1
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Shen B, Heiter D, Yang W, Xu SY, Stoddard B. Cryo-EM structures of DNA-free and DNA-bound BsaXI: architecture of a Type IIB restriction-modification enzyme. Nucleic Acids Res 2025; 53:gkaf291. [PMID: 40239994 PMCID: PMC11997821 DOI: 10.1093/nar/gkaf291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Revised: 03/25/2025] [Accepted: 03/28/2025] [Indexed: 04/18/2025] Open
Abstract
We have determined multiple cryogenic electron microscopy (cryo-EM) structures of the Type IIB restriction-modification enzyme BsaXI. Such enzymes cleave DNA on both sides of their recognition sequence and share features of Types I, II, and III restriction systems. BsaXI forms a heterotrimeric (RM)2S assemblage in the presence and absence of bound DNA. Two unique structural motifs-a multi-helical "knob" and a long antiparallel double-helical "paddle"-are involved in DNA binding and cleavage. Binding of the DNA target triggers a large conformational change from an 'open' to 'closed' configuration, resulting in a mixture of two different conformations with respect to the positioning of the S subunit and its target recognition domains on the enzyme's bipartite DNA target site. Structure-guided mutagenesis studies implicated two clusters of residues in the RM subunit as being critical for DNA cleavage, both are located proximal to a DNA cleavage site. One corresponds to a canonical PD-(D/E)xK endonuclease site in the N-terminal endonuclease domain, while the other corresponds to residues clustered within the paddle motif (near to the C-terminal end of the RM subunit). This analysis facilitates a comparison of three potential mechanisms by which such enzymes cleave DNA on each side of the bound target.
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Affiliation(s)
- Betty W Shen
- Division of Basic Sciences, Fred Hutchinson Cancer Research, 1100 Fairview Ave. N. Seattle, WA 98109, United States
| | - Dan Heiter
- New England Biolabs, 240 County Road Ipswich, MA 01938, United States
| | - Weiwei Yang
- New England Biolabs, 240 County Road Ipswich, MA 01938, United States
| | - Shuang-yong Xu
- New England Biolabs, 240 County Road Ipswich, MA 01938, United States
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research, 1100 Fairview Ave. N. Seattle, WA 98109, United States
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2
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Galià-Camps C, Pegueroles C, Turon X, Carreras C, Pascual M. Genome composition and GC content influence loci distribution in reduced representation genomic studies. BMC Genomics 2024; 25:410. [PMID: 38664648 PMCID: PMC11046876 DOI: 10.1186/s12864-024-10312-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Genomic architecture is a key evolutionary trait for living organisms. Due to multiple complex adaptive and neutral forces which impose evolutionary pressures on genomes, there is a huge variability of genomic features. However, their variability and the extent to which genomic content determines the distribution of recovered loci in reduced representation sequencing studies is largely unexplored. RESULTS Here, by using 80 genome assemblies, we observed that whereas plants primarily increase their genome size by expanding their intergenic regions, animals expand both intergenic and intronic regions, although the expansion patterns differ between deuterostomes and protostomes. Loci mapping in introns, exons, and intergenic categories obtained by in silico digestion using 2b-enzymes are positively correlated with the percentage of these regions in the corresponding genomes, suggesting that loci distribution mostly mirrors genomic architecture of the selected taxon. However, exonic regions showed a significant enrichment of loci in all groups regardless of the used enzyme. Moreover, when using selective adaptors to obtain a secondarily reduced loci dataset, the percentage and distribution of retained loci also varied. Adaptors with G/C terminals recovered a lower percentage of selected loci, with a further enrichment of exonic regions, while adaptors with A/T terminals retained a higher percentage of loci and slightly selected more intronic regions than expected. CONCLUSIONS Our results highlight how genome composition, genome GC content, RAD enzyme choice and use of base-selective adaptors influence reduced genome representation techniques. This is important to acknowledge in population and conservation genomic studies, as it determines the abundance and distribution of loci.
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Affiliation(s)
- Carles Galià-Camps
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, Barcelona, 08028, Spain.
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain.
- Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Accés Cala Sant Francesc 14, Blanes, 17300, Spain.
| | - Cinta Pegueroles
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, Barcelona, 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Xavier Turon
- Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Accés Cala Sant Francesc 14, Blanes, 17300, Spain
| | - Carlos Carreras
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, Barcelona, 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Marta Pascual
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, Barcelona, 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
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3
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Sun Z, Liu J, Zhang M, Wang T, Huang S, Weiss ST, Liu YY. Removal of false positives in metagenomics-based taxonomy profiling via targeting Type IIB restriction sites. Nat Commun 2023; 14:5321. [PMID: 37658057 PMCID: PMC10474111 DOI: 10.1038/s41467-023-41099-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/22/2023] [Indexed: 09/03/2023] Open
Abstract
Accurate species identification and abundance estimation are critical for the interpretation of whole metagenome sequencing (WMS) data. Yet, existing metagenomic profilers suffer from false-positive identifications, which can account for more than 90% of total identified species. Here, by leveraging species-specific Type IIB restriction endonuclease digestion sites as reference instead of universal markers or whole microbial genomes, we present a metagenomic profiler, MAP2B (MetAgenomic Profiler based on type IIB restriction sites), to resolve those issues. We first illustrate the pitfalls of using relative abundance as the only feature in determining false positives. We then propose a feature set to distinguish false positives from true positives, and using simulated metagenomes from CAMI2, we establish a false-positive recognition model. By benchmarking the performance in metagenomic profiling using a simulation dataset with varying sequencing depth and species richness, we illustrate the superior performance of MAP2B over existing metagenomic profilers in species identification. We further test the performance of MAP2B using real WMS data from an ATCC mock community, confirming its superior precision against sequencing depth. Finally, by leveraging WMS data from an IBD cohort, we demonstrate the taxonomic features generated by MAP2B can better discriminate IBD and predict metabolomic profiles.
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Affiliation(s)
- Zheng Sun
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jiang Liu
- Qingdao OE Biotechnology Company Limited, Qingdao, Shandong, China
| | - Meng Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
| | - Tong Wang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Shi Huang
- Faculty of Dentistry, The University of Hong Kong, Hong Kong, China
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
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4
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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: 1.7] [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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5
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Picher ÁJ, Hernández F, Budeus B, Soriano E, Avila J. Human Brain Single Nucleotide Polymorphism: Validation of DNA Sequencing. J Alzheimers Dis Rep 2018; 2:103-109. [PMID: 30480253 PMCID: PMC6159612 DOI: 10.3233/adr-170039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Genetic factors may be involved in the onset of neurodegenerative diseases like Alzheimer’s disease. In the case of the familial type, the disease is due to an inherited mutation at specific sites in three genes. Also, there are some genetic risk factors that facilitate the development of sporadic Alzheimer’s disease. All of these genetic analyses were performed using blood samples as a source of DNA. However, the presence of somatic mutations in the brain can be identified only using brain samples. In this review, we comment on a method that correctly identifies single nucleotide variations in the human brain and that can be used to validate high-through sequencing techniques. This method involves selective enrichment of the DNA population bearing the nucleotide variations, thereby facilitating posterior validation of the data by Sanger’s sequencing.
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Affiliation(s)
- Ángel J Picher
- Expedeon S.L.U., Parque Científico de Madrid, Cantoblanco, Madrid, Spain
| | - Félix Hernández
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain
| | | | - Eduardo Soriano
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain.,Department of Cell Biology and Institute of Neurosciences, University of Barcelona, Barcelona, Spain.,Vall d'Hebrón Institut de Recerca (VHIR), Barcelona, Spain.,ICREA Academia, Barcelona, Spain
| | - Jesús Avila
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain
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6
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Paterno M, Schiavina M, Aglieri G, Ben Souissi J, Boscari E, Casagrandi R, Chassanite A, Chiantore M, Congiu L, Guarnieri G, Kruschel C, Macic V, Marino IAM, Papetti C, Patarnello T, Zane L, Melià P. Population genomics meet Lagrangian simulations: Oceanographic patterns and long larval duration ensure connectivity among Paracentrotus lividus populations in the Adriatic and Ionian seas. Ecol Evol 2017; 7:2463-2479. [PMID: 28428839 PMCID: PMC5395429 DOI: 10.1002/ece3.2844] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/20/2017] [Accepted: 01/28/2017] [Indexed: 01/15/2023] Open
Abstract
Connectivity between populations influences both their dynamics and the genetic structuring of species. In this study, we explored connectivity patterns of a marine species with long-distance dispersal, the edible common sea urchin Paracentrotus lividus, focusing mainly on the Adriatic-Ionian basins (Central Mediterranean). We applied a multidisciplinary approach integrating population genomics, based on 1,122 single nucleotide polymorphisms (SNPs) obtained from 2b-RAD in 275 samples, with Lagrangian simulations performed with a biophysical model of larval dispersal. We detected genetic homogeneity among eight population samples collected in the focal Adriatic-Ionian area, whereas weak but significant differentiation was found with respect to two samples from the Western Mediterranean (France and Tunisia). This result was not affected by the few putative outlier loci identified in our dataset. Lagrangian simulations found a significant potential for larval exchange among the eight Adriatic-Ionian locations, supporting the hypothesis of connectivity of P. lividus populations in this area. A peculiar pattern emerged from the comparison of our results with those obtained from published P. lividus cytochrome b (cytb) sequences, the latter revealing genetic differentiation in the same geographic area despite a smaller sample size and a lower power to detect differences. The comparison with studies conducted using nuclear markers on other species with similar pelagic larval durations in the same Adriatic-Ionian locations indicates species-specific differences in genetic connectivity patterns and warns against generalizing single-species results to the entire community of rocky shore habitats.
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Affiliation(s)
- Marta Paterno
- Department of BiologyUniversity of PadovaPadovaItaly
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
| | - Marcello Schiavina
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
- Dipartimento di Elettronica, Informazione e BioingegneriaPolitecnico di MilanoMilanoItaly
| | - Giorgio Aglieri
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
- Department of Biological and Environmental Sciences and TechnologiesUniversity of SalentoLecceItaly
| | | | - Elisa Boscari
- Department of BiologyUniversity of PadovaPadovaItaly
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
| | - Renato Casagrandi
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
- Dipartimento di Elettronica, Informazione e BioingegneriaPolitecnico di MilanoMilanoItaly
| | - Aurore Chassanite
- USR 3278 CNRS‐EPHECRIOBEUniversité de Perpignan Via DominitiaPerpignan CedexFrance
| | - Mariachiara Chiantore
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
- Department for Earth, Environment and Life Sciences (DiSTAV)University of GenoaGenoaItaly
| | - Leonardo Congiu
- Department of BiologyUniversity of PadovaPadovaItaly
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
| | - Giuseppe Guarnieri
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
- Department of Biological and Environmental Sciences and TechnologiesUniversity of SalentoLecceItaly
| | | | - Vesna Macic
- Institute of Marine Biology Kotor (IBMK)KotorMontenegro
| | - Ilaria A. M. Marino
- Department of BiologyUniversity of PadovaPadovaItaly
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
| | - Chiara Papetti
- Department of BiologyUniversity of PadovaPadovaItaly
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
| | - Tomaso Patarnello
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroPadovaItaly
| | - Lorenzo Zane
- Department of BiologyUniversity of PadovaPadovaItaly
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
| | - Paco Melià
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
- Dipartimento di Elettronica, Informazione e BioingegneriaPolitecnico di MilanoMilanoItaly
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7
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Jiang N, Zhang F, Wu J, Chen Y, Hu X, Fang O, Leach LJ, Wang D, Luo Z. A highly robust and optimized sequence-based approach for genetic polymorphism discovery and genotyping in large plant populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1739-57. [PMID: 27316437 PMCID: PMC4983294 DOI: 10.1007/s00122-016-2736-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 05/28/2016] [Indexed: 05/14/2023]
Abstract
This optimized approach provides both a computational tool and a library construction protocol, which can maximize the number of genomic sequence reads that uniformly cover a plant genome and minimize the number of sequence reads representing chloroplast DNA and rRNA genes. One can implement the developed computational tool to feasibly design their own RAD-seq experiment to achieve expected coverage of sequence variant markers for large plant populations using information of the genome sequence and ideally, though not necessarily, information of the sequence polymorphism distribution in the genome. Advent of the next generation sequencing techniques motivates recent interest in developing sequence-based identification and genotyping of genome-wide genetic variants in large populations, with RAD-seq being a typical example. Without taking proper account for the fact that chloroplast and rRNA genes may occupy up to 60 % of the resulting sequence reads, the current RAD-seq design could be very inefficient for plant and crop species. We presented here a generic computational tool to optimize RAD-seq design in any plant species and experimentally tested the optimized design by implementing it to screen for and genotype sequence variants in four plant populations of diploid and autotetraploid Arabidopsis and potato Solanum tuberosum. Sequence data from the optimized RAD-seq experiments shows that the undesirable chloroplast and rRNA contributed sequence reads can be controlled at 3-10 %. Additionally, the optimized RAD-seq method enables pre-design of the required uniformity and density in coverage of the high quality sequence polymorphic markers over the genome of interest and genotyping of large plant or crop populations at a competitive cost in comparison to other mainstream rivals in the literature.
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Affiliation(s)
- Ning Jiang
- Department of Biostatistics and Computational Biology, SKLG, School of Life Sciences, Fudan University, Shanghai, China
| | - Fengjun Zhang
- Department of Biostatistics and Computational Biology, SKLG, School of Life Sciences, Fudan University, Shanghai, China
- Qinghai Academy of Agriculture and Forestry Sciences, Xining, Qinghai China
| | - Jinhua Wu
- Department of Biostatistics and Computational Biology, SKLG, School of Life Sciences, Fudan University, Shanghai, China
| | - Yue Chen
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Xiaohua Hu
- Department of Biostatistics and Computational Biology, SKLG, School of Life Sciences, Fudan University, Shanghai, China
| | - Ou Fang
- Department of Biostatistics and Computational Biology, SKLG, School of Life Sciences, Fudan University, Shanghai, China
| | - Lindsey J. Leach
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Di Wang
- Gansu Agricultural University, Lanzhou, Gansu China
| | - Zewei Luo
- Department of Biostatistics and Computational Biology, SKLG, School of Life Sciences, Fudan University, Shanghai, China
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
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8
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Morgan RD, Luyten YA, Johnson SA, Clough EM, Clark TA, Roberts RJ. Novel m4C modification in type I restriction-modification systems. Nucleic Acids Res 2016; 44:9413-9425. [PMID: 27580720 PMCID: PMC5100572 DOI: 10.1093/nar/gkw743] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/12/2016] [Indexed: 11/12/2022] Open
Abstract
We identify a new subgroup of Type I Restriction-Modification enzymes that modify cytosine in one DNA strand and adenine in the opposite strand for host protection. Recognition specificity has been determined for ten systems using SMRT sequencing and each recognizes a novel DNA sequence motif. Previously characterized Type I systems use two identical copies of a single methyltransferase (MTase) subunit, with one bound at each half site of the specificity (S) subunit to form the MTase. The new m4C-producing Type I systems we describe have two separate yet highly similar MTase subunits that form a heterodimeric M1M2S MTase. The MTase subunits from these systems group into two families, one of which has NPPF in the highly conserved catalytic motif IV and modifies adenine to m6A, and one having an NPPY catalytic motif IV and modifying cytosine to m4C. The high degree of similarity among their cytosine-recognizing components (MTase and S) suggest they have recently evolved, most likely from the far more common m6A Type I systems. Type I enzymes that modify cytosine exclusively were formed by replacing the adenine target recognition domain (TRD) with a cytosine-recognizing TRD. These are the first examples of m4C modification in Type I RM systems.
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Affiliation(s)
| | - Yvette A Luyten
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | | | - Emily M Clough
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Tyson A Clark
- Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA
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9
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Simons M, Diffin FM, Szczelkun MD. ClpXP protease targets long-lived DNA translocation states of a helicase-like motor to cause restriction alleviation. Nucleic Acids Res 2014; 42:12082-91. [PMID: 25260590 PMCID: PMC4231737 DOI: 10.1093/nar/gku851] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We investigated how Escherichia coli ClpXP targets the helicase-nuclease (HsdR) subunit of the bacterial Type I restriction–modification enzyme EcoKI during restriction alleviation (RA). RA is a temporary reduction in endonuclease activity that occurs when Type I enzymes bind unmodified recognition sites on the host genome. These conditions arise upon acquisition of a new system by a naïve host, upon generation of new sites by genome rearrangement/mutation or during homologous recombination between hemimethylated DNA. Using recombinant DNA and proteins in vitro, we demonstrate that ClpXP targets EcoKI HsdR during dsDNA translocation on circular DNA but not on linear DNA. Protein roadblocks did not activate HsdR proteolysis. We suggest that DNA translocation lifetime, which is elevated on circular DNA relative to linear DNA, is important to RA. To identify the ClpX degradation tag (degron) in HsdR, we used bioinformatics and biochemical assays to design N- and C-terminal mutations that were analysed in vitro and in vivo. None of the mutants produced a phenotype consistent with loss of the degron, suggesting an as-yet-unidentified recognition pathway. We note that an EcoKI nuclease mutant still produces cell death in a clpx− strain, consistent with DNA damage induced by unregulated motor activity.
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Affiliation(s)
- Michelle Simons
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Fiona M Diffin
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
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10
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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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11
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Khazanov N, Marcovitz A, Levy Y. Asymmetric DNA-search dynamics by symmetric dimeric proteins. Biochemistry 2013; 52:5335-44. [PMID: 23866074 DOI: 10.1021/bi400357m] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We focus on dimeric DNA-binding proteins from two well-studied families: orthodox type II restriction endonucleases (REs) and transcription factors (TFs). Interactions of the protein's recognition sites with the DNA and, particularly, the contribution of each of the monomers to one-dimensional (1D) sliding along nonspecific DNA were studied using computational tools. Coarse-grained molecular dynamics simulations of DNA scanning by various TFs and REs provide insights into how the symmetry of a homodimer can be broken while they nonspecifically interact with DNA. The characteristics of protein sliding along DNA, such as the average sliding length, partitioning between 1D and 3D search, and the one-dimensional diffusion coefficient D1, strongly depend on the salt concentration, which in turn affects the probability of the two monomers adopting a cooperative symmetric sliding mechanism. Indeed, we demonstrate that maximal DNA search efficiency is achieved when the protein adopts an asymmetric search mode in which one monomer slides while its partner hops. We find that proteins classified as TFs have a higher affinity for the DNA, longer sliding lengths, and an increased probability of symmetric sliding in comparison with REs. Moreover, TFs can perform their biological function over a much wider range of salt concentrations than REs. Our results demonstrate that the different biological functions of DNA-binding proteins are related to the different nonspecific DNA search mechanisms they adopt.
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Affiliation(s)
- Netaly Khazanov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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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: 0.7] [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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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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Roberts GA, Chen K, Cooper LP, White JH, Blakely GW, Dryden DTF. Removal of a frameshift between the hsdM and hsdS genes of the EcoKI Type IA DNA restriction and modification system produces a new type of system and links the different families of Type I systems. Nucleic Acids Res 2012; 40:10916-24. [PMID: 23002145 PMCID: PMC3510504 DOI: 10.1093/nar/gks876] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The EcoKI DNA methyltransferase is a trimeric protein comprised of two modification subunits (M) and one sequence specificity subunit (S). This enzyme forms the core of the EcoKI restriction/modification (RM) enzyme. The 3' end of the gene encoding the M subunit overlaps by 1 nt the start of the gene for the S subunit. Translation from the two different open reading frames is translationally coupled. Mutagenesis to remove the frameshift and fuse the two subunits together produces a functional RM enzyme in vivo with the same properties as the natural EcoKI system. The fusion protein can be purified and forms an active restriction enzyme upon addition of restriction subunits and of additional M subunit. The Type I RM systems are grouped into families, IA to IE, defined by complementation, hybridization and sequence similarity. The fusion protein forms an evolutionary intermediate form lying between the Type IA family of RM enzymes and the Type IB family of RM enzymes which have the frameshift located at a different part of the gene sequence.
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Affiliation(s)
- Gareth A Roberts
- EastChem School of Chemistry, The University of Edinburgh, The King's Buildings, Edinburgh, EH9 3JJ, UK
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15
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Pernstich C, Halford SE. Illuminating the reaction pathway of the FokI restriction endonuclease by fluorescence resonance energy transfer. Nucleic Acids Res 2011; 40:1203-13. [PMID: 21993298 PMCID: PMC3273807 DOI: 10.1093/nar/gkr809] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The FokI restriction endonuclease is a monomeric protein that recognizes an asymmetric sequence and cleaves both DNA strands at fixed loci downstream of the site. Its single active site is positioned initially near the recognition sequence, distant from its downstream target 13 nucleotides away. Moreover, to cut both strands, it has to recruit a second monomer to give an assembly with two active sites. Here, the individual steps in the FokI reaction pathway were examined by fluorescence resonance energy transfer (FRET). To monitor DNA binding and domain motion, a fluorescence donor was attached to the DNA, either downstream or upstream of the recognition site, and an acceptor placed on the catalytic domain of the protein. A FokI variant incapable of dimerization was also employed, to disentangle the signal due to domain motion from that due to protein association. Dimerization was monitored separately by using two samples of FokI labelled with donor and acceptor, respectively. The stopped-flow studies revealed a complete reaction pathway for FokI, both the sequence of events and the kinetics of each individual step.
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Affiliation(s)
- Christian Pernstich
- The DNA-proteins Interaction Unit, School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
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Stark WM, Luisi BF, Bowater RP. Machines on genes: enzymes that make, break and move DNA and RNA. Biochem Soc Trans 2010; 38:381-3. [PMID: 20298187 DOI: 10.1042/bst0380381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
As the vital information repositories of the cell, the nucleic acids DNA and RNA pose many challenges as enzyme substrates. To produce, maintain and repair DNA and RNA, and to extract the genetic information that they encode, a battery of remarkable enzymes has evolved, which includes translocases, polymerases/replicases, helicases, nucleases, topoisomerases, transposases, recombinases, repair enzymes and ribosomes. An understanding of how these enzymes function is essential if we are to have a clear view of the molecular biology of the cell and aspire to manipulate genomes and gene expression to our advantage. To bring together scientists working in this fast-developing field, the Biochemical Society held a Focused Meeting, 'Machines on Genes: Enzymes that Make, Break and Move DNA and RNA', at Robinson College, University of Cambridge, U.K., in August 2009. The present article summarizes the research presented at this meeting and the reviews associated with the talks which are published in this issue of Biochemical Society Transactions.
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Affiliation(s)
- W Marshall Stark
- Faculty of Biomedical and Life Sciences, University of Glasgow, Bower Building, Glasgow G12 8QQ, UK.
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