1
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Precise cut-and-paste DNA insertion using engineered type V-K CRISPR-associated transposases. Nat Biotechnol 2023:10.1038/s41587-022-01574-x. [PMID: 36593413 DOI: 10.1038/s41587-022-01574-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 10/14/2022] [Indexed: 01/03/2023]
Abstract
CRISPR-associated transposases (CASTs) enable recombination-independent, multi-kilobase DNA insertions at RNA-programmed genomic locations. However, the utility of type V-K CASTs is hindered by high off-target integration and a transposition mechanism that results in a mixture of desired simple cargo insertions and undesired plasmid cointegrate products. Here we overcome both limitations by engineering new CASTs with improved integration product purity and genome-wide specificity. To do so, we engineered a nicking homing endonuclease fusion to TnsB (named HELIX) to restore the 5' nicking capability needed for cargo excision on the DNA donor. HELIX enables cut-and-paste DNA insertion with up to 99.4% simple insertion product purity, while retaining robust integration efficiencies on genomic targets. HELIX has substantially higher on-target specificity than canonical CASTs, and we identify several novel factors that further regulate targeted and genome-wide integration. Finally, we extend HELIX to other type V-K orthologs and demonstrate the feasibility of HELIX-mediated integration in human cell contexts.
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2
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Zhao J, Zhao X. Sensitive miRNA Detection for Early Diagnosis of Psoriasis Based on Dual Signal Recycles. Appl Biochem Biotechnol 2023; 195:125-134. [PMID: 36066806 DOI: 10.1007/s12010-022-04114-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2022] [Indexed: 01/13/2023]
Abstract
MicroRNAs (miRNAs) play a pivotal role in regulating a variety of biological processes and can be used as biomarkers for the early diagnosis of various diseases, such as psoriasis. Herein, we depict a simple and sensitive miRNA detection method based on dual signal recycles, which is developed on the basis of strand displacement amplification (SDA). The sensor is successfully applied to the detection of miRNA-21 with a wide linear range from 100 fM to 10 nM and a lower limit of detection (LOD) of 67 fM. Because of the simple operation yet improved detection capability, we thereby believe that the developed fluorescent biosensor can be potentially applied for early clinical diagnosis as well as biological researches.
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Affiliation(s)
- Jiemei Zhao
- Department of Dermatology, Zhuji People's Hospital, Zhuji Affiliated Hospital of Shaoxing University, 9 Jianmin Road, Taozhu Street, Zhuji City, 311800, Zhejiang Province, China
| | - Xiaoqin Zhao
- Department of Dermatology, Zhuji People's Hospital, Zhuji Affiliated Hospital of Shaoxing University, 9 Jianmin Road, Taozhu Street, Zhuji City, 311800, Zhejiang Province, China.
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3
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Sensitive detection of MiRNA and CircRNA through DSN enzyme cooperating NEase assisted dual signal amplification. Anal Biochem 2022; 654:114744. [DOI: 10.1016/j.ab.2022.114744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/16/2022] [Accepted: 05/18/2022] [Indexed: 11/23/2022]
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4
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Cao S, Tang X, Chen T, Chen G. Types and Applications of Nicking Enzyme-Combined Isothermal Amplification. Int J Mol Sci 2022; 23:ijms23094620. [PMID: 35563012 PMCID: PMC9100243 DOI: 10.3390/ijms23094620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/03/2022] [Accepted: 04/11/2022] [Indexed: 02/01/2023] Open
Abstract
Due to the sudden outbreak of COVID-19 at the end of 2019, rapid detection has become an urgent need for community clinics and hospitals. The rapid development of isothermal amplification detection technology for nucleic acids in the field of molecular diagnostic point-of-care testing (POCT) has gained a great deal of attention in recent years. Thanks to intensive research on nicking enzymes, nicking enzyme-combined isothermal amplification has become a promising platform for rapid detection. This is a novel technique that uses nicking enzymes to improve ordinary isothermal amplification. It has garnered significant interest as it overcomes the complexity of traditional molecular diagnostics and is not subject to temperature limitations, relying on cleavage enzymes to efficiently amplify targets in a very short time to provide a high level of amplification efficiency. In recent years, several types of nicking enzyme-combined isothermal amplification have been developed and they have shown great potential in molecular diagnosis, immunodiagnosis, biochemical identification, and other fields. However, this kind of amplification has some disadvantages. In this review, the principles, advantages and disadvantages, and applications of several nicking enzyme-combined isothermal amplification techniques are reviewed and the prospects for the development of these techniques are also considered.
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Affiliation(s)
- Siyu Cao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China;
| | - Xiaochen Tang
- Department of Clinical Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China;
| | - Tianshu Chen
- Department of Clinical Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China;
- Correspondence: (T.C.); (G.C.)
| | - Guifang Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China;
- Correspondence: (T.C.); (G.C.)
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5
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Badawy S, Baka ZAM, Abou-Dobara MI, El-Sayed AKA, Skurnik M. Biological and molecular characterization of fEg-Eco19, a lytic bacteriophage active against an antibiotic-resistant clinical Escherichia coli isolate. Arch Virol 2022; 167:1333-1341. [PMID: 35399144 PMCID: PMC9038960 DOI: 10.1007/s00705-022-05426-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/12/2022] [Indexed: 12/30/2022]
Abstract
Characterization of bacteriophages facilitates better understanding of their biology, host specificity, genomic diversity, and adaptation to their bacterial hosts. This, in turn, is important for the exploitation of phages for therapeutic purposes, as the use of uncharacterized phages may lead to treatment failure. The present study describes the isolation and characterization of a bacteriophage effective against the important clinical pathogen Escherichia coli, which shows increasing accumulation of antibiotic resistance. Phage fEg-Eco19, which is specific for a clinical E. coli strain, was isolated from an Egyptian sewage sample. Phage fEg-Eco19 formed clear, sharp-edged, round plaques. Electron microscopy showed that the isolated phage is tailed and therefore belongs to the order Caudovirales, and morphologically, it resembles siphoviruses. The diameter of the icosahedral head of fEg-Eco19 is 68 ± 2 nm, and the non-contractile tail length and diameter are 118 ± 0.2 and 13 ± 0.6 nm, respectively. The host range of the phage was found to be narrow, as it infected only two out of 137 clinical E. coli strains tested. The phage genome is 45,805 bp in length with a GC content of 50.3% and contains 76 predicted genes. Comparison of predicted and experimental restriction digestion patterns allowed rough mapping of the physical ends of the phage genome, which was confirmed using the PhageTerm tool. Annotation of the predicted genes revealed gene products belonging to several functional groups, including regulatory proteins, DNA packaging and phage structural proteins, host lysis proteins, and proteins involved in DNA/RNA metabolism and replication.
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Affiliation(s)
- Shimaa Badawy
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00014 UH Helsinki, Finland
- Department of Botany and Microbiology, Faculty of Science, Damietta University, New Damietta, 34517 Egypt
| | - Zakaria A. M. Baka
- Department of Botany and Microbiology, Faculty of Science, Damietta University, New Damietta, 34517 Egypt
| | - Mohamed I. Abou-Dobara
- Department of Botany and Microbiology, Faculty of Science, Damietta University, New Damietta, 34517 Egypt
| | - Ahmed K. A. El-Sayed
- Department of Botany and Microbiology, Faculty of Science, Damietta University, New Damietta, 34517 Egypt
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00014 UH Helsinki, Finland
- Division of Clinical Microbiology, Helsinki University Hospital, HUSLAB, 00290 Helsinki, Finland
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6
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Xu SY. Engineering Infrequent DNA Nicking Endonuclease by Fusion of a BamHI Cleavage-Deficient Mutant and a DNA Nicking Domain. Front Microbiol 2022; 12:787073. [PMID: 35178039 PMCID: PMC8845596 DOI: 10.3389/fmicb.2021.787073] [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: 09/30/2021] [Accepted: 12/17/2021] [Indexed: 11/13/2022] Open
Abstract
Strand-specific DNA nicking endonucleases (NEases) typically nick 3–7 bp sites. Our goal is to engineer infrequent NEase with a >8 bp recognition sequence. A BamHI catalytic-deficient mutant D94N/E113K was constructed, purified, and shown to bind and protect the GGATCC site from BamHI restriction. The mutant was fused to a 76-amino acid (aa) DNA nicking domain of phage Gamma HNH (gHNH) NEase. The chimeric enzyme was purified, and it was shown to nick downstream of a composite site 5′ GGATCC-N(4-6)-AC↑CGR 3′ (R, A, or G) or to nick both sides of BamHI site at the composite site 5′ CCG↓GT-N5-GGATCC-N5-AC↑CGG 3′ (the down arrow ↓ indicates the strand shown is nicked; the up arrow↑indicates the bottom strand is nicked). Due to the attenuated activity of the small nicking domain, the fusion nickase is active in the presence of Mn2+ or Ni2+, and it has low activity in Mg2+ buffer. This work provided a proof-of-concept experiment in which a chimeric NEase could be engineered utilizing the binding specificity of a Type II restriction endonucleases (REases) in fusion with a nicking domain to generate infrequent nickase, which bridges the gap between natural REases and homing endonucleases. The engineered chimeric NEase provided a framework for further optimization in molecular diagnostic applications.
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7
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Turner D, Adriaenssens EM, Tolstoy I, Kropinski AM. Phage Annotation Guide: Guidelines for Assembly and High-Quality Annotation. PHAGE (NEW ROCHELLE, N.Y.) 2021; 2:170-182. [PMID: 35083439 PMCID: PMC8785237 DOI: 10.1089/phage.2021.0013] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
All sequencing projects of bacteriophages (phages) should seek to report an accurate and comprehensive annotation of their genomes. This article defines 14 questions for those new to phage genomics that should be addressed before submitting a genome sequence to the International Nucleotide Sequence Database Collaboration or writing a publication.
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Affiliation(s)
- Dann Turner
- Department of Applied Sciences, Faculty of Health and Applied Sciences, University of the West of England, Bristol, United Kingdom
| | | | - Igor Tolstoy
- Viral Resources, National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, Maryland, USA
| | - Andrew M Kropinski
- Department of Food Science, and University of Guelph, Guelph, Ontario, Canada.,Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
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8
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Cheng R, Huang F, Wu H, Lu X, Yan Y, Yu B, Wang X, Zhu B. A nucleotide-sensing endonuclease from the Gabija bacterial defense system. Nucleic Acids Res 2021; 49:5216-5229. [PMID: 33885789 PMCID: PMC8136825 DOI: 10.1093/nar/gkab277] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/01/2021] [Accepted: 04/08/2021] [Indexed: 01/21/2023] Open
Abstract
The arms race between bacteria and phages has led to the development of exquisite bacterial defense systems including a number of uncharacterized systems distinct from the well-known restriction-modification and CRISPR/Cas systems. Here, we report functional analyses of the GajA protein from the newly predicted Gabija system. The GajA protein is revealed as a sequence-specific DNA nicking endonuclease unique in that its activity is strictly regulated by nucleotide concentration. NTP and dNTP at physiological concentrations can fully inhibit the robust DNA cleavage activity of GajA. Interestingly, the nucleotide inhibition is mediated by an ATPase-like domain, which usually hydrolyzes ATP to stimulate the DNA cleavage when associated with other nucleases. These features suggest a mechanism of the Gabija defense in which an endonuclease activity is suppressed under normal conditions, while it is activated by the depletion of NTP and dNTP upon the replication and transcription of invading phages. This work highlights a concise strategy to utilize a DNA nicking endonuclease for phage resistance via nucleotide regulation.
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Affiliation(s)
- Rui Cheng
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Fengtao Huang
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Hui Wu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xuelin Lu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yan Yan
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Bingbing Yu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xionglue Wang
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Bin Zhu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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9
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Zhang Y, Liao YT, Salvador A, Wu VCH. Genomic Characterization of Two Shiga Toxin-Converting Bacteriophages Induced From Environmental Shiga Toxin-Producing Escherichia coli. Front Microbiol 2021; 12:587696. [PMID: 33716997 PMCID: PMC7946995 DOI: 10.3389/fmicb.2021.587696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 01/13/2021] [Indexed: 11/13/2022] Open
Abstract
Shiga toxin (Stx), encoded by stx genes located in prophage sequences, is the major agent responsible for the pathogenicity of Shiga toxin-producing Escherichia coli (STEC) and is closely associated with the development of hemolytic uremic syndrome (HUS). Although numerous Stx prophage sequences have been reported as part of STEC bacterial genomes, the information about the genomic characterization of Stx-converting bacteriophages induced from STEC strains is relatively scarce. The objectives of this study were to genomically characterize two Stx-converting phages induced from environmental STEC strains and to evaluate their correlations with published Stx-converting phages and STEC strains of different origins. The Stx1-converting phage Lys8385Vzw and the Stx2-converting phage Lys19259Vzw were induced from E. coli O103:H11 (RM8385) and E. coli O157:H7 (RM19259), respectively. Whole-genome sequencing of these phages was conducted on a MiSeq sequencer for genomic characterization. Phylogenetic analysis and comparative genomics were performed to determine the correlations between these two Stx-converting phages, 13 reference Stx-converting phages, and 10 reference STEC genomes carrying closely related Stx prophages. Both Stx-converting phages Lys8385Vzw and Lys19259Vzw had double-stranded DNA, with genome sizes of 50,953 and 61,072 bp, respectively. Approximately 40% of the annotated coding DNA sequences with the predicted functions were likely associated with the fitness for both phages and their bacterial hosts. The whole-genome–based phylogenetic analysis of these two Stx-converting phages and 13 reference Stx-converting phages revealed that the 15 Stx-converting phages were divided into three distinct clusters, and those from E. coli O157:H7, in particular, were distributed in each cluster, demonstrating the high genomic diversity of these Stx-converting phages. The genomes of Stx-converting phage Lys8385Vzw and Lys19259Vzw shared a high-nucleotide similarity with the prophage sequences of the selected STEC isolates from the clinical and environmental origin. The findings demonstrate the genomic diversity of Stx-converting phages induced from different STEC strains and provide valuable insights into the dissemination of stx genes among E. coli population via the lysogenization of Stx-converting phages.
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Affiliation(s)
- Yujie Zhang
- Produce Safety and Microbiology Research Unit, US Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Yen-Te Liao
- Produce Safety and Microbiology Research Unit, US Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Alexandra Salvador
- Produce Safety and Microbiology Research Unit, US Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Vivian C H Wu
- Produce Safety and Microbiology Research Unit, US Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
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10
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Minkiewicz P, Darewicz M, Iwaniak A, Turło M. Proposal of the Annotation of Phosphorylated Amino Acids and Peptides Using Biological and Chemical Codes. Molecules 2021; 26:molecules26030712. [PMID: 33573096 PMCID: PMC7866520 DOI: 10.3390/molecules26030712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/21/2021] [Accepted: 01/26/2021] [Indexed: 01/04/2023] Open
Abstract
Phosphorylation represents one of the most important modifications of amino acids, peptides, and proteins. By modifying the latter, it is useful in improving the functional properties of foods. Although all these substances are broadly annotated in internet databases, there is no unified code for their annotation. The present publication aims to describe a simple code for the annotation of phosphopeptide sequences. The proposed code describes the location of phosphate residues in amino acid side chains (including new rules of atom numbering in amino acids) and the diversity of phosphate residues (e.g., di- and triphosphate residues and phosphate amidation). This article also includes translating the proposed biological code into SMILES, being the most commonly used chemical code. Finally, it discusses possible errors associated with applying the proposed code and in the resulting SMILES representations of phosphopeptides. The proposed code can be extended to describe other modifications in the future.
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11
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HK97 gp74 Possesses an α-Helical Insertion in the ββα Fold That Affects Its Metal Binding, cos Site Digestion, and In Vivo Activities. J Bacteriol 2020; 202:JB.00644-19. [PMID: 31988081 DOI: 10.1128/jb.00644-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/17/2020] [Indexed: 11/20/2022] Open
Abstract
The last gene in the genome of the bacteriophage HK97 encodes gp74, an HNH endonuclease. HNH motifs contain two conserved His residues and an invariant Asn residue, and they adopt a ββα structure. gp74 is essential for phage head morphogenesis, likely because gp74 enhances the specific endonuclease activity of the HK97 terminase complex. Notably, the ability of gp74 to enhance the terminase-mediated cleavage of the phage cos site requires an intact HNH motif in gp74. Mutation of H82, the conserved metal-binding His residue in the HNH motif, to Ala abrogates gp74-mediated stimulation of terminase activity. Here, we present nuclear magnetic resonance (NMR) studies demonstrating that gp74 contains an α-helical insertion in the Ω-loop, which connects the two β-strands of the ββα fold, and a disordered C-terminal tail. NMR data indicate that the Ω-loop insert makes contacts to the ββα fold and influences the ability of gp74 to bind divalent metal ions. Further, the Ω-loop insert and C-terminal tail contribute to gp74-mediated DNA digestion and to gp74 activity in phage morphogenesis. The data presented here enrich our molecular-level understanding of how HNH endonucleases enhance terminase-mediated digestion of the cos site and contribute to the phage replication cycle.IMPORTANCE This study demonstrates that residues outside the canonical ββα fold, namely, the Ω-loop α-helical insert and a disordered C-terminal tail, regulate the activity of the HNH endonuclease gp74. The increased divalent metal ion binding when the Ω-loop insert is removed compared to reduced cos site digestion and phage formation indicates that the Ω-loop insert plays multiple regulatory roles. The data presented here provide insights into the molecular basis of the involvement of HNH proteins in phage DNA packing.
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12
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Lutz T, Flodman K, Copelas A, Czapinska H, Mabuchi M, Fomenkov A, He X, Bochtler M, Xu SY. A protein architecture guided screen for modification dependent restriction endonucleases. Nucleic Acids Res 2019; 47:9761-9776. [PMID: 31504772 PMCID: PMC6765204 DOI: 10.1093/nar/gkz755] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/18/2019] [Accepted: 08/31/2019] [Indexed: 11/15/2022] Open
Abstract
Modification dependent restriction endonucleases (MDREs) often have separate catalytic and modification dependent domains. We systematically looked for previously uncharacterized fusion proteins featuring a PUA or DUF3427 domain and HNH or PD-(D/E)XK catalytic domain. The enzymes were clustered by similarity of their putative modification sensing domains into several groups. The TspA15I (VcaM4I, CmeDI), ScoA3IV (MsiJI, VcaCI) and YenY4I groups, all featuring a PUA superfamily domain, preferentially cleaved DNA containing 5-methylcytosine or 5-hydroxymethylcytosine. ScoA3V, also featuring a PUA superfamily domain, but of a different clade, exhibited 6-methyladenine stimulated nicking activity. With few exceptions, ORFs for PUA-superfamily domain containing endonucleases were not close to DNA methyltransferase ORFs, strongly supporting modification dependent activity of the endonucleases. DUF3427 domain containing fusion proteins had very little or no endonuclease activity, despite the presence of a putative PD-(D/E)XK catalytic domain. However, their expression potently restricted phage T4gt in Escherichia coli cells. In contrast to the ORFs for PUA domain containing endonucleases, the ORFs for DUF3427 fusion proteins were frequently found in defense islands, often also featuring DNA methyltransferases.
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Affiliation(s)
- Thomas Lutz
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Kiersten Flodman
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Alyssa Copelas
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Honorata Czapinska
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Megumu Mabuchi
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Alexey Fomenkov
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Xinyi He
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Matthias Bochtler
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.,Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Shuang-Yong Xu
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
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13
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Abrosimova LA, Kisil OV, Romanova EA, Oretskaya TS, Kubareva EA. Nicking Endonucleases as Unique Tools for Biotechnology and Gene Engineering. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162019050017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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Weiditch SA, Seraphim TV, Houry WA, Kanelis V. Strategies for purification of the bacteriophage HK97 small and large terminase subunits that yield pure and homogeneous samples that are functional. Protein Expr Purif 2019; 160:45-55. [DOI: 10.1016/j.pep.2019.03.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/30/2019] [Accepted: 03/30/2019] [Indexed: 02/06/2023]
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15
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Screening substrate-binding positions by rolling circle amplification suggesting a binding model of Nt.BstNBI. Biochem J 2019; 476:1483-1496. [PMID: 31064800 DOI: 10.1042/bcj20190167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/29/2019] [Accepted: 05/04/2019] [Indexed: 02/05/2023]
Abstract
Nicking endonucleases (NEs) become increasingly attractive for their promising applications in isothermal amplification. Unfortunately, in comparison with their applications, their catalytic mechanism studies have relatively lagged behind due to a paucity of crystal structure information. Nt.BstNBI is one of those widely used NEs. However, many aspects of its catalytic mechanism still remained to be explored. Herein, we employed only rolling circle amplification (RCA) assay as a major analytic tool and succeeded in identifying the potential binding positions and regions of the DNA substrate based on locked nucleic acid modification, DNA duplex length of substrate, and substrate mismatch designs. Based on these data, we, for the first time, revealed that Nt.BstNBI was likely to recognize six adjacent positions of the recognition sequence (G1rt, A2rt, G3rt, A2rb, C3rb, and T4rb) in the major groove and hold three positions of the cleavage sequence (N3ct, N4ct, and N7cb) in the minor groove of DNA duplex for nicking. Moreover, this work also demonstrated the unexpected efficiency of RCA to study the macromolecular interaction for certain kind of nucleases in an easy and high-throughput way.
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16
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Qian C, Wang R, Wu H, Ji F, Wu J. Nicking enzyme-assisted amplification (NEAA) technology and its applications: A review. Anal Chim Acta 2019; 1050:1-15. [DOI: 10.1016/j.aca.2018.10.054] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/22/2018] [Accepted: 10/23/2018] [Indexed: 01/13/2023]
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17
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Zhang J, Ito H, Hino M, Kimura M. A RelE/ParE superfamily toxin in Vibrio parahaemolyticus has DNA nicking endonuclease activity. Biochem Biophys Res Commun 2017; 489:29-34. [PMID: 28533087 DOI: 10.1016/j.bbrc.2017.05.105] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 05/19/2017] [Indexed: 12/12/2022]
Abstract
Type II toxins in toxin-antitoxin (TA) systems fold into a similar fold and belong to the RelE/ParE superfamily. However, they display two distinct biochemical activities: RelE toxins are mRNA interferases, while ParE toxins are DNA gyrase (Gyr) inhibitors. Previously, we found a TA system, vp1842/vp1843, on the Vibrio parahaemolyticus genome whose toxin Vp1843 belongs to the RelE/ParE toxin superfamily. Vp1843, unlike RelE toxins, has neither protein synthesis inhibitory activity nor ribonuclease activity. In this study, we examined the inhibitory potency of Vp1843 with Escherichia coli Gyr. The result showed that Vp1843, unlike other ParE toxins, had little Gyr inhibitory activity, but rather converted supercoiled DNA to open-circular DNA. Analysis showed further that Vp1843 cleaves a single strand in DNA, and that the antitoxin Vp1842 neutralized the nicking endonuclease activity of Vp1843. Mutations of Lys37 and Pro45 in Vp1843 abolished its nicking activity, suggesting that they play a crucial role in nicking endonuclease activity. To our knowledge, Vp1843 is the first toxin with DNA nicking endonuclease activity among the RelE/ParE toxin superfamily.
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Affiliation(s)
- Jing Zhang
- Laboratory of Structural Biology, Graduate School of Systems Life Sciences, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
| | - Hironori Ito
- Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Graduate School, Faculty of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
| | - Madoka Hino
- Department of Health and Nutrition Sciences, Faculty of Health and Social Welfare Science, Nishikyushu University, 4490-9 Ozaki, Kanzaki-machi, Kanzaki-shi, Saga 842-8585, Japan
| | - Makoto Kimura
- Laboratory of Structural Biology, Graduate School of Systems Life Sciences, Hakozaki 6-10-1, Fukuoka 812-8581, Japan; Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Graduate School, Faculty of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan.
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Zhang L, Xu D, Huang Y, Zhu X, Rui M, Wan T, Zheng X, Shen Y, Chen X, Ma K, Gong Y. Structural and functional characterization of deep-sea thermophilic bacteriophage GVE2 HNH endonuclease. Sci Rep 2017; 7:42542. [PMID: 28211904 PMCID: PMC5304195 DOI: 10.1038/srep42542] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/10/2017] [Indexed: 01/26/2023] Open
Abstract
HNH endonucleases in bacteriophages play a variety of roles in the phage lifecycle as key components of phage DNA packaging machines. The deep-sea thermophilic bacteriophage Geobacillus virus E2 (GVE2) encodes an HNH endonuclease (GVE2 HNHE). Here, the crystal structure of GVE2 HNHE is reported. This is the first structural study of a thermostable HNH endonuclease from a thermophilic bacteriophage. Structural comparison reveals that GVE2 HNHE possesses a typical ββα-metal fold and Zn-finger motif similar to those of HNH endonucleases from other bacteriophages, apart from containing an extra α-helix, suggesting conservation of these enzymes among bacteriophages. Biochemical analysis suggests that the alanine substitutions of the conserved residues (H93, N109 and H118) in the HNH motif of GVE2 HNHE abolished 94%, 60% and 83% of nicking activity, respectively. Compared to the wild type enzyme, the H93A mutant displayed almost the same conformation while the N108A and H118A mutants had different conformations. In addition, the wild type enzyme was more thermostable than the mutants. In the presence of Mn2+ or Zn2+, the wild type enzyme displayed distinct DNA nicking patterns. However, high Mn2+ concentrations were needed for the N109A and H118A mutants to nick DNA while Zn2+ inactivated their nicking activity.
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Affiliation(s)
- Likui Zhang
- Marine Science & Technology Institute Department of Environmental Science and Engineering, Yangzhou University, China
- State Key Laboratory of Microbial Technology, Shandong University, China
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Dandan Xu
- Institute of Health Sciences and School of Life Science, Anhui University, Hefei, Anhui 230601, China
| | - Yanchao Huang
- Marine Science & Technology Institute Department of Environmental Science and Engineering, Yangzhou University, China
| | - Xinyuan Zhu
- Marine Science & Technology Institute Department of Environmental Science and Engineering, Yangzhou University, China
| | - Mianwen Rui
- Marine Science & Technology Institute Department of Environmental Science and Engineering, Yangzhou University, China
| | - Ting Wan
- Marine Science & Technology Institute Department of Environmental Science and Engineering, Yangzhou University, China
| | - Xin Zheng
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, China
| | - Yulong Shen
- State Key Laboratory of Microbial Technology, Shandong University, China
| | - Xiangdong Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Kesen Ma
- Department of Biology, University of Waterloo, Canada
| | - Yong Gong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, China
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Xu SY, Klein P, Degtyarev SK, Roberts RJ. Expression and purification of the modification-dependent restriction enzyme BisI and its homologous enzymes. Sci Rep 2016; 6:28579. [PMID: 27353146 PMCID: PMC4926085 DOI: 10.1038/srep28579] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/06/2016] [Indexed: 12/15/2022] Open
Abstract
The methylation-dependent restriction endonuclease (REase) BisI (G(m5)C ↓ NGC) is found in Bacillus subtilis T30. We expressed and purified the BisI endonuclease and 34 BisI homologs identified in bacterial genomes. 23 of these BisI homologs are active based on digestion of (m5)C-modified substrates. Two major specificities were found among these BisI family enzymes: Group I enzymes cut GCNGC containing two to four (m5)C in the two strands, or hemi-methylated sites containing two (m5)C in one strand; Group II enzymes only cut GCNGC sites containing three to four (m5)C, while one enzyme requires all four cytosines to be modified for cleavage. Another homolog, Esp638I cleaves GCS ↓ SGC (relaxed specificity RCN ↓ NGY, containing at least four (m5)C). Two BisI homologs show degenerate specificity cleaving unmodified DNA. Many homologs are small proteins ranging from 150 to 190 amino acid (aa) residues, but some homologs associated with mobile genetic elements are larger and contain an extra C-terminal domain. More than 156 BisI homologs are found in >60 bacterial genera, indicating that these enzymes are widespread in bacteria. They may play an important biological function in restricting pre-modified phage DNA.
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Affiliation(s)
- Shuang-yong Xu
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Pernelle Klein
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
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Zhang L, Huang Y, Xu D, Yang L, Qian K, Chang G, Gong Y, Zhou X, Ma K. Biochemical characterization of a thermostable HNH endonuclease from deep-sea thermophilic bacteriophage GVE2. Appl Microbiol Biotechnol 2016; 100:8003-12. [DOI: 10.1007/s00253-016-7568-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/10/2016] [Accepted: 04/18/2016] [Indexed: 12/01/2022]
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