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Yangyanqiu W, Shuwen H. Bacterial DNA involvement in carcinogenesis. Front Cell Infect Microbiol 2022; 12:996778. [PMID: 36310856 PMCID: PMC9600336 DOI: 10.3389/fcimb.2022.996778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/27/2022] [Indexed: 10/29/2023] Open
Abstract
The incidence of cancer is high worldwide, and biological factors such as viruses and bacteria play an important role in the occurrence of cancer. Helicobacter pylori, human papillomavirus, hepatitis B viruses and other organisms have been identified as carcinogens. Cancer is a disease driven by the accumulation of genome changes. Viruses can directly cause cancer by changing the genetic composition of the human body, such as cervical cancer caused by human papillomavirus DNA integration and liver cancer caused by hepatitis B virus DNA integration. Recently, bacterial DNA has been found around cancers such as pancreatic cancer, breast cancer and colorectal cancer, and the idea that bacterial genes can also be integrated into the human genome has become a hot topic. In the present paper, we reviewed the latest phenomenon and specific integration mechanism of bacterial DNA into the human genome. Based on these findings, we also suggest three sources of bacterial DNA in cancers: bacterial DNA around human tissues, free bacterial DNA in bacteremia or sepsis, and endogenous bacterial DNA in the human genome. Clarifying the theory that bacterial DNA integrates into the human genome can provide a new perspective for cancer prevention and treatment.
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Affiliation(s)
- Wang Yangyanqiu
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, China
- Graduate School of Medical college of Zhejiang University, Hangzhou, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, Huzhou, China
| | - Han Shuwen
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, China
- Graduate School of Medical college of Zhejiang University, Hangzhou, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, Huzhou, China
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2
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Restriction endonuclease T.Smu451I with new cleavage specificity-neoschizomer of T.AsuI. Folia Microbiol (Praha) 2021; 66:651-657. [PMID: 33950513 DOI: 10.1007/s12223-021-00874-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2021] [Indexed: 10/21/2022]
Abstract
A specific type II restriction endonuclease T.Smu451I has been purified to electrophoretic homogeneity from the frozen cells of soil bacterium Sphingobacterium multivorum 451 (formerly Flavobacterium multivorum 451), using ultrasonic grinding, nucleic acid removal by streptomycin sulfate, protein precipitation by ammonium sulfate and phosphocellulose P-11, DEAE-Cellulose DE-52, Hepharin-Sepharose CL-6B chromatography, and elucidated several characteristics of T.Smu451I. The molecular weight of the enzyme determined by gel filtration and SDS-polyacrylamide gel electrophoresis was calculated to be 45,000 ± 2000 D (dimer) and 23,000 ± 1000 D (monomer), respectively. The isoelectric point (pI) of T.Smu451I is 5.4. T.Smu451I recognizes pentanucleotide palindromic sequences 5'-GGNC↓C-3' and cleaves between C and C in position shown by arrow to produce 3'-cohesive terminus of trinucleotide. Therefore, T.Smu451I is a neoschizomer of T.AsuI.
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3
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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] [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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Toliusis P, Tamulaitiene G, Grigaitis R, Tuminauskaite D, Silanskas A, Manakova E, Venclovas C, Szczelkun MD, Siksnys V, Zaremba M. The H-subunit of the restriction endonuclease CglI contains a prototype DEAD-Z1 helicase-like motor. Nucleic Acids Res 2019; 46:2560-2572. [PMID: 29471489 PMCID: PMC5861437 DOI: 10.1093/nar/gky107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/08/2018] [Indexed: 11/13/2022] Open
Abstract
CglI is a restriction endonuclease from Corynebacterium glutamicum that forms a complex between: two R-subunits that have site specific-recognition and nuclease domains; and two H-subunits, with Superfamily 2 helicase-like DEAD domains, and uncharacterized Z1 and C-terminal domains. ATP hydrolysis by the H-subunits catalyses dsDNA translocation that is necessary for long-range movement along DNA that activates nuclease activity. Here, we provide biochemical and molecular modelling evidence that shows that Z1 has a fold distantly-related to RecA, and that the DEAD-Z1 domains together form an ATP binding interface and are the prototype of a previously undescribed monomeric helicase-like motor. The DEAD-Z1 motor has unusual Walker A and Motif VI sequences those nonetheless have their expected functions. Additionally, it contains DEAD-Z1-specific features: an H/H motif and a loop (aa 163–aa 172), that both play a role in the coupling of ATP hydrolysis to DNA cleavage. We also solved the crystal structure of the C-terminal domain which has a unique fold, and demonstrate that the Z1-C domains are the principal DNA binding interface of the H-subunit. Finally, we use small angle X-ray scattering to provide a model for how the H-subunit domains are arranged in a dimeric complex.
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Affiliation(s)
- Paulius Toliusis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Giedre Tamulaitiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Rokas Grigaitis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Donata Tuminauskaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Arunas Silanskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Elena Manakova
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Ceslovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Mindaugas Zaremba
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
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Xiong L, Liu S, Chen S, Xiao Y, Zhu B, Gao Y, Zhang Y, Chen B, Luo J, Deng Z, Chen X, Wang L, Chen S. A new type of DNA phosphorothioation-based antiviral system in archaea. Nat Commun 2019; 10:1688. [PMID: 30975999 PMCID: PMC6459918 DOI: 10.1038/s41467-019-09390-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 03/07/2019] [Indexed: 01/21/2023] Open
Abstract
Archaea and Bacteria have evolved different defence strategies that target virtually all steps of the viral life cycle. The diversified virion morphotypes and genome contents of archaeal viruses result in a highly complex array of archaea-virus interactions. However, our understanding of archaeal antiviral activities lags far behind our knowledges of those in bacteria. Here we report a new archaeal defence system that involves DndCDEA-specific DNA phosphorothioate (PT) modification and the PbeABCD-mediated halt of virus propagation via inhibition of DNA replication. In contrast to the breakage of invasive DNA by DndFGH in bacteria, DndCDEA-PbeABCD does not degrade or cleave viral DNA. The PbeABCD-mediated PT defence system is widespread and exhibits extensive interdomain and intradomain gene transfer events. Our results suggest that DndCDEA-PbeABCD is a new type of PT-based virus resistance system, expanding the known arsenal of defence systems as well as our understanding of host-virus interactions.
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Affiliation(s)
- Lei Xiong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
- Taihe Hospital, Hubei University of Medicine, 442000, Shiyan, Hubei, China
- Brain Center, Zhongnan Hospital, Wuhan University, 430071, Wuhan, China
| | - Siyi Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
- Brain Center, Zhongnan Hospital, Wuhan University, 430071, Wuhan, China
| | - Si Chen
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, 430023, Wuhan, China
| | - Yao Xiao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
- Brain Center, Zhongnan Hospital, Wuhan University, 430071, Wuhan, China
| | - Bochen Zhu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
- Brain Center, Zhongnan Hospital, Wuhan University, 430071, Wuhan, China
| | - Yali Gao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
- Brain Center, Zhongnan Hospital, Wuhan University, 430071, Wuhan, China
| | - Yujing Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
- Brain Center, Zhongnan Hospital, Wuhan University, 430071, Wuhan, China
| | - Beibei Chen
- College of Life Sciences, Wuhan University, 430071, Wuhan, China
| | - Jie Luo
- Taihe Hospital, Hubei University of Medicine, 442000, Shiyan, Hubei, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
| | - Xiangdong Chen
- College of Life Sciences, Wuhan University, 430071, Wuhan, China
| | - Lianrong Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
- Taihe Hospital, Hubei University of Medicine, 442000, Shiyan, Hubei, China
- Brain Center, Zhongnan Hospital, Wuhan University, 430071, Wuhan, China
| | - Shi Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China.
- Taihe Hospital, Hubei University of Medicine, 442000, Shiyan, Hubei, China.
- Brain Center, Zhongnan Hospital, Wuhan University, 430071, Wuhan, China.
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DISARM is a widespread bacterial defence system with broad anti-phage activities. Nat Microbiol 2017; 3:90-98. [PMID: 29085076 PMCID: PMC5739279 DOI: 10.1038/s41564-017-0051-0] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 09/29/2017] [Indexed: 02/06/2023]
Abstract
The evolutionary pressure imposed by phage predation on bacteria and archaea has resulted in the development of effective anti-phage defence mechanisms, including restriction-modification and CRISPR-Cas systems. Here, we report on a new defence system, DISARM (defence island system associated with restriction-modification), which is widespread in bacteria and archaea. DISARM is composed of five genes, including a DNA methylase and four other genes annotated as a helicase domain, a phospholipase D (PLD) domain, a DUF1998 domain and a gene of unknown function. Engineering the Bacillus paralicheniformis 9945a DISARM system into Bacillus subtilis has rendered the engineered bacteria protected against phages from all three major families of tailed double-stranded DNA phages. Using a series of gene deletions, we show that four of the five genes are essential for DISARM-mediated defence, with the fifth (PLD) being redundant for defence against some of the phages. We further show that DISARM restricts incoming phage DNA and that the B. paralicheniformis DISARM methylase modifies host CCWGG motifs as a marker of self DNA akin to restriction-modification systems. Our results suggest that DISARM is a new type of multi-gene restriction-modification module, expanding the arsenal of defence systems known to be at the disposal of prokaryotes against their viruses.
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7
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Toliusis P, Zaremba M, Silanskas A, Szczelkun MD, Siksnys V. CgII cleaves DNA using a mechanism distinct from other ATP-dependent restriction endonucleases. Nucleic Acids Res 2017; 45:8435-8447. [PMID: 28854738 PMCID: PMC5737866 DOI: 10.1093/nar/gkx580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/28/2017] [Indexed: 01/10/2023] Open
Abstract
The restriction endonuclease CglI from Corynebacterium glutamicum recognizes an asymmetric 5′-GCCGC-3′ site and cleaves the DNA 7 and 6/7 nucleotides downstream on the top and bottom DNA strands, respectively, in an NTP-hydrolysis dependent reaction. CglI is composed of two different proteins: an endonuclease (R.CglI) and a DEAD-family helicase-like ATPase (H.CglI). These subunits form a heterotetrameric complex with R2H2 stoichiometry. However, the R2H2·CglI complex has only one nuclease active site sufficient to cut one DNA strand suggesting that two complexes are required to introduce a double strand break. Here, we report studies to evaluate the DNA cleavage mechanism of CglI. Using one- and two-site circular DNA substrates we show that CglI does not require two sites on the same DNA for optimal catalytic activity. However, one-site linear DNA is a poor substrate, supporting a mechanism where CglI complexes must communicate along the one-dimensional DNA contour before cleavage is activated. Based on experimental data, we propose that adenosine triphosphate (ATP) hydrolysis by CglI produces translocation on DNA preferentially in a downstream direction from the target, although upstream translocation is also possible. Our results are consistent with a mechanism of CglI action that is distinct from that of other ATP-dependent restriction-modification enzymes.
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Affiliation(s)
- Paulius Toliusis
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257, Vilnius, Lithuania
| | - Mindaugas Zaremba
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257, Vilnius, Lithuania
| | - Arunas Silanskas
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257, Vilnius, Lithuania
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK
| | - Virginijus Siksnys
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257, Vilnius, Lithuania
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Zaremba M, Siksnys V. An Engineered SS Bridge Blocks the Conformational Change Required for the Nuclease Activity of BfiI. Biochemistry 2015; 54:5340-7. [PMID: 26261897 DOI: 10.1021/acs.biochem.5b00437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The type IIS restriction endonuclease BfiI is a homodimer, and each monomer is composed of the N-terminal catalytic and C-terminal DNA recognition domains connected by a 28-residue linker segment. In the crystal in the absence of cognate DNA, BfiI exists in a "closed" conformation, in which an interdomain linker occludes a putative DNA binding surface at the catalytic domain and sterically hinders access to the active site. Cognate DNA binding presumably triggers a conformational change from the inactive "closed" state to the catalytically competent "open" state. Here we show that the disulfide SS bridge engineered at the domain interface locks the enzyme in the "closed" state. In the "closed" SS-linked state, BfiI binds cognate DNA with the same affinity as the wild-type enzyme but does not cut it, indicating that cross-linking introduces a restraint on the conformational transition, which couples DNA recognition and cleavage. Disruption of the interdomain SS bridge by the reducing agent restores the DNA cleavage ability of BfiI.
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Affiliation(s)
- Mindaugas Zaremba
- Institute of Biotechnology, Vilnius University , Graiciuno 8, Vilnius LT-02241, Lithuania
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University , Graiciuno 8, Vilnius LT-02241, Lithuania
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Tamulaitiene G, Silanskas A, Grazulis S, Zaremba M, Siksnys V. Crystal structure of the R-protein of the multisubunit ATP-dependent restriction endonuclease NgoAVII. Nucleic Acids Res 2014; 42:14022-30. [PMID: 25429979 PMCID: PMC4267654 DOI: 10.1093/nar/gku1237] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The restriction endonuclease (REase) NgoAVII is composed of two proteins, R.NgoAVII and N.NgoAVII, and shares features of both Type II restriction enzymes and Type I/III ATP-dependent restriction enzymes (see accompanying paper Zaremba et al., 2014). Here we present crystal structures of the R.NgoAVII apo-protein and the R.NgoAVII C-terminal domain bound to a specific DNA. R.NgoAVII is composed of two domains: an N-terminal nucleolytic PLD domain; and a C-terminal B3-like DNA-binding domain identified previously in BfiI and EcoRII REases, and in plant transcription factors. Structural comparison of the B3-like domains of R.NgoAVII, EcoRII, BfiI and the plant transcription factors revealed a conserved DNA-binding surface comprised of N- and C-arms that together grip the DNA. The C-arms of R.NgoAVII, EcoRII, BfiI and plant B3 domains are similar in size, but the R.NgoAVII N-arm which makes the majority of the contacts to the target site is much longer. The overall structures of R.NgoAVII and BfiI are similar; however, whilst BfiI has stand-alone catalytic activity, R.NgoAVII requires an auxiliary cognate N.NgoAVII protein and ATP hydrolysis in order to cleave DNA at the target site. The structures we present will help formulate future experiments to explore the molecular mechanisms of intersubunit crosstalk that control DNA cleavage by R.NgoAVII and related endonucleases.
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Affiliation(s)
- Giedre Tamulaitiene
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Arunas Silanskas
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Saulius Grazulis
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Mindaugas Zaremba
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Virginijus Siksnys
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
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