1
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Nomburg J, Doherty EE, Price N, Bellieny-Rabelo D, Zhu YK, Doudna JA. Birth of protein folds and functions in the virome. Nature 2024; 633:710-717. [PMID: 39187718 PMCID: PMC11410667 DOI: 10.1038/s41586-024-07809-y] [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: 01/08/2024] [Accepted: 07/10/2024] [Indexed: 08/28/2024]
Abstract
The rapid evolution of viruses generates proteins that are essential for infectivity and replication but with unknown functions, due to extreme sequence divergence1. Here, using a database of 67,715 newly predicted protein structures from 4,463 eukaryotic viral species, we found that 62% of viral proteins are structurally distinct and lack homologues in the AlphaFold database2,3. Among the remaining 38% of viral proteins, many have non-viral structural analogues that revealed surprising similarities between human pathogens and their eukaryotic hosts. Structural comparisons suggested putative functions for up to 25% of unannotated viral proteins, including those with roles in the evasion of innate immunity. In particular, RNA ligase T-like phosphodiesterases were found to resemble phage-encoded proteins that hydrolyse the host immune-activating cyclic dinucleotides 3',3'- and 2',3'-cyclic GMP-AMP (cGAMP). Experimental analysis showed that RNA ligase T homologues encoded by avian poxviruses similarly hydrolyse cGAMP, showing that RNA ligase T-mediated targeting of cGAMP is an evolutionarily conserved mechanism of immune evasion that is present in both bacteriophage and eukaryotic viruses. Together, the viral protein structural database and analyses presented here afford new opportunities to identify mechanisms of virus-host interactions that are common across the virome.
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Affiliation(s)
- Jason Nomburg
- Gladstone-UCSF Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Erin E Doherty
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Nathan Price
- Gladstone-UCSF Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Daniel Bellieny-Rabelo
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Yong K Zhu
- Gladstone-UCSF Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Jennifer A Doudna
- Gladstone-UCSF Institute of Data Science and Biotechnology, San Francisco, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
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2
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Shiryaev SA, Cieplak P, Cheltsov A, Liddington RC, Terskikh AV. Dual function of Zika virus NS2B-NS3 protease. PLoS Pathog 2023; 19:e1011795. [PMID: 38011215 PMCID: PMC10723727 DOI: 10.1371/journal.ppat.1011795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/15/2023] [Accepted: 11/02/2023] [Indexed: 11/29/2023] Open
Abstract
Zika virus (ZIKV) serine protease, indispensable for viral polyprotein processing and replication, is composed of the membrane-anchored NS2B polypeptide and the N-terminal domain of the NS3 polypeptide (NS3pro). The C-terminal domain of the NS3 polypeptide (NS3hel) is necessary for helicase activity and contains an ATP-binding site. We discovered that ZIKV NS2B-NS3pro binds single-stranded RNA with a Kd of ~0.3 μM, suggesting a novel function. We tested various structural modifications of NS2B-NS3pro and observed that constructs stabilized in the recently discovered "super-open" conformation do not bind RNA. Likewise, stabilizing NS2B-NS3pro in the "closed" (proteolytically active) conformation using substrate inhibitors abolished RNA binding. We posit that RNA binding occurs when ZIKV NS2B-NS3pro adopts the "open" conformation, which we modeled using highly homologous dengue NS2B-NS3pro crystallized in the open conformation. We identified two positively charged fork-like structures present only in the open conformation of NS3pro. These forks are conserved across Flaviviridae family and could be aligned with the positively charged grove on NS3hel, providing a contiguous binding surface for the negative RNA strand exiting helicase. We propose a "reverse inchworm" model for a tightly intertwined NS2B-NS3 helicase-protease machinery, which suggests that NS2B-NS3pro cycles between open and super-open conformations to bind and release RNA enabling long-range NS3hel processivity. The transition to the closed conformation, likely induced by the substrate, enables the classical protease activity of NS2B-NS3pro.
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Affiliation(s)
- Sergey A. Shiryaev
- Sanford-Burnham-Prebys Medical Discovery Institute, Infectious and Inflammatory Disease Center, La Jolla, California, United States of America
| | - Piotr Cieplak
- Sanford-Burnham-Prebys Medical Discovery Institute, Infectious and Inflammatory Disease Center, La Jolla, California, United States of America
| | - Anton Cheltsov
- Q-mol LLC, San Diego, California, United States of America
| | - Robert C. Liddington
- Sanford-Burnham-Prebys Medical Discovery Institute, Infectious and Inflammatory Disease Center, La Jolla, California, United States of America
| | - Alexey V. Terskikh
- Sanford-Burnham-Prebys Medical Discovery Institute, Infectious and Inflammatory Disease Center, La Jolla, California, United States of America
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3
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Liu Z, Jiang W, Kim C, Peng X, Fan C, Wu Y, Xie Z, Peng F. A Pseudomonas Lysogenic Bacteriophage Crossing the Antarctic and Arctic, Representing a New Genus of Autographiviridae. Int J Mol Sci 2023; 24:ijms24087662. [PMID: 37108829 PMCID: PMC10142737 DOI: 10.3390/ijms24087662] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
Polar regions tend to support simple food webs, which are vulnerable to phage-induced gene transfer or microbial death. To further investigate phage-host interactions in polar regions and the potential linkage of phage communities between the two poles, we induced the release of a lysogenic phage, vB_PaeM-G11, from Pseudomonas sp. D3 isolated from the Antarctic, which formed clear phage plaques on the lawn of Pseudomonas sp. G11 isolated from the Arctic. From permafrost metagenomic data of the Arctic tundra, we found the genome with high-similarity to that of vB_PaeM-G11, demonstrating that vB_PaeM-G11 may have a distribution in both the Antarctic and Arctic. Phylogenetic analysis indicated that vB_PaeM-G11 is homologous to five uncultured viruses, and that they may represent a new genus in the Autographiviridae family, named Fildesvirus here. vB_PaeM-G11 was stable in a temperature range (4-40 °C) and pH (4-11), with latent and rise periods of about 40 and 10 min, respectively. This study is the first isolation and characterization study of a Pseudomonas phage distributed in both the Antarctic and Arctic, identifying its lysogenic host and lysis host, and thus provides essential information for further understanding the interaction between polar phages and their hosts and the ecological functions of phages in polar regions.
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Affiliation(s)
- Zhenyu Liu
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wenhui Jiang
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Cholsong Kim
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoya Peng
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Cong Fan
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yingliang Wu
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhixiong Xie
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Fang Peng
- College of Life Sciences, Wuhan University, Wuhan 430072, China
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4
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Stokar-Avihail A, Fedorenko T, Hör J, Garb J, Leavitt A, Millman A, Shulman G, Wojtania N, Melamed S, Amitai G, Sorek R. Discovery of phage determinants that confer sensitivity to bacterial immune systems. Cell 2023; 186:1863-1876.e16. [PMID: 37030292 DOI: 10.1016/j.cell.2023.02.029] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 01/09/2023] [Accepted: 02/20/2023] [Indexed: 04/10/2023]
Abstract
Over the past few years, numerous anti-phage defense systems have been discovered in bacteria. Although the mechanism of defense for some of these systems is understood, a major unanswered question is how these systems sense phage infection. To systematically address this question, we isolated 177 phage mutants that escape 15 different defense systems. In many cases, these escaper phages were mutated in the gene sensed by the defense system, enabling us to map the phage determinants that confer sensitivity to bacterial immunity. Our data identify specificity determinants of diverse retron systems and reveal phage-encoded triggers for multiple abortive infection systems. We find general themes in phage sensing and demonstrate that mechanistically diverse systems have converged to sense either the core replication machinery of the phage, phage structural components, or host takeover mechanisms. Combining our data with previous findings, we formulate key principles on how bacterial immune systems sense phage invaders.
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Affiliation(s)
- Avigail Stokar-Avihail
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Taya Fedorenko
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jens Hör
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jeremy Garb
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Azita Leavitt
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Adi Millman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gabriela Shulman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nicole Wojtania
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sarah Melamed
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gil Amitai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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5
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Xu L, Halma MTJ, Wuite GJL. Unravelling How Single-Stranded DNA Binding Protein Coordinates DNA Metabolism Using Single-Molecule Approaches. Int J Mol Sci 2023; 24:ijms24032806. [PMID: 36769124 PMCID: PMC9917605 DOI: 10.3390/ijms24032806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/23/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) play vital roles in DNA metabolism. Proteins of the SSB family exclusively and transiently bind to ssDNA, preventing the DNA double helix from re-annealing and maintaining genome integrity. In the meantime, they interact and coordinate with various proteins vital for DNA replication, recombination, and repair. Although SSB is essential for DNA metabolism, proteins of the SSB family have been long described as accessory players, primarily due to their unclear dynamics and mechanistic interaction with DNA and its partners. Recently-developed single-molecule tools, together with biochemical ensemble techniques and structural methods, have enhanced our understanding of the different coordination roles that SSB plays during DNA metabolism. In this review, we discuss how single-molecule assays, such as optical tweezers, magnetic tweezers, Förster resonance energy transfer, and their combinations, have advanced our understanding of the binding dynamics of SSBs to ssDNA and their interaction with other proteins partners. We highlight the central coordination role that the SSB protein plays by directly modulating other proteins' activities, rather than as an accessory player. Many possible modes of SSB interaction with protein partners are discussed, which together provide a bigger picture of the interaction network shaped by SSB.
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6
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Yin J, Fu Y, Rao G, Li Z, Tian K, Chong T, Kuang K, Wang M, Hu Z, Cao S. Structural transitions during the cooperative assembly of baculovirus single-stranded DNA-binding protein on ssDNA. Nucleic Acids Res 2022; 50:13100-13113. [PMID: 36477586 PMCID: PMC9825184 DOI: 10.1093/nar/gkac1142] [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: 09/13/2022] [Revised: 10/28/2022] [Accepted: 11/16/2022] [Indexed: 12/12/2022] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) interact with single-stranded DNA (ssDNA) to form filamentous structures with various degrees of cooperativity, as a result of intermolecular interactions between neighboring SSB subunits on ssDNA. However, it is still challenging to perform structural studies on SSB-ssDNA filaments at high resolution using the most studied SSB models, largely due to the intrinsic flexibility of these nucleoprotein complexes. In this study, HaLEF-3, an SSB protein from Helicoverpa armigera nucleopolyhedrovirus, was used for in vitro assembly of SSB-ssDNA filaments, which were structurally studied at atomic resolution using cryo-electron microscopy. Combined with the crystal structure of ssDNA-free HaLEF-3 octamers, our results revealed that the three-dimensional rearrangement of HaLEF-3 induced by an internal hinge-bending movement is essential for the formation of helical SSB-ssDNA complexes, while the contacting interface between adjacent HaLEF-3 subunits remains basically intact. We proposed a local cooperative SSB-ssDNA binding model, in which, triggered by exposure to oligonucleotides, HaLEF-3 molecules undergo ring-to-helix transition to initiate continuous SSB-SSB interactions along ssDNA. Unique structural features revealed by the assembly of HaLEF-3 on ssDNA suggest that HaLEF-3 may represent a new class of SSB.
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Affiliation(s)
| | | | | | - Zhiqiang Li
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, PR China,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Kexing Tian
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, PR China,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Tingting Chong
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, PR China,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Kai Kuang
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, PR China,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Manli Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety, Mega-Science, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Zhihong Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety, Mega-Science, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Sheng Cao
- To whom correspondence should be addressed. Tel: +86 27 87198286; Fax: +86 27 87198286;
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7
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Ratre V, Hemmadi V, Biswas S, Biswas M. Identification and Preliminary Characterization of a Novel Single-Stranded DNA Binding Protein of Staphylococcus aureus Phage Phi11 Expressed in Escherichia coli. Mol Biotechnol 2022; 65:922-933. [DOI: 10.1007/s12033-022-00598-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/28/2022] [Indexed: 11/10/2022]
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8
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Tian L, Zhu K, Chen Y, Zheng X, Zhang H, Geng Z, Li W, Ding N, Chen J, Dong Y, Cao P, Gong Y, Zhang Z. Biochemical and structural characterization of a KTSC family single-stranded DNA-binding protein from Euryarchaea. Int J Biol Macromol 2022; 216:618-628. [PMID: 35809674 DOI: 10.1016/j.ijbiomac.2022.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/24/2022] [Accepted: 07/03/2022] [Indexed: 11/05/2022]
Abstract
The lysine (K) tRNA synthetase C-terminal (KTSC) domain containing proteins are widely spread in Bacteria, Archaea and Viruses, but the function of this short domain is unclear. The occurrence of the fusion of KTSC domain to a catalytic domain or domains related to DNA or RNA metabolisms suggests its potential role in DNA or RNA binding. Here, we report the characterization of Mvu8s from Methanolobus vulcani, which consists of a single KTSC domain. Mvu8s binds specifically to ssDNA with an affinity approximately 40- and 10-fold higher than those for dsDNA and ssRNA in vitro, respectively. It shows a slight preference to the G-rich DNA sequence but barely binds the A-stretch. Crystal structure of Mvu8s shows that it forms a homo-tetramer, with each monomer composed of a four-strand antiparallel β-sheet and a helix-turn-helix in the order of β1-β2-β3-α1-α2-β4. Four basic residues (R3, R7, K54 and K58) were found to serve important roles in ssDNA-binding. And, the spiral arrangement of the DNA interfaces in Mvu8s homo-tetramer presumably results in ssDNA wrapping. Our results not only offer clues of the functions of the KTSC domain containing proteins but also expand our knowledge on the non-oligonucleotide-binding (OB) fold single-stranded DNA-binding proteins in Archaea.
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Affiliation(s)
- Lei Tian
- Department of General Surgery & Institute of General Surgery, Chinese PLA General Hospital First Medical Center, Beijing 100853, China
| | - Keli Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China; Center for Multi-disciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, 19B YuquanLu, Shijingshan District, Beijing 100049, China; Institute of Physical Science and Information Technology, Anhui University, China
| | - Yuanyuan Chen
- The Research Platform for Protein Sciences, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Xiaowei Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Heng Zhang
- Center for Multi-disciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, 19B YuquanLu, Shijingshan District, Beijing 100049, China
| | - Zhi Geng
- Center for Multi-disciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, 19B YuquanLu, Shijingshan District, Beijing 100049, China
| | - Wenqian Li
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture, College of Food Science and Nutrition-al Engineering, China Agricultural University, Beijing, 100083, China
| | - Niannian Ding
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Jingyu Chen
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture, College of Food Science and Nutrition-al Engineering, China Agricultural University, Beijing, 100083, China
| | - Yuhui Dong
- Center for Multi-disciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, 19B YuquanLu, Shijingshan District, Beijing 100049, China
| | - Peng Cao
- Faculty of Environment and Life, Beijing University of Technology, 100 Pingleyuan, Chaoyang District, Beijing 100124, China.
| | - Yong Gong
- Center for Multi-disciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, 19B YuquanLu, Shijingshan District, Beijing 100049, China.
| | - Zhenfeng Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China.
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9
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Huang C, Liu X, Chen Y, Zhou J, Li W, Ding N, Huang L, Chen J, Zhang Z. A Novel Family of Winged-Helix Single-Stranded DNA-Binding Proteins from Archaea. Int J Mol Sci 2022; 23:ijms23073455. [PMID: 35408816 PMCID: PMC8998557 DOI: 10.3390/ijms23073455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 02/04/2023] Open
Abstract
The winged helix superfamily comprises a large number of structurally related nucleic acid-binding proteins. While these proteins are often shown to bind dsDNA, few are known to bind ssDNA. Here, we report the identification and characterization of Sul7s, a novel winged-helix single-stranded DNA binding protein family highly conserved in Sulfolobaceae. Sul7s from Sulfolobus islandicus binds ssDNA with an affinity approximately 15-fold higher than that for dsDNA in vitro. It prefers binding oligo(dT)30 over oligo(dC)30 or a dG-rich 30-nt oligonucleotide, and barely binds oligo(dA)30. Further, binding by Sul7s inhibits DNA strand annealing, but shows little effect on the melting temperature of DNA duplexes. The solution structure of Sul7s determined by NMR shows a winged helix-turn-helix fold, consisting of three α-helices, three β-strands, and two short wings. It interacts with ssDNA via a large positively charged binding surface, presumably resulting in ssDNA deformation. Our results shed significant light on not only non-OB fold single-stranded DNA binding proteins in Archaea, but also the divergence of the winged-helix proteins in both function and structure during evolution.
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Affiliation(s)
- Can Huang
- MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (C.H.); (W.L.)
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China; (J.Z.); (N.D.); (L.H.)
| | - Xuehui Liu
- The Research Platform for Protein Sciences, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; (X.L.); (Y.C.)
| | - Yuanyuan Chen
- The Research Platform for Protein Sciences, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; (X.L.); (Y.C.)
| | - Junshi Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China; (J.Z.); (N.D.); (L.H.)
| | - Wenqian Li
- MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (C.H.); (W.L.)
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China; (J.Z.); (N.D.); (L.H.)
| | - Niannian Ding
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China; (J.Z.); (N.D.); (L.H.)
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China; (J.Z.); (N.D.); (L.H.)
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingyu Chen
- MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (C.H.); (W.L.)
- Correspondence: (J.C.); (Z.Z.); Tel.: +86-10-64806988 (Z.Z.)
| | - Zhenfeng Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China; (J.Z.); (N.D.); (L.H.)
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (J.C.); (Z.Z.); Tel.: +86-10-64806988 (Z.Z.)
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10
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Bocanegra R, Plaza G A I, Ibarra B. In vitro single-molecule manipulation studies of viral DNA replication. Enzymes 2021; 49:115-148. [PMID: 34696830 DOI: 10.1016/bs.enz.2021.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Faithfull replication of genomic information relies on the coordinated activity of the multi-protein machinery known as the replisome. Several constituents of the replisome operate as molecular motors that couple thermal and chemical energy to a mechanical task. Over the last few decades, in vitro single-molecule manipulation techniques have been used to monitor and manipulate mechanically the activities of individual molecular motors involved in DNA replication with nanometer, millisecond, and picoNewton resolutions. These studies have uncovered the real-time kinetics of operation of these biological systems, the nature of their transient intermediates, and the processes by which they convert energy to work (mechano-chemistry), ultimately providing new insights into their inner workings of operation not accessible by ensemble assays. In this chapter, we describe two of the most widely used single-molecule manipulation techniques for the study of DNA replication, optical and magnetic tweezers, and their application in the study of the activities of proteins involved in viral DNA replication.
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Affiliation(s)
- Rebeca Bocanegra
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, Madrid, Spain
| | - Ismael Plaza G A
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, Madrid, Spain
| | - Borja Ibarra
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, Madrid, Spain.
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11
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Blevins MS, Walker JN, Schaub JM, Finkelstein IJ, Brodbelt JS. Characterization of the T4 gp32-ssDNA complex by native, cross-linking, and ultraviolet photodissociation mass spectrometry. Chem Sci 2021; 12:13764-13776. [PMID: 34760161 PMCID: PMC8549804 DOI: 10.1039/d1sc02861h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/23/2021] [Indexed: 12/28/2022] Open
Abstract
Protein-DNA interactions play crucial roles in DNA replication across all living organisms. Here, we apply a suite of mass spectrometry (MS) tools to characterize a protein-ssDNA complex, T4 gp32·ssDNA, with results that both support previous studies and simultaneously uncover novel insight into this non-covalent biological complex. Native mass spectrometry of the protein reveals the co-occurrence of Zn-bound monomers and homodimers, while addition of differing lengths of ssDNA generates a variety of protein:ssDNA complex stoichiometries (1 : 1, 2 : 1, 3 : 1), indicating sequential association of gp32 monomers with ssDNA. Ultraviolet photodissociation (UVPD) mass spectrometry allows characterization of the binding site of the ssDNA within the protein monomer via analysis of holo ions, i.e. ssDNA-containing protein fragments, enabling interrogation of disordered regions of the protein which are inaccessible via traditional crystallographic techniques. Finally, two complementary cross-linking (XL) approaches, bottom-up analysis of the crosslinked complexes as well as MS1 analysis of the intact complexes, are used to showcase the absence of ssDNA binding with the intact cross-linked homodimer and to generate two homodimer gp32 model structures which highlight that the homodimer interface overlaps with the monomer ssDNA-binding site. These models suggest that the homodimer may function in a regulatory capacity by controlling the extent of ssDNA binding of the protein monomer. In sum, this work underscores the utility of a multi-faceted mass spectrometry approach for detailed investigation of non-covalent protein-DNA complexes.
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Affiliation(s)
- Molly S Blevins
- Department of Chemistry, University of Texas at Austin Austin TX 78712 USA
| | - Jada N Walker
- Department of Chemistry, University of Texas at Austin Austin TX 78712 USA
| | - Jeffrey M Schaub
- Department of Molecular Biosciences, University of Texas at Austin Austin TX 78712 USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin Austin TX 78712 USA
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12
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Gabashvili E, Kobakhidze S, Koulouris S, Robinson T, Kotetishvili M. Bi- and Multi-directional Gene Transfer in the Natural Populations of Polyvalent Bacteriophages, and Their Host Species Spectrum Representing Foodborne Versus Other Human and/or Animal Pathogens. FOOD AND ENVIRONMENTAL VIROLOGY 2021; 13:179-202. [PMID: 33484405 DOI: 10.1007/s12560-021-09460-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Unraveling the trends of phage-host versus phage-phage coevolution is critical for avoiding possible undesirable outcomes from the use of phage preparations intended for therapeutic, food safety or environmental safety purposes. We aimed to investigate a phenomenon of intergeneric recombination and its trajectories across the natural populations of phages predominantly linked to foodborne pathogens. The results from the recombination analyses, using a large array of the recombination detection algorithms imbedded in SplitsTree, RDP4, and Simplot software packages, provided strong evidence (fit: 100; P ≤ 0.014) for both bi- and multi-directional intergeneric recombination of the genetic loci involved collectively in phage morphogenesis, host specificity, virulence, replication, and persistence. Intergeneric recombination was determined to occur not only among conspecifics of the virulent versus temperate phages but also between the phages with these different lifestyles. The recombining polyvalent phages were suggested to interact with fairly large host species networks, including sometimes genetically very distinct species, such as e.g., Salmonella enterica and/or Escherichia coli versus Staphylococcus aureus or Yersinia pestis. Further studies are needed to understand whether phage-driven intergeneric recombination can lead to undesirable changes of intestinal and other microbiota in humans and animals.
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Affiliation(s)
- Ekaterine Gabashvili
- School of Natural Sciences and Medicine, Ilia State University, 1 Giorgi Tsereteli exit, 0162, Tbilisi, Georgia
- Division of Risk Assessment, Scientific-Research Center of Agriculture, 6 Marshal Gelovani ave., 0159, Tbilisi, Georgia
| | - Saba Kobakhidze
- Division of Risk Assessment, Scientific-Research Center of Agriculture, 6 Marshal Gelovani ave., 0159, Tbilisi, Georgia
| | - Stylianos Koulouris
- Engagement and Cooperation Unit, European Food Safety Authority, Via Carlo Magno 1A, 43126, Parma, Italy
| | - Tobin Robinson
- Scientific Committee, and Emerging Risks Unit, European Food Safety Authority, Via Carlo Magno 1A, 43126, Parma, Italy
| | - Mamuka Kotetishvili
- Division of Risk Assessment, Scientific-Research Center of Agriculture, 6 Marshal Gelovani ave., 0159, Tbilisi, Georgia.
- Hygiene and Medical Ecology, G. Natadze Scientific-Research Institute of Sanitation, 78 D. Uznadze St., 0102, Tbilisi, Georgia.
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13
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Oliveira MT, Ciesielski GL. The Essential, Ubiquitous Single-Stranded DNA-Binding Proteins. Methods Mol Biol 2021; 2281:1-21. [PMID: 33847949 DOI: 10.1007/978-1-0716-1290-3_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Maintenance of genomes is fundamental for all living organisms. The diverse processes related to genome maintenance entail the management of various intermediate structures, which may be deleterious if unresolved. The most frequent intermediate structures that result from the melting of the DNA duplex are single-stranded (ss) DNA stretches. These are thermodynamically less stable and can spontaneously fold into secondary structures, which may obstruct a variety of genome processes. In addition, ssDNA is more prone to breaking, which may lead to the formation of deletions or DNA degradation. Single-stranded DNA-binding proteins (SSBs) bind and stabilize ssDNA, preventing the abovementioned deleterious consequences and recruiting the appropriate machinery to resolve that intermediate molecule. They are present in all forms of life and are essential for their viability, with very few exceptions. Here we present an introductory chapter to a volume of the Methods in Molecular Biology dedicated to SSBs, in which we provide a general description of SSBs from various taxa.
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Affiliation(s)
- Marcos T Oliveira
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil
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14
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Foster BM, Rosenberg D, Salvo H, Stephens KL, Bintz BJ, Hammel M, Ellenberger T, Gainey MD, Wallen JR. Combined Solution and Crystal Methods Reveal the Electrostatic Tethers That Provide a Flexible Platform for Replication Activities in the Bacteriophage T7 Replisome. Biochemistry 2019; 58:4466-4479. [PMID: 31659895 DOI: 10.1021/acs.biochem.9b00525] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent structural studies of the bacteriophage T7 DNA replication system have shed light on how multiple proteins assemble to copy two antiparallel DNA strands. In T7, acidic C-terminal tails of both the primase-helicase and single-stranded DNA binding protein bind to two basic patches on the DNA polymerase to aid in replisome assembly, processivity, and coordinated DNA synthesis. Although these electrostatic interactions are essential for DNA replication, the molecular details for how these tails bind the polymerase are unknown. We have determined an X-ray crystal structure of the T7 DNA polymerase bound to both a primer/template DNA and a peptide that mimics the C-terminal tail of the primase-helicase. The structure reveals that the essential C-terminal phenylalanine of the tail binds to a hydrophobic pocket that is surrounded by positive charge on the surface of the polymerase. We show that alterations of polymerase residues that engage the tail lead to defects in viral replication. In the structure, we also observe dTTP bound in the exonuclease active site and stacked against tryptophan 160. Using both primer/extension assays and high-throughput sequencing, we show how mutations in the exonuclease active site lead to defects in mismatch repair and an increase in the level of mutagenesis of the T7 genome. Finally, using small-angle X-ray scattering, we provide the first solution structures of a complex between the single-stranded DNA binding protein and the DNA polymerase and show how a single-stranded DNA binding protein dimer engages both one and two copies of DNA polymerase.
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Affiliation(s)
- Brittni M Foster
- Department of Chemistry & Physics , Western Carolina University , Cullowhee , North Carolina 28723 , United States
| | - Daniel Rosenberg
- Molecular Biophysics and Integrated Bioimaging , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.,Graduate Group in Biophysics , University of California, Berkeley , Berkeley , California 94720 , United States
| | - Henry Salvo
- Department of Chemistry & Physics , Western Carolina University , Cullowhee , North Carolina 28723 , United States
| | - Kasie L Stephens
- Department of Chemistry & Physics , Western Carolina University , Cullowhee , North Carolina 28723 , United States
| | - Brittania J Bintz
- Department of Chemistry & Physics , Western Carolina University , Cullowhee , North Carolina 28723 , United States
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Tom Ellenberger
- Department of Biochemistry and Molecular Biophysics , Washington University School of Medicine , St. Louis , Missouri 63110 , United States
| | - Maria D Gainey
- Department of Chemistry & Physics , Western Carolina University , Cullowhee , North Carolina 28723 , United States
| | - Jamie R Wallen
- Department of Chemistry & Physics , Western Carolina University , Cullowhee , North Carolina 28723 , United States
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15
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Pant K, Anderson B, Perdana H, Malinowski MA, Win AT, Pabst C, Williams MC, Karpel RL. The role of the C-domain of bacteriophage T4 gene 32 protein in ssDNA binding and dsDNA helix-destabilization: Kinetic, single-molecule, and cross-linking studies. PLoS One 2018; 13:e0194357. [PMID: 29634784 PMCID: PMC5892887 DOI: 10.1371/journal.pone.0194357] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/01/2018] [Indexed: 11/19/2022] Open
Abstract
The model single-stranded DNA binding protein of bacteriophage T4, gene 32 protein (gp32) has well-established roles in DNA replication, recombination, and repair. gp32 is a single-chain polypeptide consisting of three domains. Based on thermodynamics and kinetics measurements, we have proposed that gp32 can undergo a conformational change where the acidic C-terminal domain binds internally to or near the single-stranded (ss) DNA binding surface in the core (central) domain, blocking ssDNA interaction. To test this model, we have employed a variety of experimental approaches and gp32 variants to characterize this conformational change. Utilizing stopped-flow methods, the association kinetics of wild type and truncated forms of gp32 with ssDNA were measured. When the C-domain is present, the log-log plot of k vs. [NaCl] shows a positive slope, whereas when it is absent (*I protein), there is little rate change with salt concentration, as expected for this model.A gp32 variant lacking residues 292-296 within the C-domain, ΔPR201, displays kinetic properties intermediate between gp32 and *I. The single molecule force-induced DNA helix-destabilizing activitiesas well as the single- and double-stranded DNA affinities of ΔPR201 and gp32 truncated at residue 295 also fall between full-length protein and *I. Finally, chemical cross-linking of recombinant C-domain and gp32 lacking both N- and C-terminal domains is inhibited by increasing concentrations of a short single-stranded oligonucleotide, and the salt dependence of cross-linking mirrors that expected for the model. Taken together, these results provide the first evidence in support of this model that have been obtained through structural probes.
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Affiliation(s)
- Kiran Pant
- Department of Physics, Northeastern University, Dana Research Center, Boston, Massachusetts, United States of America
| | - Brian Anderson
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Hilltop Circle, Baltimore, Maryland, United States of America
| | - Hendrik Perdana
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Hilltop Circle, Baltimore, Maryland, United States of America
| | - Matthew A. Malinowski
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Hilltop Circle, Baltimore, Maryland, United States of America
| | - Aye T. Win
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Hilltop Circle, Baltimore, Maryland, United States of America
| | - Christopher Pabst
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Hilltop Circle, Baltimore, Maryland, United States of America
| | - Mark C. Williams
- Department of Physics, Northeastern University, Dana Research Center, Boston, Massachusetts, United States of America
- Center for Interdisciplinary Research on Complex Systems, Northeastern University, Dana Research Center, Boston, Massachusetts, United States of America
| | - Richard L. Karpel
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Hilltop Circle, Baltimore, Maryland, United States of America
- * E-mail:
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16
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Zou Z, Wu S, Xiong J, Li H, Jiang Y, Zhang H. ssDNA hybridization facilitated by T7 ssDNA binding protein (gp2.5) rapidly initiates from the strand terminus or internally followed by a slow zippering step. Biochimie 2018; 147:1-12. [DOI: 10.1016/j.biochi.2017.12.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 12/26/2017] [Indexed: 01/23/2023]
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17
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Antony E, Lohman TM. Dynamics of E. coli single stranded DNA binding (SSB) protein-DNA complexes. Semin Cell Dev Biol 2018; 86:102-111. [PMID: 29588158 DOI: 10.1016/j.semcdb.2018.03.017] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 01/25/2023]
Abstract
Single stranded DNA binding proteins (SSB) are essential to the cell as they stabilize transiently open single stranded DNA (ssDNA) intermediates, recruit appropriate DNA metabolism proteins, and coordinate fundamental processes such as replication, repair and recombination. Escherichia coli single stranded DNA binding protein (EcSSB) has long served as the prototype for the study of SSB function. The structure, functions, and DNA binding properties of EcSSB are well established: The protein is a stable homotetramer with each subunit possessing an N-terminal DNA binding core, a C-terminal protein-protein interaction tail, and an intervening intrinsically disordered linker (IDL). EcSSB wraps ssDNA in multiple DNA binding modes and can diffuse along DNA to remove secondary structures and remodel other protein-DNA complexes. This review provides an update on these features based on recent findings, with special emphasis on the functional and mechanistic relevance of the IDL and DNA binding modes.
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Affiliation(s)
- Edwin Antony
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA.
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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18
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Hernandez AJ, Richardson CC. Gp2.5, the multifunctional bacteriophage T7 single-stranded DNA binding protein. Semin Cell Dev Biol 2018; 86:92-101. [PMID: 29588157 DOI: 10.1016/j.semcdb.2018.03.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 01/29/2018] [Accepted: 03/23/2018] [Indexed: 12/11/2022]
Abstract
The essential bacteriophage T7-encoded single-stranded DNA binding protein is the nexus of T7 DNA metabolism. Multiple layers of macromolecular interactions mediate its function in replication, recombination, repair, and the maturation of viral genomes. In addition to binding ssDNA, the protein binds to DNA polymerase and DNA helicase, regulating their activities. The protein displays potent homologous DNA annealing activity, underscoring its role in recombination.
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Affiliation(s)
- Alfredo J Hernandez
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Charles C Richardson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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19
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Cernooka E, Rumnieks J, Tars K, Kazaks A. Structural Basis for DNA Recognition of a Single-stranded DNA-binding Protein from Enterobacter Phage Enc34. Sci Rep 2017; 7:15529. [PMID: 29138440 PMCID: PMC5686142 DOI: 10.1038/s41598-017-15774-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/01/2017] [Indexed: 11/29/2022] Open
Abstract
Modern DNA sequencing capabilities have led to the discovery of a large number of new bacteriophage genomes, which are a rich source of novel proteins with an unidentified biological role. The genome of Enterobacter cancerogenus bacteriophage Enc34 contains several proteins of unknown function that are nevertheless conserved among distantly related phages. Here, we report the crystal structure of a conserved Enc34 replication protein ORF6 which contains a domain of unknown function DUF2815. Despite the low (~15%) sequence identity, the Enc34 ORF6 structurally resembles the gene 2.5 protein from bacteriophage T7, and likewise is a single-stranded DNA (ssDNA)-binding protein (SSB) that consists of a variation of the oligosaccharide/oligonucleotide-binding (OB)-fold and an unstructured C-terminal segment. We further report the crystal structure of a C-terminally truncated ORF6 in complex with an ssDNA oligonucleotide that reveals a DNA-binding mode involving two aromatic stacks and multiple electrostatic interactions, with implications for a common ssDNA recognition mechanism for all T7-type SSBs.
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Affiliation(s)
- Elina Cernooka
- Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia
| | - Janis Rumnieks
- Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia.
- Faculty of Biology, Department of Molecular Biology, Riga, LV-1004, Latvia.
| | - Andris Kazaks
- Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia.
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20
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Wallen JR, Zhang H, Weis C, Cui W, Foster BM, Ho CMW, Hammel M, Tainer JA, Gross ML, Ellenberger T. Hybrid Methods Reveal Multiple Flexibly Linked DNA Polymerases within the Bacteriophage T7 Replisome. Structure 2017; 25:157-166. [PMID: 28052235 DOI: 10.1016/j.str.2016.11.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 11/02/2016] [Accepted: 11/22/2016] [Indexed: 10/20/2022]
Abstract
The physical organization of DNA enzymes at a replication fork enables efficient copying of two antiparallel DNA strands, yet dynamic protein interactions within the replication complex complicate replisome structural studies. We employed a combination of crystallographic, native mass spectrometry and small-angle X-ray scattering experiments to capture alternative structures of a model replication system encoded by bacteriophage T7. Two molecules of DNA polymerase bind the ring-shaped primase-helicase in a conserved orientation and provide structural insight into how the acidic C-terminal tail of the primase-helicase contacts the DNA polymerase to facilitate loading of the polymerase onto DNA. A third DNA polymerase binds the ring in an offset manner that may enable polymerase exchange during replication. Alternative polymerase binding modes are also detected by small-angle X-ray scattering with DNA substrates present. Our collective results unveil complex motions within T7 replisome higher-order structures that are underpinned by multivalent protein-protein interactions with functional implications.
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Affiliation(s)
- Jamie R Wallen
- Department of Chemistry & Physics, Western Carolina University, Cullowhee, NC 28723, USA.
| | - Hao Zhang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Caroline Weis
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Weidong Cui
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Brittni M Foster
- Department of Chemistry & Physics, Western Carolina University, Cullowhee, NC 28723, USA
| | - Chris M W Ho
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, MD Anderson Cancer Center, Houston, TX 77054, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Tom Ellenberger
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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21
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Jarillo J, Morín JA, Beltrán-Heredia E, Villaluenga JPG, Ibarra B, Cao FJ. Mechanics, thermodynamics, and kinetics of ligand binding to biopolymers. PLoS One 2017; 12:e0174830. [PMID: 28380044 PMCID: PMC5381885 DOI: 10.1371/journal.pone.0174830] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 03/15/2017] [Indexed: 01/20/2023] Open
Abstract
Ligands binding to polymers regulate polymer functions by changing their physical and chemical properties. This ligand regulation plays a key role in many biological processes. We propose here a model to explain the mechanical, thermodynamic, and kinetic properties of the process of binding of small ligands to long biopolymers. These properties can now be measured at the single molecule level using force spectroscopy techniques. Our model performs an effective decomposition of the ligand-polymer system on its covered and uncovered regions, showing that the elastic properties of the ligand-polymer depend explicitly on the ligand coverage of the polymer (i.e., the fraction of the polymer covered by the ligand). The equilibrium coverage that minimizes the free energy of the ligand-polymer system is computed as a function of the applied force. We show how ligands tune the mechanical properties of a polymer, in particular its length and stiffness, in a force dependent manner. In addition, it is shown how ligand binding can be regulated applying mechanical tension on the polymer. Moreover, the binding kinetics study shows that, in the case where the ligand binds and organizes the polymer in different modes, the binding process can present transient shortening or lengthening of the polymer, caused by changes in the relative coverage by the different ligand modes. Our model will be useful to understand ligand-binding regulation of biological processes, such as the metabolism of nucleic acid. In particular, this model allows estimating the coverage fraction and the ligand mode characteristics from the force extension curves of a ligand-polymer system.
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Affiliation(s)
- Javier Jarillo
- Departamento de Física Atómica, Molecular y Nuclear. Facultad de Ciencias Físicas. Universidad Complutense de Madrid. Pza. de las Ciencias, 1. Madrid. Spain
| | - José A. Morín
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia) & CNB-CSIC-IMDEA Nanociencia Associated Unit ‘Unidad de Nanobiotecnología’, Madrid, Spain
| | - Elena Beltrán-Heredia
- Departamento de Física Atómica, Molecular y Nuclear. Facultad de Ciencias Físicas. Universidad Complutense de Madrid. Pza. de las Ciencias, 1. Madrid. Spain
| | - Juan P. G. Villaluenga
- Departamento de Física Aplicada I. Facultad de Ciencias Físicas. Universidad Complutense de Madrid. Pza. de las Ciencias, 1. Madrid. Spain
| | - Borja Ibarra
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia) & CNB-CSIC-IMDEA Nanociencia Associated Unit ‘Unidad de Nanobiotecnología’, Madrid, Spain
| | - Francisco J. Cao
- Departamento de Física Atómica, Molecular y Nuclear. Facultad de Ciencias Físicas. Universidad Complutense de Madrid. Pza. de las Ciencias, 1. Madrid. Spain
- * E-mail:
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22
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Cryo-EM structure of the replisome reveals multiple interactions coordinating DNA synthesis. Proc Natl Acad Sci U S A 2017; 114:E1848-E1856. [PMID: 28223502 DOI: 10.1073/pnas.1701252114] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We present a structure of the ∼650-kDa functional replisome of bacteriophage T7 assembled on DNA resembling a replication fork. A structure of the complex consisting of six domains of DNA helicase, five domains of RNA primase, two DNA polymerases, and two thioredoxin (processivity factor) molecules was determined by single-particle cryo-electron microscopy. The two molecules of DNA polymerase adopt a different spatial arrangement at the replication fork, reflecting their roles in leading- and lagging-strand synthesis. The structure, in combination with biochemical data, reveals molecular mechanisms for coordination of leading- and lagging-strand synthesis. Because mechanisms of DNA replication are highly conserved, the observations are relevant to other replication systems.
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23
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Korolev S. Advances in structural studies of recombination mediator proteins. Biophys Chem 2016; 225:27-37. [PMID: 27974172 DOI: 10.1016/j.bpc.2016.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/01/2016] [Accepted: 12/01/2016] [Indexed: 12/25/2022]
Abstract
Recombination mediator proteins (RMPs) are critical for genome integrity in all organisms. They include phage UvsY, prokaryotic RecF, -O, -R (RecFOR) and eukaryotic Rad52, Breast Cancer susceptibility 2 (BRCA2) and Partner and localizer of BRCA2 (PALB2) proteins. BRCA2 and PALB2 are tumor suppressors implicated in cancer. RMPs regulate binding of RecA-like recombinases to sites of DNA damage to initiate the most efficient non-mutagenic repair of broken chromosome and other deleterious DNA lesions. Mechanistically, RMPs stimulate a single-stranded DNA (ssDNA) hand-off from ssDNA binding proteins (ssbs) such as gp32, SSB and RPA, to recombinases, activating DNA repair only at the time and site of the damage event. This review summarizes structural studies of RMPs and their implications for understanding mechanism and function. Comparative analysis of RMPs is complicated due to their convergent evolution. In contrast to the evolutionary conserved ssbs and recombinases, RMPs are extremely diverse in sequence and structure. Structural studies are particularly important in such cases to reveal common features of the entire family and specific features of regulatory mechanisms for each member. All RMPs are characterized by specific DNA-binding domains and include variable protein interaction motifs. The complexity of such RMPs corresponds to the ever-growing number of DNA metabolism events they participate in under normal and pathological conditions and requires additional comprehensive structure-functional studies.
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Affiliation(s)
- S Korolev
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1100 S Grand Blvd., St. Louis, MO 63104, USA.
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24
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Chang HW, Pandey M, Kulaeva OI, Patel SS, Studitsky VM. Overcoming a nucleosomal barrier to replication. SCIENCE ADVANCES 2016; 2:e1601865. [PMID: 27847876 PMCID: PMC5106197 DOI: 10.1126/sciadv.1601865] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/11/2016] [Indexed: 05/05/2023]
Abstract
Efficient overcoming and accurate maintenance of chromatin structure and associated histone marks during DNA replication are essential for normal functioning of the daughter cells. However, the molecular mechanisms of replication through chromatin are unknown. We have studied traversal of uniquely positioned mononucleosomes by T7 replisome in vitro. Nucleosomes present a strong, sequence-dependent barrier for replication, with particularly strong pausing of DNA polymerase at the +(31-40) and +(41-65) regions of the nucleosomal DNA. The exonuclease activity of T7 DNA polymerase increases the overall rate of progression of the replisome through a nucleosome, likely by resolving nonproductive complexes. The presence of nucleosome-free DNA upstream of the replication fork facilitates the progression of DNA polymerase through the nucleosome. After replication, at least 50% of the nucleosomes assume an alternative conformation, maintaining their original positions on the DNA. Our data suggest a previously unpublished mechanism for nucleosome maintenance during replication, likely involving transient formation of an intranucleosomal DNA loop.
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Affiliation(s)
- Han-Wen Chang
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Manjula Pandey
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | | | - Smita S. Patel
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
- Corresponding author. (S.S.P.); (V.M.S.)
| | - Vasily M. Studitsky
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Corresponding author. (S.S.P.); (V.M.S.)
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Amarillas L, Chaidez C, González-Robles A, Lugo-Melchor Y, León-Félix J. Characterization of novel bacteriophage phiC119 capable of lysing multidrug-resistant Shiga toxin-producing Escherichia coli O157:H7. PeerJ 2016; 4:e2423. [PMID: 27672499 PMCID: PMC5028729 DOI: 10.7717/peerj.2423] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 08/09/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Shiga toxin-producing Escherichia coli (STEC) is one of the most common and widely distributed foodborne pathogens that has been frequently implicated in gastrointestinal and urinary tract infections. Moreover, high rates of multiple antibiotic-resistant E. coli strains have been reported worldwide. Due to the emergence of antibiotic-resistant strains, bacteriophages are considered an attractive alternative to biocontrol pathogenic bacteria. Characterization is a preliminary step towards designing a phage for biocontrol. METHODS In this study, we describe the characterization of a bacteriophage designated phiC119, which can infect and lyse several multidrug-resistant STEC strains and some Salmonella strains. The phage genome was screened to detect the stx-genes using PCR, morphological analysis, host range was determined, and genome sequencing were carried out, as well as an analysis of the cohesive ends and identification of the type of genetic material through enzymatic digestion of the genome. RESULTS Analysis of the bacteriophage particles by transmission electron microscopy showed that it had an icosahedral head and a long tail, characteristic of the family Siphoviridae. The phage exhibits broad host range against multidrug-resistant and highly virulent E. coli isolates. One-step growth experiments revealed that the phiC119 phage presented a large burst size (210 PFU/cell) and a latent period of 20 min. Based on genomic analysis, the phage contains a linear double-stranded DNA genome with a size of 47,319 bp. The phage encodes 75 putative proteins, but lysogeny and virulence genes were not found in the phiC119 genome. CONCLUSION These results suggest that phage phiC119 may be a good biological control agent. However, further studies are required to ensure its control of STEC and to confirm the safety of phage use.
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Affiliation(s)
- Luis Amarillas
- Laboratorio de Biología Molecular y Genómica Funcional, Centro de Investigación en Alimentación y Desarrollo, A. C., Culiacán, Sinaloa, México; Laboratorio de Genética, Instituto de Investigación Lightbourn, A. C., Cd. Jiménez, Chihuahua, México
| | - Cristóbal Chaidez
- Inocuidad Alimentaria, Centro de Investigación en Alimentación y Desarrollo, A. C. , Culiacán, Sinaloa , México
| | - Arturo González-Robles
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional , Ciudad de México , México
| | - Yadira Lugo-Melchor
- Laboratorio de Biología Molecular de la Unidad de Servicios Analíticos y Metrológicos, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A. C. , Guadalajara, Jalisco , México
| | - Josefina León-Félix
- Laboratorio de Biología Molecular y Genómica Funcional, Centro de Investigación en Alimentación y Desarrollo, A. C. , Culiacán, Sinaloa , México
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Delattre H, Souiai O, Fagoonee K, Guerois R, Petit MA. Phagonaute: A web-based interface for phage synteny browsing and protein function prediction. Virology 2016; 496:42-50. [PMID: 27254594 DOI: 10.1016/j.virol.2016.05.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/04/2016] [Accepted: 05/09/2016] [Indexed: 01/25/2023]
Abstract
Distant homology search tools are of great help to predict viral protein functions. However, due to the lack of profile databases dedicated to viruses, they can lack sensitivity. We constructed HMM profiles for more than 80,000 proteins from both phages and archaeal viruses, and performed all pairwise comparisons with HHsearch program. The whole resulting database can be explored through a user-friendly "Phagonaute" interface to help predict functions. Results are displayed together with their genetic context, to strengthen inferences based on remote homology. Beyond function prediction, this tool permits detections of co-occurrences, often indicative of proteins completing a task together, and observation of conserved patterns across large evolutionary distances. As a test, Herpes simplex virus I was added to Phagonaute, and 25% of its proteome matched to bacterial or archaeal viral protein counterparts. Phagonaute should therefore help virologists in their quest for protein functions and evolutionary relationships.
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Affiliation(s)
- Hadrien Delattre
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Oussema Souiai
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Khema Fagoonee
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Raphaël Guerois
- I2BC, CEA, Université Paris-Saclay, 91198 Gif-sur-Yvette, France.
| | - Marie-Agnès Petit
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
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Kazlauskas D, Krupovic M, Venclovas Č. The logic of DNA replication in double-stranded DNA viruses: insights from global analysis of viral genomes. Nucleic Acids Res 2016; 44:4551-64. [PMID: 27112572 PMCID: PMC4889955 DOI: 10.1093/nar/gkw322] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 04/13/2016] [Indexed: 11/14/2022] Open
Abstract
Genomic DNA replication is a complex process that involves multiple proteins. Cellular DNA replication systems are broadly classified into only two types, bacterial and archaeo-eukaryotic. In contrast, double-stranded (ds) DNA viruses feature a much broader diversity of DNA replication machineries. Viruses differ greatly in both completeness and composition of their sets of DNA replication proteins. In this study, we explored whether there are common patterns underlying this extreme diversity. We identified and analyzed all major functional groups of DNA replication proteins in all available proteomes of dsDNA viruses. Our results show that some proteins are common to viruses infecting all domains of life and likely represent components of the ancestral core set. These include B-family polymerases, SF3 helicases, archaeo-eukaryotic primases, clamps and clamp loaders of the archaeo-eukaryotic type, RNase H and ATP-dependent DNA ligases. We also discovered a clear correlation between genome size and self-sufficiency of viral DNA replication, the unanticipated dominance of replicative helicases and pervasive functional associations among certain groups of DNA replication proteins. Altogether, our results provide a comprehensive view on the diversity and evolution of replication systems in the DNA virome and uncover fundamental principles underlying the orchestration of viral DNA replication.
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Affiliation(s)
- Darius Kazlauskas
- Institute of Biotechnology, Vilnius University, Vilnius LT-02241, Lithuania
| | - Mart Krupovic
- Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Institut Pasteur, Paris 75015, France
| | - Česlovas Venclovas
- Institute of Biotechnology, Vilnius University, Vilnius LT-02241, Lithuania
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Wang W, Liu J, Sun L. Surface shapes and surrounding environment analysis of single- and double-stranded DNA-binding proteins in protein-DNA interface. Proteins 2016; 84:979-89. [PMID: 27038080 DOI: 10.1002/prot.25045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/15/2016] [Accepted: 03/25/2016] [Indexed: 11/12/2022]
Abstract
Protein-DNA bindings are critical to many biological processes. However, the structural mechanisms underlying these interactions are not fully understood. Here, we analyzed the residues shape (peak, flat, or valley) and the surrounding environment of double-stranded DNA-binding proteins (DSBs) and single-stranded DNA-binding proteins (SSBs) in protein-DNA interfaces. In the results, we found that the interface shapes, hydrogen bonds, and the surrounding environment present significant differences between the two kinds of proteins. Built on the investigation results, we constructed a random forest (RF) classifier to distinguish DSBs and SSBs with satisfying performance. In conclusion, we present a novel methodology to characterize protein interfaces, which will deepen our understanding of the specificity of proteins binding to ssDNA (single-stranded DNA) or dsDNA (double-stranded DNA). Proteins 2016; 84:979-989. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Wei Wang
- Department of Computer Science and Technology, College of Computer and Information Engineering, Henan Normal University, Xinxiang, 453007, China.,Laboratory of Computation Intelligence and Information Processing, Engineering Technology Research Center for Computing Intelligence and Data Mining, Henan Province, China
| | - Juan Liu
- Institute of Computer Software, School of Computer, Wuhan University, Wuhan, 430072, China
| | - Lin Sun
- Department of Computer Science and Technology, College of Computer and Information Engineering, Henan Normal University, Xinxiang, 453007, China.,Laboratory of Computation Intelligence and Information Processing, Engineering Technology Research Center for Computing Intelligence and Data Mining, Henan Province, China
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Waldman VM, Weiland E, Kozlov AG, Lohman TM. Is a fully wrapped SSB-DNA complex essential for Escherichia coli survival? Nucleic Acids Res 2016; 44:4317-29. [PMID: 27084941 PMCID: PMC4872115 DOI: 10.1093/nar/gkw262] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/30/2016] [Indexed: 11/12/2022] Open
Abstract
Escherichia coli single-stranded DNA binding protein (SSB) is an essential homotetramer that binds ssDNA and recruits multiple proteins to their sites of action during genomic maintenance. Each SSB subunit contains an N-terminal globular oligonucleotide/oligosaccharide binding fold (OB-fold) and an intrinsically disordered C-terminal domain. SSB binds ssDNA in multiple modes in vitro, including the fully wrapped (SSB)65 and (SSB)56 modes, in which ssDNA contacts all four OB-folds, and the highly cooperative (SSB)35 mode, in which ssDNA contacts an average of only two OB-folds. These modes can both be populated under physiological conditions. While these different modes might be used for different functions, this has been difficult to assess. Here we used a dimeric SSB construct with two covalently linked OB-folds to disable ssDNA binding in two of the four OB-folds thus preventing formation of fully wrapped DNA complexes in vitro, although they retain a wild-type-like, salt-dependent shift in cooperative binding to ssDNA. These variants complement wild-type SSB in vivo indicating that a fully wrapped mode is not essential for function. These results do not preclude a normal function for a fully wrapped mode, but do indicate that E. coli tolerates some flexibility with regards to its SSB binding modes.
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Affiliation(s)
- Vincent M Waldman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 660 S. Euclid Avenue, Box 8231, 63110-1093, USA
| | - Elizabeth Weiland
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 660 S. Euclid Avenue, Box 8231, 63110-1093, USA
| | - Alexander G Kozlov
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 660 S. Euclid Avenue, Box 8231, 63110-1093, USA
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 660 S. Euclid Avenue, Box 8231, 63110-1093, USA
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Abstract
I spent my childhood and adolescence in North and South Carolina, attended Duke University, and then entered Duke Medical School. One year in the laboratory of George Schwert in the biochemistry department kindled my interest in biochemistry. After one year of residency on the medical service of Duke Hospital, chaired by Eugene Stead, I joined the group of Arthur Kornberg at Stanford Medical School as a postdoctoral fellow. Two years later I accepted a faculty position at Harvard Medical School, where I remain today. During these 50 years, together with an outstanding group of students, postdoctoral fellows, and collaborators, I have pursued studies on DNA replication. I have experienced the excitement of discovering a number of important enzymes in DNA replication that, in turn, triggered an interest in the dynamics of a replisome. My associations with industry have been stimulating and fostered new friendships. I could not have chosen a better career.
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Affiliation(s)
- Charles C Richardson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115;
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Protein expression profiling in head fragments during planarian regeneration after amputation. Dev Genes Evol 2015; 225:79-93. [PMID: 25697422 DOI: 10.1007/s00427-015-0494-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 02/09/2015] [Indexed: 10/24/2022]
Abstract
Following amputation, a planarian tail fragment can regrow into a complete organism including a well-organized brain within about 2-3 weeks, thus restoring the structure and function to presurgical levels. Despite the enormous potential of these animals for regenerative medicine, our understanding of the exact mechanism of planarian regeneration is incomplete. To better understand the molecular nature of planarian head regeneration, we applied two-dimensional electrophoresis (2-DE)/matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF)/time-of-flight mass spectrometry (TOF MS) technique to analyze the dynamic proteomic expression profiles over the course of 6 to 168 h post-decapitation. This approach identified a total of 141 differentially expressed proteins, 47 of which exhibited exceptionally high fold changes (≥3-fold change). Of these, Rx protein, an important regulator of head and brain development, was considered to be closely related to planarian head regeneration because of its exceptional high expression almost throughout the time course of regeneration process. Functional annotation analysis classified the 141 proteins into eight categories: (1) signaling, (2) Ca(2+) binding and translocation, (3) transcription and translation, (4) cytoskeleton, (5) metabolism, (6) cell protection, (7) tissue differentiation, and (8) cell cycle. Signaling pathway analysis indicated that Wnt1/Ca(2+) signaling pathway was activated during head regeneration. Integrating the analyses of proteome expression profiling, functional annotation, and signaling pathway, amputation-induced head reformation requires some mechanisms to promote cell proliferation and differentiation, including differential regulation of proapoptotic and antiapoptotic proteins, and the regulation of proliferation and differentiation-related proteins. Importantly, Wnt1/Ca(2+) signaling pathway upregulates Rx expression, finally facilitating the differentiation of neoblasts into various cell types. Taken together, our study demonstrated that proteomic analysis approach used by us is a powerful tool in understanding molecular process related to head regeneration of planarian.
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Wang W, Liu J, Zhou X. Identification of single-stranded and double-stranded DNA binding proteins based on protein structure. BMC Bioinformatics 2014; 15 Suppl 12:S4. [PMID: 25474071 PMCID: PMC4243121 DOI: 10.1186/1471-2105-15-s12-s4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Background Protein-DNA interactions are essential for many biological processes. However, the structural mechanisms underlying these interactions are not fully understood. DNA binding proteins can be classified into double-stranded DNA binding proteins (DSBs) and single-stranded DNA binding proteins (SSBs), and they take part in different biological functions. DSBs usually act as transcriptional factors to regulate the genes' expressions, while SSBs usually play roles in DNA replication, recombination, and repair, etc. Understanding the binding specificity of a DNA binding protein is helpful for the research of protein functions. Results In this paper, we investigated the differences between DSBs and SSBs on surface tunnels as well as the OB-fold domain information. We detected the largest clefts on the protein surfaces, to obtain several features to be used for distinguishing the potential interfaces between SSBs and DSBs, and compared its structure with each of the six OB-fold protein templates, and use the maximal alignment score TM-score as the OB-fold feature of the protein, based on which, we constructed the support vector machine (SVM) classification model to automatically distinguish these two kinds of proteins, with prediction accuracy of 87%,83% and 83% for HOLO-set, APO-set and Mixed-set respectively. Conclusions We found that they have different ranges of tunnel lengths and tunnel curvatures; moreover, the alignment results with OB-fold templates have also found to be the discriminative feature of SSBs and DSBs. Experimental results on 10-fold cross validation indicate that the new feature set are effective to describe DNA binding proteins. The evaluation results on both bound (DNA-bound) and non-bound (DNA-free) proteins have shown the satisfactory performance of our method.
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Falero A, Marrero K, Trigueros S, Fando R. Characterization of the RstB2 protein, the DNA-binding protein of CTXϕ phage from Vibrio cholerae. Virus Genes 2014; 48:518-27. [PMID: 24643345 DOI: 10.1007/s11262-014-1053-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 02/28/2014] [Indexed: 11/25/2022]
Abstract
The low abundant protein RstB2, encoded in the RS2 region of CTXϕ, is essential for prophage formation. However, the only biochemical activity so far described is the single/double-stranded DNA-binding capacity of that protein. In this paper, a recombinant RstB2 (rRstB2) protein was overexpressed in E. coli with a yield of 58.4 mg l(-1) in shaken cultures, LB broth. The protein, purified to homogeneity, showed an identity with rRstB2 by peptide mass fingerprinting. The apparent molecular weight of the RstB2 native protein suggests that occurs mostly as a monomer in solution. The monomers were able of reacting immediately upon exposure to DNA molecules. After a year of storage at -20 °C, the protein remains biologically active. Bioinformatics analysis of the amino acid sequence of RstB2 predicts the C-end of this protein to be disordered and highly flexible, like in many other single-stranded DNA-binding proteins. When compared with the gVp of M13, conserved amino acids are found at structurally or functionally important relative positions. These results pave the way for additional studies of structure and molecular function of RstB2 for the biology of CTXϕ.
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Affiliation(s)
- Alina Falero
- National Center for Scientific Research, Ave 25 and 158, Cubanacán, Playa, PO Box 6214, Havana, Cuba,
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Mason CE, Jergic S, Lo ATY, Wang Y, Dixon NE, Beck JL. Escherichia coli single-stranded DNA-binding protein: nanoESI-MS studies of salt-modulated subunit exchange and DNA binding transactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:274-285. [PMID: 23283730 DOI: 10.1007/s13361-012-0552-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Revised: 11/28/2012] [Accepted: 11/30/2012] [Indexed: 06/01/2023]
Abstract
Single-stranded DNA-binding proteins (SSBs) are ubiquitous oligomeric proteins that bind with very high affinity to single-stranded DNA and have a variety of essential roles in DNA metabolism. Nanoelectrospray ionization mass spectrometry (nanoESI-MS) was used to monitor subunit exchange in full-length and truncated forms of the homotetrameric SSB from Escherichia coli. Subunit exchange in the native protein was found to occur slowly over a period of hours, but was significantly more rapid in a truncated variant of SSB from which the eight C-terminal residues were deleted. This effect is proposed to result from C-terminus mediated stabilization of the SSB tetramer, in which the C-termini interact with the DNA-binding cores of adjacent subunits. NanoESI-MS was also used to examine DNA binding to the SSB tetramer. Binding of single-stranded oligonucleotides [one molecule of (dT)(70), one molecule of (dT)(35), or two molecules of (dT)(35)] was found to prevent SSB subunit exchange. Transfer of SSB tetramers between discrete oligonucleotides was also observed and is consistent with predictions from solution-phase studies, suggesting that SSB-DNA complexes can be reliably analyzed by ESI mass spectrometry.
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Affiliation(s)
- Claire E Mason
- School of Chemistry, University of Wollongong, Wollongong, NSW, Australia
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Abstract
The advent of new technologies allowing the study of single biological molecules continues to have a major impact on studies of interacting systems as well as enzyme reactions. These approaches (fluorescence, optical, and magnetic tweezers), in combination with ensemble methods, have been particularly useful for mechanistic studies of protein-nucleic acid interactions and enzymes that function on nucleic acids. We review progress in the use of single-molecule methods to observe and perturb the activities of proteins and enzymes that function on flexible single-stranded DNA. These include single-stranded DNA binding proteins, recombinases (RecA/Rad51), and helicases/translocases that operate as motor proteins and play central roles in genome maintenance. We emphasize methods that have been used to detect and study the movement of these proteins (both ATP-dependent directional and random movement) along the single-stranded DNA and the mechanistic and functional information that can result from detailed analysis of such movement.
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Affiliation(s)
- Taekjip Ha
- Department of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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Marceau AH. Functions of single-strand DNA-binding proteins in DNA replication, recombination, and repair. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2012; 922:1-21. [PMID: 22976174 DOI: 10.1007/978-1-62703-032-8_1] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Double-stranded (ds) DNA contains all of the necessary genetic information, although practical use of this information requires unwinding of the duplex DNA. DNA unwinding creates single-stranded (ss) DNA intermediates that serve as templates for myriad cellular functions. Exposure of ssDNA presents several problems to the cell. First, ssDNA is thermodynamically less stable than dsDNA, which leads to spontaneous formation of duplex secondary structures that impede genome maintenance processes. Second, relative to dsDNA, ssDNA is hypersensitive to chemical and nucleolytic attacks that can cause damage to the genome. Cells deal with these potential problems by encoding specialized ssDNA-binding proteins (SSBs) that bind to and stabilize ssDNA structures required for essential genomic processes. SSBs are essential proteins found in all domains of life. SSBs bind ssDNA with high affinity and in a sequence-independent manner and, in doing so, SSBs help to form the central nucleoprotein complex substrate for DNA replication, recombination, and repair processes. While SSBs are found in every organism, the proteins themselves share surprisingly little sequence similarity, subunit composition, and oligomerization states. All SSB proteins contain at least one DNA-binding oligonucleotide/oligosaccharide binding (OB) fold, which consists minimally of a five stranded beta-sheet arranged as a beta barrel capped by a single alpha helix. The OB fold is responsible for both ssDNA binding and oligomerization (for SSBs that operate as oligomers). The overall organization of OB folds varies between bacteria, eukaryotes, and archaea. As part of SSB/ssDNA cellular structures, SSBs play direct roles in the DNA replication, recombination, and repair. In many cases, SSBs have been found to form specific complexes with diverse genome maintenance proteins, often helping to recruit SSB/ssDNA-processing enzymes to the proper cellular sites of action. This clustering of genome maintenance factors can help to stimulate and coordinate the activities of individual enzymes and is also important for dislodging SSB from ssDNA. These features support a model in which DNA metabolic processes have evolved to work on ssDNA/SSB nucleoprotein filaments rather than on naked ssDNA. In this volume, methods are described to interrogate SSB-DNA and SSB-protein binding functions along with approaches that aim to understand the cellular functions of SSB. This introductory chapter offers a general overview of SSBs that focuses on their structures, DNA-binding mechanisms, and protein-binding partners.
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Affiliation(s)
- Aimee H Marceau
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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Szczepankowska AK, Prestel E, Mariadassou M, Bardowski JK, Bidnenko E. Phylogenetic and complementation analysis of a single-stranded DNA binding protein family from lactococcal phages indicates a non-bacterial origin. PLoS One 2011; 6:e26942. [PMID: 22073223 PMCID: PMC3208561 DOI: 10.1371/journal.pone.0026942] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 10/06/2011] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The single-stranded-nucleic acid binding (SSB) protein superfamily includes proteins encoded by different organisms from Bacteria and their phages to Eukaryotes. SSB proteins share common structural characteristics and have been suggested to descend from an ancestor polypeptide. However, as other proteins involved in DNA replication, bacterial SSB proteins are clearly different from those found in Archaea and Eukaryotes. It was proposed that the corresponding genes in the phage genomes were transferred from the bacterial hosts. Recently new SSB proteins encoded by the virulent lactococcal bacteriophages (Orf14(bIL67)-like proteins) have been identified and characterized structurally and biochemically. METHODOLOGY/PRINCIPAL FINDINGS This study focused on the determination of phylogenetic relationships between Orf14(bIL67)-like proteins and other SSBs. We have performed a large scale phylogenetic analysis and pairwise sequence comparisons of SSB proteins from different phyla. The results show that, in remarkable contrast to other phage SSBs, the Orf14(bIL67)-like proteins form a distinct, self-contained and well supported phylogenetic group connected to the archaeal SSBs. Functional studies demonstrated that, despite the structural and amino acid sequence differences from bacterial SSBs, Orf14(bIL67) protein complements the conditional lethal ssb-1 mutation of Escherichia coli. CONCLUSIONS/SIGNIFICANCE Here we identified for the first time a group of phages encoded SSBs which are clearly distinct from their bacterial counterparts. All methods supported the recognition of these phage proteins as a new family within the SSB superfamily. Our findings suggest that unlike other phages, the virulent lactococcal phages carry ssb genes that were not acquired from their hosts, but transferred from an archaeal genome. This represents a unique example of a horizontal gene transfer between Archaea and bacterial phages.
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Affiliation(s)
- Agnieszka K. Szczepankowska
- Institut Micalis, UMR1319, INRA, Jouy-en-Josas, France
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | - Eric Prestel
- Institut Micalis, UMR1319, INRA, Jouy-en-Josas, France
| | | | - Jacek K. Bardowski
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
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Oliveira MT, Kaguni LS. Reduced stimulation of recombinant DNA polymerase γ and mitochondrial DNA (mtDNA) helicase by variants of mitochondrial single-stranded DNA-binding protein (mtSSB) correlates with defects in mtDNA replication in animal cells. J Biol Chem 2011; 286:40649-58. [PMID: 21953457 DOI: 10.1074/jbc.m111.289983] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mitochondrial single-stranded DNA-binding protein (mtSSB) is believed to coordinate the functions of DNA polymerase γ (pol γ) and the mitochondrial DNA (mtDNA) helicase at the mtDNA replication fork. We generated five variants of the human mtSSB bearing mutations in amino acid residues specific to metazoans that map on the protein surface, removed from the single-stranded DNA (ssDNA) binding groove. Although the mtSSB variants bound ssDNA with only slightly different affinities, they exhibited distinct capacities to stimulate the DNA polymerase activity of human pol γ and the DNA unwinding activity of human mtDNA helicase in vitro. Interestingly, we observed that the variants with defects in stimulating pol γ had unaltered capacities to stimulate the mtDNA helicase; at the same time, variants showing reduced stimulation of the mtDNA helicase activity promoted DNA synthesis by pol γ similarly to the wild-type mtSSB. The overexpression of the equivalent variants of Drosophila melanogaster mtSSB in S2 cells in culture caused mtDNA depletion under conditions of mitochondrial homeostasis. Furthermore, we observed more severe reduction of mtDNA copy number upon expression of these proteins during recovery from treatment with ethidium bromide, when mtDNA replication is stimulated in vivo. Our findings suggest that mtSSB uses distinct structural elements to interact functionally with its mtDNA replisome partners and to promote proper mtDNA replication in animal cells.
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Affiliation(s)
- Marcos T Oliveira
- Department of Biochemistry and Molecular Biology, Center for Mitochondrial Science and Medicine, and Graduate Program in Genetics, Michigan State University, East Lansing, Michigan 48824-1319, USA
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Choreography of bacteriophage T7 DNA replication. Curr Opin Chem Biol 2011; 15:580-6. [PMID: 21907611 DOI: 10.1016/j.cbpa.2011.07.024] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 07/25/2011] [Accepted: 07/27/2011] [Indexed: 11/21/2022]
Abstract
The replication system of phage T7 provides a model for DNA replication. Biochemical, structural, and single-molecule analyses together provide insight into replisome mechanics. A complex of polymerase, a processivity factor, and helicase mediates leading strand synthesis. Establishment of the complex requires an interaction of the C-terminal tail of the helicase with the polymerase. During synthesis the complex is stabilized by other interactions to provide for a processivity of 5 kilobase (kb). The C-terminal tail also interacts with a distinct region of the polymerase to captures dissociating polymerase to increase the processivity to >17kb. The lagging strand is synthesized discontinuously within a loop that forms and resolves during each cycle of Okazaki fragment synthesis. The synthesis of a primer as well as the termination of a fragment signal loop resolution.
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41
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Recombination-dependent concatemeric viral DNA replication. Virus Res 2011; 160:1-14. [PMID: 21708194 DOI: 10.1016/j.virusres.2011.06.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 06/07/2011] [Accepted: 06/10/2011] [Indexed: 11/24/2022]
Abstract
The initiation of viral double stranded (ds) DNA replication involves proteins that recruit and load the replisome at the replication origin (ori). Any block in replication fork progression or a programmed barrier may act as a factor for ori-independent remodelling and assembly of a new replisome at the stalled fork. Then replication initiation becomes dependent on recombination proteins, a process called recombination-dependent replication (RDR). RDR, which is recognized as being important for replication restart and stability in all living organisms, plays an essential role in the replication cycle of many dsDNA viruses. The SPP1 virus, which infects Bacillus subtilis cells, serves as a paradigm to understand the links between replication and recombination in circular dsDNA viruses. SPP1-encoded initiator and replisome assembly proteins control the onset of viral replication and direct the recruitment of host-encoded replisomal components at viral oriL. SPP1 uses replication fork reactivation to switch from ori-dependent θ-type (circle-to-circle) replication to σ-type RDR. Replication fork arrest leads to a double strand break that is processed by viral-encoded factors to generate a D-loop into which a new replisome is assembled, leading to σ-type viral replication. SPP1 RDR proteins are compared with similar proteins encoded by other viruses and their possible in vivo roles are discussed.
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42
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Oliveira MT, Kaguni LS. Functional roles of the N- and C-terminal regions of the human mitochondrial single-stranded DNA-binding protein. PLoS One 2010; 5:e15379. [PMID: 21060847 PMCID: PMC2965674 DOI: 10.1371/journal.pone.0015379] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 08/31/2010] [Indexed: 12/31/2022] Open
Abstract
Biochemical studies of the mitochondrial DNA (mtDNA) replisome demonstrate that the mtDNA polymerase and the mtDNA helicase are stimulated by the mitochondrial single-stranded DNA-binding protein (mtSSB). Unlike Escherichia coli SSB, bacteriophage T7 gp2.5 and bacteriophage T4 gp32, mtSSBs lack a long, negatively charged C-terminal tail. Furthermore, additional residues at the N-terminus (notwithstanding the mitochondrial presequence) are present in the sequence of species across the animal kingdom. We sought to analyze the functional importance of the N- and C-terminal regions of the human mtSSB in the context of mtDNA replication. We produced the mature wild-type human mtSSB and three terminal deletion variants, and examined their physical and biochemical properties. We demonstrate that the recombinant proteins adopt a tetrameric form, and bind single-stranded DNA with similar affinities. They also stimulate similarly the DNA unwinding activity of the human mtDNA helicase (up to 8-fold). Notably, we find that unlike the high level of stimulation that we observed previously in the Drosophila system, stimulation of DNA synthesis catalyzed by human mtDNA polymerase is only moderate, and occurs over a narrow range of salt concentrations. Interestingly, each of the deletion variants of human mtSSB stimulates DNA synthesis at a higher level than the wild-type protein, indicating that the termini modulate negatively functional interactions with the mitochondrial replicase. We discuss our findings in the context of species-specific components of the mtDNA replisome, and in comparison with various prokaryotic DNA replication machineries.
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Affiliation(s)
- Marcos T. Oliveira
- Department of Biochemistry and Molecular Biology, Center for Mitochondrial Science and Medicine, and Graduate Program in Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Laurie S. Kaguni
- Department of Biochemistry and Molecular Biology, Center for Mitochondrial Science and Medicine, and Graduate Program in Genetics, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
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43
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AmrZ beta-sheet residues are essential for DNA binding and transcriptional control of Pseudomonas aeruginosa virulence genes. J Bacteriol 2010; 192:5390-401. [PMID: 20709902 DOI: 10.1128/jb.00711-10] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
AmrZ is a putative ribbon-helix-helix (RHH) transcriptional regulator. RHH proteins utilize residues within the β-sheet for DNA binding, while the α-helices promote oligomerization. AmrZ is of interest due to its dual roles as a transcriptional activator and as a repressor, regulating genes encoding virulence factors associated with both chronic and acute Pseudomonas aeruginosa infection. In this study, cross-linking revealed that AmrZ forms oligomers in solution but that the amino terminus, containing an unordered region and a β-sheet, were not required for oligomerization. The first 12 unordered residues (extended amino terminus) contributed minimally to DNA binding. Mutagenesis of the AmrZ β-sheet demonstrated that residues 18, 20, and 22 were essential for DNA binding at both activation and repressor sites, suggesting that AmrZ utilizes a similar mechanism for binding to these sites. Mice infected with amrZ mutants exhibited reduced bacterial burden, morbidity, and mortality. Direct in vivo competition assays showed a 5-fold competitive advantage for the wild type over an isogenic amrZ mutant. Finally, the reduced infection phenotype of the amrZ-null strain was similar to that of a strain expressing a DNA-binding-deficient AmrZ variant, indicating that DNA binding and transcriptional regulation by AmrZ is responsible for the in vivo virulence defect. These recent infection data, along with previously identified AmrZ-regulated virulence factors, suggest the necessity of AmrZ transcriptional regulation for optimal virulence during acute infection.
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44
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Chaurasiya KR, Paramanathan T, McCauley MJ, Williams MC. Biophysical characterization of DNA binding from single molecule force measurements. Phys Life Rev 2010; 7:299-341. [PMID: 20576476 DOI: 10.1016/j.plrev.2010.06.001] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 05/19/2010] [Accepted: 05/20/2010] [Indexed: 11/25/2022]
Abstract
Single molecule force spectroscopy is a powerful method that uses the mechanical properties of DNA to explore DNA interactions. Here we describe how DNA stretching experiments quantitatively characterize the DNA binding of small molecules and proteins. Small molecules exhibit diverse DNA binding modes, including binding into the major and minor grooves and intercalation between base pairs of double-stranded DNA (dsDNA). Histones bind and package dsDNA, while other nuclear proteins such as high mobility group proteins bind to the backbone and bend dsDNA. Single-stranded DNA (ssDNA) binding proteins slide along dsDNA to locate and stabilize ssDNA during replication. Other proteins exhibit binding to both dsDNA and ssDNA. Nucleic acid chaperone proteins can switch rapidly between dsDNA and ssDNA binding modes, while DNA polymerases bind both forms of DNA with high affinity at distinct binding sites at the replication fork. Single molecule force measurements quantitatively characterize these DNA binding mechanisms, elucidating small molecule interactions and protein function.
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Affiliation(s)
- Kathy R Chaurasiya
- Department of Physics, Northeastern University, 111 Dana Research Center, Boston, MA 02115, USA
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45
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Ghosh S, Hamdan SM, Richardson CC. Two modes of interaction of the single-stranded DNA-binding protein of bacteriophage T7 with the DNA polymerase-thioredoxin complex. J Biol Chem 2010; 285:18103-12. [PMID: 20375019 DOI: 10.1074/jbc.m110.107656] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The DNA polymerase encoded by bacteriophage T7 has low processivity. Escherichia coli thioredoxin binds to a segment of 76 residues in the thumb subdomain of the polymerase and increases the processivity. The binding of thioredoxin leads to the formation of two basic loops, loops A and B, located within the thioredoxin-binding domain (TBD). Both loops interact with the acidic C terminus of the T7 helicase. A relatively weak electrostatic mode involves the C-terminal tail of the helicase and the TBD, whereas a high affinity interaction that does not involve the C-terminal tail occurs when the polymerase is in a polymerization mode. T7 gene 2.5 single-stranded DNA-binding protein (gp2.5) also has an acidic C-terminal tail. gp2.5 also has two modes of interaction with the polymerase, but both involve the C-terminal tail of gp2.5. An electrostatic interaction requires the basic residues in loops A and B, and gp2.5 binds to both loops with similar affinity as measured by surface plasmon resonance. When the polymerase is in a polymerization mode, the C terminus of gene 2.5 protein interacts with the polymerase in regions outside the TBD. gp2.5 increases the processivity of the polymerase-helicase complex during leading strand synthesis. When loop B of the TBD is altered, abortive DNA products are observed during leading strand synthesis. Loop B appears to play an important role in communication with the helicase and gp2.5, whereas loop A plays a stabilizing role in these interactions.
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Affiliation(s)
- Sharmistha Ghosh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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46
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de Souza RF, Iyer LM, Aravind L. Diversity and evolution of chromatin proteins encoded by DNA viruses. BIOCHIMICA ET BIOPHYSICA ACTA 2010; 1799:302-18. [PMID: 19878744 PMCID: PMC3243496 DOI: 10.1016/j.bbagrm.2009.10.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Revised: 10/21/2009] [Accepted: 10/22/2009] [Indexed: 11/23/2022]
Abstract
Double-stranded DNA viruses display a great variety of proteins that interact with host chromatin. Using the wealth of available genomic and functional information, we have systematically surveyed chromatin-related proteins encoded by dsDNA viruses. The distribution of viral chromatin-related proteins is primarily influenced by viral genome size and the superkingdom to which the host of the virus belongs. Smaller viruses usually encode multifunctional proteins that mediate several distinct interactions with host chromatin proteins and viral or host DNA. Larger viruses additionally encode several enzymes, which catalyze manipulations of chromosome structure, chromatin remodeling and covalent modifications of proteins and DNA. Among these viruses, it is also common to encounter transcription factors and DNA-packaging proteins such as histones and IHF/HU derived from cellular genomes, which might play a role in constituting virus-specific chromatin states. Through all size ranges a subset of domains in viral chromatin proteins appears to have been derived from those found in host proteins. Examples include the Zn-finger domains of the E6 and E7 proteins of papillomaviruses, SET domain methyltransferases and Jumonji-related demethylases in certain nucleocytoplasmic large DNA viruses and BEN domains in poxviruses and polydnaviruses. In other cases, chromatin-interacting modules, such as the LXCXE motif, appear to have been widely disseminated across distinct viral lineages, resulting in similar retinoblastoma targeting strategies. Viruses, especially those with large linear genomes, have evolved a number of mechanisms to manipulate viral chromosomes in the process of replication-associated recombination. These include topoisomerases, Rad50/SbcC-like ABC ATPases and a novel recombinase system in bacteriophages utilizing RecA and Rad52 homologs. Larger DNA viruses also encode SWI2/SNF2 and A18-like ATPases which appear to play specialized roles in transcription and recombination. Finally, it also appears that certain domains of viral provenance have given rise to key functions in eukaryotic chromatin such as a HEH domain of chromosome tethering proteins and the TET/JBP-like cytosine and thymine hydroxylases.
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Affiliation(s)
- Robson F. de Souza
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States of America
| | - Lakshminarayan M. Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States of America
| | - L. Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States of America
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47
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Lopes A, Amarir-Bouhram J, Faure G, Petit MA, Guerois R. Detection of novel recombinases in bacteriophage genomes unveils Rad52, Rad51 and Gp2.5 remote homologs. Nucleic Acids Res 2010; 38:3952-62. [PMID: 20194117 PMCID: PMC2896510 DOI: 10.1093/nar/gkq096] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Homologous recombination is a key in contributing to bacteriophages genome repair, circularization and replication. No less than six kinds of recombinase genes have been reported so far in bacteriophage genomes, two (UvsX and Gp2.5) from virulent, and four (Sak, Redβ, Erf and Sak4) from temperate phages. Using profile–profile comparisons, structure-based modelling and gene-context analyses, we provide new views on the global landscape of recombinases in 465 bacteriophages. We show that Sak, Redβ and Erf belong to a common large superfamily adopting a shortcut Rad52-like fold. Remote homologs of Sak4 are predicted to adopt a shortcut Rad51/RecA fold and are discovered widespread among phage genomes. Unexpectedly, within temperate phages, gene-context analyses also pinpointed the presence of distant Gp2.5 homologs, believed to be restricted to virulent phages. All in all, three major superfamilies of phage recombinases emerged either related to Rad52-like, Rad51-like or Gp2.5-like proteins. For two newly detected recombinases belonging to the Sak4 and Gp2.5 families, we provide experimental evidence of their recombination activity in vivo. Temperate versus virulent lifestyle together with the importance of genome mosaicism is discussed in the light of these novel recombinases. Screening for these recombinases in genomes can be performed at http://biodev.extra.cea.fr/virfam.
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Affiliation(s)
- Anne Lopes
- CEA, iBiTecS, F-91191 Gif sur Yvette, France
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48
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Solomun T, Seitz H, Sturm H. DNA damage by low-energy electron impact: dependence on guanine content. J Phys Chem B 2010; 113:11557-9. [PMID: 19645513 DOI: 10.1021/jp905263x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Single-stranded DNA oligonucleotides (33-mers) containing different numbers of guanines (n=1-4) were tethered to a gold surface and exposed to 1 eV electrons. The electrons induced DNA damage, which was analyzed with fluorescence and infrared spectroscopy methods. The damage was identified as strand breaks and found to correlate linearly with the number of guanines in the sequence. This sequence dependence indicates that the electron capture by the DNA bases plays an important role in the damage reaction mechanism.
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Affiliation(s)
- T Solomun
- Institute of Chemistry and Biochemistry, Free University Berlin, Takustrasse 3, D-14195 Berlin, Germany.
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49
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Szczepańska AK. Bacteriophage-encoded functions engaged in initiation of homologous recombination events. Crit Rev Microbiol 2010; 35:197-220. [PMID: 19563302 DOI: 10.1080/10408410902983129] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Recombination plays a significant role in bacteriophage biology. Functions promoting recombination are involved in key stages of phage multiplication and drive phage evolution. Their biological role is reflected by the great variety of phages existing in the environment. This work presents the role of recombination in the phage life cycle and highlights the discrete character of phage-encoded recombination functions (anti-RecBCD activities, 5' --> 3' DNA exonucleases, single-stranded DNA binding proteins, single-stranded DNA annealing proteins, and recombinases). The focus of this review is on phage proteins that initiate genetic exchange. Importance of recombination is reviewed based on the accepted coli-phages T4 and lambda models, the recombination system of phage P22, and the recently characterized recombination functions of Bacillus subtilis phage SPP1 and mycobacteriophage Che9c. Key steps of the molecular mechanisms involving phage recombination functions and their application in molecular engineering are discussed.
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Affiliation(s)
- Agnieszka K Szczepańska
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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50
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Jeong YJ, Park K, Kim DE. Isothermal DNA amplification in vitro: the helicase-dependent amplification system. Cell Mol Life Sci 2009; 66:3325-36. [PMID: 19629390 PMCID: PMC11115679 DOI: 10.1007/s00018-009-0094-3] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Revised: 06/26/2009] [Accepted: 07/01/2009] [Indexed: 01/27/2023]
Abstract
Since the development of polymerase chain reaction, amplification of nucleic acids has emerged as an elemental tool for molecular biology, genomics, and biotechnology. Amplification methods often use temperature cycling to exponentially amplify nucleic acids; however, isothermal amplification methods have also been developed, which do not require heating the double-stranded nucleic acid to dissociate the synthesized products from templates. Among the several methods used for isothermal DNA amplification, the helicase-dependent amplification (HDA) is discussed in this review with an emphasis on the reconstituted DNA replication system. Since DNA helicase can unwind the double-stranded DNA without the need for heating, the HDA system provides a very useful tool to amplify DNA in vitro under isothermal conditions with a simplified reaction scheme. This review describes components and detailed aspects of current HDA systems using Escherichia coli UvrD helicase and T7 bacteriophage gp4 helicase with consideration of the processivity and efficiency of DNA amplification.
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Affiliation(s)
- Yong-Joo Jeong
- Department of Bio and Nanochemistry, Kookmin University, 861-1 Jeongneung-dong, Seongbuk-gu, Seoul, 136-702 Republic of Korea
| | - Kkothanahreum Park
- Department of Bioscience and Biotechnology, Konkuk University, 1 Hwayang-dong, Gwanjin-gu, Seoul, 143-701 Republic of Korea
| | - Dong-Eun Kim
- Department of Bioscience and Biotechnology, Konkuk University, 1 Hwayang-dong, Gwanjin-gu, Seoul, 143-701 Republic of Korea
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