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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: 6] [Impact Index Per Article: 3.0] [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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Filloux A. Bacterial protein secretion systems: Game of types. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35536734 DOI: 10.1099/mic.0.001193] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein trafficking across the bacterial envelope is a process that contributes to the organisation and integrity of the cell. It is the foundation for establishing contact and exchange between the environment and the cytosol. It helps cells to communicate with one another, whether they establish symbiotic or competitive behaviours. It is instrumental for pathogenesis and for bacteria to subvert the host immune response. Understanding the formation of envelope conduits and the manifold strategies employed for moving macromolecules across these channels is a fascinating playground. The diversity of the nanomachines involved in this process logically resulted in an attempt to classify them, which is where the protein secretion system types emerged. As our knowledge grew, so did the number of types, and their rightful nomenclature started to be questioned. While this may seem a semantic or philosophical issue, it also reflects scientific rigour when it comes to assimilating findings into textbooks and science history. Here I give an overview on bacterial protein secretion systems, their history, their nomenclature and why it can be misleading for newcomers in the field. Note that I do not try to suggest a new nomenclature. Instead, I explore the reasons why naming could have escaped our control and I try to reiterate basic concepts that underlie protein trafficking cross membranes.
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Affiliation(s)
- Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
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3
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Wu X, Zhao Y, Sun L, Jiang M, Wang Q, Wang Q, Yang W, Wu Y. Crystal structure of CagV, the Helicobacter pylori homologue of the T4SS protein VirB8. FEBS J 2019; 286:4294-4309. [PMID: 31230405 DOI: 10.1111/febs.14971] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/13/2019] [Accepted: 06/21/2019] [Indexed: 12/15/2022]
Abstract
The VirB/D type IV secretion system (T4SS) plays an essential role in materials transport between host cells and pathogenic Helicobacter pylori and is considered the major pathogenic mediator of H. pylori-associated gastric disease. VirB8, an inner membrane protein that interacts with many other proteins, is a crucial component for secretory function. Here, we present a crystal structure of the periplasmic domain of CagV, the VirB8 counterpart in the H. pylori Cag-T4SS. The structure reveals a fold similar to that of other VirB8 members except for the absence of the α5 helix, a discontinuous β1 strand, a larger angle between the α2 and α3 helices, a more hydrophobic surface groove, but exhibits a different dimer interface. Whether the dimerization occurs in solution was proved by mutagenesis, size-exclusion chromatography and cross-linking assays. Unlike the classical dimerization mode, the interface of the CagV dimer is principally formed by several hydrogen bonds, which indicates instability of dimerization. The structure here demonstrates the difference in dimerization among VirB8 homologues and indicates the considerable compositional and functional diversity of them in T4SS. DATABASE: Coordinates and structure factors have been deposited in the Protein Data Bank under accession codes 6IQT.
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Affiliation(s)
- Xiuling Wu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Yanhe Zhao
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lifang Sun
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China
| | - Meiqin Jiang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Qin Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - QianChao Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Wendi Yang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Yunkun Wu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou, China
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4
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Cianciotto NP. Many substrates and functions of type II secretion: lessons learned from Legionella pneumophila. Future Microbiol 2009; 4:797-805. [PMID: 19722835 DOI: 10.2217/fmb.09.53] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Type II secretion is one of six systems that exist in Gram-negative bacteria for the purpose of secreting proteins into the extracellular milieu and/or into host cells. This article will review the various recent studies of Legionella pneumophila that have increased our appreciation of the numbers, types and novelties of proteins that can be secreted via the type II system, as well as the many ways in which type II secretion can promote bacterial physiology, growth, ecology, intracellular infection and virulence. In this context, type II secretion represents a potentially important target for industrial and biomedical applications.
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Affiliation(s)
- Nicholas P Cianciotto
- Department of Microbiology & Immunology, Northwestern University Medical School, 320 East Superior St., Chicago, IL 60611, USA.
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5
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Saier MH, Ma CH, Rodgers L, Tamang DG, Yen MR. Protein secretion and membrane insertion systems in bacteria and eukaryotic organelles. ADVANCES IN APPLIED MICROBIOLOGY 2009; 65:141-97. [PMID: 19026865 DOI: 10.1016/s0065-2164(08)00606-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Milton H Saier
- Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116, USA
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6
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Ream W. Agrobacterium tumefaciens and A. rhizogenes use different proteins to transport bacterial DNA into the plant cell nucleus. Microb Biotechnol 2009; 2:416-27. [PMID: 21255274 PMCID: PMC3815903 DOI: 10.1111/j.1751-7915.2009.00104.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Agrobacterium tumefaciens and A. rhizogenes transport single‐stranded DNA (ssDNA; T‐strands) and virulence proteins into plant cells through a type IV secretion system. DNA transfer initiates when VirD2 nicks border sequences in the tumour‐inducing plasmid, attaches to the 5′ end, and pilots T‐strands into plant cells. Agrobacterium tumefaciens translocates ssDNA‐binding protein VirE2 into plant cells where it targets T‐strands into the nucleus. Some A. rhizogenes strains lack VirE2 but transfer T‐strands efficiently due to the GALLS gene, which complements an A. tumefaciens virE2 mutant. VirE2 and full‐length GALLS (GALLS‐FL) contain nuclear localization sequences that target these proteins to the plant cell nucleus. VirE2 binds cooperatively to T‐strands allowing it to move ssDNA without ATP hydrolysis. Unlike VirE2, GALLS‐FL contains ATP‐binding and helicase motifs similar to those in TraA, a strand transferase involved in conjugation. VirE2 may accumulate in the nucleus and pull T‐strands into the nucleus using the force generated by cooperative DNA binding. GALLS‐FL accumulates inside the nucleus where its predicted ATP‐dependent strand transferase may pull T‐strands into the nucleus. These different mechanisms for nuclear import of T‐strands may affect the efficiency and quality of transgenic events in plant biotechnology applications.
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Affiliation(s)
- Walt Ream
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA.
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Mrsny RJ. Lessons from nature: "Pathogen-Mimetic" systems for mucosal nano-medicines. Adv Drug Deliv Rev 2009; 61:172-92. [PMID: 19146895 DOI: 10.1016/j.addr.2008.09.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Accepted: 09/22/2008] [Indexed: 12/13/2022]
Abstract
Mucosal surfaces establish an interface with external environments that provide a protective barrier with the capacity to selectively absorb and secrete materials important for homeostasis of the organism. In man, mucosal surfaces such as those in the gastrointestinal tract, respiratory tree and genitourinary system also represent significant barrier to the successful administration of certain pharmaceutical agents and the delivery of newly designed nano-scale therapeutic systems. This review examines morphological, physiological and biochemical aspects of these mucosal barriers and presents currently understood mechanisms used by a variety of virulence factors used by pathogenic bacteria to overcome various aspects of these mucosal barriers. Such information emphasizes the impediments that biologically active materials must overcome for absorption across these mucosal surfaces and provides a template for strategies to overcome these barriers for the successful delivery of nano-scale bioactive materials, also known as nano-medicines.
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8
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Lin YH, Gao R, Binns AN, Lynn DG. Capturing the VirA/VirG TCS of Agrobacterium tumefaciens. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008; 631:161-77. [PMID: 18792688 DOI: 10.1007/978-0-387-78885-2_11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Two-component systems (TCS) regulate pathogenic commitment in many interactions and provide an opportunity for unique therapeutic intervention. The VirA/VirG TCS of Agrobacterium tumefaciens mediates inter-kingdom gene transfer in the development of host tumors and sets in motion the events that underlie the great success of this multi-host plant pathogen. Significant proof for the feasibility of interventions has now emerged with the discovery of a natural product that effectively "blinds" the pathogen to the host via inhibition of VirA/VirG signal transduction. Moreover, the emerging studies on the mechanism of signal perception have revealed general sites suitable for intervention of TCS signaling. Given the extensive functional homology, it should now be possible to transfer the models discovered for VirA/VirG broadly to other pathogenic interactions.
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Affiliation(s)
- Yi-Han Lin
- Center for Fundamental and Applied Molecular Evolution, Department of Chemistry, Emory University, Atlanta, GA 30322, USA
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9
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Saier MH. Protein Secretion and Membrane Insertion Systems in Gram-Negative Bacteria. J Membr Biol 2007; 214:75-90. [PMID: 17546510 DOI: 10.1007/s00232-006-0049-7] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Revised: 11/07/2006] [Indexed: 12/30/2022]
Abstract
In contrast to other organisms, gram-negative bacteria have evolved numerous systems for protein export. Eight types are known that mediate export across or insertion into the cytoplasmic membrane, while eight specifically mediate export across or insertion into the outer membrane. Three of the former secretory pathway (SP) systems, type I SP (ISP, ABC), IIISP (Fla/Path) and IVSP (Conj/Vir), can export proteins across both membranes in a single energy-coupled step. A fourth generalized mechanism for exporting proteins across the two-membrane envelope in two distinct steps (which we here refer to as type II secretory pathways [IISP]) utilizes either the general secretory pathway (GSP or Sec) or the twin-arginine targeting translocase for translocation across the inner membrane, and either the main terminal branch or one of several protein-specific export systems for translocation across the outer membrane. We here survey the various well-characterized protein translocation systems found in living organisms and then focus on the systems present in gram-negative bacteria. Comparisons between these systems suggest specific biogenic, mechanistic and evolutionary similarities as well as major differences.
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Affiliation(s)
- Milton H Saier
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA.
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10
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DebRoy S, Dao J, Söderberg M, Rossier O, Cianciotto NP. Legionella pneumophila type II secretome reveals unique exoproteins and a chitinase that promotes bacterial persistence in the lung. Proc Natl Acad Sci U S A 2006; 103:19146-51. [PMID: 17148602 PMCID: PMC1748190 DOI: 10.1073/pnas.0608279103] [Citation(s) in RCA: 168] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Type II protein secretion is critical for Legionella pneumophila infection of amoebae, macrophages, and mice. Previously, we found several enzymes to be secreted by this (Lsp) secretory pathway. To better define the L. pneumophila type II secretome, a 2D electrophoresis proteomic approach was used to compare proteins in wild-type and type II mutant supernatants. We identified 20 proteins that are type II-dependent, including aminopeptidases, an RNase, and chitinase, as well as proteins with no homology to known proteins. Because a chitinase had not been previously reported in Legionella, we determined that wild type secretes activity against both p-nitrophenyl triacetyl chitotriose and glycol chitin. An lsp mutant had a 70-75% reduction in activity, confirming the type II dependency of the secreted chitinase. Newly constructed chitinase (chiA) mutants also had approximately 75% less activity, and reintroduction of chiA restored the mutants to normal levels of activity. Although chiA mutants were not impaired for in vitro intracellular infection, they were defective upon intratracheal inoculation into the lungs of A/J mice, and antibodies against ChiA were detectable in infected animals. In contrast, mutants lacking a secreted phosphatase, protease, or one of several lipolytic enzymes were not defective in vivo. In sum, this study shows that the output of type II secretion is greater in magnitude than previously appreciated and includes previously undescribed proteins. Our data also indicate that an enzyme with chitinase activity can promote infection of a mammalian host.
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Affiliation(s)
- Sruti DebRoy
- Department of Microbiology–Immunology, Northwestern University Medical School, Chicago, IL 60611
| | - Jenny Dao
- Department of Microbiology–Immunology, Northwestern University Medical School, Chicago, IL 60611
| | - Maria Söderberg
- Department of Microbiology–Immunology, Northwestern University Medical School, Chicago, IL 60611
| | - Ombeline Rossier
- Department of Microbiology–Immunology, Northwestern University Medical School, Chicago, IL 60611
| | - Nicholas P. Cianciotto
- Department of Microbiology–Immunology, Northwestern University Medical School, Chicago, IL 60611
- *To whom correspondence should be addressed. E-mail:
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11
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Worden AZ, Cuvelier ML, Bartlett DH. In-depth analyses of marine microbial community genomics. Trends Microbiol 2006; 14:331-6. [PMID: 16820296 DOI: 10.1016/j.tim.2006.06.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Revised: 05/18/2006] [Accepted: 06/19/2006] [Indexed: 11/21/2022]
Abstract
Marine microbes have evolved to live along extreme environmental gradients, whether at the microscale, in proximity to particles or over the entire water column. Using community genomics, DeLong et al. highlight deduced biological differences that result from open-ocean depth gradients. The power of the large-insert libraries used is that both phylogeny and function can be inferred from the genetic material obtained--even for uncultured microbes. Together with complete genomes of marine isolates and advances in physiology and ecology, this study paves the way for ecosystems biology approaches to dynamics and controls of marine microbial populations.
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Affiliation(s)
- Alexandra Z Worden
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, FL 33149, USA.
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