1
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Shibata T, Ikawa S, Iwasaki W, Sasanuma H, Masai H, Hirota K. Homology recognition without double-stranded DNA-strand separation in D-loop formation by RecA. Nucleic Acids Res 2024; 52:2565-2577. [PMID: 38214227 PMCID: PMC10954442 DOI: 10.1093/nar/gkad1260] [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: 12/30/2023] [Indexed: 01/13/2024] Open
Abstract
RecA protein and RecA/Rad51 orthologues are required for homologous recombination and DNA repair in all living creatures. RecA/Rad51 catalyzes formation of the D-loop, an obligatory recombination intermediate, through an ATP-dependent reaction consisting of two phases: homology recognition between double-stranded (ds)DNA and single-stranded (ss)DNA to form a hybrid-duplex core of 6-8 base pairs and subsequent hybrid-duplex/D-loop processing. How dsDNA recognizes homologous ssDNA is controversial. The aromatic residue at the tip of the β-hairpin loop (L2) was shown to stabilize dsDNA-strand separation. We tested a model in which dsDNA strands were separated by the aromatic residue before homology recognition and found that the aromatic residue was not essential to homology recognition, but was required for D-loop processing. Contrary to the model, we found that the double helix was not unwound even a single turn during search for sequence homology, but rather was unwound only after the homologous sequence was recognized. These results suggest that dsDNA recognizes its homologous ssDNA before strand separation. The search for homologous sequence with homologous ssDNA without dsDNA-strand separation does not generate stress within the dsDNA; this would be an advantage for dsDNA to express homology-dependent functions in vivo and also in vitro.
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Affiliation(s)
- Takehiko Shibata
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami Ohsawa, Hachioji, Tokyo 192-0397, Japan
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
- Cellular & Molecular Biology Laboratory, RIKEN, Wako-shi, Saitama 351-0198, Japan
| | - Shukuko Ikawa
- Cellular & Molecular Biology Laboratory, RIKEN, Wako-shi, Saitama 351-0198, Japan
| | - Wakana Iwasaki
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroyuki Sasanuma
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Hisao Masai
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami Ohsawa, Hachioji, Tokyo 192-0397, Japan
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2
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Wang G, Li J. Review, analysis, and optimization of the CRISPR Streptococcus pyogenes Cas9 system. MEDICINE IN DRUG DISCOVERY 2021. [DOI: 10.1016/j.medidd.2021.100080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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3
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Shibata T, Iwasaki W, Hirota K. The intrinsic ability of double-stranded DNA to carry out D-loop and R-loop formation. Comput Struct Biotechnol J 2020; 18:3350-3360. [PMID: 33294131 PMCID: PMC7677664 DOI: 10.1016/j.csbj.2020.10.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/22/2020] [Accepted: 10/25/2020] [Indexed: 12/03/2022] Open
Abstract
Double-stranded (ds)DNA, not dsRNA, has an ability to form a homologous complex with single-stranded (ss)DNA or ssRNA of homologous sequence. D-loops and homologous triplexes are homologous complexes formed with ssDNA by RecA/Rad51-family homologous-pairing proteins, and are a key intermediate of homologous (genetic/DNA) recombination. R-loop formation independent of transcription (R-loop formation in trans) was recently found to play roles in gene regulation and development of mammals and plants. In addition, the crRNA-Cas effector complex in CRISPR-Cas systems also relies on R-loop formation to recognize specific target. In homologous complex formation, ssDNA/ssRNA finds a homologous sequence in dsDNA by Watson-Crick base-pairing. crRNA-Cas effector complexes appear to actively melt dsDNA to make its bases available for annealing to crRNA. On the other hand, in D-loop formation and homologous-triplex formation, it is likely that dsDNA recognizes the homologous sequence before the melting of its double helix by using its intrinsic molecular function depending on CH2 at the 2'-position of the deoxyribose, and that the major role of RecA is the extension of ssDNA and the holding dsDNA at a position suitable for homology search. This intrinsic dsDNA function would also play a role in R-loop formation. The dependency of homologous-complex formation on 2'-CH2 of the deoxyribose would explain the absence of homologous complex formation by dsRNA, and dsDNA as sole genome molecule in all cellular organisms.
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Affiliation(s)
- Takehiko Shibata
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Wakana Iwasaki
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Tsurumi, Yokohama, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
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4
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Knadler C, Rolfsmeier M, Vallejo A, Haseltine C. Characterization of an archaeal recombinase paralog that exhibits novel anti-recombinase activity. Mutat Res 2020; 821:111703. [PMID: 32416400 DOI: 10.1016/j.mrfmmm.2020.111703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/01/2020] [Indexed: 01/31/2023]
Abstract
The process of homologous recombination is heavily dependent on the RecA family of recombinases for repair of DNA double-strand breaks. These recombinases are responsible for identifying homologies and forming heteroduplex DNA between substrate ssDNA and dsDNA templates, activities that are modified by various accessory factors. In this work we describe the biochemical functions of the SsoRal2 recombinase paralog from the crenarchaeon Sulfolobus solfataricus. We found that the SsoRal2 protein is a DNA-independent ATPase that, unlike the other S. solfataricus paralogs, does not bind either ss- or dsDNA. Instead, SsoRal2 alters the ssDNA binding activity of the SsoRadA recombinase in conjunction with another paralog, SsoRal1. In the presence of SsoRal1, SsoRal2 has a modest effect on strand invasion but effectively abrogates strand exchange activity. Taken together, these results indicate that SsoRal2 assists in nucleoprotein filament modulation and control of strand exchange in S. solfataricus.
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Affiliation(s)
- Corey Knadler
- Washington State University, Biotech/LifeSciences Rm 137, Pullman, 99164, United States
| | - Michael Rolfsmeier
- Washington State University, Biotech/LifeSciences Rm 137, Pullman, 99164, United States
| | - Antonia Vallejo
- Washington State University, Biotech/LifeSciences Rm 137, Pullman, 99164, United States
| | - Cynthia Haseltine
- Washington State University, Biotech/LifeSciences Rm 137, Pullman, 99164, United States.
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5
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Chang Y, Shao J, Gao Y, Liu W, Gao Z, Hu Y, Chang H. Reporter gene knock-in into Marc-145 cells using CRISPR/Cas9-mediated homologous recombination. Biotechnol Lett 2020; 42:1317-1325. [PMID: 32185620 DOI: 10.1007/s10529-020-02860-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/06/2020] [Indexed: 12/31/2022]
Abstract
OBJECTIVES Marc-145 cells (monkey embryonic kidney epithelial cells) play a critical role in the biotechnology industry as certain virus host cells. To investigate the expression of enhanced green fluorescent protein (eGFP) gene as a foreign gene in Marc-145 cells, which we developed an approach of foreign gene site-specific knock-in into Marc-145 cells by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) and putatively explored appropriate genomic recombination sites in Marc-145 cells. RESULTS Our study demonstrated that the specific homologous recombination (HR) site between the Rac GTPase activating protein 1 (RACGAP1) and the acid-sensing ion channel subunit 1 (ASIC1) genes of the 11th chromosome could be used as the target site of Cas9 for the generation of target gene knock-in into Marc-145 cells, by the insertion of the eGFP cassette into the specific HR site and subsequent expression. CONCLUSIONS Junction PCR, sequencing, Southern blot and fluorescence assay determined eGFP gene-specific knock-in HR site between the RACGAP1 and ASIC1 genes of the 11th chromosome, which was identified by the genomic safe harbours in Marc-145 cells. Our study encouraged a broader range of applications, such as Marc-145 cells development and engineering for virus adaption and yield increase in the vaccine biotechnology industry.
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Affiliation(s)
- Yanyan Chang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, Gansu, China
| | - Junjun Shao
- State Key Laboratory of Veterinary Etiological Biology, OIE/China National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, China
| | - Yuan Gao
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, Gansu, China
| | - Wei Liu
- State Key Laboratory of Veterinary Etiological Biology, OIE/China National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, China
| | - Zhan Gao
- State Key Laboratory of Veterinary Etiological Biology, OIE/China National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, China
| | - Yonghao Hu
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, Gansu, China.
| | - Huiyun Chang
- State Key Laboratory of Veterinary Etiological Biology, OIE/China National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, China.
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6
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Miné-Hattab J, Taddei A. Physical principles and functional consequences of nuclear compartmentalization in budding yeast. Curr Opin Cell Biol 2019; 58:105-113. [PMID: 30928833 DOI: 10.1016/j.ceb.2019.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/28/2019] [Accepted: 02/20/2019] [Indexed: 12/19/2022]
Abstract
One striking feature of eukaryotic nuclei is the existence of discrete regions, in which specific factors concentrate while others are excluded, thus forming microenvironments with different molecular compositions and biological functions. These domains are often referred to as subcompartments even though they are not membrane enclosed. Despite their functional importance the physical nature of these structures remains largely unknown. Here, we describe how the Saccharomyces cerevisiae nucleus is compartmentalized and discuss possible physical models underlying the formation and maintenance of chromatin associated subcompartments. Focusing on three particular examples, the nucleolus, silencing foci, and repair foci, we discuss the biological implications of these different models as well as possible approaches to challenge them in living cells.
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Affiliation(s)
- Judith Miné-Hattab
- Institut Curi-PSL Research University, CNRS, Sorbonne Université, UMR3664, F-75005, Paris, France
| | - Angela Taddei
- Institut Curi-PSL Research University, CNRS, Sorbonne Université, UMR3664, F-75005, Paris, France.
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7
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Chen J, Tang Q, Guo S, Lu C, Le S, Yan J. Parallel triplex structure formed between stretched single-stranded DNA and homologous duplex DNA. Nucleic Acids Res 2017; 45:10032-10041. [PMID: 28973442 PMCID: PMC5622322 DOI: 10.1093/nar/gkx628] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 07/11/2017] [Indexed: 02/01/2023] Open
Abstract
The interaction between the single-stranded DNA and the homologous duplex DNA is essential for DNA homologous repair. Here, we report that parallel triplex structure can form spontaneously between a mechanically extended ssDNA and a homologous dsDNA in protein-free condition. The triplex has a contour length close to that of a B-form DNA duplex and remains stable after force is released. The binding energy between the ssDNA and the homologous dsDNA in the triplex is estimated to be comparable to the basepairing energy in a B-form dsDNA. As ssDNA is in a similar extended conformation within recombinase-coated nucleoprotein filaments, we propose that the parallel triplex may form and serve as an intermediate during recombinase-catalyzed homologous joint formation.
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Affiliation(s)
- Jin Chen
- Mechanobiology Institute, National University of Singapore, 117411, Singapore
| | - Qingnan Tang
- Department of Physics, National University of Singapore, 117542, Singapore
| | - Shiwen Guo
- Mechanobiology Institute, National University of Singapore, 117411, Singapore
| | - Chen Lu
- Mechanobiology Institute, National University of Singapore, 117411, Singapore.,Centre for Bioimaging Sciences, National University of Singapore, 117546, Singapore
| | - Shimin Le
- Mechanobiology Institute, National University of Singapore, 117411, Singapore.,Department of Physics, National University of Singapore, 117542, Singapore
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, 117411, Singapore.,Department of Physics, National University of Singapore, 117542, Singapore.,Centre for Bioimaging Sciences, National University of Singapore, 117546, Singapore
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8
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Shao S, Ren C, Liu Z, Bai Y, Chen Z, Wei Z, Wang X, Zhang Z, Xu K. Enhancing CRISPR/Cas9-mediated homology-directed repair in mammalian cells by expressing Saccharomyces cerevisiae Rad52. Int J Biochem Cell Biol 2017; 92:43-52. [DOI: 10.1016/j.biocel.2017.09.012] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 09/09/2017] [Accepted: 09/15/2017] [Indexed: 12/01/2022]
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9
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Jha JK, Ramachandran R, Chattoraj DK. Opening the Strands of Replication Origins-Still an Open Question. Front Mol Biosci 2016; 3:62. [PMID: 27747216 PMCID: PMC5043065 DOI: 10.3389/fmolb.2016.00062] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 09/16/2016] [Indexed: 11/22/2022] Open
Abstract
The local separation of duplex DNA strands (strand opening) is necessary for initiating basic transactions on DNA such as transcription, replication, and homologous recombination. Strand opening is commonly a stage at which these processes are regulated. Many different mechanisms are used to open the DNA duplex, the details of which are of great current interest. In this review, we focus on a few well-studied cases of DNA replication origin opening in bacteria. In particular, we discuss the opening of origins that support the theta (θ) mode of replication, which is used by all chromosomal origins and many extra-chromosomal elements such as plasmids and phages. Although the details of opening can vary among different origins, a common theme is binding of the initiator to multiple sites at the origin, causing stress that opens an adjacent and intrinsically unstable A+T rich region. The initiator stabilizes the opening by capturing one of the open strands. How the initiator binding energy is harnessed for strand opening remains to be understood.
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Affiliation(s)
- Jyoti K Jha
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda, MD, USA
| | - Revathy Ramachandran
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda, MD, USA
| | - Dhruba K Chattoraj
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda, MD, USA
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10
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Peng Y, Feng Y, Deng GJ, He YM, Fan QH. From Weakness to Strength: C-H/π-Interaction-Guided Self-Assembly and Gelation of Poly(benzyl ether) Dendrimers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:9313-9320. [PMID: 27538342 DOI: 10.1021/acs.langmuir.6b02672] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The C-H/π interactions as the key driving force for the construction of supramolecular gels remain a great challenge because of their weak nature. We hereby employed for the first time weak C-H/π interactions for the construction of supramolecular dendritic gels based on peripherally methyl-functionalized poly(benzyl ether) dendrimers. Their gelation property is highly dependent on the nature of the peripheral methyl groups. Furthermore, single-crystal X-ray analysis and NMR spectroscopy revealed that multiple C-H/π interactions between the proton of the methyl group and the electron-rich peripheral methyl-substituted aryl ring played significant roles in the formation of supramolecular nanofibers and organogels. This study uncovers the critical role of weak noncovalent interactions and provides new insights into the further design of self-assembled nanomaterials.
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Affiliation(s)
- Yi Peng
- Beijing National Laboratory for Molecule Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University , Xiangtan 411105, China
| | - Yu Feng
- Beijing National Laboratory for Molecule Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Guo-Jun Deng
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University , Xiangtan 411105, China
| | - Yan-Mei He
- Beijing National Laboratory for Molecule Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Qing-Hua Fan
- Beijing National Laboratory for Molecule Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
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11
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He Y, Wang M, Sun Q, Pawlowski WP. Mapping Recombination Initiation Sites Using Chromatin Immunoprecipitation. Methods Mol Biol 2016; 1429:177-88. [PMID: 27511175 DOI: 10.1007/978-1-4939-3622-9_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Genome-wide maps of recombination sites provide valuable information not only on the recombination pathway itself but also facilitate the understanding of genome dynamics and evolution. Here, we describe a chromatin immunoprecipitation (ChIP) protocol to map the sites of recombination initiation in plants with maize used as an example. ChIP is a method that allows identification of chromosomal sites occupied by specific proteins. Our protocol utilizes RAD51, a protein involved in repair of double-strand breaks (DSBs) that initiate meiotic recombination, to identify DSB formation hotspots. Chromatin is extracted from meiotic flowers, sheared and enriched in fragments bound to RAD51. Genomic location of the protein is then identified by next-generation sequencing. This protocol can also be used in other species of plants, animals, and fungi.
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Affiliation(s)
- Yan He
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100083, China
| | - Minghui Wang
- Institute of Biotechnology, Biotechnology Resource Center and Section of Plant Biology in School of IntegrativePlant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Qi Sun
- Institute of Biotechnology, Biotechnology Resource Center, Cornell University, Ithaca, NY, 14853, USA
| | - Wojciech P Pawlowski
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
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12
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Kikukawa H, Sakuradani E, Ando A, Okuda T, Ochiai M, Shimizu S, Ogawa J. Disruption of lig4 improves gene targeting efficiency in the oleaginous fungus Mortierella alpina 1S-4. J Biotechnol 2015; 208:63-9. [PMID: 26052021 DOI: 10.1016/j.jbiotec.2015.05.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/19/2015] [Accepted: 05/29/2015] [Indexed: 11/28/2022]
Abstract
The oil-producing zygomycete Mortierella alpina 1S-4 is known to accumulate beneficial polyunsaturated fatty acids. We identified the lig4 gene that encodes for a DNA ligase 4 homolog, which functions to repair double strand breaks by non-homologous end joining. We disrupted the lig4 gene to improve the gene targeting efficiency in M. alpina. The M. alpina 1S-4 Δlig4 strains showed no defect in vegetative growth, formation of spores, and fatty acid production, but exhibited high sensitivity to methyl methansulfonate, an agent that causes DNA double-strand breaks. Importantly, gene replacement of ura5 marker by CBXB marker occurred in 67% of Δlig4 strains and the gene targeting efficiency was 21-fold greater than that observed in disruption of the lig4 gene in the M. alpina 1S-4 host strain. Further metabolic engineering of the Δlig4 strains is expected to result in strains that produce higher levels of rare and beneficial polyunsaturated fatty acids and contribute to basic research on the zygomycete.
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Affiliation(s)
- Hiroshi Kikukawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Eiji Sakuradani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan; Institute of Technology and Science, Tokushima University, 2-1 Minami-Josanjima, Tokushima 770-8506, Japan
| | - Akinori Ando
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan; Research Unit for Physiological Chemistry, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Tomoyo Okuda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Misa Ochiai
- Research Institute, Suntory Global Innovation Center Ltd., 1-1-1 Wakayamadai, Shimamoto-cho, Mishima-gun, Osaka 618-8503, Japan
| | - Sakayu Shimizu
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan; Department of Bioscience and Biotechnology, Faculty of Bioenvironmental Science, Kyoto Gakuen University, 1-1 Nanjo, Sogabe, Kameoka 621-8555, Japan
| | - Jun Ogawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan; Research Unit for Physiological Chemistry, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
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13
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Kikukawa H, Sakuradani E, Nakatani M, Ando A, Okuda T, Sakamoto T, Ochiai M, Shimizu S, Ogawa J. Gene targeting in the oil-producing fungus Mortierella alpina 1S-4 and construction of a strain producing a valuable polyunsaturated fatty acid. Curr Genet 2015; 61:579-89. [PMID: 25782448 DOI: 10.1007/s00294-015-0481-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/26/2015] [Accepted: 02/28/2015] [Indexed: 11/26/2022]
Abstract
To develop an efficient gene-targeting system in Mortierella alpina 1S-4, we identified the ku80 gene encoding the Ku80 protein, which is involved in the nonhomologous end-joining pathway in genomic double-strand break (DSB) repair, and constructed ku80 gene-disrupted strains via single-crossover homologous recombination. The Δku80 strain from M. alpina 1S-4 showed no negative effects on vegetative growth, formation of spores, and fatty acid productivity, and exhibited high sensitivity to methyl methanesulfonate, which causes DSBs. Dihomo-γ-linolenic acid (DGLA)-producing strains were constructed by disruption of the Δ5-desaturase gene, encoding a key enzyme of bioconversion of DGLA to ARA, using the Δku80 strain as a host strain. The significant improvement of gene-targeting efficiency was not observed by disruption of the ku80 gene, but the construction of DGLA-producing strain by disruption of the Δ5-desaturase gene was succeeded using the Δku80 strain as a host strain. This report describes the first study on the identification and disruption of the ku80 gene in zygomycetes and construction of a DGLA-producing transformant using a gene-targeting system in M. alpina 1S-4.
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Affiliation(s)
- Hiroshi Kikukawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Eiji Sakuradani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
- Institute of Technology and Science, Tokushima University, 2-1 Minami-josanjima, Tokushima, 770-8506, Japan
| | - Masato Nakatani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Akinori Ando
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
- Research Unit for Physiological Chemistry, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tomoyo Okuda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Takaiku Sakamoto
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Misa Ochiai
- Research Institute, Suntory Global Innovation Center Ltd., 1-1-1 Wakayamadai, Shimamoto-cho, Mishima-gun, Osaka, 618-8503, Japan
| | - Sakayu Shimizu
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
- Department of Bioscience and Biotechnology, Faculty of Bioenvironmental Science, Kyoto Gakuen University, 1-1 Nanjo, Sogabe, Kameoka, 621-8555, Japan
| | - Jun Ogawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.
- Research Unit for Physiological Chemistry, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.
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14
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Shinohara T, Ikawa S, Iwasaki W, Hiraki T, Hikima T, Mikawa T, Arai N, Kamiya N, Shibata T. Loop L1 governs the DNA-binding specificity and order for RecA-catalyzed reactions in homologous recombination and DNA repair. Nucleic Acids Res 2015; 43:973-86. [PMID: 25561575 PMCID: PMC4333409 DOI: 10.1093/nar/gku1364] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 12/14/2014] [Accepted: 12/18/2014] [Indexed: 11/16/2022] Open
Abstract
In all organisms, RecA-family recombinases catalyze homologous joint formation in homologous genetic recombination, which is essential for genome stability and diversification. In homologous joint formation, ATP-bound RecA/Rad51-recombinases first bind single-stranded DNA at its primary site and then interact with double-stranded DNA at another site. The underlying reason and the regulatory mechanism for this conserved binding order remain unknown. A comparison of the loop L1 structures in a DNA-free RecA crystal that we originally determined and in the reported DNA-bound active RecA crystals suggested that the aspartate at position 161 in loop L1 in DNA-free RecA prevented double-stranded, but not single-stranded, DNA-binding to the primary site. This was confirmed by the effects of the Ala-replacement of Asp-161 (D161A), analyzed directly by gel-mobility shift assays and indirectly by DNA-dependent ATPase activity and SOS repressor cleavage. When RecA/Rad51-recombinases interact with double-stranded DNA before single-stranded DNA, homologous joint-formation is suppressed, likely by forming a dead-end product. We found that the D161A-replacement reduced this suppression, probably by allowing double-stranded DNA to bind preferentially and reversibly to the primary site. Thus, Asp-161 in the flexible loop L1 of wild-type RecA determines the preference for single-stranded DNA-binding to the primary site and regulates the DNA-binding order in RecA-catalyzed recombinase reactions.
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Affiliation(s)
- Takeshi Shinohara
- Cellular & Molecular Biology Unit, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama 351-0198, Japan Department of Supramolecular Biology, Graduate School of Nanobiosciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shukuko Ikawa
- Cellular & Molecular Biology Unit, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama 351-0198, Japan
| | - Wakana Iwasaki
- Cellular & Molecular Biology Unit, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Toshiki Hiraki
- Advanced Photon Technology Division, Research Infrastructure Group, RIKEN SPring-8 Center, RIKEN Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Takaaki Hikima
- Advanced Photon Technology Division, Research Infrastructure Group, RIKEN SPring-8 Center, RIKEN Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Tsutomu Mikawa
- Cellular & Molecular Biology Unit, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Naoto Arai
- Department of Applied Biological Science, Nihon University College of Bioresource Sciences, 1866 Kameino, Fujisawa-shi, Kanagawa 252-8510, Japan
| | - Nobuo Kamiya
- Advanced Photon Technology Division, Research Infrastructure Group, RIKEN SPring-8 Center, RIKEN Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Takehiko Shibata
- Cellular & Molecular Biology Unit, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama 351-0198, Japan Department of Supramolecular Biology, Graduate School of Nanobiosciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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15
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Zhao C, Li P, Smith MD, Pellechia PJ, Shimizu KD. Experimental Study of the Cooperativity of CH−π Interactions. Org Lett 2014; 16:3520-3. [DOI: 10.1021/ol5014729] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Chen Zhao
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ping Li
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Mark D. Smith
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Perry J. Pellechia
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ken D. Shimizu
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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16
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Simultaneous Use of MutS and RecA for Suppression of Nonspecific Amplification during PCR. J Nucleic Acids 2013; 2013:823730. [PMID: 23970956 PMCID: PMC3736406 DOI: 10.1155/2013/823730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 06/21/2013] [Indexed: 11/25/2022] Open
Abstract
Thermus thermophilus MutS, a thermostable mismatch-recognizing protein, is utilized in PCR to suppress nonspecific amplification by preventing synthesis from mismatched primers. T. thermophilus RecA also decreases nonspecific amplification by promoting proper hybridization between the primer and template. We observed that MutS and RecA function under the same reaction conditions and that MutS and RecA do not preclude each other. Furthermore, there were some DNA sequences for which only one of the 2 proteins effectively suppressed nonspecific amplification. The simultaneous use of MutS and RecA is a more attractive error-suppressing technique than the use of either of the 2 proteins alone.
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17
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An archaeal RadA paralog influences presynaptic filament formation. DNA Repair (Amst) 2013; 12:403-13. [PMID: 23622866 DOI: 10.1016/j.dnarep.2013.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 02/28/2013] [Accepted: 03/02/2013] [Indexed: 11/24/2022]
Abstract
Recombinases of the RecA family play vital roles in homologous recombination, a high-fidelity mechanism to repair DNA double-stranded breaks. These proteins catalyze strand invasion and exchange after forming dynamic nucleoprotein filaments on ssDNA. Increasing evidence suggests that stabilization of these dynamic filaments is a highly conserved function across diverse species. Here, we analyze the presynaptic filament formation and DNA binding characteristics of the Sulfolobus solfataricus recombinase SsoRadA in conjunction with the SsoRadA paralog SsoRal1. In addition to constraining SsoRadA ssDNA-dependent ATPase activity, the paralog also enhances SsoRadA ssDNA binding, effectively influencing activities necessary for presynaptic filament formation. These activities result in enhanced SsoRadA-mediated strand invasion in the presence of SsoRal1 and suggest a filament stabilization function for the SsoRal1 protein.
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18
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Kimura Y, Goto Y, Oana H, Washizu M. Optical sequence probing with the homologous recombination protein RecA. J Biotechnol 2013; 164:254-9. [DOI: 10.1016/j.jbiotec.2012.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 07/23/2012] [Accepted: 08/19/2012] [Indexed: 12/01/2022]
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19
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He Y, Sidhu G, Pawlowski WP. Chromatin immunoprecipitation for studying chromosomal localization of meiotic proteins in maize. Methods Mol Biol 2013; 990:191-201. [PMID: 23559215 DOI: 10.1007/978-1-62703-333-6_19] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Chromatin immunoprecipitation (ChIP) is a method that allows identification of chromosomal sites occupied by specific proteins. In this technique, chromatin is extracted from cells, sheared, and, using a specific antibody, enriched in fragments that contain a protein of interest. Genomic location of the protein can then be identified by hybridization of the resulting DNA to tiling microarrays or by sequencing. Thanks to advances in high-throughput sequencing methods, studying protein localization using ChIP has become possible even in species with relatively large genomes. Here, we describe a ChIP protocol that we developed to examine localization of meiotic proteins in maize.
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Affiliation(s)
- Yan He
- Cornell University, Ithaca, NY, USA
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20
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Graham WJ, Haseltine CA. A recombinase paralog from the hyperthermophilic crenarchaeon Sulfolobus solfataricus enhances SsoRadA ssDNA binding and strand displacement. Gene 2012; 515:128-39. [PMID: 23220019 DOI: 10.1016/j.gene.2012.11.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 11/14/2012] [Accepted: 11/19/2012] [Indexed: 11/16/2022]
Abstract
Homologous recombination (HR) is a major pathway for the repair of double-strand DNA breaks, a highly deleterious form of DNA damage. The main catalytic protein in HR is the essential RecA-family recombinase, which is conserved across all three domains of life. Eukaryotes and archaea encode varying numbers of proteins paralogous to their main recombinase. Although there is increasing evidence for the functions of some of these paralog proteins, overall their mechanism of action remains largely unclear. Here we present the first biochemical characterization of one of the paralog proteins, SsoRal3, from the crenarchaeaon Sulfolobus solfataricus. The SsoRal3 protein is a ssDNA-dependent ATPase that can catalyze strand invasion at both saturating and subsaturating concentrations. It can bind both ssDNA and dsDNA, but its binding preference is altered by the presence or absence of ATP. Addition of SsoRal3 to SsoRadA nucleoprotein filaments reduces total ATPase activity. Subsaturating concentrations of SsoRal3 increase the ssDNA binding activity of SsoRadA approximately 9-fold and also increase the persistence of SsoRadA catalyzed strand invasion products. Overall, these results suggest that SsoRal3 functions to stabilize the SsoRadA presynaptic filament.
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Affiliation(s)
- William J Graham
- School of Molecular Biosciences, Washington State University, Pullman, WA 99163, USA
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21
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Wilce J, Vivian J, Wilce M. Oligonucleotide binding proteins: the occurrence of dimer and multimer formation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 747:91-104. [PMID: 22949113 DOI: 10.1007/978-1-4614-3229-6_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Protein dimers and multimers are often employed by nature for DNA and RNA handling and formation of specific, high-affinity protein-oligonucleotide complexes. The repeating structure of dsDNA lends itself to recognition by multimeric protein complexes that can assemble about the helical structure. In the cases of both DNA and RNA, specific recognition of nucleotide sequences can be achieved by multidomain proteins or protein multimers. Furthermore large multimeric assemblies are utilised for the stable formation of structures such as rings and filaments. Also, the assembly of multimeric structures by interchangeable subunits can add layers of regulation and increase functional complexity. Thus there appear to be many advantages to oligonucleotide interactions that are conferred by dimerisation or multimerisation.
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Affiliation(s)
- Jackie Wilce
- Department of Biochemistry and Molecular Biology, and School of Biomedical Sciences, Monash Univerity, Melbourne, Victoria, Australia.
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22
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Algebraic distribution of segmental duplication lengths in whole-genome sequence self-alignments. PLoS One 2011; 6:e18464. [PMID: 21779315 PMCID: PMC3136455 DOI: 10.1371/journal.pone.0018464] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 03/08/2011] [Indexed: 01/25/2023] Open
Abstract
Distributions of duplicated sequences from genome self-alignment are characterized, including forward and backward alignments in bacteria and eukaryotes. A Markovian process without auto-correlation should generate an exponential distribution expected from local effects of point mutation and selection on localised function; however, the observed distributions show substantial deviation from exponential form – they are roughly algebraic instead – suggesting a novel kind of long-distance correlation that must be non-local in origin.
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23
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Zhang Z, Luo Y, Chen J, Dong S, Yu Y, Ma Z, Huang F. Formation of Linear Supramolecular Polymers That Is Driven by CH⋅⋅⋅π Interactions in Solution and in the Solid State. Angew Chem Int Ed Engl 2011; 50:1397-401. [DOI: 10.1002/anie.201006693] [Citation(s) in RCA: 656] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 11/18/2010] [Indexed: 11/11/2022]
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24
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Zhang Z, Luo Y, Chen J, Dong S, Yu Y, Ma Z, Huang F. Formation of Linear Supramolecular Polymers That Is Driven by CH⋅⋅⋅π Interactions in Solution and in the Solid State. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201006693] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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25
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Masuda T, Ito Y, Terada T, Shibata T, Mikawa T. A non-canonical DNA structure enables homologous recombination in various genetic systems. J Biol Chem 2009; 284:30230-9. [PMID: 19729448 DOI: 10.1074/jbc.m109.043810] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Homologous recombination, which is critical to genetic diversity, depends on homologous pairing (HP). HP is the switch from parental to recombinant base pairs, which requires expansion of inter-base pair spaces. This expansion unavoidably causes untwisting of the parental double-stranded DNA. RecA/Rad51-catalyzed ATP-dependent HP is extensively stimulated in vitro by negative supercoils, which compensates for untwisting. However, in vivo, double-stranded DNA is relaxed by bound proteins and thus is an unfavorable substrate for RecA/Rad51. In contrast, Mhr1, an ATP-independent HP protein required for yeast mitochondrial homologous recombination, catalyzes HP without the net untwisting of double-stranded DNA. Therefore, we questioned whether Mhr1 uses a novel strategy to promote HP. Here, we found that, like RecA, Mhr1 induced the extension of bound single-stranded DNA. In addition, this structure was induced by all evolutionarily and structurally distinct HP proteins so far tested, including bacterial RecO, viral RecT, and human Rad51. Thus, HP includes the common non-canonical DNA structure and uses a common core mechanism, independent of the species of HP proteins. We discuss the significance of multiple types of HP proteins.
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Affiliation(s)
- Tokiha Masuda
- Graduate School of Nanobioscience, Yokohama City University, Yokohama 230-0045, USA
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26
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Watanabe K, Pacher M, Dukowic S, Schubert V, Puchta H, Schubert I. The STRUCTURAL MAINTENANCE OF CHROMOSOMES 5/6 complex promotes sister chromatid alignment and homologous recombination after DNA damage in Arabidopsis thaliana. THE PLANT CELL 2009; 21:2688-99. [PMID: 19737979 PMCID: PMC2768936 DOI: 10.1105/tpc.108.060525] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2008] [Revised: 07/13/2009] [Accepted: 08/24/2009] [Indexed: 05/18/2023]
Abstract
Sister chromatids are often arranged as incompletely aligned entities in interphase nuclei of Arabidopsis thaliana. The STRUCTURAL MAINTENANCE OF CHROMOSOMES (SMC) 5/6 complex, together with cohesin, is involved in double-strand break (DSB) repair by sister chromatid recombination in yeasts and mammals. Here, we analyzed the function of genes in Arabidopsis. The wild-type allele of SMC5 is essential for seed development. Each of the two SMC6 homologs of Arabidopsis is required for efficient repair of DNA breakage via intermolecular homologous recombination in somatic cells. Alignment of sister chromatids is enhanced transiently after X-irradiation (and mitomycin C treatment) in wild-type nuclei. In the smc5/6 mutants, the x-ray-mediated increase in sister chromatid alignment is much lower and delayed. The reduced S phase-established cohesion caused by a knockout mutation in one of the alpha-kleisin genes, SYN1, also perturbed enhancement of sister chromatid alignment after irradiation, suggesting that the S phase-established cohesion is a prerequisite for correct DSB-dependent cohesion. The radiation-sensitive51 mutant, deficient in heteroduplex formation during DSB repair, showed wild-type frequencies of sister chromatid alignment after X-irradiation, implying that the irradiation-mediated increase in sister chromatid alignment is a prerequisite for, rather than a consequence of, DNA strand exchange between sister chromatids. Our results suggest that the SMC5/6 complex promotes sister chromatid cohesion after DNA breakage and facilitates homologous recombination between sister chromatids.
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Affiliation(s)
- Koichi Watanabe
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Michael Pacher
- Botanical Institute II, University Karlsruhe, 76128 Karlsruhe, Germany
| | - Stefanie Dukowic
- Botanical Institute II, University Karlsruhe, 76128 Karlsruhe, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Holger Puchta
- Botanical Institute II, University Karlsruhe, 76128 Karlsruhe, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
- Address correspondence to
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27
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Bressan FF, De Bem THC, Perecin F, Lopes FL, Ambrosio CE, Meirelles FV, Miglino MA. Unearthing the roles of imprinted genes in the placenta. Placenta 2009; 30:823-34. [PMID: 19679348 DOI: 10.1016/j.placenta.2009.07.007] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Accepted: 07/22/2009] [Indexed: 11/17/2022]
Abstract
Mammalian fetal survival and growth are dependent on a well-established and functional placenta. Although transient, the placenta is the first organ to be formed during pregnancy and is responsible for important functions during development, such as the control of metabolism and fetal nutrition, gas and metabolite exchange, and endocrine control. Epigenetic marks and gene expression patterns in early development play an essential role in embryo and fetal development. Specifically, the epigenetic phenomenon known as genomic imprinting, represented by the non-equivalence of the paternal and maternal genome, may be one of the most important regulatory pathways involved in the development and function of the placenta in eutherian mammals. A lack of pattern or an imprecise pattern of genomic imprinting can lead to either embryonic losses or a disruption in fetal and placental development. Genetically modified animals present a powerful approach for revealing the interplay between gene expression and placental function in vivo and allow a single gene disruption to be analyzed, particularly focusing on its role in placenta function. In this paper, we review the recent transgenic strategies that have been successfully created in order to provide a better understanding of the epigenetic patterns of the placenta, with a special focus on imprinted genes. We summarize a number of phenotypes derived from the genetic manipulation of imprinted genes and other epigenetic modulators in an attempt to demonstrate that gene-targeting studies have contributed considerably to the knowledge of placentation and conceptus development.
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Affiliation(s)
- F F Bressan
- Department of Basic Sciences, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
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28
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Ling F, Yoshida M, Shibata T. Heteroduplex joint formation free of net topological change by Mhr1, a mitochondrial recombinase. J Biol Chem 2009; 284:9341-53. [PMID: 19193646 DOI: 10.1074/jbc.m900023200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Homologous pairing, an essential process for homologous recombination, is the formation of a heteroduplex joint by an invading single-stranded DNA tail and a complementary sequence within double-stranded DNA (dsDNA). The base rotation of the parental dsDNA, to switch from parental base pairs to heteroduplex ones with the invading single-stranded DNA, sterically requires vertical extension between adjacent base pairs, which inevitably induces untwisting of the dsDNA. RecA is a prototype of the RecA/Rad51/Dmc1 family proteins, which promote ATP-dependent homologous pairing in homologous DNA recombination in vivo, except in mitochondria. As predicted by the requirement for the untwisting, dsDNA bound to RecA is extended and untwisted, and homologous pairing by RecA in vitro is extensively stimulated by the negative supercoils of dsDNA substrates. D-loop formation in negatively supercoiled dsDNA, which serves as an assay for homologous pairing, is also catalyzed in an ATP-independent manner by proteins structurally unrelated to RecA, such as Mhr1. Mhr1 is required for yeast mitochondrial DNA recombination instead of RecA family proteins. Inconsistent with the topological requirements, tests for the effects of negative supercoils revealed that Mhr1 catalyzes homologous pairing with relaxed closed circular dsDNA much more efficiently than with negatively supercoiled dsDNA. Topological analyses indicated that neither the process nor the products of homologous pairing by Mhr1 involve a net topological change of closed circular dsDNA. This would be favorable for homologous recombination in mitochondria, where dsDNA is unlikely to be under topological stress toward unwinding. We propose a novel topological mechanism wherein Mhr1 induces untwisting without net topological change.
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Affiliation(s)
- Feng Ling
- Chemical Genetics Laboratory, RIKEN Advanced Science Institute, Hirosawa 2-1, Wako-city, Saitama 351-0198, Japan.
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29
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Nishio M, Umezawa Y, Honda K, Tsuboyama S, Suezawa H. CH/π hydrogen bonds in organic and organometallic chemistry. CrystEngComm 2009. [DOI: 10.1039/b902318f] [Citation(s) in RCA: 481] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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30
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Abstract
Brh2, the ortholog of the BRCA2 tumor suppressor in Ustilago maydis, works hand in hand with Rad51 to promote repair of DNA by homologous recombination. Previous studies established that Brh2 can stimulate DNA strand exchange by enabling Rad51 nucleoprotein filament formation on replication protein A-coated ssDNA. But, more recently, it was noted that Brh2 has an inherent DNA annealing activity, raising the notion that it might have roles in recombination in addition to or beyond the mediator function. Here, we found that Brh2 can autonomously promote the formation of D-loops in reactions with plasmid DNA and homologous single-stranded oligonucleotides. The reaction differs from that catalyzed by Rad51 in having no requirement for cofactors or preloading phase on ssDNA. D-loop formation was most effective when Brh2 was mixed with plasmid DNA before addition of single-stranded oligomer. D-loop formation catalyzed by Rad51 was also enhanced when Brh2 was premixed with plasmid DNA. Brh2 rendered defective in Rad51 interaction by mutation in the BRC element was still capable of promoting D-loop formation. However, the mutant protein was unable to enhance the Rad51-catalyzed reaction. The results suggest a model in which Brh2 binding to plasmid DNA attracts and helps capture Rad51-coated ssDNA.
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31
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Miné J, Disseau L, Takahashi M, Cappello G, Dutreix M, Viovy JL. Real-time measurements of the nucleation, growth and dissociation of single Rad51-DNA nucleoprotein filaments. Nucleic Acids Res 2007; 35:7171-87. [PMID: 17947332 PMCID: PMC2175369 DOI: 10.1093/nar/gkm752] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Human Rad51 (hRad51), the protein central to DNA pairing and strand exchange during homologous recombination, polymerizes on DNA to form nucleoprotein filaments. By making use of magnetic tweezers to manipulate individual DNA molecules, we measured the nucleation and growth of hRad51 nucleoprotein filaments, and their subsequent disassembly in real time. The dependence of the initial polymerization rate upon the concentration of hRad51 suggests that the rate-limiting step is the formation of a nucleus involving 5.5 +/- 1.5 hRad51 monomers, corresponding to one helical turn of the hRad51 nucleoprotein filament. Polymerization is highly cooperative (i.e. a nucleation-limited reaction) at low concentrations and less cooperative (a growth-limited reaction) at high concentrations of the protein. We show that the observed preference of hRad51 to form nucleoprotein filaments on double-stranded DNA rather than on single-stranded DNA is due to the fact that it depolymerizes much faster from ssDNA than from dsDNA: indeed, hRad51 polymerizes faster on ssDNA than on dsDNA. Hydrolysis of ATP by hRad51 does not correlate with its dissociation from dsDNA. This suggests that hRad51 does not depolymerize rapidly from dsDNA after strand exchange but stays bound to the heteroduplex, highlighting the importance of partner proteins to facilitate hRad51 depolymerization from dsDNA.
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Affiliation(s)
- Judith Miné
- Laboratoire Physico-Chimie Curie, UMR CNRS 168, Institut Curie, Paris, France
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32
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Nishinaka T, Doi Y, Hara R, Yashima E. Elastic behavior of RecA-DNA helical filaments. J Mol Biol 2007; 370:837-45. [PMID: 17559876 DOI: 10.1016/j.jmb.2007.05.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2007] [Revised: 05/09/2007] [Accepted: 05/10/2007] [Indexed: 10/23/2022]
Abstract
Escherichia coli RecA protein forms a right-handed helical filament with DNA molecules and has an ATP-dependent activity that exchanges homologous strands between single-stranded DNA (ssDNA) and duplex DNA. We show that the RecA-ssDNA filamentous complex is an elastic helical molecule whose length is controlled by the binding and release of nucleotide cofactors. RecA-ssDNA filaments were fluorescently labelled and attached to a glass surface inside a flow chamber. When the chamber solution was replaced by a buffer solution without nucleotide cofactors, the RecA-ssDNA filament rapidly contracted approximately 0.68-fold with partial filament dissociation. The contracted filament elongated up to 1.25-fold when a buffer solution containing ATPgammaS was injected, and elongated up to 1.17-fold when a buffer solution containing ATP or dATP was injected. This contraction-elongation behavior was able to be repeated by the successive injection of dATP and non-nucleotide buffers. We propose that this elastic motion couples to the elastic motion and/or the twisting rotation of DNA strands within the filament by adjusting their helical phases.
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Affiliation(s)
- Taro Nishinaka
- Yashima Super-structured Helix Project, ERATO, Japan Science and Technology Agency, 101 Creation Core Nagoya, 2266-22 Anagahora, Shimoshidami, Nagoya 463-0003, Japan.
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33
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Gómez-Gómez JM, Manfredi C, Alonso JC, Blázquez J. A novel role for RecA under non-stress: promotion of swarming motility in Escherichia coli K-12. BMC Biol 2007; 5:14. [PMID: 17391508 PMCID: PMC1852089 DOI: 10.1186/1741-7007-5-14] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2006] [Accepted: 03/28/2007] [Indexed: 12/23/2022] Open
Abstract
Background Bacterial motility is a crucial factor in the colonization of natural environments. Escherichia coli has two flagella-driven motility types: swimming and swarming. Swimming motility consists of individual cell movement in liquid medium or soft semisolid agar, whereas swarming is a coordinated cellular behaviour leading to a collective movement on semisolid surfaces. It is known that swimming motility can be influenced by several types of environmental stress. In nature, environmentally induced DNA damage (e.g. UV irradiation) is one of the most common types of stress. One of the key proteins involved in the response to DNA damage is RecA, a multifunctional protein required for maintaining genome integrity and the generation of genetic variation. Results The ability of E. coli cells to develop swarming migration on semisolid surfaces was suppressed in the absence of RecA. However, swimming motility was not affected. The swarming defect of a ΔrecA strain was fully complemented by a plasmid-borne recA gene. Although the ΔrecA cells grown on semisolidsurfaces exhibited flagellar production, they also presented impaired individual movement as well as a fully inactive collective swarming migration. Both the comparative analysis of gene expression profiles in wild-type and ΔrecA cells grown on a semisolid surface and the motility of lexA1 [Ind-] mutant cells demonstrated that the RecA effect on swarming does not require induction of the SOS response. By using a RecA-GFP fusion protein we were able to segregate the effect of RecA on swarming from its other functions. This protein fusion failed to regulate the induction of the SOS response, the recombinational DNA repair of UV-treated cells and the genetic recombination, however, it was efficient in rescuing the swarming motility defect of the ΔrecA mutant. The RecA-GFP protein retains a residual ssDNA-dependent ATPase activity but does not perform DNA strand exchange. Conclusion The experimental evidence presented in this work supports a novel role for RecA: the promotion of swarming motility. The defective swarming migration of ΔrecA cells does not appear to be associated with defective flagellar production; rather, it seems to be associated with an abnormal flagellar propulsion function. Our results strongly suggest that the RecA effect on swarming motility does not require an extensive canonical RecA nucleofilament formation. RecA is the first reported cellular factor specifically affecting swarming but not swimming motility in E. coli. The integration of two apparently disconnected biologically important processes, such as the maintenance of genome integrity and motility in a unique protein, may have important evolutive consequences.
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Affiliation(s)
- José-María Gómez-Gómez
- Departamento de Biotecnología Microbiana. Centro Nacional de Biotecnología, C/Darwin, 3, 28049-Madrid, Spain
| | - Candela Manfredi
- Departamento de Biotecnología Microbiana. Centro Nacional de Biotecnología, C/Darwin, 3, 28049-Madrid, Spain
| | - Juan-Carlos Alonso
- Departamento de Biotecnología Microbiana. Centro Nacional de Biotecnología, C/Darwin, 3, 28049-Madrid, Spain
| | - Jesús Blázquez
- Departamento de Biotecnología Microbiana. Centro Nacional de Biotecnología, C/Darwin, 3, 28049-Madrid, Spain
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34
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The bacterial RecA protein: structure, function, and regulation. MOLECULAR GENETICS OF RECOMBINATION 2007. [DOI: 10.1007/978-3-540-71021-9_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Okoshi K, Nishinaka T, Doi Y, Hara R, Hashimoto M, Yashima E. Liquid crystal formation of RecA–DNA filamentous complexes. Chem Commun (Camb) 2007:2022-4. [PMID: 17713065 DOI: 10.1039/b702982a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Spontaneous optical birefringence of RecA-bound linear and closed circular single-stranded DNA filaments, as well as RecA self-assembled polymer, was observed in aqueous buffer solutions, which demonstrates the formation of lyotropic liquid crystalline phases.
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Affiliation(s)
- Kento Okoshi
- Yashima Super-structured Helix Project, Exploratory Research for Advanced Technology (ERA TO), Japan Science and Technology Agency (JST), Shimoshidami, Moriyama-ku, Nagoya 463-0003, Japan.
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36
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Takahashi T, Masuda T, Koyama Y. Enhanced gene targeting frequency in ku70 and ku80 disruption mutants of Aspergillus sojae and Aspergillus oryzae. Mol Genet Genomics 2006; 275:460-70. [PMID: 16470383 DOI: 10.1007/s00438-006-0104-1] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2005] [Accepted: 01/13/2006] [Indexed: 02/03/2023]
Abstract
In the koji molds Aspergillus sojae and Aspergillus oryzae, exogenous DNA is integrated in the genome, in most cases irrespective of the sequence homology, suggesting that DNA integration occurs predominantly through a nonhomologous end joining pathway where two ku genes, namely, ku70 and ku80, play a key role. To determine the effect of ku gene disruption on the gene targeting frequency, we constructed ku70-, ku80-, and ku70-ku80-disrupted strains of A. sojae and A. oryzae. The gene targeting frequency of the tannase gene in ku70 and ku80 strains of both Aspergillus species was markedly enhanced as compared with that of the parental strains. The gene targeting frequency of the aflR and ku80 genes was also enhanced in an A. sojae ku70 background. Therefore, the koji mold strains with ku-disrupted genes will be excellent tools as hosts for efficient gene targeting.
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Affiliation(s)
- Tadashi Takahashi
- Noda Institute for Scientific Research, 399 Noda, 278-0037, Noda City, Chiba, Japan.
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37
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Tsuchiya H, Harashima H, Kamiya H. Factors affecting SFHR gene correction efficiency with single-stranded DNA fragment. Biochem Biophys Res Commun 2005; 336:1194-200. [PMID: 16171787 DOI: 10.1016/j.bbrc.2005.08.258] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2005] [Accepted: 08/30/2005] [Indexed: 12/17/2022]
Abstract
A 606-nt single-stranded (ss) DNA fragment, prepared by restriction enzyme digestion of ss phagemid DNA, improves the gene correction efficiency by 12-fold as compared with a PCR fragment, which is the conventional type of fragment used in the small fragment homologous replacement method [H. Tsuchiya, H. Harashima, H. Kamiya, Increased SFHR gene correction efficiency with sense single-stranded DNA, J. Gene Med. 7 (2005) 486-493]. To reveal the characteristic features of this gene correction with the ss DNA fragment, the effects on the gene correction in CHO-K1 cells of the chain length, 5'-phosphate, adenine methylation, and transcription were studied. Moreover, the possibility that the ss DNA fragment is integrated into the target DNA was examined with a radioactively labeled ss DNA fragment. The presence of methylated adenine, but not the 5'-phosphate, enhanced the gene correction efficiency, and the optimal length of the ss DNA fragment (approximately 600 nt) was determined. Transcription of the target gene did not affect the gene correction efficiency. In addition, the target DNA recovered from the transfected CHO-K1 cells was radioactive. The results obtained in this study indicate that length and adenine methylation were important factors affecting the gene correction efficiency, and that the ss DNA fragment was integrated into the double-stranded target DNA.
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Affiliation(s)
- Hiroyuki Tsuchiya
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
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38
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Abstract
During the last decade, chimeric RNA-DNA oligonucleotides (RDOs) and single-stranded oligodeoxynucleotides have been used to make permanent and specific sequence changes in the genome, with the ultimate goal of curing human genetic disorders caused by mutations. There have been large variations observed in the rate of gene repair in these studies. This has been due, at least in part, to the lack of standardized assay conditions and the paucity of mechanistic studies in the early developmental stages. Previously, it was proposed that strand pairing is the rate-limiting step and mismatch DNA repair is involved in the gene repair process. We propose an alternative model, in which an oligonucleotide is assimilated to the target DNA during active transcription, leading to formation of a transient D-loop. The trafficking of RNA polymerase is interrupted by the D-loop, and the stalled RNA polymerase complex may signal for recruitment of DNA repair proteins, including transcription-coupled DNA repair and nucleotide-excision repair. Thus, oligonucleotides can be considered as a class of DNA-damaging agents that cause a transient but major structural change in DNA. Understanding of the recognition and repair pathways to process this unusual DNA structure may have relevance in physiologic processes, transcription, and DNA replication.
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Affiliation(s)
- Olga Igoucheva
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Jefferson Medical College, Philadelphia, PA 19107, USA
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39
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Yoon K. Montagna symposium on epidermal stem cells oligonucleotide-directed gene correction in epidermis. J Investig Dermatol Symp Proc 2005; 9:276-83. [PMID: 15369224 DOI: 10.1111/j.1087-0024.2004.09303.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Oligonucleotide-directed gene alteration produces a targeted DNA sequence change in the genome of mammalian cells. The advantage of this approach is that expression of the corrected gene is regulated in the same way as a normal gene. Reliable, sensitive, and standardized assays played a critical role in the measurement of gene correction frequency among different cell types and in evaluating the structure-activity relationship of oligonucleotides. Mechanistic studies using these assays have become critical for understanding the gene repair process and setting realistic expectations on the capability of this technology. The epidermis is an ideal tissue where oligonucleotides can be administered locally and the treated sites can be monitored easily. But given the low frequency of gene correction, general selection procedures and amplification of corrected cells via epidermal stem cells are ultimately needed to make the gene repair technology practical. Recent data suggest that the in vivo application of oligonucleotides may be capable of gene correction in epidermal stem cells and the subsequent expansion of the corrected cells may result in an apparent high-level and long-lasting gene repair. Advances in oligonucleotide delivery and targeting of epidermal stem cells will be required for potential application of oligonucleotides toward treatment of genodermatoses.
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Affiliation(s)
- Kyonggeun Yoon
- Department of Dermatology and Cutaneous Biology, Jefferson Medical College, Philadelphia, Pennsylvania 19107, USA.
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40
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Rybalchenko N, Golub EI, Bi B, Radding CM. Strand invasion promoted by recombination protein beta of coliphage lambda. Proc Natl Acad Sci U S A 2004; 101:17056-60. [PMID: 15574500 PMCID: PMC535401 DOI: 10.1073/pnas.0408046101] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Studies of phage lambda in vivo have indicated that its own recombination enzymes, beta protein and lambda exonuclease, are capable of catalyzing two dissimilar pathways of homologous recombination that are widely distributed in nature: single-strand annealing and strand invasion. The former is an enzymatic splicing of overlapping ends of broken homologous DNA molecules, whereas the latter is characterized by the formation of a three-stranded synaptic intermediate and subsequent strand exchange. Previous studies in vitro have shown that beta protein has annealing activity, and that lambda exonuclease, acting on branched substrates, can produce a perfect splice that requires only ligation for completion. The present study shows that beta protein can initiate strand invasion in vitro, as evidenced both by the formation of displacement loops (D-loops) in superhelical DNA and by strand exchange between colinear single-stranded and double-stranded molecules. Thus, beta protein can catalyze steps that are central to both strand annealing and strand invasion pathways of recombination. These observations add beta protein to a set of diverse proteins that appear to promote recognition of homology by a unitary mechanism governed by the intrinsic dynamic properties of base pairs in DNA.
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Affiliation(s)
- Nataliya Rybalchenko
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
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41
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Folta-Stogniew E, O'Malley S, Gupta R, Anderson KS, Radding CM. Exchange of DNA base pairs that coincides with recognition of homology promoted by E. coli RecA protein. Mol Cell 2004; 15:965-75. [PMID: 15383285 DOI: 10.1016/j.molcel.2004.08.017] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2004] [Revised: 06/06/2004] [Accepted: 07/01/2004] [Indexed: 11/26/2022]
Abstract
The unresolved mechanism by which a single strand of DNA recognizes homology in duplex DNA is central to understanding genetic recombination and repair of double-strand breaks. Using stopped-flow fluorescence we monitored strand exchange catalyzed by E. coli RecA protein, measuring simultaneously the rate of exchange of A:T base pairs and the rates of formation and dissociation of the three-stranded intermediates called synaptic complexes. The rate of exchange of A:T base pairs was indistinguishable from the rate of formation of synaptic complexes, whereas the rate of displacement of a single strand from complexes was five to ten times slower. This physical evidence shows that a subset of bases exchanges at a rate that is fast enough to account for recognition of homology. Together, several studies suggest that a mechanism governed by the dynamic structure of DNA and catalyzed by diverse enzymes underlies both recognition of homology and initiation of strand exchange.
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Affiliation(s)
- Ewa Folta-Stogniew
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
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42
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Abstract
The primordial genetic code probably has been a drastically simplified ancestor of the canonical code that is used by contemporary cells. In order to understand how the present-day code came about we first need to explain how the language of the building plan can change without destroying the encoded information. In this work we introduce a minimal organism model that is based on biophysically reasonable descriptions of RNA and protein, namely secondary structure folding and knowledge based potentials. The evolution of a population of such organism under competition for a common resource is simulated explicitly at the level of individual replication events. Starting with very simple codes, and hence greatly reduced amino acid alphabets, we observe a diversification of the codes in most simulation runs. The driving force behind this effect is the possibility to produce fitter proteins when the repertoire of amino acids is enlarged.
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Affiliation(s)
- Günter Weberndorfer
- Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien, Wien, Austria
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43
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Pawlowski WP, Golubovskaya IN, Cande WZ. Altered nuclear distribution of recombination protein RAD51 in maize mutants suggests the involvement of RAD51 in meiotic homology recognition. THE PLANT CELL 2003; 15:1807-16. [PMID: 12897254 PMCID: PMC167171 DOI: 10.1105/tpc.012898] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2003] [Accepted: 06/11/2003] [Indexed: 05/17/2023]
Abstract
The recombination protein RAD51 is a component of the meiotic recombination pathway and has been proposed to play a role in the homology search, a process by which homologous chromosomes find each other before they pair in the prophase of meiosis. To study the relationship between recombination and chromosome pairing, we examined the distribution of RAD51 foci on meiotic chromosomes in maize mutants with defects in chromosome pairing. The patterns of RAD51 distribution showed dramatic variation among the meiotic mutants. The mutants generally exhibited significant decreases in the number of RAD51 foci at zygotene, corresponding to the degree of their pairing defects. These results provide evidence for a key role of RAD51 structures in the homology search.
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Affiliation(s)
- Wojciech P Pawlowski
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3200, USA.
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44
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Yoshida J, Umezu K, Maki H. Positive and negative roles of homologous recombination in the maintenance of genome stability in Saccharomyces cerevisiae. Genetics 2003; 164:31-46. [PMID: 12750319 PMCID: PMC1462549 DOI: 10.1093/genetics/164.1.31] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In previous studies of the loss of heterozygosity (LOH), we analyzed a hemizygous URA3 marker on chromosome III in S. cerevisiae and showed that homologous recombination is involved in processes that lead to LOH in multiple ways, including allelic recombination, chromosome size alterations, and chromosome loss. To investigate the role of homologous recombination more precisely, we examined LOH events in rad50 Delta, rad51 Delta, rad52 Delta, rad50 Delta rad52 Delta, and rad51 Delta rad52 Delta mutants. As compared to Rad(+) cells, the frequency of LOH was significantly increased in all mutants, and most events were chromosome loss. Other LOH events were differentially affected in each mutant: the frequencies of all types of recombination were decreased in rad52 mutants and enhanced in rad50 mutants. The rad51 mutation increased the frequency of ectopic but not allelic recombination. Both the rad52 and rad51 mutations increased the frequency of intragenic point mutations approximately 25-fold, suggesting that alternative mutagenic pathways partially substitute for homologous recombination. Overall, these results indicate that all of the genes are required for chromosome maintenance and that they most likely function in homologous recombination between sister chromatids. In contrast, other recombination pathways can occur at a substantial level even in the absence of one of the genes and contribute to generating various chromosome rearrangements.
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Affiliation(s)
- Jumpei Yoshida
- Department of Molecular Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.
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45
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Cui Z, Yang Y, Kaufman CD, Agalliu D, Hackett PB. RecA-mediated, targeted mutagenesis in zebrafish. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2003; 5:174-184. [PMID: 12876654 DOI: 10.1007/s10126-002-0059-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2002] [Accepted: 04/29/2002] [Indexed: 05/24/2023]
Abstract
We have evaluated the efficacy of RecA, a prokaryotic protein involved with homologous recombination, to direct site-specific mutagenesis in zebrafish embryos. For this we coinjected a vector containing a mutated enhanced green fluorescent protein (EGFP) gene plus 236-nucleotide corrective single-stranded DNAs coated with RecA into 1-cell zebrafish embryos. Twenty-hours after fertilization, about 5% to 20% of injected embryos showed EGFP expression in 1 or more cells when RecA-coated corrective DNAs were used, but not when RecA was omitted. Mutated EGFP genes with 1-bp insertions or deletions were inefficiently activated, whereas those with 7-bp insertions were activated about 4-fold more efficiently. RecA-coated template strand had a higher efficiency than its complementary strand in activation of EGFP expression. Prior irradiation of the embryos with UV light enhanced RecA-mediated restoration of gene activity, suggesting that the effects we observed were augmented by one or more factors of zebrafish DNA repair systems.
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Affiliation(s)
- Zongbin Cui
- Department of Genetics, Cell Biology and Development and The Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, St. Paul, MN 55108-1095, USA
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46
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Noirot P, Gupta RC, Radding CM, Kolodner RD. Hallmarks of homology recognition by RecA-like recombinases are exhibited by the unrelated Escherichia coli RecT protein. EMBO J 2003; 22:324-34. [PMID: 12514138 PMCID: PMC140102 DOI: 10.1093/emboj/cdg027] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Homologous recombination is a fundamental process for genome maintenance and evolution. Various proteins capable of performing homology recognition and pairing of DNA strands have been isolated from many organisms. The RecA family of proteins exhibits a number of biochemical properties that are considered hallmarks of homology recognition. Here, we investigated whether the unrelated Escherichia coli RecT protein, which mediates homologous pairing and strand exchange, also exhibits such properties. We found that, like RecA and known RecA homologs: (i) RecT promotes the co-aggregation of ssDNA with duplex DNA, which is known to facilitate homologous contacts; (ii) RecT binding to ssDNA mediates unstacking of the bases, a key step in homology recognition; (iii) RecT mediates the formation of a three-strand synaptic intermediate where pairing is facilitated by local helix destabilization, and the preferential switching of A:T base pairs mediates recognition of homology; and (iv) RecT-mediated pairing occurs from both 3'- and 5'-single-stranded ends. Taken together, our results show that RecT shares fundamental homology-recognition properties with the RecA homologs, and provide new insights on an underlying universal mechanism of homologous recognition.
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Affiliation(s)
| | - Ravindra C. Gupta
- Laboratoire de Génétique Microbienne, INRA, 78352 Jouy en Josas Cedex, France,
Department of Biological Sciences, SUNY at Albany, 1400 Washington Avenue, Albany, NY 12222, Department of Genetics, Yale University School of Medicine, New Haven, CT 06520 and Ludwig Institute for Cancer Research, Cancer Center and Department of Medicine, University of California-San Diego School of Medicine, La Jolla, CA 92093, USA Corresponding author e-mail:
| | - Charles M. Radding
- Laboratoire de Génétique Microbienne, INRA, 78352 Jouy en Josas Cedex, France,
Department of Biological Sciences, SUNY at Albany, 1400 Washington Avenue, Albany, NY 12222, Department of Genetics, Yale University School of Medicine, New Haven, CT 06520 and Ludwig Institute for Cancer Research, Cancer Center and Department of Medicine, University of California-San Diego School of Medicine, La Jolla, CA 92093, USA Corresponding author e-mail:
| | - Richard D. Kolodner
- Laboratoire de Génétique Microbienne, INRA, 78352 Jouy en Josas Cedex, France,
Department of Biological Sciences, SUNY at Albany, 1400 Washington Avenue, Albany, NY 12222, Department of Genetics, Yale University School of Medicine, New Haven, CT 06520 and Ludwig Institute for Cancer Research, Cancer Center and Department of Medicine, University of California-San Diego School of Medicine, La Jolla, CA 92093, USA Corresponding author e-mail:
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47
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Ling F, Shibata T. Recombination-dependent mtDNA partitioning: in vivo role of Mhr1p to promote pairing of homologous DNA. EMBO J 2002; 21:4730-40. [PMID: 12198175 PMCID: PMC126199 DOI: 10.1093/emboj/cdf466] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2002] [Revised: 07/09/2002] [Accepted: 07/16/2002] [Indexed: 11/12/2022] Open
Abstract
Yeast mhr1-1 was isolated as a defective mutation in mitochondrial DNA (mtDNA) recombination. About half of mhr1-1 cells lose mtDNA during growth at a higher temperature. Here, we show that mhr1-1 exhibits a defect in the partitioning of nascent mtDNA into buds and is a base-substitution mutation in MHR1 encoding a mitochondrial matrix protein. We found that the Mhr1 protein (Mhr1p) has activity to pair single-stranded DNA and homologous double-stranded DNA to form heteroduplex joints in vitro, and that mhr1-1 causes the loss of this activity, indicating its role in homologous mtDNA recombination. While the majority of the mtDNA in the mother cells consists of head-to-tail concatemers, more than half of the mtDNA in the buds exists as genome-sized monomers. The mhr1-1 deltacce1 double mutant cells do not maintain any mtDNA, indicating the strict dependence of mtDNA maintenance on recombination functions. These results suggest a mechanism for mtDNA inheritance similar to that operating in the replication and packaging of phage DNA.
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MESH Headings
- Amino Acid Substitution
- DNA/genetics
- DNA/metabolism
- DNA, Circular/genetics
- DNA, Circular/metabolism
- DNA, Fungal/genetics
- DNA, Fungal/metabolism
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/metabolism
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- Extrachromosomal Inheritance/genetics
- Models, Genetic
- Mutation, Missense
- Nuclear Proteins/genetics
- Nuclear Proteins/physiology
- Point Mutation
- Recombination, Genetic/genetics
- Reproduction, Asexual
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/growth & development
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/physiology
- Sequence Homology, Nucleic Acid
- Transcription Factors
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Affiliation(s)
- Feng Ling
- Cellular & Molecular Biology Laboratory, RIKEN, Hirosawa 2-1, Wako-shi, Saitama 351-0198 and CREST, Japan Science and Technology Corporation (JST), Japan Corresponding author at: Cellular & Molecular Biology Laboratory, RIKEN, Hirosawa 2-1, Wako-shi, Saitama 351-0198, Japan e-mail:
| | - Takehiko Shibata
- Cellular & Molecular Biology Laboratory, RIKEN, Hirosawa 2-1, Wako-shi, Saitama 351-0198 and CREST, Japan Science and Technology Corporation (JST), Japan Corresponding author at: Cellular & Molecular Biology Laboratory, RIKEN, Hirosawa 2-1, Wako-shi, Saitama 351-0198, Japan e-mail:
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48
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Sekkai D, Dausse E, Di Primo C, Darfeuille F, Boiziau C, Toulmé JJ. In vitro selection of DNA aptamers against the HIV-1 TAR RNA hairpin. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 2002; 12:265-74. [PMID: 12238815 DOI: 10.1089/108729002320351584] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In vitro selection was performed to identify DNA aptamers against the TAR RNA stem-loop structure of HIV-1. A counterselection step allowed the elimination of kissing complex-forming aptamers previously selected (Boiziau et al. J. Biol. Chem. 1999; 274:12730). This led to the emergence of oligonucleotides, most of which contained two consensus sequences, one targeted to the stem 3'-strand (5'-CCCTAGTTA) and the other complementary to the TAR apical loop (5'-CTCCC). The best aptamer could be shortened to a 19-mer oligonucleotide, characterized by a dissociation constant of 50 nM. A 16-mer oligonucleotide complementary to the TAR stem 3'-strand could also be derived from the identified aptamers, with an equal affinity (Kd = 50 nM). Experiments performed to elucidate the interaction between TAR and the aptamers (UV melting measures, enzymatic and chemical footprints) demonstrated that the TAR stem 5'-strand was not simply displaced as a result of the complex formation but unexpectedly remained associated on contact with the antisense oligonucleotide. We suggest that a multistranded structure could be formed.
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Affiliation(s)
- Dalila Sekkai
- INSERM U 386, Université Victor Segalen Bordeaux 2, France
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49
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Xiao J, Singleton SF. Elucidating a key intermediate in homologous DNA strand exchange: structural characterization of the RecA-triple-stranded DNA complex using fluorescence resonance energy transfer. J Mol Biol 2002; 320:529-58. [PMID: 12096908 DOI: 10.1016/s0022-2836(02)00462-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The RecA protein of Escherichia coli plays essential roles in homologous recombination and restarting stalled DNA replication forks. In vitro, the protein mediates DNA strand exchange between single-stranded (ssDNA) and homologous double-stranded DNA (dsDNA) molecules that serves as a model system for the in vivo processes. To date, no high-resolution structure of the key intermediate, comprised of three DNA strands simultaneously bound to a RecA filament (RecA-tsDNA complex), has been reported. We present a systematic characterization of the helical geometries of the three DNA strands of the RecA-tsDNA complex using fluorescence resonance energy transfer (FRET) under physiologically relevant solution conditions. FRET donor and acceptor dyes were used to label different DNA strands, and the interfluorophore distances were inferred from energy transfer efficiencies measured as a function of the base-pair separation between the two dyes. The energy transfer efficiencies were first measured on a control RecA-dsDNA complex, and the calculated helical parameters (h approximately 5 A, Omega(h) approximately 20 degrees ) were consistent with structural conclusions derived from electron microscopy (EM) and other classic biochemical methods. Measurements of the helical parameters for the RecA-tsDNA complex revealed that all three DNA strands adopt extended and unwound conformations similar to those of RecA-bound dsDNA. The structural data are consistent with the hypothesis that this complex is a late, post-strand-exchange intermediate with the outgoing strand shifted by about three base-pairs with respect to its registry with the incoming and complementary strands. Furthermore, the bases of the incoming and complementary strands are displaced away from the helix axis toward the minor groove of the heteroduplex, and the bases of the outgoing strand lie in the major groove of the heteroduplex. We present a model for the strand exchange intermediate in which homologous contacts preceding strand exchange arise in the minor groove of the substrate dsDNA.
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Affiliation(s)
- Jie Xiao
- Department of Chemistry, Rice University, P.O. Box 1892, MS 65, Houston, TX 77005, USA
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Abstract
Mutation plays the primary role in evolution that Weismann mistakenly attributed to sex. Homologous recombination, as in sex, is important for population genetics--shuffling of minor variants, but relatively insignificant for large-scale evolution. Major evolutionary innovations depend much more on illegitimate recombination, which makes novel genes by gene duplication and by gene chimaerisation--essentially mutational forces. The machinery of recombination and sex evolved in two distinct bouts of quantum evolution separated by nearly 3 Gy of stasis; I discuss their nature and causes. The dominant selective force in the evolution of recombination and sex has been selection for replicational fidelity and viability; without the recombination machinery, accurate reproduction, stasis, resistance to radical deleterious evolutionary change and preservation of evolutionary innovations would be impossible. Recombination proteins betray in their phylogeny and domain structure a key role for gene duplication and chimaerisation in their own origin. They arose about 3.8 Gy ago to enable faithful replication and segregation of the first circular DNA genomes in precellular ancestors of Gram-negative eubacteria. Then they were recruited and modified by selfish genetic parasites (viruses; transposons) to help them spread from host to host. Bacteria differ fundamentally from eukaryotes in that gene transfer between cells, whether incidental to their absorptive feeding on DNA and virus infection or directly by plasmids, involves only genomic fragments. This was radically changed by the neomuran revolution about 850 million years ago when a posibacterium evolved into the thermophilic cenancestor of eukaryotes and archaebacteria (jointly called neomurans), radically modifying or substituting its DNA-handling enzymes (those responsible for transcription as well as for replication, repair and recombination) as a coadaptive consequence of the origin of core histones to stabilise its chromosome. Substitution of glycoprotein for peptidoglycan walls in the neomuran ancestor and the evolution of an endoskeleton and endomembrane system in eukaryotes alone required the origin of nuclei, mitosis and novel cell cycle controls and enabled them to evolve cell fusion and thereby the combination of whole genomes from different cells. Meiosis evolved because of resulting selection for periodic ploidy reduction, with incidental consequences for intrapopulation genetic exchange. Little modification was needed to recombination enzymes or to the ancient bacterial catalysts of homology search by spontaneous base pairing to mediate chromosome pairing. The key innovation was the origin of meiotic cohesins delaying centromere splitting to allow two successive divisions before reversion to vegetative growth and replication, necessarily yielding two-step meiosis. Also significant was the evolution of synaptonemal complexes to stabilise bivalents and of monopolins to orient sister centromeres to one spindle pole. The primary significance of sex was not to promote evolutionary change but to limit it by facilitating ploidy cycles to balance the conflicting selective forces acting on rapidly growing phagotrophic protozoa and starved dormant cysts subject to radiation and other damage.
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Affiliation(s)
- T Cavalier-Smith
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
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