located at the replication terminus region of the chromosome. The septal protein FtsK controls the initiation of the dimer resolution reaction, so that recombination occurs at the right time (immediately prior to cell division) and at the right place (cell division septum). XerCD and FtsK have been detected in nearly all sequenced eubacterial genomes including Proteobacteria, Archaea, and Firmicutes. However, in Streptococci and Lactococci, an alternative system has been found, composed of a single recombinase (XerS) genetically linked to an atypical 31 bp recombination site (difSL). A similar recombination system has also been found in 𝜀-proteobacteria such as Campylobacter and Helicobacter, where a single recombinase (XerH) acts at a resolution site called difH. Most Archaea contain a recombinase called XerA that acts on a highly conserved 28 bp sequence dif, which appears to act independently of FtsK. Additionally, several mobile elements have been found to exploit the dif/Xer system to integrate their genomes into the host chromosome in Vibrio cholerae, Neisseria gonorrhoeae, and Enterobacter cloacae. This review highlights the versatility of dif/Xer recombinase systems in prokaryotes and summarizes our current understanding of homologs of dif/Xer machineries.
Collapse
Affiliation(s)
- Fabio Castillo
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, MontréalQC, Canada
| | | | - George Szatmari
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, MontréalQC, Canada
| |
Collapse
|
26
|
Kamagata K, Murata A, Itoh Y, Takahashi S. Characterization of facilitated diffusion of tumor suppressor p53 along DNA using single-molecule fluorescence imaging. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2017. [DOI: 10.1016/j.jphotochemrev.2017.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
27
|
Kinetics of large-scale chromosomal movement during asymmetric cell division in Escherichia coli. PLoS Genet 2017; 13:e1006638. [PMID: 28234902 PMCID: PMC5345879 DOI: 10.1371/journal.pgen.1006638] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 03/10/2017] [Accepted: 02/15/2017] [Indexed: 11/19/2022] Open
Abstract
Coordination between cell division and chromosome replication is essential for a cell to produce viable progeny. In the commonly accepted view, Escherichia coli realize this coordination via the accurate positioning of its cell division apparatus relative to the nucleoids. However, E. coli lacking proper positioning of its cell division planes can still successfully propagate. Here, we characterize how these cells partition their chromosomes into daughters during such asymmetric divisions. Using quantitative time-lapse imaging, we show that DNA translocase, FtsK, can pump as much as 80% (3.7 Mb) of the chromosome between daughters at an average rate of 1700±800 bp/s. Pauses in DNA translocation are rare, and in no occasions did we observe reversals at experimental time scales of a few minutes. The majority of DNA movement occurs at the latest stages of cell division when the cell division protein ZipA has already dissociated from the septum, and the septum has closed to a narrow channel with a diameter much smaller than the resolution limit of the microscope (~250 nm). Our data suggest that the narrow constriction is necessary for effective translocation of DNA by FtsK. DNA translocases are conserved throughout bacteria. While at atomic and molecular levels they have been well characterized, their ability to partition DNA in vegetatively growing cells has remained less clear. Here we show that E. coli translocase, FtsK, can move as much as 80% (3.7 Mb) of the chromosomal DNA across the closing septum in asymmetrically dividing cells at an average rate of 1700 bp/s. The majority of DNA movement occurs at the latest stages of cell division when the septum has closed to a narrow channel. Our data implies that a narrow septal opening is needed for effective translocation of DNA by FtsK.
Collapse
|
28
|
El Najjar N, Kaimer C, Rösch T, Graumann PL. Requirements for Septal Localization and Chromosome Segregation Activity of the DNA Translocase SftA from Bacillus subtilis. J Mol Microbiol Biotechnol 2017; 27:29-42. [PMID: 28110333 DOI: 10.1159/000450725] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 09/09/2016] [Indexed: 11/19/2022] Open
Abstract
Bacillus subtilis possesses 2 DNA translocases that affect late stages of chromosome segregation: SftA separates nonsegregated DNA prior to septum closure, while SpoIIIE rescues septum-entrapped DNA. We provide evidence that SftA is associated with the division machinery via a stretch of 47 amino acids within its N-terminus, suggesting that SftA is recruited by protein-protein interactions with a component of the division machinery. SftA was also recruited to mid-cell in the absence of its first 20 amino acids, which are proposed to contain a membrane-binding motif. Cell fractionation experiments showed that SftA can be found in the cytosolic fraction, and to a minor degree in the membrane fraction, showing that it is a soluble protein in vivo. The expression of truncated SftA constructs led to a dominant sftA deletion phenotype, even at very low induction rates of the truncated proteins, indicating that the incorporation of nonfunctional monomers into SftA hexamers abolishes functionality. Mobility shift experiments and surface plasmon binding studies showed that SftA binds to DNA in a cooperative manner, and demonstrated low ATPase activity when binding to short nucleotides rather than to long stretches of DNA.
Collapse
Affiliation(s)
- Nina El Najjar
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, and Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | | | | | | |
Collapse
|
29
|
Kim KI, Lee S, Jin X, Kim SJ, Jo K, Lee JH. DNA Binding Peptide Directed Synthesis of Continuous DNA Nanowires for Analysis of Large DNA Molecules by Scanning Electron Microscope. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1601926. [PMID: 27813273 DOI: 10.1002/smll.201601926] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/04/2016] [Indexed: 06/06/2023]
Abstract
Synthesis of smooth and continuous DNA nanowires, preserving the original structure of native DNA, and allowing its analysis by scanning electron microscope (SEM), is demonstrated. Gold nanoparticles densely assembled on the DNA backbone via thiol-tagged DNA binding peptides work as seeds for metallization of DNA. This method allows whole analysis of DNA molecules with entangled 3D features.
Collapse
Affiliation(s)
- Kyung-Il Kim
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, 04107, Republic of Korea
| | - Xuelin Jin
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, 04107, Republic of Korea
| | - Su Ji Kim
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, 04107, Republic of Korea
| | - Jung Heon Lee
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| |
Collapse
|
30
|
Rad4 recognition-at-a-distance: Physical basis of conformation-specific anomalous diffusion of DNA repair proteins. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 127:93-104. [PMID: 27939760 DOI: 10.1016/j.pbiomolbio.2016.12.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 12/06/2016] [Indexed: 11/20/2022]
Abstract
Since Robert Brown's first observations of random walks by pollen particles suspended in solution, the concept of diffusion has been subject to countless theoretical and experimental studies in diverse fields from finance and social sciences, to physics and biology. Diffusive transport of macromolecules in cells is intimately linked to essential cellular functions including nutrient uptake, signal transduction, gene expression, as well as DNA replication and repair. Advancement in experimental techniques has allowed precise measurements of these diffusion processes. Mathematical and physical descriptions and computer simulations have been applied to model complicated biological systems in which anomalous diffusion, in addition to simple Brownian motion, was observed. The purpose of this review is to provide an overview of the major physical models of anomalous diffusion and corresponding experimental evidence on the target search problem faced by DNA-binding proteins, with an emphasis on DNA repair proteins and the role of anomalous diffusion in DNA target recognition.
Collapse
|
31
|
Abstract
Homologous recombination is an important pathway involved in the repair of double-stranded DNA breaks. Genetic studies form the foundation of our knowledge on homologous recombination. Significant progress has also been made toward understanding the biochemical and biophysical properties of the proteins, complexes, and reaction intermediates involved in this essential DNA repair pathway. However, heterogeneous or transient recombination intermediates remain extremely difficult to assess through traditional ensemble methods, leaving an incomplete mechanistic picture of many steps that take place during homologous recombination. To help overcome some of these limitations, we have established DNA curtain methodologies as an experimental platform for studying homologous DNA recombination in real-time at the single-molecule level. Here, we present a detailed overview describing the preparation and use of single-stranded DNA curtains in applications related to the study of homologous DNA recombination with emphasis on recent work related to the study of the eukaryotic recombinase Rad51.
Collapse
|
32
|
Pi F, Zhao Z, Chelikani V, Yoder K, Kvaratskhelia M, Guo P. Development of Potent Antiviral Drugs Inspired by Viral Hexameric DNA-Packaging Motors with Revolving Mechanism. J Virol 2016; 90:8036-46. [PMID: 27356896 PMCID: PMC5008075 DOI: 10.1128/jvi.00508-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The intracellular parasitic nature of viruses and the emergence of antiviral drug resistance necessitate the development of new potent antiviral drugs. Recently, a method for developing potent inhibitory drugs by targeting biological machines with high stoichiometry and a sequential-action mechanism was described. Inspired by this finding, we reviewed the development of antiviral drugs targeting viral DNA-packaging motors. Inhibiting multisubunit targets with sequential actions resembles breaking one bulb in a series of Christmas lights, which turns off the entire string. Indeed, studies on viral DNA packaging might lead to the development of new antiviral drugs. Recent elucidation of the mechanism of the viral double-stranded DNA (dsDNA)-packaging motor with sequential one-way revolving motion will promote the development of potent antiviral drugs with high specificity and efficiency. Traditionally, biomotors have been classified into two categories: linear and rotation motors. Recently discovered was a third type of biomotor, including the viral DNA-packaging motor, beside the bacterial DNA translocases, that uses a revolving mechanism without rotation. By analogy, rotation resembles the Earth's rotation on its own axis, while revolving resembles the Earth's revolving around the Sun (see animations at http://rnanano.osu.edu/movie.html). Herein, we review the structures of viral dsDNA-packaging motors, the stoichiometries of motor components, and the motion mechanisms of the motors. All viral dsDNA-packaging motors, including those of dsDNA/dsRNA bacteriophages, adenoviruses, poxviruses, herpesviruses, mimiviruses, megaviruses, pandoraviruses, and pithoviruses, contain a high-stoichiometry machine composed of multiple components that work cooperatively and sequentially. Thus, it is an ideal target for potent drug development based on the power function of the stoichiometries of target complexes that work sequentially.
Collapse
Affiliation(s)
- Fengmei Pi
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, Department of Physiology and Cell Biology, College of Medicine, and the Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, USA
| | - Zhengyi Zhao
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, Department of Physiology and Cell Biology, College of Medicine, and the Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, USA
| | - Venkata Chelikani
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Canterbury, New Zealand
| | - Kristine Yoder
- Department of Molecular Virology, Immunology, and Medical Genetics, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Mamuka Kvaratskhelia
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, Department of Physiology and Cell Biology, College of Medicine, and the Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, USA
| | - Peixuan Guo
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, Department of Physiology and Cell Biology, College of Medicine, and the Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, USA
| |
Collapse
|
33
|
Moolman MC, Tiruvadi Krishnan S, Kerssemakers JWJ, de Leeuw R, Lorent V, Sherratt DJ, Dekker NH. The progression of replication forks at natural replication barriers in live bacteria. Nucleic Acids Res 2016; 44:6262-73. [PMID: 27166373 PMCID: PMC5291258 DOI: 10.1093/nar/gkw397] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 04/27/2016] [Accepted: 04/28/2016] [Indexed: 01/07/2023] Open
Abstract
Protein-DNA complexes are one of the principal barriers the replisome encounters during replication. One such barrier is the Tus-ter complex, which is a direction dependent barrier for replication fork progression. The details concerning the dynamics of the replisome when encountering these Tus-ter barriers in the cell are poorly understood. By performing quantitative fluorescence microscopy with microfuidics, we investigate the effect on the replisome when encountering these barriers in live Escherichia coli cells. We make use of an E. coli variant that includes only an ectopic origin of replication that is positioned such that one of the two replisomes encounters a Tus-ter barrier before the other replisome. This enables us to single out the effect of encountering a Tus-ter roadblock on an individual replisome. We demonstrate that the replisome remains stably bound after encountering a Tus-ter complex from the non-permissive direction. Furthermore, the replisome is only transiently blocked, and continues replication beyond the barrier. Additionally, we demonstrate that these barriers affect sister chromosome segregation by visualizing specific chromosomal loci in the presence and absence of the Tus protein. These observations demonstrate the resilience of the replication fork to natural barriers and the sensitivity of chromosome alignment to fork progression.
Collapse
Affiliation(s)
- M Charl Moolman
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Sriram Tiruvadi Krishnan
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Jacob W J Kerssemakers
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Roy de Leeuw
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Vincent Lorent
- Université Paris 13, Sorbonne Paris Cité, Laboratoire de Physique des Lasers, CNRS, (UMR 7538), F-93430 Villetaneuse, France
| | - David J Sherratt
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| |
Collapse
|
34
|
|
35
|
FtsK translocation permits discrimination between an endogenous and an imported Xer/dif recombination complex. Proc Natl Acad Sci U S A 2016; 113:7882-7. [PMID: 27317749 DOI: 10.1073/pnas.1523178113] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In bacteria, the FtsK/Xer/dif (chromosome dimer resolution site) system is essential for faithful vertical genetic transmission, ensuring the resolution of chromosome dimers during their segregation to daughter cells. This system is also targeted by mobile genetic elements that integrate into chromosomal dif sites. A central question is thus how Xer/dif recombination is tuned to both act in chromosome segregation and stably maintain mobile elements. To explore this question, we focused on pathogenic Neisseria species harboring a genomic island in their dif sites. We show that the FtsK DNA translocase acts differentially at the recombination sites flanking the genomic island. It stops at one Xer/dif complex, activating recombination, but it does not stop on the other site, thus dismantling it. FtsK translocation thus permits cis discrimination between an endogenous and an imported Xer/dif recombination complex.
Collapse
|
36
|
Stigler J, Çamdere GÖ, Koshland DE, Greene EC. Single-Molecule Imaging Reveals a Collapsed Conformational State for DNA-Bound Cohesin. Cell Rep 2016; 15:988-998. [PMID: 27117417 PMCID: PMC4856582 DOI: 10.1016/j.celrep.2016.04.003] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 02/05/2016] [Accepted: 03/28/2016] [Indexed: 11/30/2022] Open
Abstract
Cohesin is essential for the hierarchical organization of the eukaryotic genome and plays key roles in many aspects of chromosome biology. The conformation of cohesin bound to DNA remains poorly defined, leaving crucial gaps in our understanding of how cohesin fulfills its biological functions. Here, we use single-molecule microscopy to directly observe the dynamic and functional characteristics of cohesin bound to DNA. We show that cohesin can undergo rapid one-dimensional (1D) diffusion along DNA, but individual nucleosomes, nucleosome arrays, and other protein obstacles significantly restrict its mobility. Furthermore, we demonstrate that DNA motor proteins can readily push cohesin along DNA, but they cannot pass through the interior of the cohesin ring. Together, our results reveal that DNA-bound cohesin has a central pore that is substantially smaller than anticipated. These findings have direct implications for understanding how cohesin and other SMC proteins interact with and distribute along chromatin.
Collapse
Affiliation(s)
- Johannes Stigler
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Gamze Ö Çamdere
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Douglas E Koshland
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| |
Collapse
|
37
|
Biological Nanomotors with a Revolution, Linear, or Rotation Motion Mechanism. Microbiol Mol Biol Rev 2016; 80:161-86. [PMID: 26819321 DOI: 10.1128/mmbr.00056-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The ubiquitous biological nanomotors were classified into two categories in the past: linear and rotation motors. In 2013, a third type of biomotor, revolution without rotation (http://rnanano.osu.edu/movie.html), was discovered and found to be widespread among bacteria, eukaryotic viruses, and double-stranded DNA (dsDNA) bacteriophages. This review focuses on recent findings about various aspects of motors, including chirality, stoichiometry, channel size, entropy, conformational change, and energy usage rate, in a variety of well-studied motors, including FoF1 ATPase, helicases, viral dsDNA-packaging motors, bacterial chromosome translocases, myosin, kinesin, and dynein. In particular, dsDNA translocases are used to illustrate how these features relate to the motion mechanism and how nature elegantly evolved a revolution mechanism to avoid coiling and tangling during lengthy dsDNA genome transportation in cell division. Motor chirality and channel size are two factors that distinguish rotation motors from revolution motors. Rotation motors use right-handed channels to drive the right-handed dsDNA, similar to the way a nut drives the bolt with threads in same orientation; revolution motors use left-handed motor channels to revolve the right-handed dsDNA. Rotation motors use small channels (<2 nm in diameter) for the close contact of the channel wall with single-stranded DNA (ssDNA) or the 2-nm dsDNA bolt; revolution motors use larger channels (>3 nm) with room for the bolt to revolve. Binding and hydrolysis of ATP are linked to different conformational entropy changes in the motor that lead to altered affinity for the substrate and allow work to be done, for example, helicase unwinding of DNA or translocase directional movement of DNA.
Collapse
|
38
|
Lee S, Wang C, Song J, Kim DG, Oh Y, Ko W, Lee J, Park J, Lee HS, Jo K. Investigation of various fluorescent protein–DNA binding peptides for effectively visualizing large DNA molecules. RSC Adv 2016. [DOI: 10.1039/c6ra08683g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Single-molecule DNA visualization with fluorescent protein DNA binding peptides.
Collapse
Affiliation(s)
- Seonghyun Lee
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Cong Wang
- Department of Mechanical Engineering
- Sogang University
- Seoul
- Korea
| | - Junghyun Song
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Do-geun Kim
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Yeeun Oh
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Wooseok Ko
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Jinyong Lee
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Jungyul Park
- Department of Mechanical Engineering
- Sogang University
- Seoul
- Korea
| | - Hyun Soo Lee
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Kyubong Jo
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| |
Collapse
|
39
|
Deniz AA. Deciphering Complexity in Molecular Biophysics with Single-Molecule Resolution. J Mol Biol 2015; 428:301-307. [PMID: 26707199 DOI: 10.1016/j.jmb.2015.12.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 12/16/2015] [Accepted: 12/16/2015] [Indexed: 01/12/2023]
Abstract
The structural features and dynamics of biological macromolecules underlie the molecular biology and correct functioning of cells. However, heterogeneity and other complexity of these molecules and their interactions often lead to loss of important information in traditional biophysical experiments. Single-molecule methods have dramatically altered the conceptual thinking and experimental tests available for such studies, leveraging their ability to avoid ensemble averaging. Here, I discuss briefly the rise of fluorescence single-molecule methods over the past two decades, a few key applications, and end with a view to challenges and future prospects.
Collapse
Affiliation(s)
- Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| |
Collapse
|
40
|
Gros J, Kumar C, Lynch G, Yadav T, Whitehouse I, Remus D. Post-licensing Specification of Eukaryotic Replication Origins by Facilitated Mcm2-7 Sliding along DNA. Mol Cell 2015; 60:797-807. [PMID: 26656162 DOI: 10.1016/j.molcel.2015.10.022] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 08/28/2015] [Accepted: 10/09/2015] [Indexed: 12/11/2022]
Abstract
Eukaryotic genomes are replicated from many origin sites that are licensed by the loading of the replicative DNA helicase, Mcm2-7. How eukaryotic origin positions are specified remains elusive. Here we show that, contrary to the bacterial paradigm, eukaryotic replication origins are not irrevocably defined by selection of the helicase loading site, but can shift in position after helicase loading. Using purified proteins we show that DNA translocases, including RNA polymerase, can push budding yeast Mcm2-7 double hexamers along DNA. Displaced Mcm2-7 double hexamers support DNA replication initiation distal to the loading site in vitro. Similarly, in yeast cells that are defective for transcription termination, collisions with RNA polymerase induce a redistribution of Mcm2-7 complexes along the chromosomes, resulting in a corresponding shift in DNA replication initiation sites. These results reveal a eukaryotic origin specification mechanism that departs from the classical replicon model, helping eukaryotic cells to negotiate transcription-replication conflict.
Collapse
Affiliation(s)
- Julien Gros
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center (MSKCC), 1275 York Avenue, New York, NY 10065, USA
| | - Charanya Kumar
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center (MSKCC), 1275 York Avenue, New York, NY 10065, USA
| | - Gerard Lynch
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center (MSKCC), 1275 York Avenue, New York, NY 10065, USA
| | - Tejas Yadav
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center (MSKCC), 1275 York Avenue, New York, NY 10065, USA; Weill-Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Iestyn Whitehouse
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center (MSKCC), 1275 York Avenue, New York, NY 10065, USA
| | - Dirk Remus
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center (MSKCC), 1275 York Avenue, New York, NY 10065, USA.
| |
Collapse
|
41
|
Liu N, Chistol G, Bustamante C. Two-subunit DNA escort mechanism and inactive subunit bypass in an ultra-fast ring ATPase. eLife 2015; 4. [PMID: 26452092 PMCID: PMC4728128 DOI: 10.7554/elife.09224] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 10/08/2015] [Indexed: 11/17/2022] Open
Abstract
SpoIIIE is a homo-hexameric dsDNA translocase responsible for completing chromosome segregation in Bacillus subtilis. Here, we use a single-molecule approach to monitor SpoIIIE translocation when challenged with neutral-backbone DNA and non-hydrolyzable ATP analogs. We show that SpoIIIE makes multiple essential contacts with phosphates on the 5'→3' strand in the direction of translocation. Using DNA constructs with two neutral-backbone segments separated by a single charged base pair, we deduce that SpoIIIE’s step size is 2 bp. Finally, experiments with non-hydrolyzable ATP analogs suggest that SpoIIIE can operate with non-consecutive inactive subunits. We propose a two-subunit escort translocation mechanism that is strict enough to enable SpoIIIE to track one DNA strand, yet sufficiently compliant to permit the motor to bypass inactive subunits without arrest. We speculate that such a flexible mechanism arose for motors that, like SpoIIIE, constitute functional bottlenecks where the inactivation of even a single motor can be lethal for the cell. DOI:http://dx.doi.org/10.7554/eLife.09224.001 Bacillus subtilis is a bacterium that lives in the soil. When food is in short supply, B. subtilis stops reproducing and individual bacterial cells transform into spores that lay dormant until conditions improve. While, B subtilis is generally harmless, it forms spores in a similar way to other bacteria that cause diseases such as anthrax. During spore formation, a membrane forms to divide the cell into a large mother cell and a smaller “forespore” cell. Then, a copy of the mother cell’s DNA – which is made of building blocks called bases – moves into the forespore. A group of proteins called SpoIIIE is instrumental in this process as it uses energy from a molecule called ATP to pump the DNA across the membrane at the rapid speed of 5,000 base pairs of DNA per second. SpoIIIE contains six individual protein subunits that form a ring-shaped motor structure that spans the membrane. It belongs to a large family of proteins that are found in all living organisms and drive many vital processes. How does SpoIIIE interact with DNA and how do the individual subunits coordinate their behaviour? Liu, Chistol et al. address these questions by using instruments called optical tweezers, which use a laser beam to hold and manipulate tiny objects. The experiments show that to move a fragment of DNA across a membrane, SpoIIIE only makes contact with one of the two strands that make up the DNA molecule. The experiments suggest that the DNA is handed over from one SpoIIIE subunit to another in a sequential order. This would allow the DNA to remain bound to SpoIIIE at all times as it passes through the membrane. Next, Liu, Chistol et al. measured how SpoIIIE steps along the DNA and found that each subunit takes a small two base pair step when energy is released from a single molecule of ATP. There is an element of flexibility in the system, because SpoIIIE can still move DNA normally even if some subunits cannot use energy from ATP. This provides a fail-safe mechanism that still allows the cells to form spores in the event that one subunit is disabled. Future work will concentrate in understanding how the subunits communicate around the ring to coordinate their sequential use of ATP and their DNA pumping activity. DOI:http://dx.doi.org/10.7554/eLife.09224.002
Collapse
Affiliation(s)
- Ninning Liu
- Jason L. Choy Laboratory of Single Molecule Biophysics, University of California, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | - Gheorghe Chistol
- Jason L. Choy Laboratory of Single Molecule Biophysics, University of California, Berkeley, United States.,Department of Physics, University of California, Berkeley, United States
| | - Carlos Bustamante
- Jason L. Choy Laboratory of Single Molecule Biophysics, University of California, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, United States.,Department of Physics, University of California, Berkeley, United States.,California Institute for Quantitative Biosciences, Berkeley, United States.,Department of Chemistry, Howard Hughes Medical Institute, University of California, Berkeley, United States.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Kavli Energy NanoSciences Institute at the University of California, Berkeley and the Lawrence Berkeley National Laboratory, Berkeley, United States
| |
Collapse
|
42
|
Gallardo IF, Pasupathy P, Brown M, Manhart CM, Neikirk DP, Alani E, Finkelstein IJ. High-Throughput Universal DNA Curtain Arrays for Single-Molecule Fluorescence Imaging. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:10310-7. [PMID: 26325477 PMCID: PMC4624423 DOI: 10.1021/acs.langmuir.5b02416] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Single-molecule studies of protein-DNA interactions have shed critical insights into the molecular mechanisms of nearly every aspect of DNA metabolism. The development of DNA curtains-a method for organizing arrays of DNA molecules on a fluid lipid bilayer-has greatly facilitated these studies by increasing the number of reactions that can be observed in a single experiment. However, the utility of DNA curtains is limited by the challenges associated with depositing nanometer-scale lipid diffusion barriers onto quartz microscope slides. Here, we describe a UV lithography-based method for large-scale fabrication of chromium (Cr) features and organization of DNA molecules at these features for high-throughput single-molecule studies. We demonstrate this approach by assembling 792 independent DNA arrays (containing >900,000 DNA molecules) within a single microfluidic flowcell. As a first proof of principle, we track the diffusion of Mlh1-Mlh3-a heterodimeric complex that participates in DNA mismatch repair and meiotic recombination. To further highlight the utility of this approach, we demonstrate a two-lane flowcell that facilitates concurrent experiments on different DNA substrates. Our technique greatly reduces the challenges associated with assembling DNA curtains and paves the way for the rapid acquisition of large statistical data sets from individual single-molecule experiments.
Collapse
Affiliation(s)
| | | | | | - Carol M Manhart
- Department of Molecular Biology and Genetics, Cornell University , Ithaca, New York 14853, United States
| | | | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University , Ithaca, New York 14853, United States
| | | |
Collapse
|
43
|
Assembly, translocation, and activation of XerCD-dif recombination by FtsK translocase analyzed in real-time by FRET and two-color tethered fluorophore motion. Proc Natl Acad Sci U S A 2015; 112:E5133-41. [PMID: 26324908 DOI: 10.1073/pnas.1510814112] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The FtsK dsDNA translocase functions in bacterial chromosome unlinking by activating XerCD-dif recombination in the replication terminus region. To analyze FtsK assembly and translocation, and the subsequent activation of XerCD-dif recombination, we extended the tethered fluorophore motion technique, using two spectrally distinct fluorophores to monitor two effective lengths along the same tethered DNA molecule. We observed that FtsK assembled stepwise on DNA into a single hexamer, and began translocation rapidly (∼ 0.25 s). Without extruding DNA loops, single FtsK hexamers approached XerCD-dif and resided there for ∼ 0.5 s irrespective of whether XerCD-dif was synapsed or unsynapsed. FtsK then dissociated, rather than reversing. Infrequently, FtsK activated XerCD-dif recombination when it encountered a preformed synaptic complex, and dissociated before the completion of recombination, consistent with each FtsK-XerCD-dif encounter activating only one round of recombination.
Collapse
|
44
|
Briggs K, Fischer CJ. All motors have to decide is what to do with the DNA that is given them. Biomol Concepts 2015; 5:383-95. [PMID: 25367619 DOI: 10.1515/bmc-2014-0017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 09/09/2014] [Indexed: 11/15/2022] Open
Abstract
DNA translocases are a diverse group of molecular motors responsible for a wide variety of cellular functions. The goal of this review is to identify common aspects in the mechanisms for how these enzymes couple the binding and hydrolysis of ATP to their movement along DNA. Not surprisingly, the shared structural components contained within the catalytic domains of several of these motors appear to give rise to common aspects of DNA translocation. Perhaps more interesting, however, are the differences between the families of translocases and the potential associated implications both for the functions of the members of these families and for the evolution of these families. However, as there are few translocases for which complete characterizations of the mechanisms of DNA binding, DNA translocation, and DNA-stimulated ATPase have been completed, it is difficult to form many inferences. We therefore hope that this review motivates the necessary further experimentation required for broader comparisons and conclusions.
Collapse
|
45
|
Berghuis BA, Dulin D, Xu ZQ, van Laar T, Cross B, Janissen R, Jergic S, Dixon NE, Depken M, Dekker NH. Strand separation establishes a sustained lock at the Tus-Ter replication fork barrier. Nat Chem Biol 2015; 11:579-85. [PMID: 26147356 DOI: 10.1038/nchembio.1857] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 05/20/2015] [Indexed: 01/30/2023]
Abstract
The bidirectional replication of a circular chromosome by many bacteria necessitates proper termination to avoid the head-on collision of the opposing replisomes. In Escherichia coli, replisome progression beyond the termination site is prevented by Tus proteins bound to asymmetric Ter sites. Structural evidence indicates that strand separation on the blocking (nonpermissive) side of Tus-Ter triggers roadblock formation, but biochemical evidence also suggests roles for protein-protein interactions. Here DNA unzipping experiments demonstrate that nonpermissively oriented Tus-Ter forms a tight lock in the absence of replicative proteins, whereas permissively oriented Tus-Ter allows nearly unhindered strand separation. Quantifying the lock strength reveals the existence of several intermediate lock states that are impacted by mutations in the lock domain but not by mutations in the DNA-binding domain. Lock formation is highly specific and exceeds reported in vivo efficiencies. We postulate that protein-protein interactions may actually hinder, rather than promote, proper lock formation.
Collapse
Affiliation(s)
- Bojk A Berghuis
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - David Dulin
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Zhi-Qiang Xu
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Theo van Laar
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Bronwen Cross
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Richard Janissen
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Slobodan Jergic
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Nicholas E Dixon
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Martin Depken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| |
Collapse
|
46
|
Männik J, Bailey MW. Spatial coordination between chromosomes and cell division proteins in Escherichia coli. Front Microbiol 2015; 6:306. [PMID: 25926826 PMCID: PMC4396457 DOI: 10.3389/fmicb.2015.00306] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 03/27/2015] [Indexed: 11/13/2022] Open
Abstract
To successfully propagate, cells need to coordinate chromosomal replication and segregation with cell division to prevent formation of DNA-less cells and cells with damaged DNA. Here, we review molecular systems in Escherichia coli that are known to be involved in positioning the divisome and chromosome relative to each other. Interestingly, this well-studied micro-organism has several partially redundant mechanisms to achieve this task; none of which are essential. Some of these systems determine the localization of the divisome relative to chromosomes such as SlmA-dependent nucleoid occlusion, some localize the chromosome relative to the divisome such as DNA translocation by FtsK, and some are likely to act on both systems such as the Min system and newly described Ter linkage. Moreover, there is evidence that E. coli harbors other divisome-chromosome coordination systems in addition to those known. The review also discusses the minimal requirements of coordination between chromosomes and cell division proteins needed for cell viability. Arguments are presented that cells can propagate without any dedicated coordination between their chromosomes and cell division machinery at the expense of lowered fitness.
Collapse
Affiliation(s)
- Jaan Männik
- Department of Physics and Astronomy, University of Tennessee , Knoxville, TN, USA ; Department of Biochemistry and Molecular and Cellular Biology, University of Tennessee , Knoxville, TN, USA
| | - Matthew W Bailey
- Department of Physics and Astronomy, University of Tennessee , Knoxville, TN, USA
| |
Collapse
|
47
|
Crozat E, Rousseau P, Fournes F, Cornet F. The FtsK family of DNA translocases finds the ends of circles. J Mol Microbiol Biotechnol 2015; 24:396-408. [PMID: 25732341 DOI: 10.1159/000369213] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A global view of bacterial chromosome choreography during the cell cycle is emerging, highlighting as a next challenge the description of the molecular mechanisms and factors involved. Here, we review one such factor, the FtsK family of DNA translocases. FtsK is a powerful and fast translocase that reads chromosome polarity. It couples segregation of the chromosome with cell division and controls the last steps of segregation in time and space. The second model protein of the family SpoIIIE acts in the transfer of the Bacillus subtilis chromosome during sporulation. This review focuses on the molecular mechanisms used by FtsK and SpoIIIE to segregate chromosomes with emphasis on the latest advances and open questions.
Collapse
Affiliation(s)
- Estelle Crozat
- Laboratoire de Microbiologie et de Génétique Moléculaires, CNRS, and Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | | | | | | |
Collapse
|
48
|
Qi Z, Redding S, Lee JY, Gibb B, Kwon Y, Niu H, Gaines WA, Sung P, Greene EC. DNA sequence alignment by microhomology sampling during homologous recombination. Cell 2015; 160:856-869. [PMID: 25684365 DOI: 10.1016/j.cell.2015.01.029] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 11/18/2014] [Accepted: 01/09/2015] [Indexed: 11/19/2022]
Abstract
Homologous recombination (HR) mediates the exchange of genetic information between sister or homologous chromatids. During HR, members of the RecA/Rad51 family of recombinases must somehow search through vast quantities of DNA sequence to align and pair single-strand DNA (ssDNA) with a homologous double-strand DNA (dsDNA) template. Here, we use single-molecule imaging to visualize Rad51 as it aligns and pairs homologous DNA sequences in real time. We show that Rad51 uses a length-based recognition mechanism while interrogating dsDNA, enabling robust kinetic selection of 8-nucleotide (nt) tracts of microhomology, which kinetically confines the search to sites with a high probability of being a homologous target. Successful pairing with a ninth nucleotide coincides with an additional reduction in binding free energy, and subsequent strand exchange occurs in precise 3-nt steps, reflecting the base triplet organization of the presynaptic complex. These findings provide crucial new insights into the physical and evolutionary underpinnings of DNA recombination.
Collapse
Affiliation(s)
- Zhi Qi
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA
| | - Sy Redding
- Department of Chemistry, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA
| | - Ja Yil Lee
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA
| | - Bryan Gibb
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA
| | - YoungHo Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Hengyao Niu
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - William A Gaines
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA; Howard Hughes Medical Institute, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA.
| |
Collapse
|
49
|
Accessory Replicative Helicases and the Replication of Protein-Bound DNA. J Mol Biol 2014; 426:3917-3928. [DOI: 10.1016/j.jmb.2014.10.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 09/29/2014] [Accepted: 10/06/2014] [Indexed: 12/29/2022]
|
50
|
Besprozvannaya M, Burton BM. Do the same traffic rules apply? Directional chromosome segregation by SpoIIIE and FtsK. Mol Microbiol 2014; 93:599-608. [PMID: 25040776 DOI: 10.1111/mmi.12708] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2014] [Indexed: 11/28/2022]
Abstract
Over a decade of studies have tackled the question of how FtsK/SpoIIIE translocases establish and maintain directional DNA translocation during chromosome segregation in bacteria. FtsK/SpoIIIE translocases move DNA in a highly processive, directional manner, where directionality is facilitated by sequences on the substrate DNA molecules that are being transported. In recent years, structural, biochemical, single-molecule and high-resolution microscopic studies have provided new insight into the mechanistic details of directional DNA segregation. Out of this body of work, a series of models have emerged and, ultimately, yielded two seemingly opposing models: the loading model and the target search model. We review these recent mechanistic insights into directional DNA movement and discuss the data that may serve to unite these suggested models, as well as propose future directions that may ultimately solve the debate.
Collapse
Affiliation(s)
- Marina Besprozvannaya
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA
| | | |
Collapse
|