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Hayashi M, Wada Y, Yamamura A, Inoue H, Yamashita N, Ichimura S, Iida Y. Evaluation of the enzymatic properties of DNA (cytosine-5)-methyltransferase M.ApeKI from archaea in the presence of metal ions. Biosci Biotechnol Biochem 2024; 88:1155-1163. [PMID: 39085041 DOI: 10.1093/bbb/zbae106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 07/16/2024] [Indexed: 08/02/2024]
Abstract
We previously identified M.ApeKI from Aeropyum pernix K1 as a highly thermostable DNA (cytosine-5)-methyltransferase. M.ApeKI uses the type II restriction-modification system (R-M system), among the best-studied R-M systems. Although endonucleases generally utilize Mg (II) as a cofactor, several reports have shown that MTases exhibit different reactions in the presence of metal ions. This study aim was to evaluate the enzymatic properties of DNA (cytosine-5)-methyltransferase M.ApeKI from archaea in the presence of metal ions. We evaluated the influence of metal ions on the catalytic activity and DNA binding of M.ApeKI. The catalytic activity was inhibited by Cu (II), Mg (II), Mn (II), and Zn (II), each at 5 m m. DNA binding was more strongly inhibited by 5 m m Cu (II) and 10 m m Zn (II). To our knowledge, this is the first report showing that DNA binding of type II MTase is inhibited by metal ions.
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Affiliation(s)
- Mao Hayashi
- Department of Applied Chemistry and Bioscience, Graduate School of Engineering, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
| | - Yoshinari Wada
- Department of Applied Bioscience, Faculty of Applied Bioscience, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
| | - Akira Yamamura
- Department of Applied Chemistry and Bioscience, Graduate School of Engineering, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
- Department of Applied Bioscience, Faculty of Applied Bioscience, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
| | - Hideki Inoue
- Department of Applied Chemistry and Bioscience, Graduate School of Engineering, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
- Department of Applied Bioscience, Faculty of Applied Bioscience, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
| | - Naoya Yamashita
- Department of Applied Chemistry and Bioscience, Graduate School of Engineering, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
- Department of Applied Bioscience, Faculty of Applied Bioscience, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
| | - Shigetoshi Ichimura
- Department of Applied Chemistry and Bioscience, Graduate School of Engineering, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
- Department of Applied Bioscience, Faculty of Applied Bioscience, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
| | - Yasuhiro Iida
- Department of Applied Chemistry and Bioscience, Graduate School of Engineering, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
- Department of Applied Bioscience, Faculty of Applied Bioscience, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
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2
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Frank PH, Hong M, Higgins B, Perkins S, Taylor T, Wall VE, Drew M, Waybright T, Gillette W, Esposito D, Messing S. Adapting recombinant bacterial alkaline phosphatase for nucleotide exchange of small GTPases. Protein Expr Purif 2024; 218:106446. [PMID: 38395209 PMCID: PMC11000209 DOI: 10.1016/j.pep.2024.106446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/05/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024]
Abstract
The small GTPase Rat sarcoma virus proteins (RAS) are key regulators of cell growth and involved in 20-30% of cancers. RAS switches between its active state and inactive state via exchange of GTP (active) and GDP (inactive). Therefore, to study active protein, it needs to undergo nucleotide exchange to a non-hydrolysable GTP analog. Calf intestine alkaline phosphatase bound to agarose beads (CIP-agarose) is regularly used in a nucleotide exchange protocol to replace GDP with a non-hydrolysable analog. Due to pandemic supply problems and product shortages, we found the need for an alternative to this commercially available product. Here we describe how we generated a bacterial alkaline phosphatase (BAP) with an affinity tag bound to an agarose bead. This BAP completely exchanges the nucleotide in our samples, thereby demonstrating an alternative to the commercially available product using generally available laboratory equipment.
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Affiliation(s)
- Peter H Frank
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Min Hong
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Brianna Higgins
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Shelley Perkins
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Troy Taylor
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Vanessa E Wall
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Matthew Drew
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Timothy Waybright
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - William Gillette
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
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3
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Gulati P, Singh A, Patra S, Bhat S, Verma A. Restriction modification systems in archaea: A panoramic outlook. Heliyon 2024; 10:e27382. [PMID: 38644887 PMCID: PMC11033074 DOI: 10.1016/j.heliyon.2024.e27382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/19/2024] [Accepted: 02/28/2024] [Indexed: 04/23/2024] Open
Abstract
Restriction modification (RM) systems are one of the ubiquitous yet primitive defense responses employed by bacteria and archaea with the primary role of safeguarding themselves against invading bacteriophages. Protection of the host occurs by the cleavage of the invading foreign DNA via restriction endonucleases with concomitant methylation of host DNA with the aid of a methyltransferase counterpart. RM systems have been extensively studied in bacteria, however, in the case of archaea there are limited reports of RM enzymes that are investigated to date owing to their inhospitable growth demands. This review aims to broaden the knowledge about what is known about the diversity of RM systems in archaea and encapsulate the current knowledge on restriction and modification enzymes characterized in archaea so far and the role of RM systems in the milieu of archaeal biology.
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Affiliation(s)
- Pallavi Gulati
- Department of Microbiology, Ram Lal Anand College, University of Delhi South Campus, New Delhi 110021, India
| | - Ashish Singh
- Department of Microbiology, University of Delhi South Campus, New Delhi 110021, India
| | - Sandeep Patra
- Department of Microbiology, Ram Lal Anand College, University of Delhi South Campus, New Delhi 110021, India
| | - Shreyas Bhat
- Department of Microbiology, Ram Lal Anand College, University of Delhi South Campus, New Delhi 110021, India
| | - Anil Verma
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA-15213, USA
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4
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Gao Q, Lu S, Wang Y, He L, Wang M, Jia R, Chen S, Zhu D, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Mao S, Ou X, Sun D, Tian B, Cheng A. Bacterial DNA methyltransferase: A key to the epigenetic world with lessons learned from proteobacteria. Front Microbiol 2023; 14:1129437. [PMID: 37032876 PMCID: PMC10073500 DOI: 10.3389/fmicb.2023.1129437] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/27/2023] [Indexed: 04/11/2023] Open
Abstract
Epigenetics modulates expression levels of various important genes in both prokaryotes and eukaryotes. These epigenetic traits are heritable without any change in genetic DNA sequences. DNA methylation is a universal mechanism of epigenetic regulation in all kingdoms of life. In bacteria, DNA methylation is the main form of epigenetic regulation and plays important roles in affecting clinically relevant phenotypes, such as virulence, host colonization, sporulation, biofilm formation et al. In this review, we survey bacterial epigenomic studies and focus on the recent developments in the structure, function, and mechanism of several highly conserved bacterial DNA methylases. These methyltransferases are relatively common in bacteria and participate in the regulation of gene expression and chromosomal DNA replication and repair control. Recent advances in sequencing techniques capable of detecting methylation signals have enabled the characterization of genome-wide epigenetic regulation. With their involvement in critical cellular processes, these highly conserved DNA methyltransferases may emerge as promising targets for developing novel epigenetic inhibitors for biomedical applications.
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Affiliation(s)
- Qun Gao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
| | - Shuwei Lu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuwei Wang
- Key Laboratory of Livestock and Poultry Provenance Disease Research in Mianyang, Sichuan, China
| | - Longgui He
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Renyong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shun Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mafeng Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xinxin Zhao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qiao Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ying Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shaqiu Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Juan Huang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Sai Mao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xumin Ou
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Di Sun
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bin Tian
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
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5
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Seo PW, Hofmann A, Kim JH, Hwangbo SA, Kim JH, Kim JW, Huynh TYL, Choy HE, Kim SJ, Lee J, Lee JO, Jin KS, Park SY, Kim JS. Structural features of a minimal intact methyltransferase of a type I restriction-modification system. Int J Biol Macromol 2022; 208:381-389. [PMID: 35337914 DOI: 10.1016/j.ijbiomac.2022.03.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 11/05/2022]
Abstract
Type I restriction-modification enzymes are oligomeric proteins composed of methylation (M), DNA sequence-recognition (S), and restriction (R) subunits. The different bipartite DNA sequences of 2-4 consecutive bases are recognized by two discerned target recognition domains (TRDs) located at the two-helix bundle of the two conserved regions (CRs). Two M-subunits and a single S-subunit form an oligomeric protein that functions as a methyltransferase (M2S1 MTase). Here, we present the crystal structure of the intact MTase from Vibrio vulnificus YJ016 in complex with the DNA-mimicking Ocr protein and the S-adenosyl-L-homocysteine (SAH). This MTase includes the M-domain with a helix tail (M-tail helix) and the S1/2-domain of a TRD and a CR α-helix. The Ocr binds to the cleft of the TRD surface and SAH is located in the pocket within the M-domain. The solution- and negative-staining electron microscopy-based reconstructed (M1S1/2)2 structure reveals a symmetric (S1/2)2 assembly using two CR-helices and two M-tail helices as a pivot, which is plausible for recognizing two DNA regions of same sequence. The conformational flexibility of the minimal M1S1/2 MTase dimer indicates a particular state resembling the structure of M2S1 MTases.
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Affiliation(s)
- Pil-Won Seo
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia; Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 95326 Kulmbach, Germany
| | - Jun-Ha Kim
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea; Department of Chemical Engineering, Kumoh National Institute of Technology, 61, Daehak-ro, Gumi, Gyeongbuk 39177, Republic of Korea
| | - Seung-A Hwangbo
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea; Department of Life Sciences and Institute of Membrane Proteins, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jun-Hong Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Ji-Won Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Thi Yen Ly Huynh
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hyon E Choy
- Department of Microbiology, Basic Medical Research Building, Chonnam National University Medical College, Hwasun, Jeonnam 58128, Republic of Korea
| | - Soo-Jung Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jimin Lee
- Department of Life Sciences and Institute of Membrane Proteins, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jie-Oh Lee
- Department of Life Sciences and Institute of Membrane Proteins, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Kyeong Sik Jin
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea.
| | - Suk-Youl Park
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea.
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea.
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6
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Li D, Li P, Peng M, Zhao X, Jiang X, Wang D, Yuan Y, Guo Q, Wang M, Xu X, Wang M. Transmission barrier of the blaKPC plasmid mediated by type I restriction-modification systems in Escherichia coli. J Antimicrob Chemother 2022; 77:952-956. [PMID: 35040978 DOI: 10.1093/jac/dkab489] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 12/06/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Transportation of carbapenem-resistant plasmids contributes to carbapenem resistance in Gram-negative bacteria. KPC enzymes are the most clinically important enzymes among carbapenem-resistant Klebsiella pneumoniae, whereas the rate of blaKPC in Escherichia coli is low. The CRISPR-Cas system and restriction-modification system (R-M system) in bacteria defend against invading genomes. Currently, the role of the immune systems in the low rate of KPC-producing E. coli remains unclear. OBJECTIVES We investigated the relationship between immune systems and the low detection rate of blaKPC in E. coli. METHODS We searched for blaKPC among 1039 E. coli whole genomes available in GenBank using nucleotide BLAST. CRISPR-Cas systems and the R-M system were detected in all strains having the ST as blaKPC-positive strains. Nucleotide BLAST was used to search for protospacers on blaKPC plasmids. A conjugation assay was performed to determine whether the R-M system influences the acquisition of blaKPC plasmids by E. coli. RESULTS ST131 was the dominant ST of KPC-producing E. coli and IncN was the main plasmid type (12/32). CRISPR-Cas systems were frequently present in E. coli carrying blaKPC. Furthermore, CRISPR-Cas systems in E. coli didn't target plasmids with blaKPC. Type I R-M systems were rare in KPC-producing E. coli, but significantly over-represented in KPC-negative strains. E. coli DH5α with hsdR deletion accepted blaKPC-carrying plasmids, whereas those with hsdR complementation impeded blaKPC-carrying plasmid conjugation. CONCLUSIONS Horizontal transmission of blaKPC occurs among E. coli. The type I R-M system is associated with the defence against blaKPC plasmid transport into E. coli.
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Affiliation(s)
- Dan Li
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People's Republic of China
| | - Pei Li
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People's Republic of China
| | - Mingjia Peng
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People's Republic of China
| | - Xiaoyu Zhao
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People's Republic of China
| | - Xiaoying Jiang
- The First Department of Critical Care Medicine, Gansu Provincial Hospital, Gansu, People's Republic of China
| | - Dongliang Wang
- The First Department of Critical Care Medicine, Gansu Provincial Hospital, Gansu, People's Republic of China
| | - Yuan Yuan
- The First Department of Critical Care Medicine, Gansu Provincial Hospital, Gansu, People's Republic of China
| | - Qinglan Guo
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People's Republic of China
| | - Minghua Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People's Republic of China
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People's Republic of China
| | - Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People's Republic of China
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7
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Ren J, Lee HM, Shen J, Na D. Advanced biotechnology using methyltransferase and its applications in bacteria: a mini review. Biotechnol Lett 2021; 44:33-44. [PMID: 34820721 DOI: 10.1007/s10529-021-03208-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/12/2021] [Indexed: 11/26/2022]
Abstract
Since prokaryotic restriction-modification (RM) systems protect the host by cleaving foreign DNA by restriction endonucleases, it is difficult to introduce engineered plasmid DNAs into newly isolated microorganisms whose RM system is not discovered. The prokaryotes also possess methyltransferases to protect their own DNA from the endonucleases. As those methyltransferases can be utilized to methylate engineered plasmid DNAs before transformation and to enhance the stability within the cells, the study on methyltransferases in newly isolated bacteria is essential for genetic engineering. Here, we introduce the mechanism of the RM system, specifically the methyltransferases and their biotechnological applications. These biotechnological strategies could facilitate plasmid DNA-based genetic engineering in bacteria strains that strongly defend against foreign DNA.
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Affiliation(s)
- Jun Ren
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyang-Mi Lee
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - JunHao Shen
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea.
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8
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Tumuluri VS, Rajgor V, Xu SY, Chouhan OP, Saikrishnan K. Mechanism of DNA cleavage by the endonuclease SauUSI: a major barrier to horizontal gene transfer and antibiotic resistance in Staphylococcus aureus. Nucleic Acids Res 2021; 49:2161-2178. [PMID: 33533920 PMCID: PMC7913695 DOI: 10.1093/nar/gkab042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 01/11/2021] [Accepted: 01/31/2021] [Indexed: 02/06/2023] Open
Abstract
Acquisition of foreign DNA by Staphylococcus aureus, including vancomycin resistance genes, is thwarted by the ATP-dependent endonuclease SauUSI. Deciphering the mechanism of action of SauUSI could unravel the reason how it singularly plays a major role in preventing horizontal gene transfer (HGT) in S. aureus. Here, we report a detailed biochemical and structural characterization of SauUSI, which reveals that in the presence of ATP, the enzyme can cleave DNA having a single or multiple target site/s. Remarkably, in the case of multiple target sites, the entire region of DNA flanked by two target sites is shred into smaller fragments by SauUSI. Crystal structure of SauUSI reveals a stable dimer held together by the nuclease domains, which are spatially arranged to hydrolyze the phosphodiester bonds of both strands of the duplex. Thus, the architecture of the dimeric SauUSI facilitates cleavage of either single-site or multi-site DNA. The structure also provides insights into the molecular basis of target recognition by SauUSI. We show that target recognition activates ATP hydrolysis by the helicase-like ATPase domain, which powers active directional movement (translocation) of SauUSI along the DNA. We propose that a pile-up of multiple translocating SauUSI molecules against a stationary SauUSI bound to a target site catalyzes random double-stranded breaks causing shredding of the DNA between two target sites. The extensive and irreparable damage of the foreign DNA by shredding makes SauUSI a potent barrier against HGT.
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Affiliation(s)
| | - Vrunda Rajgor
- Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India
| | - Shuang-Yong Xu
- New England Biolabs Inc., Research Department, Ipswich, MA 01938, USA
| | - Om Prakash Chouhan
- Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India
| | - Kayarat Saikrishnan
- Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India
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9
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Hosford CJ, Adams MC, Niu Y, Chappie JS. The N-terminal domain of Staphylothermus marinus McrB shares structural homology with PUA-like RNA binding proteins. J Struct Biol 2020; 211:107572. [PMID: 32652237 DOI: 10.1016/j.jsb.2020.107572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 12/27/2022]
Abstract
McrBC is a conserved modification-dependent restriction system that in Escherichia coli specifically targets foreign DNA containing methylated cytosines. Crystallographic data show that the N-terminal domain of Escherichia coli McrB binds substrates via a base flipping mechanism. This region is poorly conserved among the plethora of McrB homologs, suggesting that other species may use alternative binding strategies and/or recognize different targets. Here we present the crystal structure of the N-terminal domain from Stayphlothermus marinus McrB (Sm3-180) at 1.92 Å, which adopts a PUA-like EVE fold that is closely related to the YTH and ASCH RNA binding domains. Unlike most PUA-like domains, Sm3-180 binds DNA and can associate with different modified substrates. We find the canonical 'aromatic cage' binding pocket that confers specificity for methylated bases in other EVE/YTH domains is degenerate and occluded in Sm3-180, which may contribute to its promiscuity in target recognition. Further structural comparison between different PUA-like domains identifies motifs and conformational variations that correlate with the preference for binding either DNA or RNA. Together these data have important implications for PUA-like domain specificity and suggest a broader biological versatility for the McrBC family than previously described.
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Affiliation(s)
| | - Myfanwy C Adams
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Yiming Niu
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA.
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Hosford CJ, Bui AQ, Chappie JS. The structure of the Thermococcus gammatolerans McrB N-terminal domain reveals a new mode of substrate recognition and specificity among McrB homologs. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49932-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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11
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Hosford CJ, Bui AQ, Chappie JS. The structure of the Thermococcus gammatolerans McrB N-terminal domain reveals a new mode of substrate recognition and specificity among McrB homologs. J Biol Chem 2019; 295:743-756. [PMID: 31822563 DOI: 10.1074/jbc.ra119.010188] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 12/07/2019] [Indexed: 01/12/2023] Open
Abstract
McrBC is a two-component, modification-dependent restriction system that cleaves foreign DNA-containing methylated cytosines. Previous crystallographic studies have shown that Escherichia coli McrB uses a base-flipping mechanism to recognize these modified substrates with high affinity. The side chains stabilizing both the flipped base and the distorted duplex are poorly conserved among McrB homologs, suggesting that other mechanisms may exist for binding modified DNA. Here we present the structures of the Thermococcus gammatolerans McrB DNA-binding domain (TgΔ185) both alone and in complex with a methylated DNA substrate at 1.68 and 2.27 Å resolution, respectively. The structures reveal that TgΔ185 consists of a YT521-B homology (YTH) domain, which is commonly found in eukaryotic proteins that bind methylated RNA and is structurally unrelated to the E. coli McrB DNA-binding domain. Structural superposition and co-crystallization further show that TgΔ185 shares a conserved aromatic cage with other YTH domains, which forms the binding pocket for a flipped-out base. Mutational analysis of this aromatic cage supports its role in conferring specificity for the methylated adenines, whereas an extended basic surface present in TgΔ185 facilitates its preferential binding to duplex DNA rather than RNA. Together, these findings establish a new binding mode and specificity among McrB homologs and expand the biological roles of YTH domains.
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Affiliation(s)
| | - Anthony Q Bui
- Department of Molecular Medicine, Cornell University, Ithaca, New York 14853
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, New York 14853
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12
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Mtimka S, Pillay P, Rashamuse K, Gildenhuys S, Tsekoa TL. Functional screening of a soil metagenome for DNA endonucleases by acquired resistance to bacteriophage infection. Mol Biol Rep 2019; 47:353-361. [PMID: 31643043 DOI: 10.1007/s11033-019-05137-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/10/2019] [Indexed: 11/27/2022]
Abstract
Endonucleases play a crucial role as reagents in laboratory research and diagnostics. Here, metagenomics was used to functionally screen a fosmid library for endonucleases. A fosmid library was constructed using metagenomic DNA isolated from soil sampled from the unique environment of the Kogelberg Nature Reserve in the Western Cape of South Africa. The principle of acquired immunity against phage infection was used to develop a plate-based screening technique for the isolation of restriction endonucleases from the library. Using next-generation sequencing and bioinformatics tools, sequence data were generated and analysed, revealing 113 novel open reading frames (ORFs) encoding putative endonuclease genes and ORFs of unknown identity and function. One endonuclease designated Endo52 was selected from the putative endonuclease ORFs and was recombinantly produced in Escherichia coli Rosetta™ (DE3) pLysS. Endo52 was purified by immobilised metal affinity chromatography and yielded 0.437 g per litre of cultivation volume. Its enzyme activity was monitored by cleaving lambda DNA and pUC19 plasmid as substrates, and it demonstrated non-specific endonuclease activity. In addition to endonuclease-like genes, the screen identified several unknown genes. These could present new phage resistance mechanisms and are an opportunity for future investigations.
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Affiliation(s)
- Sibongile Mtimka
- Biomanufacturing Technologies, CSIR Future Production: Chemicals, P O Box 395, Pretoria, 0001, South Africa.,Department of Life & Consumer Sciences, College of Agriculture & Environmental Sciences, University of South Africa, Florida Campus (The Science Hub), Florida, P O Box 392, Johannesburg, South Africa
| | - Priyen Pillay
- Biomanufacturing Technologies, CSIR Future Production: Chemicals, P O Box 395, Pretoria, 0001, South Africa
| | - Konanani Rashamuse
- Biomanufacturing Technologies, CSIR Future Production: Chemicals, P O Box 395, Pretoria, 0001, South Africa
| | - Samantha Gildenhuys
- Department of Life & Consumer Sciences, College of Agriculture & Environmental Sciences, University of South Africa, Florida Campus (The Science Hub), Florida, P O Box 392, Johannesburg, South Africa
| | - Tsepo L Tsekoa
- Biomanufacturing Technologies, CSIR Future Production: Chemicals, P O Box 395, Pretoria, 0001, South Africa.
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Gao W, He Y, Zhang F, Zhao F, Huang C, Zhang Y, Zhao Q, Wang S, Yang C. Metabolic engineering of Bacillus amyloliquefaciens LL3 for enhanced poly-γ-glutamic acid synthesis. Microb Biotechnol 2019; 12:932-945. [PMID: 31219230 PMCID: PMC6680638 DOI: 10.1111/1751-7915.13446] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/17/2019] [Indexed: 01/29/2023] Open
Abstract
Poly-γ-glutamic acid (γ-PGA) is a biocompatible and biodegradable polypeptide with wide-ranging applications in foods, cosmetics, medicine, agriculture and wastewater treatment. Bacillus amyloliquefaciens LL3 can produce γ-PGA from sucrose that can be obtained easily from sugarcane and sugar beet. In our previous work, it was found that low intracellular glutamate concentration was the limiting factor for γ-PGA production by LL3. In this study, the γ-PGA synthesis by strain LL3 was enhanced by chromosomally engineering its glutamate metabolism-relevant networks. First, the downstream metabolic pathways were partly blocked by deleting fadR, lysC, aspB, pckA, proAB, rocG and gudB. The resulting strain NK-A6 synthesized 4.84 g l-1 γ-PGA, with a 31.5% increase compared with strain LL3. Second, a strong promoter PC 2up was inserted into the upstream of icd gene, to generate strain NK-A7, which further led to a 33.5% improvement in the γ-PGA titre, achieving 6.46 g l-1 . The NADPH level was improved by regulating the expression of pgi and gndA. Third, metabolic evolution was carried out to generate strain NK-A9E, which showed a comparable γ-PGA titre with strain NK-A7. Finally, the srf and itu operons were deleted respectively, from the original strains NK-A7 and NK-A9E. The resulting strain NK-A11 exhibited the highest γ-PGA titre (7.53 g l-1 ), with a 2.05-fold improvement compared with LL3. The results demonstrated that the approaches described here efficiently enhanced γ-PGA production in B. amyloliquefaciens fermentation.
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Affiliation(s)
- Weixia Gao
- Key Laboratory of Molecular Microbiology and Technology for Ministry of EducationNankai UniversityTianjin300071China
- State Key Laboratory of Medicinal Chemical BiologyNankai UniversityTianjin300071China
| | - Yulian He
- Prenatal Diagnosis and Genetic Diagnosis CenterTangshan Maternal and Child Health Care HospitalTangshan063000China
| | - Fang Zhang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of EducationNankai UniversityTianjin300071China
| | - Fengjie Zhao
- Key Laboratory of Molecular Microbiology and Technology for Ministry of EducationNankai UniversityTianjin300071China
| | - Chao Huang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of EducationNankai UniversityTianjin300071China
| | - Yiting Zhang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of EducationNankai UniversityTianjin300071China
| | - Qiang Zhao
- State Key Laboratory of Medicinal Chemical BiologyNankai UniversityTianjin300071China
| | - Shufang Wang
- State Key Laboratory of Medicinal Chemical BiologyNankai UniversityTianjin300071China
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of EducationNankai UniversityTianjin300071China
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Pikin SA, Pikina ES. On DNA Motions under Action of Enzymes of Different Types. II. CRYSTALLOGR REP+ 2019. [DOI: 10.1134/s106377451901019x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abstract
Enterococcus faecium has a highly variable genome prone to recombination and horizontal gene transfer. Here, we have identified a novel genetic island with an insertion locus and mobilization genes similar to those of staphylococcus cassette chromosome elements SCCmec This novel element termed the enterococcus cassette chromosome (ECC) element was located in the 3' region of rlmH and encoded large serine recombinases ccrAB similar to SCCmec Horizontal transfer of an ECC element termed ECC::cat containing a knock-in cat chloramphenicol resistance determinant occurred in the presence of a conjugative rep pLG1 plasmid. We determined the ECC::cat insertion site in the 3' region of rlmH in the E. faecium recipient by long-read sequencing. ECC::cat also mobilized by homologous recombination through sequence identity between flanking insertion sequence (IS) elements in ECC::cat and the conjugative plasmid. The ccrABEnt genes were found in 69 of 516 E. faecium genomes in GenBank. Full-length ECC elements were retrieved from 32 of these genomes. ECCs were flanked by attR and attL sites of approximately 50 bp. The attECC sequences were found by PCR and sequencing of circularized ECCs in three strains. The genes in ECCs contained an amalgam of common and rare E. faecium genes. Taken together, our data imply that ECC elements act as hot spots for genetic exchange and contribute to the large variation of accessory genes found in E. faecium IMPORTANCE Enterococcus faecium is a bacterium found in a great variety of environments, ranging from the clinic as a nosocomial pathogen to natural habitats such as mammalian intestines, water, and soil. They are known to exchange genetic material through horizontal gene transfer and recombination, leading to great variability of accessory genes and aiding environmental adaptation. Identifying mobile genetic elements causing sequence variation is important to understand how genetic content variation occurs. Here, a novel genetic island, the enterococcus cassette chromosome, is shown to contain a wealth of genes, which may aid E. faecium in adapting to new environments. The transmission mechanism involves the only two conserved genes within ECC, ccrAB Ent, large serine recombinases that insert ECC into the host genome similarly to SCC elements found in staphylococci.
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17
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Grinkevich P, Sinha D, Iermak I, Guzanova A, Weiserova M, Ludwig J, Mesters JR, Ettrich RH. Crystal structure of a novel domain of the motor subunit of the Type I restriction enzyme EcoR124 involved in complex assembly and DNA binding. J Biol Chem 2018; 293:15043-15054. [PMID: 30054276 DOI: 10.1074/jbc.ra118.003978] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/19/2018] [Indexed: 01/30/2023] Open
Abstract
Although EcoR124 is one of the better-studied Type I restriction-modification enzymes, it still presents many challenges to detailed analyses because of its structural and functional complexity and missing structural information. In all available structures of its motor subunit HsdR, responsible for DNA translocation and cleavage, a large part of the HsdR C terminus remains unresolved. The crystal structure of the C terminus of HsdR, obtained with a crystallization chaperone in the form of pHluorin fusion and refined to 2.45 Å, revealed that this part of the protein forms an independent domain with its own hydrophobic core and displays a unique α-helical fold. The full-length HsdR model, based on the WT structure and the C-terminal domain determined here, disclosed a proposed DNA-binding groove lined by positively charged residues. In vivo and in vitro assays with a C-terminal deletion mutant of HsdR supported the idea that this domain is involved in complex assembly and DNA binding. Conserved residues identified through sequence analysis of the C-terminal domain may play a key role in protein-protein and protein-DNA interactions. We conclude that the motor subunit of EcoR124 comprises five structural and functional domains, with the fifth, the C-terminal domain, revealing a unique fold characterized by four conserved motifs in the IC subfamily of Type I restriction-modification systems. In summary, the structural and biochemical results reported here support a model in which the C-terminal domain of the motor subunit HsdR of the endonuclease EcoR124 is involved in complex assembly and DNA binding.
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Affiliation(s)
- Pavel Grinkevich
- From the Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Zamek 136, 373 33 Nove Hrady, Czech Republic.,the Faculty of Sciences, University of South Bohemia in Ceske Budejovice, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Dhiraj Sinha
- From the Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Zamek 136, 373 33 Nove Hrady, Czech Republic
| | - Iuliia Iermak
- From the Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Zamek 136, 373 33 Nove Hrady, Czech Republic.,the Department of Structural Cell Biology, Molecular Mechanisms of DNA Repair, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Alena Guzanova
- the Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Marie Weiserova
- the Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Jost Ludwig
- From the Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Zamek 136, 373 33 Nove Hrady, Czech Republic
| | - Jeroen R Mesters
- the Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, Lübeck, Germany, and
| | - Rüdiger H Ettrich
- From the Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Zamek 136, 373 33 Nove Hrady, Czech Republic, .,the College of Biomedical Sciences, Larkin University, Miami, Florida 33169
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Seib KL, Jen FEC, Scott AL, Tan A, Jennings MP. Phase variation of DNA methyltransferases and the regulation of virulence and immune evasion in the pathogenic Neisseria. Pathog Dis 2017; 75:3966716. [DOI: 10.1093/femspd/ftx080] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/13/2017] [Indexed: 01/31/2023] Open
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19
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Bialevich V, Sinha D, Shamayeva K, Guzanova A, Řeha D, Csefalvay E, Carey J, Weiserova M, Ettrich RH. The helical domain of the EcoR124I motor subunit participates in ATPase activity and dsDNA translocation. PeerJ 2017; 5:e2887. [PMID: 28133570 PMCID: PMC5248579 DOI: 10.7717/peerj.2887] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/08/2016] [Indexed: 01/20/2023] Open
Abstract
Type I restriction-modification enzymes are multisubunit, multifunctional molecular machines that recognize specific DNA target sequences, and their multisubunit organization underlies their multifunctionality. EcoR124I is the archetype of Type I restriction-modification family IC and is composed of three subunit types: HsdS, HsdM, and HsdR. DNA cleavage and ATP-dependent DNA translocation activities are housed in the distinct domains of the endonuclease/motor subunit HsdR. Because the multiple functions are integrated in this large subunit of 1,038 residues, a large number of interdomain contacts might be expected. The crystal structure of EcoR124I HsdR reveals a surprisingly sparse number of contacts between helicase domain 2 and the C-terminal helical domain that is thought to be involved in assembly with HsdM. Only two potential hydrogen-bonding contacts are found in a very small contact region. In the present work, the relevance of these two potential hydrogen-bonding interactions for the multiple activities of EcoR124I is evaluated by analysing mutant enzymes using in vivo and in vitro experiments. Molecular dynamics simulations are employed to provide structural interpretation of the functional data. The results indicate that the helical C-terminal domain is involved in the DNA translocation, cleavage, and ATPase activities of HsdR, and a role in controlling those activities is suggested.
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Affiliation(s)
- Vitali Bialevich
- Center for Nanobiology and Structural Biology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic
- Faculty of Sciences, University of South Bohemia in Ceske Budejovice, Nove Hrady, Czech Republic
| | - Dhiraj Sinha
- Center for Nanobiology and Structural Biology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic
- Faculty of Sciences, University of South Bohemia in Ceske Budejovice, Nove Hrady, Czech Republic
| | - Katsiaryna Shamayeva
- Center for Nanobiology and Structural Biology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic
| | - Alena Guzanova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - David Řeha
- Center for Nanobiology and Structural Biology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic
- Faculty of Sciences, University of South Bohemia in Ceske Budejovice, Nove Hrady, Czech Republic
| | - Eva Csefalvay
- Center for Nanobiology and Structural Biology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic
| | - Jannette Carey
- Center for Nanobiology and Structural Biology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic
- Chemistry Department, Princeton University, Princeton, NJ, United States
| | - Marie Weiserova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Rüdiger H. Ettrich
- Center for Nanobiology and Structural Biology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic
- Faculty of Sciences, University of South Bohemia in Ceske Budejovice, Nove Hrady, Czech Republic
- College of Medical Sciences, Nova Southeastern University, Fort Lauderdale, FL, United States
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Grinkevich P, Iermak I, Luedtke NA, Mesters JR, Ettrich R, Ludwig J. pHluorin-assisted expression, purification, crystallization and X-ray diffraction data analysis of the C-terminal domain of the HsdR subunit of the Escherichia coli type I restriction-modification system EcoR124I. Acta Crystallogr F Struct Biol Commun 2016; 72:672-6. [PMID: 27599856 PMCID: PMC5012205 DOI: 10.1107/s2053230x16011626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/16/2016] [Indexed: 11/10/2022] Open
Abstract
The HsdR subunit of the type I restriction-modification system EcoR124I is responsible for the translocation as well as the restriction activity of the whole complex consisting of the HsdR, HsdM and HsdS subunits, and while crystal structures are available for the wild type and several mutants, the C-terminal domain comprising approximately 150 residues was not resolved in any of these structures. Here, three fusion constructs with the GFP variant pHluorin developed to overexpress, purify and crystallize the C-terminal domain of HsdR are reported. The shortest of the three encompassed HsdR residues 887-1038 and yielded crystals that belonged to the orthorhombic space group C2221, with unit-cell parameters a = 83.42, b = 176.58, c = 126.03 Å, α = β = γ = 90.00° and two molecules in the asymmetric unit (VM = 2.55 Å(3) Da(-1), solvent content 50.47%). X-ray diffraction data were collected to a resolution of 2.45 Å.
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Affiliation(s)
- Pavel Grinkevich
- Center for Nanobiology and Structural Biology, Institute of Microbiology ASCR, v.v.i., Zamek 136, 37333 Nove Hrady, Czech Republic
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 31, 37005 Ceske Budejovice, Czech Republic
| | - Iuliia Iermak
- Center for Nanobiology and Structural Biology, Institute of Microbiology ASCR, v.v.i., Zamek 136, 37333 Nove Hrady, Czech Republic
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 31, 37005 Ceske Budejovice, Czech Republic
| | - Nicholas A. Luedtke
- Center for Nanobiology and Structural Biology, Institute of Microbiology ASCR, v.v.i., Zamek 136, 37333 Nove Hrady, Czech Republic
- Ripon College, 300 Seward Street, Ripon, WI 54971, USA
| | - Jeroen R. Mesters
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, Lübeck, Germany
| | - Rüdiger Ettrich
- Center for Nanobiology and Structural Biology, Institute of Microbiology ASCR, v.v.i., Zamek 136, 37333 Nove Hrady, Czech Republic
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 31, 37005 Ceske Budejovice, Czech Republic
| | - Jost Ludwig
- Center for Nanobiology and Structural Biology, Institute of Microbiology ASCR, v.v.i., Zamek 136, 37333 Nove Hrady, Czech Republic
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 31, 37005 Ceske Budejovice, Czech Republic
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Ershova AS, Rusinov IS, Spirin SA, Karyagina AS, Alexeevski AV. Role of Restriction-Modification Systems in Prokaryotic Evolution and Ecology. BIOCHEMISTRY (MOSCOW) 2016; 80:1373-86. [PMID: 26567582 DOI: 10.1134/s0006297915100193] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Restriction-modification (R-M) systems are able to methylate or cleave DNA depending on methylation status of their recognition site. It allows them to protect bacterial cells from invasion by foreign DNA. Comparative analysis of a large number of available bacterial genomes and methylomes clearly demonstrates that the role of R-M systems in bacteria is wider than only defense. R-M systems maintain heterogeneity of a bacterial population and are involved in adaptation of bacteria to change in their environmental conditions. R-M systems can be essential for host colonization by pathogenic bacteria. Phase variation and intragenomic recombinations are sources of the fast evolution of the specificity of R-M systems. This review focuses on the influence of R-M systems on evolution and ecology of prokaryotes.
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Affiliation(s)
- A S Ershova
- Belozerksy Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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Urulangodi M, Dhanaraju R, Gupta K, Roy RP, Bujnicki JM, Rao DN. Asymmetric DNA methylation by dimeric EcoP15I DNA methyltransferase. Biochimie 2016; 128-129:70-82. [PMID: 27422119 DOI: 10.1016/j.biochi.2016.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 07/11/2016] [Indexed: 11/16/2022]
Abstract
EcoP15I DNA methyltransferase (M.EcoP15I) recognizes short asymmetric sequence, 5'-CAGCAG-3', and methylates the second adenine only on one strand of the double-stranded DNA (dsDNA). In vivo, this methylation is sufficient to protect the host DNA from cleavage by the cognate restriction endonuclease, R.EcoP15I, because of the stringent cleavage specificity requirements. Biochemical and structural characterization support the notion that purified M.EcoP15I exists and functions as dimer. However, the exact role of dimerization in M.EcoP15I reaction mechanism remains elusive. Here we engineered M.EcoP15I to a stable monomeric form and studied the role of dimerization in enzyme catalyzed methylation reaction. While the monomeric form binds single-stranded DNA (ssDNA) containing the recognition sequence it is unable to methylate it. Further we show that, while the monomeric form has AdoMet binding and Mg(2+) binding motifs intact, optimal dsDNA binding required for methylation is dependent on dimerization. Together, our biochemical data supports a unique subunit organization for M.EcoP15I to catalyze the methylation reaction.
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Affiliation(s)
| | - Rajkumar Dhanaraju
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Kanchan Gupta
- National Institute of Immunology, New Delhi 110 067, India
| | - Rajendra P Roy
- National Institute of Immunology, New Delhi 110 067, India
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, PL-02-109 Warsaw, Poland
| | - Desirazu N Rao
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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Weigele P, Raleigh EA. Biosynthesis and Function of Modified Bases in Bacteria and Their Viruses. Chem Rev 2016; 116:12655-12687. [PMID: 27319741 DOI: 10.1021/acs.chemrev.6b00114] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Naturally occurring modification of the canonical A, G, C, and T bases can be found in the DNA of cellular organisms and viruses from all domains of life. Bacterial viruses (bacteriophages) are a particularly rich but still underexploited source of such modified variant nucleotides. The modifications conserve the coding and base-pairing functions of DNA, but add regulatory and protective functions. In prokaryotes, modified bases appear primarily to be part of an arms race between bacteriophages (and other genomic parasites) and their hosts, although, as in eukaryotes, some modifications have been adapted to convey epigenetic information. The first half of this review catalogs the identification and diversity of DNA modifications found in bacteria and bacteriophages. What is known about the biogenesis, context, and function of these modifications are also described. The second part of the review places these DNA modifications in the context of the arms race between bacteria and bacteriophages. It focuses particularly on the defense and counter-defense strategies that turn on direct recognition of the presence of a modified base. Where modification has been shown to affect other DNA transactions, such as expression and chromosome segregation, that is summarized, with reference to recent reviews.
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Affiliation(s)
- Peter Weigele
- Chemical Biology, New England Biolabs , Ipswich, Massachusetts 01938, United States
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Kwiatek A, Mrozek A, Bacal P, Piekarowicz A, Adamczyk-Popławska M. Type III Methyltransferase M.NgoAX from Neisseria gonorrhoeae FA1090 Regulates Biofilm Formation and Interactions with Human Cells. Front Microbiol 2015; 6:1426. [PMID: 26733970 PMCID: PMC4685087 DOI: 10.3389/fmicb.2015.01426] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/30/2015] [Indexed: 11/24/2022] Open
Abstract
Neisseria gonorrhoeae is the etiological factor of the sexually transmitted gonorrhea disease that may lead, under specific conditions, to systemic infections. The gonococcal genome encodes many restriction modification (RM) systems, which main biological role is to defend the pathogen from potentially harmful foreign DNA. However, RM systems seem also to be involved in several other functions. In this study, we examined the effect of inactivation the N. gonorrhoeae FA1090 ngoAXmod gene encoding M.NgoAX methyltransferase on the global gene expression, biofilm formation, interactions with human epithelial host cells and overall bacterial growth. Expression microarrays showed at least a twofold deregulation of a total of 121 genes in the NgoAX knock-out mutant compared to the wild-type (wt) strain under standard grow conditions. Genes with changed expression levels encoded mostly proteins involved in cell metabolism, DNA replication and repair or regulating cellular processes and signaling (such as cell wall/envelop biogenesis). As determined by the assay with crystal violet, the NgoAX knock-out strain formed a slightly larger biofilm biomass per cell than the wt strain. Live biofilm observations showed that the biofilm formed by the gonococcal ngoAXmod gene mutant is more relaxed, dispersed and thicker than the one formed by the wt strain. This more relaxed feature of the biofilm, in respect to adhesion and bacterial interactions, can be involved in pathogenesis. Moreover, the overall adhesion of mutant bacterial cells to human cells was lower than adhesion of the wt gonococci [adhesion index = 0.672 (±0.2) and 2.15 (±1.53), respectively]; yet, a higher number of mutant than wt bacteria were found inside the Hec-1-B epithelial cells [invasion index = 3.38 (±0.93) × 105 for mutant and 4.67 (±3.09) × 104 for the wt strain]. These results indicate that NgoAX knock-out cells have lower ability to attach to human cells, but more easily penetrate inside the host cells. All these data suggest that the NgoAX methyltransferase, may be implicated in N. gonorrhoeae pathogenicity, involving regulation of biofilm formation, adhesion to host cells and epithelial cell invasion.
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Affiliation(s)
- Agnieszka Kwiatek
- Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Agnieszka Mrozek
- Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Pawel Bacal
- Laboratory of Theory and Applications of Electrodes, Faculty of Chemistry, University of Warsaw Warsaw, Poland
| | - Andrzej Piekarowicz
- Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
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Zautner AE, Goldschmidt AM, Thürmer A, Schuldes J, Bader O, Lugert R, Groß U, Stingl K, Salinas G, Lingner T. SMRT sequencing of the Campylobacter coli BfR-CA-9557 genome sequence reveals unique methylation motifs. BMC Genomics 2015; 16:1088. [PMID: 26689587 PMCID: PMC4687069 DOI: 10.1186/s12864-015-2317-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 12/15/2015] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Campylobacter species are the most prevalent bacterial pathogen causing acute enteritis worldwide. In contrast to Campylobacter jejuni, about 5 % of Campylobacter coli strains exhibit susceptibility to restriction endonuclease digestion by DpnI cutting specifically 5'-G(m)ATC-3' motifs. This indicates significant differences in DNA methylation between both microbial species. The goal of the study was to analyze the methylome of a C. coli strain susceptible to DpnI digestion, to identify its methylation motifs and restriction modification systems (RM-systems), and compare them to related organisms like C. jejuni and Helicobacter pylori. RESULTS Using one SMRT cell and the PacBio RS sequencing technology followed by PacBio Modification and Motif Analysis the complete genome of the DpnI susceptible strain C. coli BfR-CA-9557 was sequenced to 500-fold coverage and assembled into a single contig of 1.7 Mbp. The genome contains a CJIE1-like element prophage and is phylogenetically closer to C. coli clade 1 isolates than clade 3. 45,881 6-methylated adenines (ca. 2.7 % of genome positions) that are predominantly arranged in eight different methylation motifs and 1,788 4-methylated cytosines (ca. 0.1 %) have been detected. Only two of these motifs correspond to known restriction modification motifs. Characteristic for this methylome was the very high fraction of methylation of motifs with mostly above 99 %. CONCLUSIONS Only five dominant methylation motifs have been identified in C. jejuni, which have been associated with known RM-systems. C. coli BFR-CA-9557 shares one (RAATTY) of these, but four ORFs could be assigned to putative Type I RM-systems, seven ORFs to Type II RM-systems and three ORFs to Type IV RM-systems. In accordance with DpnI prescreening RM-system IIP, methylation of GATC motifs was detected in C. coli BfR-CA-9557. A homologous IIP RM-system has been described for H. pylori. The remaining methylation motifs are specific for C. coli BfR-CA-9557 and have been neither detected in C. jejuni nor in H. pylori. The results of this study give us new insights into epigenetics of Campylobacteraceae and provide the groundwork to resolve the function of RM-systems in C. coli.
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Affiliation(s)
- Andreas E Zautner
- Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, D-37075, Göttingen, Germany.
| | - Anne-Marie Goldschmidt
- Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, D-37075, Göttingen, Germany
| | - Andrea Thürmer
- Institute for Microbiology and Genetics, Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Jörg Schuldes
- Institute for Microbiology and Genetics, Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Oliver Bader
- Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, D-37075, Göttingen, Germany
| | - Raimond Lugert
- Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, D-37075, Göttingen, Germany
| | - Uwe Groß
- Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, D-37075, Göttingen, Germany
| | - Kerstin Stingl
- Federal Institute for Risk Assessment (BfR), Department of Biological Safety - National Reference Laboratory for Campylobacter, D-12277, Berlin, Germany
| | - Gabriela Salinas
- Microarray and Deep-Sequencing Core Facility, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, D-37077, Göttingen, Germany
| | - Thomas Lingner
- Microarray and Deep-Sequencing Core Facility, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, D-37077, Göttingen, Germany
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26
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In silico approaches for the identification of virulence candidates amongst hypothetical proteins of Mycoplasma pneumoniae 309. Comput Biol Chem 2015; 59 Pt A:67-80. [DOI: 10.1016/j.compbiolchem.2015.09.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 09/08/2015] [Accepted: 09/14/2015] [Indexed: 01/25/2023]
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27
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Chand MK, Nirwan N, Diffin FM, van Aelst K, Kulkarni M, Pernstich C, Szczelkun MD, Saikrishnan K. Translocation-coupled DNA cleavage by the Type ISP restriction-modification enzymes. Nat Chem Biol 2015; 11:870-7. [PMID: 26389736 PMCID: PMC4636054 DOI: 10.1038/nchembio.1926] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 08/27/2015] [Indexed: 01/21/2023]
Abstract
Production of endonucleolytic double-strand DNA breaks requires separate strand cleavage events. Although catalytic mechanisms for simple, dimeric endonucleases are known, there are many complex nuclease machines that are poorly understood. Here we studied the single polypeptide Type ISP restriction-modification (RM) enzymes, which cleave random DNA between distant target sites when two enzymes collide after convergent ATP-driven translocation. We report the 2.7-Å resolution X-ray crystal structure of a Type ISP enzyme-DNA complex, revealing that both the helicase-like ATPase and nuclease are located upstream of the direction of translocation, an observation inconsistent with simple nuclease-domain dimerization. Using single-molecule and biochemical techniques, we demonstrate that each ATPase remodels its DNA-protein complex and translocates along DNA without looping it, leading to a collision complex in which the nuclease domains are distal. Sequencing of the products of single cleavage events suggests a previously undescribed endonuclease model, where multiple, stochastic strand-nicking events combine to produce DNA scission.
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Affiliation(s)
- Mahesh Kumar Chand
- Division of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Neha Nirwan
- Division of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Fiona M. Diffin
- DNA-Protein Interactions Unit, School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Kara van Aelst
- DNA-Protein Interactions Unit, School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Manasi Kulkarni
- Division of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Christian Pernstich
- DNA-Protein Interactions Unit, School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Mark D. Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Kayarat Saikrishnan
- Division of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
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28
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Hoskisson PA, Sumby P, Smith MCM. The phage growth limitation system in Streptomyces coelicolor A(3)2 is a toxin/antitoxin system, comprising enzymes with DNA methyltransferase, protein kinase and ATPase activity. Virology 2015; 477:100-109. [PMID: 25592393 PMCID: PMC4365076 DOI: 10.1016/j.virol.2014.12.036] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/20/2014] [Accepted: 12/22/2014] [Indexed: 11/19/2022]
Abstract
The phage growth limitation system of Streptomyces coelicolor A3(2) is an unusual bacteriophage defence mechanism. Progeny ϕC31 phage from an initial infection are thought to be modified such that subsequent infections are attenuated in a Pgl(+) host but normal in a Pgl(-) strain. Earlier work identified four genes required for phage resistance by Pgl. Here we demonstrate that Pgl is an elaborate and novel phage restriction system that, in part, comprises a toxin/antitoxin system where PglX, a DNA methyltransferase is toxic in the absence of a functional PglZ. In addition, the ATPase activity of PglY and a protein kinase activity in PglW are shown to be essential for phage resistance by Pgl. We conclude that on infection of a Pgl(+) cell by bacteriophage ϕC31, PglW transduces a signal, probably via phosphorylation, to other Pgl proteins resulting in the activation of the DNA methyltransferase, PglX and this leads to phage restriction.
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Affiliation(s)
- Paul A Hoskisson
- Department of Molecular and Cell Biology, University of Aberdeen, Institute of Medical Science, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Paul Sumby
- Department of Genetics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, UK
| | - Margaret C M Smith
- Department of Molecular and Cell Biology, University of Aberdeen, Institute of Medical Science, Foresterhill, Aberdeen AB25 2ZD, UK.
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29
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Chaikind B, Ostermeier M. Directed evolution of improved zinc finger methyltransferases. PLoS One 2014; 9:e96931. [PMID: 24810747 PMCID: PMC4014571 DOI: 10.1371/journal.pone.0096931] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 04/14/2014] [Indexed: 01/09/2023] Open
Abstract
The ability to target DNA methylation toward a single, user-designated CpG site in vivo may have wide applicability for basic biological and biomedical research. A tool for targeting methylation toward single sites could be used to study the effects of individual methylation events on transcription, protein recruitment to DNA, and the dynamics of such epigenetic alterations. Although various tools for directing methylation to promoters exist, none offers the ability to localize methylation solely to a single CpG site. In our ongoing research to create such a tool, we have pursued a strategy employing artificially bifurcated DNA methyltransferases; each methyltransferase fragment is fused to zinc finger proteins with affinity for sequences flanking a targeted CpG site for methylation. We sought to improve the targeting of these enzymes by reducing the methyltransferase activity at non-targeted sites while maintaining high levels of activity at a targeted site. Here we demonstrate an in vitro directed evolution selection strategy to improve methyltransferase specificity and use it to optimize an engineered zinc finger methyltransferase derived from M.SssI. The unusual restriction enzyme McrBC is a key component of this strategy and is used to select against methyltransferases that methylate multiple sites on a plasmid. This strategy allowed us to quickly identify mutants with high levels of methylation at the target site (up to ∼80%) and nearly unobservable levels of methylation at a off-target sites (<1%), as assessed in E. coli. We also demonstrate that replacing the zinc finger domains with new zinc fingers redirects the methylation to a new target CpG site flanked by the corresponding zinc finger binding sequences.
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Affiliation(s)
- Brian Chaikind
- Chemistry-Biology Interface Graduate Program, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Marc Ostermeier
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
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30
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Furuta Y, Namba-Fukuyo H, Shibata TF, Nishiyama T, Shigenobu S, Suzuki Y, Sugano S, Hasebe M, Kobayashi I. Methylome diversification through changes in DNA methyltransferase sequence specificity. PLoS Genet 2014; 10:e1004272. [PMID: 24722038 PMCID: PMC3983042 DOI: 10.1371/journal.pgen.1004272] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Accepted: 02/13/2014] [Indexed: 12/20/2022] Open
Abstract
Epigenetic modifications such as DNA methylation have large effects on gene expression and genome maintenance. Helicobacter pylori, a human gastric pathogen, has a large number of DNA methyltransferase genes, with different strains having unique repertoires. Previous genome comparisons suggested that these methyltransferases often change DNA sequence specificity through domain movement--the movement between and within genes of coding sequences of target recognition domains. Using single-molecule real-time sequencing technology, which detects N6-methyladenines and N4-methylcytosines with single-base resolution, we studied methylated DNA sites throughout the H. pylori genome for several closely related strains. Overall, the methylome was highly variable among closely related strains. Hypermethylated regions were found, for example, in rpoB gene for RNA polymerase. We identified DNA sequence motifs for methylation and then assigned each of them to a specific homology group of the target recognition domains in the specificity-determining genes for Type I and other restriction-modification systems. These results supported proposed mechanisms for sequence-specificity changes in DNA methyltransferases. Knocking out one of the Type I specificity genes led to transcriptome changes, which suggested its role in gene expression. These results are consistent with the concept of evolution driven by DNA methylation, in which changes in the methylome lead to changes in the transcriptome and potentially to changes in phenotype, providing targets for natural or artificial selection.
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Affiliation(s)
- Yoshikazu Furuta
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan
| | - Hiroe Namba-Fukuyo
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
| | | | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | - Shuji Shigenobu
- National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki, Japan
| | - Ichizo Kobayashi
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan
- * E-mail:
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31
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Huynh Thi Yen L, Park SY, Kim JS. Cloning, crystallization and preliminary X-ray diffraction analysis of an intact DNA methyltransferase of a type I restriction-modification enzyme from Vibrio vulnificus. Acta Crystallogr F Struct Biol Commun 2014; 70:489-92. [PMID: 24699746 PMCID: PMC3976070 DOI: 10.1107/s2053230x14004543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 02/27/2014] [Indexed: 11/10/2022] Open
Abstract
Independently of the restriction (HsdR) subunit, the specificity (HsdS) and methylation (HsdM) subunits interact with each other, and function as a methyltransferase in type I restriction-modification systems. A single gene that combines the HsdS and HsdM subunits in Vibrio vulnificus YJ016 was expressed and purified. A crystal suitable for X-ray diffraction was obtained from 25%(w/v) polyethylene glycol monomethylether 5000, 0.1 M HEPES pH 8.0, 0.2 M ammonium sulfate at 291 K by hanging-drop vapour diffusion. Diffraction data were collected to a resolution of 2.31 Å using synchrotron radiation. The crystal belonged to the primitive monoclinic space group P21, with unit-cell parameters a = 93.25, b = 133.04, c = 121.49 Å, β = 109.7°. With four molecules in the asymmetric unit, the crystal volume per unit protein weight was 2.61 Å(3) Da(-1), corresponding to a solvent content of 53%.
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Affiliation(s)
- Ly Huynh Thi Yen
- Department of Chemistry, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Suk-Youl Park
- Department of Chemistry, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju 500-757, Republic of Korea
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32
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Smith RM, Pernstich C, Halford SE. TstI, a Type II restriction-modification protein with DNA recognition, cleavage and methylation functions in a single polypeptide. Nucleic Acids Res 2014; 42:5809-22. [PMID: 24634443 PMCID: PMC4027205 DOI: 10.1093/nar/gku187] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Type II restriction–modification systems cleave and methylate DNA at specific sequences. However, the Type IIB systems look more like Type I than conventional Type II schemes as they employ the same protein for both restriction and modification and for DNA recognition. Several Type IIB proteins, including the archetype BcgI, are assemblies of two polypeptides: one with endonuclease and methyltransferase roles, another for DNA recognition. Conversely, some IIB proteins express all three functions from separate segments of a single polypeptide. This study analysed one such single-chain protein, TstI. Comparison with BcgI showed that the one- and the two-polypeptide systems differ markedly. Unlike the heterologous assembly of BcgI, TstI forms a homotetramer. The tetramer bridges two recognition sites before eventually cutting the DNA in both strands on both sides of the sites, but at each site the first double-strand break is made long before the second. In contrast, BcgI cuts all eight target bonds at two sites in a single step. TstI also differs from BcgI in either methylating or cleaving unmodified sites at similar rates. The site may thus be modified before TstI can make the second double-strand break. TstI MTase acts best at hemi-methylated sites.
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Affiliation(s)
- Rachel M Smith
- The DNA-proteins Interaction Unit, School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Christian Pernstich
- The DNA-proteins Interaction Unit, School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Stephen E Halford
- The DNA-proteins Interaction Unit, School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
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Restriction-Modification Systems as a Barrier for Genetic Manipulation of Staphylococcus aureus. Methods Mol Biol 2014; 1373:9-23. [PMID: 25646604 DOI: 10.1007/7651_2014_180] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genetic manipulation is a powerful approach to study fundamental aspects of bacterial physiology, metabolism, and pathogenesis. Most Staphylococcus aureus strains are remarkably difficult to genetically manipulate as they possess strong host defense mechanisms that protect bacteria from cellular invasion by foreign DNA. In S. aureus these bacterial "immunity" mechanisms against invading genomes are mainly associated with restriction-modification systems. To date, prokaryotic restriction-modification systems are classified into four different types (Type I-IV), all of which have been found in the sequenced S. aureus genomes. This chapter describes the roles, classification, mechanisms of action of different types of restriction-modification systems and the recent advances in the biology of restriction and modification in S. aureus.
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Loenen WAM, Dryden DTF, Raleigh EA, Wilson GG. Type I restriction enzymes and their relatives. Nucleic Acids Res 2014; 42:20-44. [PMID: 24068554 PMCID: PMC3874165 DOI: 10.1093/nar/gkt847] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 08/26/2013] [Accepted: 08/29/2013] [Indexed: 12/24/2022] Open
Abstract
Type I restriction enzymes (REases) are large pentameric proteins with separate restriction (R), methylation (M) and DNA sequence-recognition (S) subunits. They were the first REases to be discovered and purified, but unlike the enormously useful Type II REases, they have yet to find a place in the enzymatic toolbox of molecular biologists. Type I enzymes have been difficult to characterize, but this is changing as genome analysis reveals their genes, and methylome analysis reveals their recognition sequences. Several Type I REases have been studied in detail and what has been learned about them invites greater attention. In this article, we discuss aspects of the biochemistry, biology and regulation of Type I REases, and of the mechanisms that bacteriophages and plasmids have evolved to evade them. Type I REases have a remarkable ability to change sequence specificity by domain shuffling and rearrangements. We summarize the classic experiments and observations that led to this discovery, and we discuss how this ability depends on the modular organizations of the enzymes and of their S subunits. Finally, we describe examples of Type II restriction-modification systems that have features in common with Type I enzymes, with emphasis on the varied Type IIG enzymes.
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Affiliation(s)
- Wil A. M. Loenen
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands, EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9, 3JJ, Scotland, UK and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
| | - David T. F. Dryden
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands, EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9, 3JJ, Scotland, UK and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
| | - Elisabeth A. Raleigh
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands, EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9, 3JJ, Scotland, UK and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
| | - Geoffrey G. Wilson
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands, EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9, 3JJ, Scotland, UK and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
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35
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Loenen WAM, Dryden DTF, Raleigh EA, Wilson GG, Murray NE. Highlights of the DNA cutters: a short history of the restriction enzymes. Nucleic Acids Res 2014; 42:3-19. [PMID: 24141096 PMCID: PMC3874209 DOI: 10.1093/nar/gkt990] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 09/24/2013] [Accepted: 10/02/2013] [Indexed: 11/16/2022] Open
Abstract
In the early 1950's, 'host-controlled variation in bacterial viruses' was reported as a non-hereditary phenomenon: one cycle of viral growth on certain bacterial hosts affected the ability of progeny virus to grow on other hosts by either restricting or enlarging their host range. Unlike mutation, this change was reversible, and one cycle of growth in the previous host returned the virus to its original form. These simple observations heralded the discovery of the endonuclease and methyltransferase activities of what are now termed Type I, II, III and IV DNA restriction-modification systems. The Type II restriction enzymes (e.g. EcoRI) gave rise to recombinant DNA technology that has transformed molecular biology and medicine. This review traces the discovery of restriction enzymes and their continuing impact on molecular biology and medicine.
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Affiliation(s)
- Wil A. M. Loenen
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - David T. F. Dryden
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Elisabeth A. Raleigh
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Geoffrey G. Wilson
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
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36
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Zemlyanskaya EV, Degtyarev SK. Substrate specificity and properties of methyl-directed site-specific DNA endonucleases. Mol Biol 2013. [DOI: 10.1134/s0026893313060186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Krebes J, Morgan RD, Bunk B, Spröer C, Luong K, Parusel R, Anton BP, König C, Josenhans C, Overmann J, Roberts RJ, Korlach J, Suerbaum S. The complex methylome of the human gastric pathogen Helicobacter pylori. Nucleic Acids Res 2013; 42:2415-32. [PMID: 24302578 PMCID: PMC3936762 DOI: 10.1093/nar/gkt1201] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The genome of Helicobacter pylori is remarkable for its large number of restriction-modification (R-M) systems, and strain-specific diversity in R-M systems has been suggested to limit natural transformation, the major driving force of genetic diversification in H. pylori. We have determined the comprehensive methylomes of two H. pylori strains at single base resolution, using Single Molecule Real-Time (SMRT®) sequencing. For strains 26695 and J99-R3, 17 and 22 methylated sequence motifs were identified, respectively. For most motifs, almost all sites occurring in the genome were detected as methylated. Twelve novel methylation patterns corresponding to nine recognition sequences were detected (26695, 3; J99-R3, 6). Functional inactivation, correction of frameshifts as well as cloning and expression of candidate methyltransferases (MTases) permitted not only the functional characterization of multiple, yet undescribed, MTases, but also revealed novel features of both Type I and Type II R-M systems, including frameshift-mediated changes of sequence specificity and the interaction of one MTase with two alternative specificity subunits resulting in different methylation patterns. The methylomes of these well-characterized H. pylori strains will provide a valuable resource for future studies investigating the role of H. pylori R-M systems in limiting transformation as well as in gene regulation and host interaction.
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Affiliation(s)
- Juliane Krebes
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany, German Center for Infection Research, Hannover-Braunschweig Site, Carl-Neuberg-Straße 1, 30625 Hannover, Germany, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany and Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA
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38
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Exploring the roles of DNA methylation in the metal-reducing bacterium Shewanella oneidensis MR-1. J Bacteriol 2013; 195:4966-74. [PMID: 23995632 DOI: 10.1128/jb.00935-13] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We performed whole-genome analyses of DNA methylation in Shewanella oneidensis MR-1 to examine its possible role in regulating gene expression and other cellular processes. Single-molecule real-time (SMRT) sequencing revealed extensive methylation of adenine (N6mA) throughout the genome. These methylated bases were located in five sequence motifs, including three novel targets for type I restriction/modification enzymes. The sequence motifs targeted by putative methyltranferases were determined via SMRT sequencing of gene knockout mutants. In addition, we found that S. oneidensis MR-1 cultures grown under various culture conditions displayed different DNA methylation patterns. However, the small number of differentially methylated sites could not be directly linked to the much larger number of differentially expressed genes under these conditions, suggesting that DNA methylation is not a major regulator of gene expression in S. oneidensis MR-1. The enrichment of methylated GATC motifs in the origin of replication indicates that DNA methylation may regulate genome replication in a manner similar to that seen in Escherichia coli. Furthermore, comparative analyses suggest that many Gammaproteobacteria, including all members of the Shewanellaceae family, may also utilize DNA methylation to regulate genome replication.
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39
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Algire MA, Montague MG, Vashee S, Lartigue C, Merryman C. A Type III restriction-modification system in Mycoplasma mycoides subsp. capri. Open Biol 2013; 2:120115. [PMID: 23155485 PMCID: PMC3498834 DOI: 10.1098/rsob.120115] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 10/10/2012] [Indexed: 12/24/2022] Open
Abstract
The sequenced genome of Mycoplasma mycoides subsp. capri revealed the presence of a Type III restriction–modification system (MmyCI). The methyltransferase (modification) subunit of MmyCI (M.MmyCI) was shown to recognize the sequence 5′-TGAG-3′ and methylate the adenine. The coding region of the methyltransferase gene contains 12 consecutive AG dinucleotide repeats that result in a translational termination at a TAA codon immediately beyond the repeat region. This strain does not have MmyCI activity. A clone was found with 10 AG repeats such that the gene is in frame, and this strain has MmyCI activity, suggesting that the expression of the MmyCI methyltransferase may be phase variable.
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Affiliation(s)
- Mikkel A Algire
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.
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40
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Schwarz FW, Tóth J, van Aelst K, Cui G, Clausing S, Szczelkun MD, Seidel R. The helicase-like domains of type III restriction enzymes trigger long-range diffusion along DNA. Science 2013; 340:353-6. [PMID: 23599494 PMCID: PMC3646237 DOI: 10.1126/science.1231122] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Helicases are ubiquitous adenosine triphosphatases (ATPases) with widespread roles in genome metabolism. Here, we report a previously undescribed functionality for ATPases with helicase-like domains; namely, that ATP hydrolysis can trigger ATP-independent long-range protein diffusion on DNA in one dimension (1D). Specifically, using single-molecule fluorescence microscopy we show that the Type III restriction enzyme EcoP15I uses its ATPase to switch into a distinct structural state that diffuses on DNA over long distances and long times. The switching occurs only upon binding to the target site and requires hydrolysis of ~30 ATPs. We define the mechanism for these enzymes and show how ATPase activity is involved in DNA target site verification and 1D signaling, roles that are common in DNA metabolism: for example, in nucleotide excision and mismatch repair.
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Affiliation(s)
- Friedrich W. Schwarz
- DNA motors group, Biotechnology Center, Technische Universität Dresden, 01062 Dresden, Germany
| | - Júlia Tóth
- DNA-Protein Interactions Unit, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK
| | - Kara van Aelst
- DNA-Protein Interactions Unit, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK
| | - Guanshen Cui
- DNA-Protein Interactions Unit, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK
| | - Sylvia Clausing
- DNA motors group, Biotechnology Center, Technische Universität Dresden, 01062 Dresden, Germany
| | - Mark D. Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK
| | - Ralf Seidel
- DNA motors group, Biotechnology Center, Technische Universität Dresden, 01062 Dresden, Germany
- Institute of Molecular Cell Biology, University of Münster, 48149 Münster, Germany
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41
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Makarova KS, Wolf YI, Koonin EV. Comparative genomics of defense systems in archaea and bacteria. Nucleic Acids Res 2013; 41:4360-77. [PMID: 23470997 PMCID: PMC3632139 DOI: 10.1093/nar/gkt157] [Citation(s) in RCA: 297] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Our knowledge of prokaryotic defense systems has vastly expanded as the result of comparative genomic analysis, followed by experimental validation. This expansion is both quantitative, including the discovery of diverse new examples of known types of defense systems, such as restriction-modification or toxin-antitoxin systems, and qualitative, including the discovery of fundamentally new defense mechanisms, such as the CRISPR-Cas immunity system. Large-scale statistical analysis reveals that the distribution of different defense systems in bacterial and archaeal taxa is non-uniform, with four groups of organisms distinguishable with respect to the overall abundance and the balance between specific types of defense systems. The genes encoding defense system components in bacterial and archaea typically cluster in defense islands. In addition to genes encoding known defense systems, these islands contain numerous uncharacterized genes, which are candidates for new types of defense systems. The tight association of the genes encoding immunity systems and dormancy- or cell death-inducing defense systems in prokaryotic genomes suggests that these two major types of defense are functionally coupled, providing for effective protection at the population level.
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Affiliation(s)
- Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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42
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Vasu K, Nagaraja V. Diverse functions of restriction-modification systems in addition to cellular defense. Microbiol Mol Biol Rev 2013; 77:53-72. [PMID: 23471617 PMCID: PMC3591985 DOI: 10.1128/mmbr.00044-12] [Citation(s) in RCA: 383] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Restriction-modification (R-M) systems are ubiquitous and are often considered primitive immune systems in bacteria. Their diversity and prevalence across the prokaryotic kingdom are an indication of their success as a defense mechanism against invading genomes. However, their cellular defense function does not adequately explain the basis for their immaculate specificity in sequence recognition and nonuniform distribution, ranging from none to too many, in diverse species. The present review deals with new developments which provide insights into the roles of these enzymes in other aspects of cellular function. In this review, emphasis is placed on novel hypotheses and various findings that have not yet been dealt with in a critical review. Emerging studies indicate their role in various cellular processes other than host defense, virulence, and even controlling the rate of evolution of the organism. We also discuss how R-M systems could have successfully evolved and be involved in additional cellular portfolios, thereby increasing the relative fitness of their hosts in the population.
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Affiliation(s)
- Kommireddy Vasu
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
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43
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Smith RM, Jacklin AJ, Marshall JJT, Sobott F, Halford SE. Organization of the BcgI restriction-modification protein for the transfer of one methyl group to DNA. Nucleic Acids Res 2012; 41:405-17. [PMID: 23147004 PMCID: PMC3592466 DOI: 10.1093/nar/gks1000] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Type IIB restriction–modification protein BcgI contains A and B subunits in a
2:1 ratio: A has the active sites for both endonuclease and methyltransferase functions
while B recognizes the DNA. Like almost all Type IIB systems, BcgI needs two unmethylated
sites for nuclease activity; it cuts both sites upstream and downstream of the recognition
sequence, hydrolyzing eight phosphodiester bonds in a single synaptic complex. This
complex may incorporate four A2B protomers to give the eight catalytic centres
(one per A subunit) needed to cut all eight bonds. The BcgI recognition sequence contains
one adenine in each strand that can be N6-methylated. Although most DNA
methyltransferases operate at both unmethylated and hemi-methylated sites, BcgI
methyltransferase is only effective at hemi-methylated sites, where the nuclease component
is inactive. Unlike the nuclease, the methyltransferase acts at solitary sites,
functioning catalytically rather than stoichiometrically. Though it transfers one methyl
group at a time, presumably through a single A subunit, BcgI methyltransferase can be
activated by adding extra A subunits, either individually or as part of A2B
protomers, which indicates that it requires an assembly containing at least two
A2B units.
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Affiliation(s)
- Rachel M Smith
- The DNA-protein Interactions Unit, School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
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44
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Smith RM, Marshall JJT, Jacklin AJ, Retter SE, Halford SE, Sobott F. Organization of the BcgI restriction-modification protein for the cleavage of eight phosphodiester bonds in DNA. Nucleic Acids Res 2012; 41:391-404. [PMID: 23147005 PMCID: PMC3592470 DOI: 10.1093/nar/gks1023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Type IIB restriction-modification systems, such as BcgI, feature a single protein with
both endonuclease and methyltransferase activities. Type IIB nucleases require two
recognition sites and cut both strands on both sides of their unmodified sites. BcgI cuts
all eight target phosphodiester bonds before dissociation. The BcgI protein contains A and
B polypeptides in a 2:1 ratio: A has one catalytic centre for each activity; B recognizes
the DNA. We show here that BcgI is organized as A2B protomers, with B at its
centre, but that these protomers self-associate to assemblies containing several
A2B units. Moreover, like the well known FokI nuclease, BcgI bound to its
site has to recruit additional protomers before it can cut DNA. DNA-bound BcgI can
alternatively be activated by excess A subunits, much like the activation of FokI by its
catalytic domain. Eight A subunits, each with one centre for nuclease activity, are
presumably needed to cut the eight bonds cleaved by BcgI. Its nuclease reaction may thus
involve two A2B units, each bound to a recognition site, with two more
A2B units bridging the complexes by protein–protein interactions
between the nuclease domains.
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Affiliation(s)
- Rachel M Smith
- The DNA-proteins Interaction Unit, School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
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45
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Park SY, Lee HJ, Song JM, Sun J, Hwang HJ, Nishi K, Kim JS. Structural characterization of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1570-7. [PMID: 23090406 DOI: 10.1107/s0907444912038826] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 09/10/2012] [Indexed: 11/10/2022]
Abstract
In multifunctional type I restriction enzymes, active methyltransferases (MTases) are constituted of methylation (HsdM) and specificity (HsdS) subunits. In this study, the crystal structure of a putative HsdM subunit from Vibrio vulnificus YJ016 (vvHsdM) was elucidated at a resolution of 1.80 Å. A cofactor-binding site for S-adenosyl-L-methionine (SAM, a methyl-group donor) is formed within the C-terminal domain of an α/β-fold, in which a number of residues are conserved, including the GxGG and (N/D)PP(F/Y) motifs, which are likely to interact with several functional moieties of the SAM methyl-group donor. Comparison with the N6 DNA MTase of Thermus aquaticus and other HsdM structures suggests that two aromatic rings (Phe199 and Phe312) in the motifs that are conserved among the HsdMs may sandwich both sides of the adenine ring of the recognition sequence so that a conserved Asn residue (Asn309) can interact with the N6 atom of the target adenine base (a methyl-group acceptor) and locate the target adenine base close to the transferred SAM methyl group.
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Affiliation(s)
- Suk-Youl Park
- Department of Chemistry, Chonnam National University, Gwangju 500-757, Republic of Korea
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46
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Zaremba M, Sasnauskas G, Siksnys V. The link between restriction endonuclease fidelity and oligomeric state: a study with Bse634I. FEBS Lett 2012; 586:3324-9. [PMID: 22828280 DOI: 10.1016/j.febslet.2012.07.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 07/02/2012] [Accepted: 07/06/2012] [Indexed: 11/18/2022]
Abstract
Type II restriction endonucleases (REases) exist in multiple oligomeric forms. The tetrameric REases have two DNA binding interfaces and must synapse two recognition sites to achieve cleavage. It was hypothesised that binding of two recognition sites by tetrameric enzymes contributes to their fidelity. Here, we experimentally determined the fidelity for Bse634I REase in different oligomeric states. Surprisingly, we find that tetramerisation does not increase REase fidelity in comparison to the dimeric variant. Instead, an inherent ability to act concertedly at two sites provides tetrameric REase with a safety-catch to prevent host DNA cleavage if a single unmodified site becomes available.
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47
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Furuta Y, Kobayashi I. Movement of DNA sequence recognition domains between non-orthologous proteins. Nucleic Acids Res 2012; 40:9218-32. [PMID: 22821560 PMCID: PMC3467074 DOI: 10.1093/nar/gks681] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Comparisons of proteins show that they evolve through the movement of domains. However, in many cases, the underlying mechanisms remain unclear. Here, we observed the movements of DNA recognition domains between non-orthologous proteins within a prokaryote genome. Restriction-modification (RM) systems, consisting of a sequence-specific DNA methyltransferase and a restriction enzyme, contribute to maintenance/evolution of genomes/epigenomes. RM systems limit horizontal gene transfer but are themselves mobile. We compared Type III RM systems in Helicobacter pylori genomes and found that target recognition domain (TRD) sequences are mobile, moving between different orthologous groups that occupy unique chromosomal locations. Sequence comparisons suggested that a likely underlying mechanism is movement through homologous recombination of similar DNA sequences that encode amino acid sequence motifs that are conserved among Type III DNA methyltransferases. Consistent with this movement, incongruence was observed between the phylogenetic trees of TRD regions and other regions in proteins. Horizontal acquisition of diverse TRD sequences was suggested by detection of homologs in other Helicobacter species and distantly related bacterial species. One of these RM systems in H. pylori was inactivated by insertion of another RM system that likely transferred from an oral bacterium. TRD movement represents a novel route for diversification of DNA-interacting proteins.
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Affiliation(s)
- Yoshikazu Furuta
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan
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48
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Tóth J, van Aelst K, Salmons H, Szczelkun MD. Dissociation from DNA of Type III Restriction-Modification enzymes during helicase-dependent motion and following endonuclease activity. Nucleic Acids Res 2012; 40:6752-64. [PMID: 22523084 PMCID: PMC3413136 DOI: 10.1093/nar/gks328] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
DNA cleavage by the Type III Restriction–Modification (RM) enzymes requires the binding of a pair of RM enzymes at two distant, inversely orientated recognition sequences followed by helicase-catalysed ATP hydrolysis and long-range communication. Here we addressed the dissociation from DNA of these enzymes at two stages: during long-range communication and following DNA cleavage. First, we demonstrated that a communicating species can be trapped in a DNA domain without a recognition site, with a non-specific DNA association lifetime of ∼200 s. If free DNA ends were present the lifetime became too short to measure, confirming that ends accelerate dissociation. Secondly, we observed that Type III RM enzymes can dissociate upon DNA cleavage and go on to cleave further DNA molecules (they can ‘turnover’, albeit inefficiently). The relationship between the observed cleavage rate and enzyme concentration indicated independent binding of each site and a requirement for simultaneous interaction of at least two enzymes per DNA to achieve cleavage. In light of various mechanisms for helicase-driven motion on DNA, we suggest these results are most consistent with a thermally driven random 1D search model (i.e. ‘DNA sliding’).
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Affiliation(s)
- Júlia Tóth
- DNA-Protein Interactions Unit, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK
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49
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Gupta R, Capalash N, Sharma P. Restriction endonucleases: natural and directed evolution. Appl Microbiol Biotechnol 2012; 94:583-99. [PMID: 22398859 DOI: 10.1007/s00253-012-3961-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 02/08/2012] [Accepted: 02/09/2012] [Indexed: 10/28/2022]
Abstract
Type II restriction endonucleases (REs) are highly sequence-specific compared with other classes of nucleases. PD-(D/E)XK nucleases, initially represented by only type II REs, now comprise a large and extremely diverse superfamily of proteins and, although sharing a structurally conserved core, typically display little or no detectable sequence similarity except for the active site motifs. Sequence similarity can only be observed in methylases and few isoschizomers. As a consequence, REs are classified according to combinations of functional properties rather than on the basis of genetic relatedness. New alignment matrices and classification systems based on structural core connectivity and cleavage mechanisms have been developed to characterize new REs and related proteins. REs recognizing more than 300 distinct specificities have been identified in RE database (REBASE: http://rebase.neb.com/cgi-bin/statlist ) but still the need for newer specificities is increasing due to the advancement in molecular biology and applications. The enzymes have undergone constant evolution through structural changes in protein scaffolds which include random mutations, homologous recombinations, insertions, and deletions of coding DNA sequences but rational mutagenesis or directed evolution delivers protein variants with new functions in accordance with defined biochemical or environmental pressures. Redesigning through random mutation, addition or deletion of amino acids, methylation-based selection, synthetic molecules, combining recognition and cleavage domains from different enzymes, or combination with domains of additional functions change the cleavage specificity or substrate preference and stability. There is a growing number of patents awarded for the creation of engineered REs with new and enhanced properties.
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Affiliation(s)
- Richa Gupta
- Department of Biotechnology, Panjab University, Chandigarh, India 160014
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50
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Rusling DA, Laurens N, Pernstich C, Wuite GJL, Halford SE. DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations. Nucleic Acids Res 2012; 40:4977-87. [PMID: 22362745 PMCID: PMC3367207 DOI: 10.1093/nar/gks183] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Most restriction endonucleases, including FokI, interact with two copies of their recognition sequence before cutting DNA. On DNA with two sites they act in cis looping out the intervening DNA. While many restriction enzymes operate symmetrically at palindromic sites, FokI acts asymmetrically at a non-palindromic site. The directionality of its sequence means that two FokI sites can be bridged in either parallel or anti-parallel alignments. Here we show by biochemical and single-molecule biophysical methods that FokI aligns two recognition sites on separate DNA molecules in parallel and that the parallel arrangement holds for sites in the same DNA regardless of whether they are in inverted or repeated orientations. The parallel arrangement dictates the topology of the loop trapped between sites in cis: the loop from inverted sites has a simple 180° bend, while that with repeated sites has a convoluted 360° turn. The ability of FokI to act at asymmetric sites thus enabled us to identify the synapse geometry for sites in trans and in cis, which in turn revealed the relationship between synapse geometry and loop topology.
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Affiliation(s)
- David A Rusling
- The DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
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