1
|
Mre11-Rad50: the DNA end game. Biochem Soc Trans 2023; 51:527-538. [PMID: 36892213 DOI: 10.1042/bst20220754] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/09/2023] [Accepted: 02/17/2023] [Indexed: 03/10/2023]
Abstract
The Mre11-Rad50-(Nbs1/Xrs2) complex is an evolutionarily conserved factor for the repair of DNA double-strand breaks and other DNA termini in all kingdoms of life. It is an intricate DNA associated molecular machine that cuts, among other functions, a large variety of free and obstructed DNA termini for DNA repair by end joining or homologous recombination, yet leaves undamaged DNA intact. Recent years have brought progress in both the structural and functional analyses of Mre11-Rad50 orthologs, revealing mechanisms of DNA end recognition, endo/exonuclease activities, nuclease regulation and DNA scaffolding. Here, I review our current understanding and recent progress on the functional architecture Mre11-Rad50 and how this chromosome associated coiled-coil ABC ATPase acts as DNA topology specific endo-/exonuclease.
Collapse
|
2
|
Boss BL, Wanees AE, Zaslow SJ, Normile TG, Izquierdo JA. Comparative genomics of the plant-growth promoting bacterium Sphingobium sp. strain AEW4 isolated from the rhizosphere of the beachgrass Ammophila breviligulata. BMC Genomics 2022; 23:508. [PMID: 35831788 PMCID: PMC9281055 DOI: 10.1186/s12864-022-08738-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/04/2022] [Indexed: 11/29/2022] Open
Abstract
Background The genus Sphingobium within the class Alpha-proteobacteria contains a small number of plant-growth promoting rhizobacteria (PGPR), although it is mostly comprised of organisms that play an important role in biodegradation and bioremediation in sediments and sandy soils. A Sphingobium sp. isolate was obtained from the rhizosphere of the beachgrass Ammophila breviligulata with a variety of plant growth-promoting properties and designated as Sphingobium sp. strain AEW4. Results Analysis of the 16S rRNA gene as well as full genome nucleotide and amino acid identities revealed that this isolate is most similar to Sphingobium xenophagum and Sphingobium hydrophobicum. Comparative genomics analyses indicate that the genome of strain AEW4 contains unique features that explain its relationship with a plant host as a PGPR, including pathways involved in monosaccharide utilization, fermentation pathways, iron sequestration, and resistance to osmotic stress. Many of these unique features are not broadly distributed across the genus. In addition, pathways involved in the metabolism of salicylate and catechol, phenyl acetate degradation, and DNA repair were also identified in this organism but not in most closely related organisms. Conclusion The genome of Sphingobium sp. strain AEW4 contains a number of distinctive features that are crucial to explain its role as a plant-growth promoting rhizobacterium, and comparative genomics analyses support its classification as a relevant Sphingobium strain involved in plant growth promotion of beachgrass and other plants. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08738-8.
Collapse
Affiliation(s)
- Brianna L Boss
- Department of Biology, Hofstra University, Hempstead, NY, 11549, USA
| | - Abanoub E Wanees
- Department of Biology, Hofstra University, Hempstead, NY, 11549, USA
| | - Shari J Zaslow
- Department of Biology, Hofstra University, Hempstead, NY, 11549, USA
| | - Tyler G Normile
- Department of Biology, Hofstra University, Hempstead, NY, 11549, USA
| | | |
Collapse
|
3
|
Panigrahi R, Glover JNM. Structural insights into DNA double-strand break signaling. Biochem J 2021; 478:135-156. [PMID: 33439989 DOI: 10.1042/bcj20200066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/10/2020] [Accepted: 12/15/2020] [Indexed: 12/14/2022]
Abstract
Genomic integrity is most threatened by double-strand breaks, which, if left unrepaired, lead to carcinogenesis or cell death. The cell generates a network of protein-protein signaling interactions that emanate from the DNA damage which are now recognized as a rich basis for anti-cancer therapy development. Deciphering the structures of signaling proteins has been an uphill task owing to their large size and complex domain organization. Recent advances in mammalian protein expression/purification and cryo-EM-based structure determination have led to significant progress in our understanding of these large multidomain proteins. This review is an overview of the structural principles that underlie some of the key signaling proteins that function at the double-strand break site. We also discuss some plausible ideas that could be considered for future structural approaches to visualize and build a more complete understanding of protein dynamics at the break site.
Collapse
Affiliation(s)
- Rashmi Panigrahi
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| |
Collapse
|
4
|
Li B, Yan J, Zhang Y, Li W, Zeng C, Zhao W, Hou X, Zhang C, Dong Y. CRISPR-Cas12a Possesses Unconventional DNase Activity that Can Be Inactivated by Synthetic Oligonucleotides. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 19:1043-1052. [PMID: 32045875 PMCID: PMC7015830 DOI: 10.1016/j.omtn.2019.12.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/26/2019] [Accepted: 12/27/2019] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas12a (CRISPR-Cpf1) was reported to have multiple types of cleavage activities. Without the assistance of CRISPR RNA (crRNA), we investigated DNase activity and substrate specificity of Cas12a orthologs in the presence of diverse divalent metal ions. Cas12a from different species are capable of degrading single-stranded DNA (ssDNA) and/or double-stranded DNA (dsDNA), depending on the metal ions used. In spite of sharing high sequence similarity and functional domains among diverse Cas12a orthologs, only Acidaminococcus sp. Cas12a (AsCas12a) showed a predominant preference for cleaving ssDNA, but no detectable activity toward dsDNA substrate in the presence of magnesium (II) ions. In addition, we found that both AsCas12a and Francisella novicida Cas12a (FnCas12a) caused substantial dsDNA cleavage in the presence of manganese (II) ion. More importantly, the DNase activities can be inhibited by synthetic DNA oligonucleotides with phosphorothioate linkage modifications. Overall, ssDNase activity of the Cas12a orthologs uncovered a distinct approach for DNA cleavage compared with crRNA-guided dsDNA breaks, and provided insights into potential biological and therapeutic applications.
Collapse
Affiliation(s)
- Bin Li
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; Department of Infectious Disease, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518020, China
| | - Jingyue Yan
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Youxi Zhang
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Wenqing Li
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Chunxi Zeng
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Weiyu Zhao
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Xucheng Hou
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Chengxiang Zhang
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Yizhou Dong
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; Department of Biomedical Engineering, The Ohio State University, Columbus, OH 43210, USA; The Center for Clinical and Translational Science, The Ohio State University, Columbus, OH 43210, USA; James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart & Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA; Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA.
| |
Collapse
|
5
|
Tatebe H, Lim CT, Konno H, Shiozaki K, Shinohara A, Uchihashi T, Furukohri A. Rad50 zinc hook functions as a constitutive dimerization module interchangeable with SMC hinge. Nat Commun 2020; 11:370. [PMID: 31953386 PMCID: PMC6969161 DOI: 10.1038/s41467-019-14025-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 12/10/2019] [Indexed: 01/11/2023] Open
Abstract
The human Mre11/Rad50 complex is one of the key factors in genome maintenance pathways. Previous nanoscale imaging by atomic force microscopy (AFM) showed that the ring-like structure of the human Mre11/Rad50 complex transiently opens at the zinc hook of Rad50. However, imaging of the human Mre11/Rad50 complex by high-speed AFM shows that the Rad50 coiled-coil arms are consistently bridged by the dimerized hooks while the Mre11/Rad50 ring opens by disconnecting the head domains; resembling other SMC proteins such as cohesin or condensin. These architectural features are conserved in the yeast and bacterial Mre11/Rad50 complexes. Yeast strains harboring the chimeric Mre11/Rad50 complex containing the SMC hinge of bacterial condensin MukB instead of the RAD50 hook properly functions in DNA repair. We propose that the basic role of the Rad50 hook is similar to that of the SMC hinge, which serves as rather stable dimerization interface.
Collapse
Affiliation(s)
- Hisashi Tatebe
- Nara Institute of Science and Technology, Graduate School of Biological Sciences, Ikoma, Nara, 630-0192, Japan
| | - Chew Theng Lim
- Nara Institute of Science and Technology, Graduate School of Biological Sciences, Ikoma, Nara, 630-0192, Japan
| | - Hiroki Konno
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Kazuhiro Shiozaki
- Nara Institute of Science and Technology, Graduate School of Biological Sciences, Ikoma, Nara, 630-0192, Japan
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, 95616, USA
| | - Akira Shinohara
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Takayuki Uchihashi
- Department of Physics, Nagoya University, Nagoya, 464-8602, Japan.
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan.
| | - Asako Furukohri
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan.
| |
Collapse
|
6
|
Hamilton NA, Wendel BM, Weber EA, Courcelle CT, Courcelle J. RecBCD, SbcCD and ExoI process a substrate created by convergent replisomes to complete DNA replication. Mol Microbiol 2019; 111:1638-1651. [PMID: 30883946 PMCID: PMC6561825 DOI: 10.1111/mmi.14242] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2019] [Indexed: 12/11/2022]
Abstract
The accurate completion of DNA replication on the chromosome requires RecBCD and structure specific SbcCD and ExoI nucleases. However, the substrates and mechanism by which this reaction occurs remains unknown. Here we show that these completion enzymes operate on plasmid substrates containing two replisomes, but are not required for plasmids containing one replisome. Completion on the two-replisome plasmids requires RecBCD, but does not require RecA and no broken intermediates accumulate in its absence, indicating that the completion reaction occurs normally in the absence of any double-strand breaks. Further, similar to the chromosome, we show that when the normal completion reaction is prevented, an aberrant RecA-mediated recombination process leads to amplifications that drive most of the instabilities associated with the two-replisome substrates. The observations imply that the substrate SbcCD, ExoI and RecBCD act upon in vivo is created specifically by two convergent replisomes, and demonstrate that the function of RecBCD in completing replication is independent of double-strand break repair, and likely promotes joining of the strands of the convergent replication forks.
Collapse
Affiliation(s)
- Nicklas A. Hamilton
- To whom correspondence should be addressed: Department of Biology, Portland State University, PO Box 751 Portland, Oregon, 97207-0751;
| | | | - Emma A. Weber
- Department of Biology, Portland State University, Portland, OR 97201
| | | | - Justin Courcelle
- Department of Biology, Portland State University, Portland, OR 97201
| |
Collapse
|
7
|
Saathoff JH, Käshammer L, Lammens K, Byrne RT, Hopfner KP. The bacterial Mre11-Rad50 homolog SbcCD cleaves opposing strands of DNA by two chemically distinct nuclease reactions. Nucleic Acids Res 2018; 46:11303-11314. [PMID: 30277537 PMCID: PMC6265447 DOI: 10.1093/nar/gky878] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/14/2018] [Accepted: 09/19/2018] [Indexed: 12/22/2022] Open
Abstract
The Mre11-Rad50 complex is a DNA double-strand break sensor that cleaves blocked DNA ends and hairpins by an ATP-dependent endo/exonuclease activity for subsequent repair. For that, Mre11-Rad50 complexes, including the Escherichia coli homolog SbcCD, can endonucleolytically cleave one or both strands near a protein block and process free DNA ends via a 3'-5' exonuclease, but a unified basis for these distinct activities is lacking. Here we analyzed DNA binding, ATPase and nuclease reactions on different DNA substrates. SbcCD clips terminal bases of both strands of the DNA end in the presence of ATPγS. It introduces a DNA double-strand break around 20-25 bp from a blocked end after multiple rounds of ATP hydrolysis in a reaction that correlates with local DNA meltability. Interestingly, we find that nuclease reactions on opposing strands are chemically distinct, leaving a 5' phosphate on one strand, but a 3' phosphate on the other strand. Collectively, our results identify an unexpected chemical variability of the nuclease, indicating that the complex is oriented at a free DNA end and facing a block with opposite polarity. This suggests a unified model for ATP-dependent endo- and exonuclease reactions at internal DNA near a block and at free DNA ends.
Collapse
Affiliation(s)
- Jan-Hinnerk Saathoff
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
| | - Lisa Käshammer
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
| | - Katja Lammens
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
| | - Robert Thomas Byrne
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
| | - Karl-Peter Hopfner
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
- Center for Integrated Protein Science, Munich, Germany
| |
Collapse
|