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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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PacBio sequencing output increased through uniform and directional fivefold concatenation. Sci Rep 2021; 11:18065. [PMID: 34508117 PMCID: PMC8433307 DOI: 10.1038/s41598-021-96829-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/17/2021] [Indexed: 12/20/2022] Open
Abstract
Advances in sequencing technology have allowed researchers to sequence DNA with greater ease and at decreasing costs. Main developments have focused on either sequencing many short sequences or fewer large sequences. Methods for sequencing mid-sized sequences of 600-5,000 bp are currently less efficient. For example, the PacBio Sequel I system yields ~ 100,000-300,000 reads with an accuracy per base pair of 90-99%. We sought to sequence several DNA populations of ~ 870 bp in length with a sequencing accuracy of 99% and to the greatest depth possible. We optimised a simple, robust method to concatenate genes of ~ 870 bp five times and then sequenced the resulting DNA of ~ 5,000 bp by PacBioSMRT long-read sequencing. Our method improved upon previously published concatenation attempts, leading to a greater sequencing depth, high-quality reads and limited sample preparation at little expense. We applied this efficient concatenation protocol to sequence nine DNA populations from a protein engineering study. The improved method is accompanied by a simple and user-friendly analysis pipeline, DeCatCounter, to sequence medium-length sequences efficiently at one-fifth of the cost.
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Bower EKM, Cooper LP, Roberts GA, White JH, Luyten Y, Morgan RD, Dryden DTF. A model for the evolution of prokaryotic DNA restriction-modification systems based upon the structural malleability of Type I restriction-modification enzymes. Nucleic Acids Res 2019; 46:9067-9080. [PMID: 30165537 PMCID: PMC6158711 DOI: 10.1093/nar/gky760] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 08/21/2018] [Indexed: 12/28/2022] Open
Abstract
Restriction Modification (RM) systems prevent the invasion of foreign genetic material into bacterial cells by restriction and protect the host's genetic material by methylation. They are therefore important in maintaining the integrity of the host genome. RM systems are currently classified into four types (I to IV) on the basis of differences in composition, target recognition, cofactors and the manner in which they cleave DNA. Comparing the structures of the different types, similarities can be observed suggesting an evolutionary link between these different types. This work describes the ‘deconstruction’ of a large Type I RM enzyme into forms structurally similar to smaller Type II RM enzymes in an effort to elucidate the pathway taken by Nature to form these different RM enzymes. Based upon the ability to engineer new enzymes from the Type I ‘scaffold’, an evolutionary pathway and the evolutionary pressures required to move along the pathway from Type I RM systems to Type II RM systems are proposed. Experiments to test the evolutionary model are discussed.
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Affiliation(s)
- Edward K M Bower
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FJ, UK
| | - Laurie P Cooper
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FJ, UK
| | - Gareth A Roberts
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FJ, UK
| | - John H White
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FJ, UK
| | - Yvette Luyten
- New England Biolabs, 240 County Road, Ipswich, MA 01938-2723, USA
| | - Richard D Morgan
- New England Biolabs, 240 County Road, Ipswich, MA 01938-2723, USA
| | - David T F Dryden
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
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