1
|
Freeman KG, Mondal S, Macale LS, Podgorski J, White SJ, Silva BH, Ortiz V, Huet A, Perez RJ, Narsico JT, Ho MC, Jacobs-Sera D, Lowary TL, Conway JF, Park D, Hatfull GF. Structure and infection dynamics of mycobacteriophage Bxb1. Cell 2025:S0092-8674(25)00345-9. [PMID: 40239650 DOI: 10.1016/j.cell.2025.03.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 11/27/2024] [Accepted: 03/14/2025] [Indexed: 04/18/2025]
Abstract
Mycobacteriophage Bxb1 is a well-characterized virus of Mycobacterium smegmatis with double-stranded DNA and a long, flexible tail. Mycobacteriophages show considerable potential as therapies for Mycobacterium infections, but little is known about the structural details of these phages or how they bind to and traverse the complex Mycobacterium cell wall. Here, we report the complete structure and atomic model of phage Bxb1, including the arrangement of immunodominant domains of both the capsid and tail tube subunits, as well as the assembly of the protein subunits in the tail-tip complex. The structure contains protein assemblies with 3-, 5-, 6-, and 12-fold symmetries, which interact to satisfy several symmetry mismatches. Cryoelectron tomography of phage particles bound to M. smegmatis reveals the structural transitions that occur for free phage particles to bind to the cell surface and navigate through the cell wall to enable DNA transfer into the cytoplasm.
Collapse
Affiliation(s)
- Krista G Freeman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sudipta Mondal
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Lourriel S Macale
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Jennifer Podgorski
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Simon J White
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Benjamin H Silva
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Valery Ortiz
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Alexis Huet
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Ronelito J Perez
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Joemark T Narsico
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Todd L Lowary
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - James F Conway
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Donghyun Park
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA.
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
| |
Collapse
|
2
|
Liu X, Hu J, Wang W, Yang H, Tao E, Ma Y, Sha S. Mycobacterial Biofilm: Mechanisms, Clinical Problems, and Treatments. Int J Mol Sci 2024; 25:7771. [PMID: 39063012 PMCID: PMC11277187 DOI: 10.3390/ijms25147771] [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: 06/02/2024] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/28/2024] Open
Abstract
Tuberculosis (TB) remains a threat to human health worldwide. Mycobacterium tuberculosis (Mtb) and other nontuberculous mycobacteria (NTM) can form biofilms, and in vitro and animal experiments have shown that biofilms cause serious drug resistance and mycobacterial persistence. Deeper investigations into the mechanisms of mycobacterial biofilm formation and, consequently, the exploration of appropriate antibiofilm treatments to improve the efficiency of current anti-TB drugs will be useful for curing TB. In this review, the genes and molecules that have been recently reported to be involved in mycobacterial biofilm development, such as ABC transporter, Pks1, PpiB, GroEL1, MprB, (p)ppGpp, poly(P), and c-di-GMP, are summarized. Biofilm-induced clinical problems, including biofilm-related infections and enhanced virulence, as well as their possible mechanisms, are also discussed in detail. Moreover, we also illustrate newly synthesized anti-TB agents that target mycobacterial biofilm, as well as some assistant methods with high efficiency in reducing biofilms in hosts, such as the use of nanoparticles.
Collapse
Affiliation(s)
- Xining Liu
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China; (X.L.); (J.H.); (W.W.); (E.T.)
| | - Junxing Hu
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China; (X.L.); (J.H.); (W.W.); (E.T.)
| | - Wenzhen Wang
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China; (X.L.); (J.H.); (W.W.); (E.T.)
| | - Hanyu Yang
- The Queen’s University of Belfast Joint College, China Medical University, Shenyang 110122, China;
| | - Erning Tao
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China; (X.L.); (J.H.); (W.W.); (E.T.)
| | - Yufang Ma
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China; (X.L.); (J.H.); (W.W.); (E.T.)
| | - Shanshan Sha
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China; (X.L.); (J.H.); (W.W.); (E.T.)
| |
Collapse
|
3
|
Dulberger CL, Guerrero-Bustamante CA, Owen SV, Wilson S, Wuo MG, Garlena RA, Serpa LA, Russell DA, Zhu J, Braunecker BJ, Squyres GR, Baym M, Kiessling LL, Garner EC, Rubin EJ, Hatfull GF. Mycobacterial nucleoid-associated protein Lsr2 is required for productive mycobacteriophage infection. Nat Microbiol 2023; 8:695-710. [PMID: 36823286 PMCID: PMC10066036 DOI: 10.1038/s41564-023-01333-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/23/2023] [Indexed: 02/25/2023]
Abstract
Mycobacteriophages are a diverse group of viruses infecting Mycobacterium with substantial therapeutic potential. However, as this potential becomes realized, the molecular details of phage infection and mechanisms of resistance remain ill-defined. Here we use live-cell fluorescence microscopy to visualize the spatiotemporal dynamics of mycobacteriophage infection in single cells and populations, showing that infection is dependent on the host nucleoid-associated Lsr2 protein. Mycobacteriophages preferentially adsorb at Mycobacterium smegmatis sites of new cell wall synthesis and following DNA injection, Lsr2 reorganizes away from host replication foci to establish zones of phage DNA replication (ZOPR). Cells lacking Lsr2 proceed through to cell lysis when infected but fail to generate consecutive phage bursts that trigger epidemic spread of phage particles to neighbouring cells. Many mycobacteriophages code for their own Lsr2-related proteins, and although their roles are unknown, they do not rescue the loss of host Lsr2.
Collapse
Affiliation(s)
- Charles L Dulberger
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | | | - Siân V Owen
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sean Wilson
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Michael G Wuo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rebecca A Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lexi A Serpa
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Junhao Zhu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ben J Braunecker
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Georgia R Squyres
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Michael Baym
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Laura L Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
| |
Collapse
|
4
|
Armianinova DK, Karpov DS, Kotliarova MS, Goncharenko AV. Genetic Engineering in Mycobacteria. Mol Biol 2022. [DOI: 10.1134/s0026893322060036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Abstract
Genetic tools for targeted modification of the mycobacterial genome contribute to the understanding of the physiology and virulence mechanisms of mycobacteria. Human and animal pathogens, such as the Mycobacterium tuberculosis complex, which causes tuberculosis, and M. leprae, which causes leprosy, are of particular importance. Genetic research opens up novel opportunities to identify and validate new targets for antibacterial drugs and to develop improved vaccines. Although mycobacteria are difficult to work with due to their slow growth rate and a limited possibility to transfer genetic information, significant progress has been made in developing genetic engineering methods for mycobacteria. The review considers the main approaches to changing the mycobacterial genome in a targeted manner, including homologous and site-specific recombination and use of the CRISPR/Cas system.
Collapse
|
5
|
Abstract
Mycobacteriophages-bacteriophages infecting Mycobacterium hosts-contribute substantially to our understanding of viral diversity and evolution, provide resources for advancing Mycobacterium genetics, are the basis of high-impact science education programs, and show considerable therapeutic potential. Over 10,000 individual mycobacteriophages have been isolated by high school and undergraduate students using the model organism Mycobacterium smegmatis mc2155 and 2,100 have been completely sequenced, giving a high-resolution view of the phages that infect a single common host strain. The phage genomes are revealed to be highly diverse and architecturally mosaic and are replete with genes of unknown function. Mycobacteriophages have provided many widely used tools for Mycobacterium genetics including integration-proficient vectors and recombineering systems, as well as systems for efficient delivery of reporter genes, transposons, and allelic exchange substrates. The genomic insights and engineering tools have facilitated exploration of phages for treatment of Mycobacterium infections, although their full therapeutic potential has yet to be realized.
Collapse
Affiliation(s)
- Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States of America
| |
Collapse
|
6
|
Liu K, Lin GH, Liu K, Liu YJ, Tao XY, Gao B, Zhao M, Wei DZ, Wang FQ. Multiplexed site-specific genome engineering in Mycolicibacterium neoaurum by Att/Int system. Synth Syst Biotechnol 2022; 7:1002-1011. [PMID: 35782483 PMCID: PMC9213222 DOI: 10.1016/j.synbio.2022.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/04/2022] [Accepted: 05/25/2022] [Indexed: 11/10/2022] Open
Abstract
Genomic integration of genes and pathway-sized DNA cassettes is often an indispensable way to construct robust and productive microbial cell factories. For some uncommon microbial hosts, such as Mycolicibacterium and Mycobacterium species, however, it is a challenge. Here, we present a multiplexed integrase-assisted site-specific recombination (miSSR) method to precisely and iteratively integrate genes/pathways with controllable copies in the chromosomes of Mycolicibacteria for the purpose of developing cell factories. First, a single-step multi-copy integration method was established in M. neoaurum by a combination application of mycobacteriophage L5 integrase and two-step allelic exchange strategy, the efficiencies of which were ∼100% for no more than three-copy integration events and decreased sharply to ∼20% for five-copy integration events. Second, the R4, Bxb1 and ΦC31 bacteriophage Att/Int systems were selected to extend the available integration toolbox for multiplexed gene integration events. Third, a reconstructed mycolicibacterial Xer recombinases (Xer-cise) system was employed to recycle the selection marker of gene recombination to facilitate the iterative gene manipulation. As a proof of concept, the biosynthetic pathway of ergothioneine (EGT) in Mycolicibacterium neoaurum ATCC 25795 was achieved by remodeling its metabolic pathway with a miSSR system. With six copies of the biosynthetic gene clusters (BGCs) of EGT and pentose phosphate isomerase (PRT), the titer of EGT in the resulting strain in a 30 mL shake flask within 5 days was enhanced to 66 mg/L, which was 3.77 times of that in the wild strain. The improvements indicated that the miSSR system was an effective, flexible, and convenient tool to engineer the genomes of Mycolicibacteria as well as other strains in the Mycobacteriaceae due to their proximate evolutionary relationships.
Collapse
|
7
|
Efficient targeted transgenesis of large donor DNA into multiple mouse genetic backgrounds using bacteriophage Bxb1 integrase. Sci Rep 2022; 12:5424. [PMID: 35361849 PMCID: PMC8971409 DOI: 10.1038/s41598-022-09445-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/23/2022] [Indexed: 12/12/2022] Open
Abstract
The development of mouse models of human disease and synthetic biology research by targeted transgenesis of large DNA constructs represent a significant genetic engineering hurdle. We developed an efficient, precise, single-copy integration of large transgenes directly into zygotes using multiple mouse genetic backgrounds. We used in vivo Bxb1 mediated recombinase-mediated cassette exchange (RMCE) with a transgene “landing pad” composed of dual heterologous Bxb1 attachment (att) sites in cis, within the Gt(ROSA)26Sor safe harbor locus. RMCE of donor was achieved by microinjection of vector DNA carrying cognate attachment sites flanking the donor transgene with Bxb1-integrase mRNA. This approach achieves perfect vector-free integration of donor constructs at efficiencies > 40% with up to ~ 43 kb transgenes. Coupled with a nanopore-based Cas9-targeted sequencing (nCATS), complete verification of precise insertion sequence was achieved. As a proof-of-concept we describe the development of C57BL/6J and NSG Krt18-ACE2 models for SARS-CoV2 research with verified heterozygous N1 animals within ~ 4 months. Additionally, we created a series of mice with diverse backgrounds carrying a single att site including FVB/NJ, PWK/PhJ, NOD/ShiLtJ, CAST/EiJ and DBA/2J allowing for rapid transgene insertion. Combined, this system enables predictable, rapid development with simplified characterization of precisely targeted transgenic animals across multiple genetic backgrounds.
Collapse
|
8
|
Freeman KG, Wetzel KS, Zhang Y, Zack KM, Jacobs-Sera D, Walters SM, Barbeau DJ, McElroy AK, Williams JV, Hatfull GF. A Mycobacteriophage-Based Vaccine Platform: SARS-CoV-2 Antigen Expression and Display. Microorganisms 2021; 9:2414. [PMID: 34946016 PMCID: PMC8704799 DOI: 10.3390/microorganisms9122414] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 11/16/2022] Open
Abstract
The explosion of SARS-CoV-2 infections in 2020 prompted a flurry of activity in vaccine development and exploration of various vaccine platforms, some well-established and some new. Phage-based vaccines were described previously, and we explored the possibility of using mycobacteriophages as a platform for displaying antigens of SARS-CoV-2 or other infectious agents. The potential advantages of using mycobacteriophages are that a large and diverse variety of them have been described and genomically characterized, engineering tools are available, and there is the capacity to display up to 700 antigen copies on a single particle approximately 100 nm in size. The phage body may itself be a good adjuvant, and the phages can be propagated easily, cheaply, and to high purity. Furthermore, the recent use of these phages therapeutically, including by intravenous administration, suggests an excellent safety profile, although efficacy can be restricted by neutralizing antibodies. We describe here the potent immunogenicity of mycobacteriophage Bxb1, and Bxb1 recombinants displaying SARS-CoV-2 Spike protein antigens.
Collapse
Affiliation(s)
- Krista G. Freeman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA; (K.G.F.); (K.S.W.); (K.M.Z.); (D.J.-S.)
| | - Katherine S. Wetzel
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA; (K.G.F.); (K.S.W.); (K.M.Z.); (D.J.-S.)
| | - Yu Zhang
- UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15260, USA; (Y.Z.); (S.M.W.); (A.K.M.); (J.V.W.)
- Center for Vaccine Research, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA;
| | - Kira M. Zack
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA; (K.G.F.); (K.S.W.); (K.M.Z.); (D.J.-S.)
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA; (K.G.F.); (K.S.W.); (K.M.Z.); (D.J.-S.)
| | - Sara M. Walters
- UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15260, USA; (Y.Z.); (S.M.W.); (A.K.M.); (J.V.W.)
| | - Dominique J. Barbeau
- Center for Vaccine Research, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA;
| | - Anita K. McElroy
- UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15260, USA; (Y.Z.); (S.M.W.); (A.K.M.); (J.V.W.)
- Center for Vaccine Research, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA;
| | - John V. Williams
- UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15260, USA; (Y.Z.); (S.M.W.); (A.K.M.); (J.V.W.)
- Center for Vaccine Research, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA;
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA; (K.G.F.); (K.S.W.); (K.M.Z.); (D.J.-S.)
| |
Collapse
|
9
|
Gao H, Taylor G, Evans SK, Fogg PCM, Smith MCM. Application of serine integrases for secondary metabolite pathway assembly in Streptomyces. Synth Syst Biotechnol 2020; 5:111-119. [PMID: 32596521 PMCID: PMC7306541 DOI: 10.1016/j.synbio.2020.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 11/29/2022] Open
Abstract
Serine integrases have been shown to be efficient tools for metabolic pathway assembly. To further improve the flexibility and efficiency of pathway engineering via serine integrases, we explored how multiple orthogonally active serine integrases can be applied for use in vitro for the heterologous expression of complex biosynthesis pathways in Streptomyces spp., the major producers of useful bioactive natural products. The results show that multiple orthogonal serine integrases efficiently assemble the genes from a complex biosynthesis pathway in a single in vitro recombination reaction, potentially permitting a versatile combinatorial assembly approach. Furthermore, the assembly strategy also permitted the incorporation of a well-characterised promoter upstream of each gene for expression in a heterologous host. The results demonstrate how site-specific recombination based on orthogonal serine integrases can be applied in Streptomyces spp.
Collapse
Affiliation(s)
- Hong Gao
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Gabrielle Taylor
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Stephanie K Evans
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Paul C M Fogg
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Margaret C M Smith
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
| |
Collapse
|
10
|
Borgers K, Vandewalle K, Festjens N, Callewaert N. A guide to Mycobacterium mutagenesis. FEBS J 2019; 286:3757-3774. [PMID: 31419030 DOI: 10.1111/febs.15041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/05/2019] [Accepted: 08/12/2019] [Indexed: 12/18/2022]
Abstract
The genus Mycobacterium includes several pathogens that cause severe disease in humans, like Mycobacterium tuberculosis (M. tb), the infectious agent causing tuberculosis. Genetic tools to engineer mycobacterial genomes, in a targeted or random fashion, have provided opportunities to investigate M. tb infection and pathogenesis. Furthermore, they have allowed the identification and validation of potential targets for the diagnosis, prevention, and treatment of tuberculosis. This review describes the various methods that are available for the generation of mutants in Mycobacterium species, focusing specifically on tools for altering slow-growing mycobacteria from the M. tb complex. Among others, it incorporates the recent new molecular biological technologies (e.g. ORBIT) to rapidly and/or genome-wide comprehensively obtain targeted mutants in mycobacteria. As such, this review can be used as a guide to select the appropriate genetic tools to generate mycobacterial mutants of interest, which can be used as tools to aid understanding of M. tb infection or to help developing TB intervention strategies.
Collapse
Affiliation(s)
- Katlyn Borgers
- VIB-UGhent Center for Medical Biotechnology, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Belgium
| | - Kristof Vandewalle
- VIB-UGhent Center for Medical Biotechnology, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Belgium
| | - Nele Festjens
- VIB-UGhent Center for Medical Biotechnology, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Belgium
| | - Nico Callewaert
- VIB-UGhent Center for Medical Biotechnology, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Belgium
| |
Collapse
|
11
|
Bacteriophage gene products as potential antimicrobials against tuberculosis. Biochem Soc Trans 2019; 47:847-860. [PMID: 31085613 DOI: 10.1042/bst20180506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 04/02/2019] [Accepted: 04/08/2019] [Indexed: 01/20/2023]
Abstract
Tuberculosis (TB) is recognised as one of the most pressing global health threats among infectious diseases. Bacteriophages are adapted for killing of their host, and they were exploited in antibacterial therapy already before the discovery of antibiotics. Antibiotics as broadly active drugs overshadowed phage therapy for a long time. However, owing to the rapid spread of antibiotic resistance and the increasing complexity of treatment of drug-resistant TB, mycobacteriophages are being studied for their antimicrobial potential. Besides phage therapy, which is the administration of live phages to infected patients, the development of drugs of phage origin is gaining interest. This path of medical research might provide us with a new pool of previously undiscovered inhibition mechanisms and molecular interactions which are also of interest in basic research of cellular processes, such as transcription. The current state of research on mycobacteriophage-derived anti-TB treatment is reviewed in comparison with inhibitors from other phages, and with focus on transcription as the host target process.
Collapse
|
12
|
Abstract
Mycobacteriophages are viruses that infect mycobacterial hosts. A large number of mycobacteriophages have been isolated and genomically characterized, providing insights into viral diversity and evolution, as well as fueling development of tools for mycobacterial genetics. Mycobacteriophages have intimate relationships with their hosts and provide insights into the genetics and physiology of the mycobacteria and tools for potential clinical applications such as drug development, diagnosis, vaccines, and potentially therapy.
Collapse
|
13
|
Murphy KC, Nelson SJ, Nambi S, Papavinasasundaram K, Baer CE, Sassetti CM. ORBIT: a New Paradigm for Genetic Engineering of Mycobacterial Chromosomes. mBio 2018; 9:e01467-18. [PMID: 30538179 PMCID: PMC6299477 DOI: 10.1128/mbio.01467-18] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/19/2018] [Indexed: 11/20/2022] Open
Abstract
Two efficient recombination systems were combined to produce a versatile method for chromosomal engineering that obviates the need to prepare double-stranded DNA (dsDNA) recombination substrates. A synthetic "targeting oligonucleotide" is incorporated into the chromosome via homologous recombination mediated by the phage Che9c RecT annealase. This oligonucleotide contains a site-specific recombination site for the directional Bxb1 integrase (Int), which allows the simultaneous integration of a "payload plasmid" that contains a cognate recombination site and a selectable marker. The targeting oligonucleotide and payload plasmid are cotransformed into a RecT- and Int-expressing strain, and drug-resistant homologous recombinants are selected in a single step. A library of reusable target-independent payload plasmids is available to generate gene knockouts, promoter replacements, or C-terminal tags. This new system is called ORBIT (for "oligonucleotide-mediated recombineering followed by Bxb1 integrase targeting") and is ideally suited for the creation of libraries consisting of large numbers of deletions, insertions, or fusions in a bacterial chromosome. We demonstrate the utility of this "drag and drop" strategy by the construction of insertions or deletions in over 100 genes in Mycobacteriumtuberculosis and M. smegmatisIMPORTANCE We sought to develop a system that could increase the usefulness of oligonucleotide-mediated recombineering of bacterial chromosomes by expanding the types of modifications generated by an oligonucleotide (i.e., insertions and deletions) and by making recombinant formation a selectable event. This paper describes such a system for use in M. smegmatis and M. tuberculosis By incorporating a single-stranded DNA (ssDNA) version of the phage Bxb1 attP site into the oligonucleotide and coelectroporating it with a nonreplicative plasmid that carries an attB site and a drug selection marker, we show both formation of a chromosomal attP site and integration of the plasmid in a single transformation. No target-specific dsDNA substrates are required. This system will allow investigators studying mycobacterial diseases, including tuberculosis, to easily generate multiple mutants for analysis of virulence factors, identification of new drug targets, and development of new vaccines.
Collapse
Affiliation(s)
- Kenan C Murphy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Samantha J Nelson
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Subhalaxmi Nambi
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Kadamba Papavinasasundaram
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Christina E Baer
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| |
Collapse
|
14
|
Bhawsinghka N, Dutta A, Mukhopadhyay J, Das Gupta SK. A transcriptomic analysis of the mycobacteriophage D29 genome reveals the presence of novel stoperator-associated promoters in its right arm. Microbiology (Reading) 2018; 164:1168-1179. [DOI: 10.1099/mic.0.000693] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Niketa Bhawsinghka
- 1Department of Microbiology, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, India
| | - Arkajyoti Dutta
- 2Department of Chemistry, Bose Institute, 93/1 APC Road, Kolkata 700009, India
| | | | - Sujoy K. Das Gupta
- 1Department of Microbiology, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, India
| |
Collapse
|
15
|
Lima-Junior JD, Viana-Niero C, Conde Oliveira DV, Machado GE, Rabello MCDS, Martins-Junior J, Martins LF, Digiampietri LA, da Silva AM, Setubal JC, Russell DA, Jacobs-Sera D, Pope WH, Hatfull GF, Leão SC. Characterization of mycobacteria and mycobacteriophages isolated from compost at the São Paulo Zoo Park Foundation in Brazil and creation of the new mycobacteriophage Cluster U. BMC Microbiol 2016; 16:111. [PMID: 27316672 PMCID: PMC4912749 DOI: 10.1186/s12866-016-0734-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 06/08/2016] [Indexed: 01/13/2023] Open
Abstract
Background A large collection of sequenced mycobacteriophages capable of infecting a single host strain of Mycobacterium smegmatis shows considerable genomic diversity with dozens of distinctive types (clusters) and extensive variation within those sharing evident nucleotide sequence similarity. Here we profiled the mycobacterial components of a large composting system at the São Paulo zoo. Results We isolated and sequenced eight mycobacteriophages using Mycobacterium smegmatis mc2155 as a host. None of these eight phages infected any of mycobacterial strains isolated from the same materials. The phage isolates span considerable genomic diversity, including two phages (Barriga, Nhonho) related to Subcluster A1 phages, two Cluster B phages (Pops, Subcluster B1; Godines, Subcluster B2), three Subcluster F1 phages (Florinda, Girafales, and Quico), and Madruga, a relative of phage Patience with which it constitutes the new Cluster U. Interestingly, the two Subcluster A1 phages and the three Subcluster F1 phages have genomic relationships indicating relatively recent evolution within a geographically isolated niche in the composting system. Conclusions We predict that composting systems such as those used to obtain these mycobacteriophages will be a rich source for the isolation of additional phages that will expand our view of bacteriophage diversity and evolution. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0734-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- James Daltro Lima-Junior
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Cristina Viana-Niero
- Departmento de Ciências Biológicas, Universidade Federal de São Paulo, campus Diadema, São Paulo, Brazil
| | - Daniel V Conde Oliveira
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Gabriel Esquitini Machado
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Joaquim Martins-Junior
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Layla Farage Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Virginia Bioinformatics Institute, Blacksburg, VA, 24060, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 1524, USA
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 1524, USA
| | - Welkin H Pope
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 1524, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 1524, USA
| | - Sylvia Cardoso Leão
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil.
| |
Collapse
|
16
|
Mouse embryonic stem cells with a multi-integrase mouse artificial chromosome for transchromosomic mouse generation. Transgenic Res 2015; 24:717-27. [PMID: 26055730 PMCID: PMC4504986 DOI: 10.1007/s11248-015-9884-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 05/28/2015] [Indexed: 01/25/2023]
Abstract
The mouse artificial chromosome (MAC) has several advantages as a gene delivery vector, including stable episomal maintenance of the exogenous genetic material and the ability to carry large and/or multiple gene inserts including their regulatory elements. Previously, a MAC containing multi-integration site (MI-MAC) was generated to facilitate transfer of multiple genes into desired cells. To generate transchromosomic (Tc) mice containing a MI-MAC with genes of interest, the desired genes were inserted into MI-MAC in CHO cells, and then the MI-MAC was transferred to mouse embryonic stem (mES) cells via microcell-mediated chromosome transfer (MMCT). However, the efficiency of MMCT from CHO to mES cells is very low (<10−6). In this study, we constructed mES cell lines containing a MI-MAC vector to directly insert a gene of interest into the MI-MAC in mES cells via a simple transfection method for Tc mouse generation. The recombination rate of the GFP gene at each attachment site (FRT, PhiC31attP, R4attP, TP901-1attP and Bxb1attP) on MI-MAC was greater than 50 % in MI-MAC mES cells. Chimeric mice with high coat colour chimerism were generated from the MI-MAC mES cell lines and germline transmission from the chimera was observed. As an example for the generation of Tc mice with a desired gene by the MI-MAC mES approach, a Tc mouse strain ubiquitously expressing Emerald luciferase was efficiently established. Thus, the findings suggest that this new Tc strategy employing mES cells and a MI-MAC vector is efficient and useful for animal transgenesis.
Collapse
|
17
|
Arutyunov D, Singh U, El-Hawiet A, Seckler HDS, Nikjah S, Joe M, Bai Y, Lowary TL, Klassen JS, Evoy S, Szymanski CM. Mycobacteriophage cell binding proteins for the capture of mycobacteria. BACTERIOPHAGE 2014; 4:e960346. [PMID: 26713219 DOI: 10.4161/21597073.2014.960346] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 08/20/2014] [Accepted: 08/28/2014] [Indexed: 12/20/2022]
Abstract
Slow growing Mycobacteriumavium subsp. paratuberculosis (MAP) causes a deadly condition in cattle known as Johne's disease where asymptomatic carriers are the major source of disease transmission. MAP was also shown to be associated with chronic Crohn's disease in humans. Mycobacterium smegmatis is a model mycobacterium that can cause opportunistic infections in a number of human tissues and, rarely, a respiratory disease. Currently, there are no rapid, culture-independent, reliable and inexpensive tests for the diagnostics of MAP or M. smegmatis infections. Bacteriophages are viruses producing a number of proteins that effectively and specifically recognize the cell envelopes of their bacterial hosts. We demonstrate that the mycobacterial phage L5 minor tail protein Gp6 and lysin Gp10 are useful tools for the rapid capture of mycobacteria. Immobilized Gp10 was able to bind both MAP and M. smegmatis cells whereas Gp6 was M. smegmatis specific. Neither of the 2 proteins was able to capture E. coli, salmonella, campylobacter or Mycobacterium marinum cells. Gp6 was detected previously as a component of the phage particle and shows no homology to proteins with known function. Therefore, electrospray ionization mass spectrometry was used to determine whether recombinant Gp6 could bind to a number of chemically synthesized fragments of mycobacterial surface glycans. These findings demonstrate that mycobacteriophage proteins could be used as a pathogen capturing platform that can potentially improve the effectiveness of existing diagnostic methods.
Collapse
Affiliation(s)
- Denis Arutyunov
- Department of Biological Sciences; University of Alberta , Edmonton, AB Canada ; Alberta Glycomics Center; University of Alberta ; Edmonton, AB Canada
| | - Upasana Singh
- Department of Electrical and Computer Engineering; University of Alberta ; Edmonton, AB Canada
| | - Amr El-Hawiet
- Alberta Glycomics Center; University of Alberta ; Edmonton, AB Canada ; Department of Chemistry; University of Alberta ; Edmonton, AB Canada
| | - Henrique Dos Santos Seckler
- Department of Biological Sciences; University of Alberta , Edmonton, AB Canada ; Alberta Glycomics Center; University of Alberta ; Edmonton, AB Canada
| | - Sanaz Nikjah
- Alberta Glycomics Center; University of Alberta ; Edmonton, AB Canada ; Department of Chemistry; University of Alberta ; Edmonton, AB Canada
| | - Maju Joe
- Alberta Glycomics Center; University of Alberta ; Edmonton, AB Canada ; Department of Chemistry; University of Alberta ; Edmonton, AB Canada
| | - Yu Bai
- Alberta Glycomics Center; University of Alberta ; Edmonton, AB Canada ; Department of Chemistry; University of Alberta ; Edmonton, AB Canada
| | - Todd L Lowary
- Alberta Glycomics Center; University of Alberta ; Edmonton, AB Canada ; Department of Chemistry; University of Alberta ; Edmonton, AB Canada
| | - John S Klassen
- Alberta Glycomics Center; University of Alberta ; Edmonton, AB Canada ; Department of Chemistry; University of Alberta ; Edmonton, AB Canada
| | - Stephane Evoy
- Department of Electrical and Computer Engineering; University of Alberta ; Edmonton, AB Canada
| | - Christine M Szymanski
- Department of Biological Sciences; University of Alberta , Edmonton, AB Canada ; Alberta Glycomics Center; University of Alberta ; Edmonton, AB Canada
| |
Collapse
|
18
|
Adriaenssens EM, Edwards R, Nash JHE, Mahadevan P, Seto D, Ackermann HW, Lavigne R, Kropinski AM. Integration of genomic and proteomic analyses in the classification of the Siphoviridae family. Virology 2014; 477:144-154. [PMID: 25466308 DOI: 10.1016/j.virol.2014.10.016] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 09/08/2014] [Accepted: 10/17/2014] [Indexed: 11/26/2022]
Abstract
Using a variety of genomic (BLASTN, ClustalW) and proteomic (Phage Proteomic Tree, CoreGenes) tools we have tackled the taxonomic status of members of the largest bacteriophage family, the Siphoviridae. In all over 400 phages were examined and we were able to propose 39 new genera, comprising 216 phage species, and add 62 species to two previously defined genera (Phic3unalikevirus; L5likevirus) grouping, in total, 390 fully sequenced phage isolates. Many of the remainders are orphans which the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) chooses not to ascribe genus status at the time being.
Collapse
Affiliation(s)
- Evelien M Adriaenssens
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of Pretoria, Lynnwood Road, Pretoria 0028, South Africa
| | - Rob Edwards
- Geology, Mathematics, and Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - John H E Nash
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 110 Stone Road West, Guelph, ON, Canada N1G 3W4
| | | | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20110, USA
| | - Hans-Wolfgang Ackermann
- Département de Microbiologie-infectiologie et immunologie, Faculté de médecine, Université Laval, Québec, QC, Canada G1K 7P4
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, KasteelparkArenberg 21 - b2462, Heverlee 3001, Belgium.
| | - Andrew M Kropinski
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 110 Stone Road West, Guelph, ON, Canada N1G 3W4; Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada N1G 2A1.
| |
Collapse
|
19
|
Abstract
Virology encompasses a broad spectrum of topics touching upon many aspects of our everyday lives. However, appreciation of this impact is too often restricted to those who have specialized training and participate in virology research. The Phage Hunters Integrating Research and Education (PHIRE) program and the This Week in Virology (TWiV) podcast seek to bring virology to new audiences through two different approaches—direct involvement of undergraduates in discovering and genomically characterizing bacteriophages (PHIRE) and clear, accessible, and free discussions among experts of all topics in virology (TWiV). Here we discuss these two high-impact programs, the audiences that they serve, their broader impacts, and their future potential.
Collapse
Affiliation(s)
- Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Vincent Racaniello
- Department of Microbiology and Immunology, Columbia University, New York, NY 10032
| |
Collapse
|
20
|
Mutational analysis of the mycobacteriophage BPs promoter PR reveals context-dependent sequences for mycobacterial gene expression. J Bacteriol 2014; 196:3589-97. [PMID: 25092027 DOI: 10.1128/jb.01801-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The PR promoter of mycobacteriophage BPs directs early lytic gene expression and is under the control of the BPs repressor, gp33. Reporter gene fusions showed that PR has modest activity in an extrachromosomal context but has activity that is barely detectable in an integrated context, even in the absence of its repressor. Mutational dissection of PR showed that it uses a canonical -10 hexamer recognized by SigA, and mutants with mutations to the sequence 5'-TATAMT had the greatest activities. It does not contain a 5'-TGN-extended -10 sequence, although mutants with mutations creating an extended -10 sequence had substantially increased promoter activity. Mutations in the -35 hexamer also influenced promoter activity but were strongly context dependent, and similar substitutions in the -35 hexamer differentially affected promoter activity, depending on the -10 and extended -10 motifs. This warrants caution in the construction of synthetic promoters or the bioinformatic prediction of promoter activity. Combinations of mutations throughout PR generated a calibrated series of promoters for expression of stably integrated recombinant genes in both Mycobacterium smegmatis and M. tuberculosis, with maximal promoter activity being more than 2-fold that of the strong hsp60 promoter.
Collapse
|
21
|
N-Terminal Region of Chitinase I ofBacillus circulansKA-304 Contained New Chitin-Biding Domain. Biosci Biotechnol Biochem 2014; 75:299-304. [DOI: 10.1271/bbb.100659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
22
|
Shao M, Kumar S, Thomson JG. Precise excision of plastid DNA by the large serine recombinase Bxb1. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:322-9. [PMID: 24261912 DOI: 10.1111/pbi.12139] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 09/12/2013] [Accepted: 10/03/2013] [Indexed: 05/08/2023]
Abstract
Marker genes are essential for the selection and identification of rarely occurring transformation events generated in biotechnology. This includes plastid transformation, which requires that multiple copies of the modified chloroplast genome be present to obtain genetically stable transplastomic plants. However, the marker gene becomes dispensable when homoplastomic plants are obtained. Here, we demonstrate the precise excision of attP- and attB-flanked DNA from the plastid genome mediated by the large serine recombinase Bxb1. We transformed the tobacco plastid genome with the pTCH-PB vector containing a stuffer fragment of DNA flanked by directly oriented nonhomologous attP and attB recombinase recognition sites. In the absence of the Bxb1 recombinase, the transformed plastid genomes were stable and heritable. Nuclear-transformed transgenic tobacco plants expressing a plastid-targeted Bxb1 recombinase were crossed with transplastomic pTCH-PB plants, and the T₁ hybrids exhibited efficient excision of the target sequence. The Bxb1-att system should prove to be a useful tool for site-specifically manipulating the plastid genome and generating marker-free transplastomic plants.
Collapse
Affiliation(s)
- Min Shao
- Department of Plant Sciences, UC Davis, Davis, CA, USA
| | | | | |
Collapse
|
23
|
Abstract
ABSTRACT
Mycobacteriophages have provided numerous essential tools for mycobacterial genetics, including delivery systems for transposons, reporter genes, and allelic exchange substrates, and components for plasmid vectors and mutagenesis. Their genetically diverse genomes also reveal insights into the broader nature of the phage population and the evolutionary mechanisms that give rise to it. The substantial advances in our understanding of the biology of mycobacteriophages including a large collection of completely sequenced genomes indicates a rich potential for further contributions in tuberculosis genetics and beyond.
Collapse
|
24
|
Hermann M, Stillhard P, Wildner H, Seruggia D, Kapp V, Sánchez-Iranzo H, Mercader N, Montoliu L, Zeilhofer HU, Pelczar P. Binary recombinase systems for high-resolution conditional mutagenesis. Nucleic Acids Res 2014; 42:3894-907. [PMID: 24413561 PMCID: PMC3973285 DOI: 10.1093/nar/gkt1361] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Conditional mutagenesis using Cre recombinase expressed from tissue specific promoters facilitates analyses of gene function and cell lineage tracing. Here, we describe two novel dual-promoter-driven conditional mutagenesis systems designed for greater accuracy and optimal efficiency of recombination. Co-Driver employs a recombinase cascade of Dre and Dre-respondent Cre, which processes loxP-flanked alleles only when both recombinases are expressed in a predetermined temporal sequence. This unique property makes Co-Driver ideal for sequential lineage tracing studies aimed at unraveling the relationships between cellular precursors and mature cell types. Co-InCre was designed for highly efficient intersectional conditional transgenesis. It relies on highly active trans-splicing inteins and promoters with simultaneous transcriptional activity to reconstitute Cre recombinase from two inactive precursor fragments. By generating native Cre, Co-InCre attains recombination rates that exceed all other binary SSR systems evaluated in this study. Both Co-Driver and Co-InCre significantly extend the utility of existing Cre-responsive alleles.
Collapse
Affiliation(s)
- Mario Hermann
- Institute of Laboratory Animal Science, University of Zurich, Sternwartstrasse 6, CH-8091 Zurich, Switzerland, Institute of Neuropathology, University Hospital of Zurich, Schmelzbergstrasse 12, CH-8091 Zurich, Switzerland, Institute of Pharmacology and Toxicology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland, National Centre for Biotechnology (CNB-CSIC), Darwin 3, 28049 Madrid, Spain, CIBERER-ISCIII, Darwin 3, 28049 Madrid, Spain, Program of Cardiovascular Development, Department of Cardiovascular Development and Repair, Centro Nacional de Investigaciones Cardiovasculares Carlos III, calle Melchor Fernández Almagro 3, 28029 Madrid, Spain and Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Cluster M mycobacteriophages Bongo, PegLeg, and Rey with unusually large repertoires of tRNA isotypes. J Virol 2013; 88:2461-80. [PMID: 24335314 DOI: 10.1128/jvi.03363-13] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
UNLABELLED Genomic analysis of a large set of phages infecting the common host Mycobacterium smegmatis mc(2)155 shows that they span considerable genetic diversity. There are more than 20 distinct types that lack nucleotide similarity with each other, and there is considerable diversity within most of the groups. Three newly isolated temperate mycobacteriophages, Bongo, PegLeg, and Rey, constitute a new group (cluster M), with the closely related phages Bongo and PegLeg forming subcluster M1 and the more distantly related Rey forming subcluster M2. The cluster M mycobacteriophages have siphoviral morphologies with unusually long tails, are homoimmune, and have larger than average genomes (80.2 to 83.7 kbp). They exhibit a variety of features not previously described in other mycobacteriophages, including noncanonical genome architectures and several unusual sets of conserved repeated sequences suggesting novel regulatory systems for both transcription and translation. In addition to containing transfer-messenger RNA and RtcB-like RNA ligase genes, their genomes encode 21 to 24 tRNA genes encompassing complete or nearly complete sets of isotypes. We predict that these tRNAs are used in late lytic growth, likely compensating for the degradation or inadequacy of host tRNAs. They may represent a complete set of tRNAs necessary for late lytic growth, especially when taken together with the apparent lack of codons in the same late genes that correspond to tRNAs that the genomes of the phages do not obviously encode. IMPORTANCE The bacteriophage population is vast, dynamic, and old and plays a central role in bacterial pathogenicity. We know surprisingly little about the genetic diversity of the phage population, although metagenomic and phage genome sequencing indicates that it is great. Probing the depth of genetic diversity of phages of a common host, Mycobacterium smegmatis, provides a higher resolution of the phage population and how it has evolved. Three new phages constituting a new cluster M further expand the diversity of the mycobacteriophages and introduce novel features. As such, they provide insights into phage genome architecture, virion structure, and gene regulation at the transcriptional and translational levels.
Collapse
|
26
|
Abstract
The study of mycobacteriophages provides insights into viral diversity and evolution, as well as the genetics and physiology of their pathogenic hosts. Genomic characterization of 80 mycobacteriophages reveals a high degree of genetic diversity and an especially rich reservoir of interesting genes. These include a vast number of genes of unknown function that do not match known database entries and many genes whose functions can be predicted but which are not typically found as components of phage genomes. Thus many mysteries surround these genomes, such as why the genes are there, what do they do, how are they expressed and regulated, how do they influence the physiology of the host bacterium, and what forces of evolution directed them to their genomic homes? Although the genetic diversity and novelty of these phages is full of intrigue, it is a godsend for the mycobacterial geneticist, presenting an abundantly rich toolbox that can be exploited to devise new and effective ways for understanding the genetics and physiology of human tuberculosis. As the number of sequenced genomes continues to grow, their mysteries continue to thicken, and the time has come to learn more about the secret lives of mycobacteriophages.
Collapse
Affiliation(s)
- Graham F Hatfull
- Department of Biological Sciences, Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, Pennslyvania, USA
| |
Collapse
|
27
|
Rewritable digital data storage in live cells via engineered control of recombination directionality. Proc Natl Acad Sci U S A 2012; 109:8884-9. [PMID: 22615351 DOI: 10.1073/pnas.1202344109] [Citation(s) in RCA: 233] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The use of synthetic biological systems in research, healthcare, and manufacturing often requires autonomous history-dependent behavior and therefore some form of engineered biological memory. For example, the study or reprogramming of aging, cancer, or development would benefit from genetically encoded counters capable of recording up to several hundred cell division or differentiation events. Although genetic material itself provides a natural data storage medium, tools that allow researchers to reliably and reversibly write information to DNA in vivo are lacking. Here, we demonstrate a rewriteable recombinase addressable data (RAD) module that reliably stores digital information within a chromosome. RAD modules use serine integrase and excisionase functions adapted from bacteriophage to invert and restore specific DNA sequences. Our core RAD memory element is capable of passive information storage in the absence of heterologous gene expression for over 100 cell divisions and can be switched repeatedly without performance degradation, as is required to support combinatorial data storage. We also demonstrate how programmed stochasticity in RAD system performance arising from bidirectional recombination can be achieved and tuned by varying the synthesis and degradation rates of recombinase proteins. The serine recombinase functions used here do not require cell-specific cofactors and should be useful in extending computing and control methods to the study and engineering of many biological systems.
Collapse
|
28
|
Mycobacteriophage Marvin: a new singleton phage with an unusual genome organization. J Virol 2012; 86:4762-75. [PMID: 22357284 DOI: 10.1128/jvi.00075-12] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Mycobacteriophages represent a genetically diverse group of viruses that infect mycobacterial hosts. Although more than 80 genomes have been sequenced, these still poorly represent the likely diversity of the broader population of phages that can infect the host, Mycobacterium smegmatis mc(2)155. We describe here a newly discovered phage, Marvin, which is a singleton phage, having no previously identified close relatives. The 65,100-bp genome contains 107 predicted protein-coding genes arranged in a noncanonical genomic architecture in which a subset of the minor tail protein genes are displaced about 20 kbp from their typical location, situated among nonstructural genes anticipated to be expressed early in lytic growth. Marvin is not temperate, and stable lysogens cannot be recovered from infections, although the presence of a putative xis gene suggests that Marvin could be a relatively recent derivative of a temperate parent. The Marvin genome is replete with novel genes not present in other mycobacteriophage genomes, and although most are of unknown function, the presence of amidoligase and glutamine amidotransferase genes suggests intriguing possibilities for the interactions of Marvin with its mycobacterial hosts.
Collapse
|
29
|
Catalão MJ, Milho C, Gil F, Moniz-Pereira J, Pimentel M. A second endolysin gene is fully embedded in-frame with the lysA gene of mycobacteriophage Ms6. PLoS One 2011; 6:e20515. [PMID: 21694774 PMCID: PMC3111421 DOI: 10.1371/journal.pone.0020515] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 05/02/2011] [Indexed: 11/24/2022] Open
Abstract
Mycobacteriophages are dsDNA viruses that infect mycobacterial hosts. The mycobacteriophage Ms6 accomplishes lysis by producing two cell wall hydrolytic enzymes, Lysin A (LysA) that possesses a central peptidoglycan recognition protein (PGRP) super-family conserved domain with the amidase catalytic site, that cleaves the amide bond between the N-acetylmuramic acid and L-alanine residues in the oligopeptide crosslinking chains of the peptidoglycan and Lysin B (LysB) a mycolylarabinogalactan esterase that hydrolyzes the mycolic acids from the mycolyl-arabinogalactan-peptidoglycan complex. Examination of the endolysin (lysA) DNA sequence revealed the existence of an embedded gene (lysA241) encoded in the same reading frame and preceded by a consensus ribosome-binding site. In the present work we show that, even though lysA is essential for Ms6 viability, phage mutants that express only the longer (Lysin384) or the shorter (Lysin241) endolysin are viable, but defective in the normal timing, progression and completion of host cell lysis. In addition, both endolysins have peptidoglycan hydrolase activity and demonstrated broad growth inhibition activity against various Gram-positive bacteria and mycobacteria.
Collapse
Affiliation(s)
- Maria João Catalão
- Centro de Patogénese Molecular, Unidade dos Retrovírus e Infecções Associadas, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Catarina Milho
- Centro de Patogénese Molecular, Unidade dos Retrovírus e Infecções Associadas, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Filipa Gil
- Centro de Patogénese Molecular, Unidade dos Retrovírus e Infecções Associadas, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - José Moniz-Pereira
- Centro de Patogénese Molecular, Unidade dos Retrovírus e Infecções Associadas, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Madalena Pimentel
- Centro de Patogénese Molecular, Unidade dos Retrovírus e Infecções Associadas, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
- * E-mail:
| |
Collapse
|
30
|
A method for producing transgenic cells using a multi-integrase system on a human artificial chromosome vector. PLoS One 2011; 6:e17267. [PMID: 21390305 PMCID: PMC3044732 DOI: 10.1371/journal.pone.0017267] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 01/24/2011] [Indexed: 11/19/2022] Open
Abstract
The production of cells capable of expressing gene(s) of interest is important for a variety of applications in biomedicine and biotechnology, including gene therapy and animal transgenesis. The ability to insert transgenes at a precise location in the genome, using site-specific recombinases such as Cre, FLP, and ΦC31, has major benefits for the efficiency of transgenesis. Recent work on integrases from ΦC31, R4, TP901-1 and Bxb1 phages demonstrated that these recombinases catalyze site-specific recombination in mammalian cells. In the present study, we examined the activities of integrases on site-specific recombination and gene expression in mammalian cells. We designed a human artificial chromosome (HAC) vector containing five recombination sites (ΦC31 attP, R4 attP, TP901-1 attP, Bxb1 attP and FRT; multi-integrase HAC vector) and de novo mammalian codon-optimized integrases. The multi-integrase HAC vector has several functions, including gene integration in a precise locus and avoiding genomic position effects; therefore, it was used as a platform to investigate integrase activities. Integrases carried out site-specific recombination at frequencies ranging from 39.3-96.8%. Additionally, we observed homogenous gene expression in 77.3-87.5% of colonies obtained using the multi-integrase HAC vector. This vector is also transferable to another cell line, and is capable of accepting genes of interest in this environment. These data suggest that integrases have high DNA recombination efficiencies in mammalian cells. The multi-integrase HAC vector enables us to produce transgene-expressing cells efficiently and create platform cell lines for gene expression.
Collapse
|
31
|
Abstract
Viruses are powerful tools for investigating and manipulating their hosts, but the enormous size and amazing genetic diversity of the bacteriophage population have emerged as something of a surprise. In light of the evident importance of mycobacteria to human health--especially Mycobacterium tuberculosis, which causes tuberculosis--and the difficulties that have plagued their genetic manipulation, mycobacteriophages are especially appealing subjects for discovery, genomic characterization, and manipulation. With more than 70 complete genome sequences available, the mycobacteriophages have provided a wealth of information on the diversity of phages that infect a common bacterial host, revealed the pervasively mosaic nature of phage genome architectures, and identified a huge number of genes of unknown function. Mycobacteriophages have provided key tools for tuberculosis genetics, and new methods for simple construction of mycobacteriophage recombinants will facilitate postgenomic explorations into mycobacteriophage biology.
Collapse
Affiliation(s)
- Graham F Hatfull
- Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.
| |
Collapse
|
32
|
Deschavanne P, DuBow MS, Regeard C. The use of genomic signature distance between bacteriophages and their hosts displays evolutionary relationships and phage growth cycle determination. Virol J 2010; 7:163. [PMID: 20637121 PMCID: PMC2917420 DOI: 10.1186/1743-422x-7-163] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Accepted: 07/17/2010] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Bacteriophage classification is mainly based on morphological traits and genome characteristics combined with host information and in some cases on phage growth lifestyle. A lack of molecular tools can impede more precise studies on phylogenetic relationships or even a taxonomic classification. The use of methods to analyze genome sequences without the requirement for homology has allowed advances in classification. RESULTS Here, we proposed to use genome sequence signature to characterize bacteriophages and to compare them to their host genome signature in order to obtain host-phage relationships and information on their lifestyle. We analyze the host-phage relationships in the four most representative groups of Caudoviridae, the dsDNA group of phages. We demonstrate that the use of phage genomic signature and its comparison with that of the host allows a grouping of phages and is also able to predict the host-phage relationships (lytic vs. temperate). CONCLUSIONS We can thus condense, in relatively simple figures, this phage information dispersed over many publications.
Collapse
Affiliation(s)
- Patrick Deschavanne
- Molécules Thérapeutiques in Silico MTI, INSERM UMR-M 973, Université Paris Diderot - Paris 7, Bât Lamarck, 75205, Paris Cedex 13, France.
| | | | | |
Collapse
|
33
|
Analyses of bifidobacterial prophage-like sequences. Antonie Van Leeuwenhoek 2010; 98:39-50. [DOI: 10.1007/s10482-010-9426-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Accepted: 03/03/2010] [Indexed: 10/19/2022]
|
34
|
Henry M, O'Sullivan O, Sleator RD, Coffey A, Ross RP, McAuliffe O, O'Mahony JM. In silico analysis of Ardmore, a novel mycobacteriophage isolated from soil. Gene 2010; 453:9-23. [DOI: 10.1016/j.gene.2009.12.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 12/16/2009] [Accepted: 12/16/2009] [Indexed: 10/20/2022]
|
35
|
Hatfull GF, Jacobs-Sera D, Lawrence JG, Pope WH, Russell DA, Ko CC, Weber RJ, Patel MC, Germane KL, Edgar RH, Hoyte NN, Bowman CA, Tantoco AT, Paladin EC, Myers MS, Smith AL, Grace MS, Pham TT, O'Brien MB, Vogelsberger AM, Hryckowian AJ, Wynalek JL, Donis-Keller H, Bogel MW, Peebles CL, Cresawn SG, Hendrix RW. Comparative genomic analysis of 60 Mycobacteriophage genomes: genome clustering, gene acquisition, and gene size. J Mol Biol 2010; 397:119-43. [PMID: 20064525 DOI: 10.1016/j.jmb.2010.01.011] [Citation(s) in RCA: 234] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 12/08/2009] [Accepted: 01/05/2010] [Indexed: 10/20/2022]
Abstract
Mycobacteriophages are viruses that infect mycobacterial hosts. Expansion of a collection of sequenced phage genomes to a total of 60-all infecting a common bacterial host-provides further insight into their diversity and evolution. Of the 60 phage genomes, 55 can be grouped into nine clusters according to their nucleotide sequence similarities, 5 of which can be further divided into subclusters; 5 genomes do not cluster with other phages. The sequence diversity between genomes within a cluster varies greatly; for example, the 6 genomes in Cluster D share more than 97.5% average nucleotide similarity with one another. In contrast, similarity between the 2 genomes in Cluster I is barely detectable by diagonal plot analysis. In total, 6858 predicted open-reading frames have been grouped into 1523 phamilies (phams) of related sequences, 46% of which possess only a single member. Only 18.8% of the phams have sequence similarity to non-mycobacteriophage database entries, and fewer than 10% of all phams can be assigned functions based on database searching or synteny. Genome clustering facilitates the identification of genes that are in greatest genetic flux and are more likely to have been exchanged horizontally in relatively recent evolutionary time. Although mycobacteriophage genes exhibit a smaller average size than genes of their host (205 residues compared with 315), phage genes in higher flux average only 100 amino acids, suggesting that the primary units of genetic exchange correspond to single protein domains.
Collapse
Affiliation(s)
- Graham F Hatfull
- Department of Biological Sciences, Pittsburgh Bacteriophage Institute, Pittsburgh, PA 15260, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Arakane Y, Muthukrishnan S. Insect chitinase and chitinase-like proteins. Cell Mol Life Sci 2010; 67:201-16. [PMID: 19816755 PMCID: PMC11115512 DOI: 10.1007/s00018-009-0161-9] [Citation(s) in RCA: 230] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2009] [Revised: 09/21/2009] [Accepted: 09/23/2009] [Indexed: 12/24/2022]
Abstract
Insect chitinases belong to family 18 glycosylhydrolases that hydrolyze chitin by an endo-type of cleavage while retaining the anomeric beta-(1-->4) configuration of products. There are multiple genes encoding chitinases and chitinase-like proteins in all insect species studied using bioinformatics searches. These chitinases differ in size, domain organization, physical, chemical and enzymatic properties, and in patterns of their expression during development. There are also differences in tissue specificity of expression. Based on a phylogenetic analysis, insect chitinases and chitinase-like proteins have been classified into several different groups. Results of RNA interference experiments demonstrate that at least some of these chitinases belonging to different groups serve non-redundant functions and are essential for insect survival, molting or development. Chitinases have been utilized for biological control of insect pests on transgenic plants either alone or in combination with other insecticidal proteins. Specific chitinases may prove to be useful as biocontrol agents and/or as vaccines.
Collapse
Affiliation(s)
- Yasuyuki Arakane
- Department of Biochemistry, Kansas State University, 141 Chalmers Hall, Manhattan, KS 66506-3702 USA
| | - Subbaratnam Muthukrishnan
- Department of Biochemistry, Kansas State University, 141 Chalmers Hall, Manhattan, KS 66506-3702 USA
| |
Collapse
|
37
|
Payne K, Sun Q, Sacchettini J, Hatfull GF. Mycobacteriophage Lysin B is a novel mycolylarabinogalactan esterase. Mol Microbiol 2009; 73:367-81. [PMID: 19555454 PMCID: PMC2774421 DOI: 10.1111/j.1365-2958.2009.06775.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Mycobacteriophages encounter a unique problem among phages of Gram-positive bacteria, in that lysis must not only degrade the peptidoglycan layer but also circumvent a mycolic acid-rich outer membrane covalently attached to the arabinogalactan-peptidoglycan complex. Mycobacteriophages accomplish this by producing two lysis enzymes, Lysin A (LysA) that hydrolyses peptidoglycan, and Lysin B (LysB), a novel mycolylarabinogalactan esterase, that cleaves the mycolylarabinogalactan bond to release free mycolic acids. The D29 LysB structure shows an alpha/beta hydrolase organization with a catalytic triad common to cutinases, but which contains an additional four-helix domain implicated in the binding of lipid substrates. Whereas LysA is essential for mycobacterial lysis, a Giles DeltalysB mutant mycobacteriophage is viable, but defective in the normal timing, progression and completion of host cell lysis. We propose that LysB facilitates lysis by compromising the integrity of the mycobacterial outer membrane linkage to the arabinogalactan-peptidoglycan layer.
Collapse
Affiliation(s)
- Kimberly Payne
- Department of Biological Sciences University of Pittsburgh Pittsburgh, PA 15260 Tel: 412 624 4350
| | - Qingan Sun
- Department of Biochemistry & Biophysics 103 Biochemisty/Biophysics Building Texas A&M University 2128 TAMU College Station, TX 77843-2128
| | - James Sacchettini
- Department of Biochemistry & Biophysics 103 Biochemisty/Biophysics Building Texas A&M University 2128 TAMU College Station, TX 77843-2128
| | - Graham F. Hatfull
- Department of Biological Sciences University of Pittsburgh Pittsburgh, PA 15260 Tel: 412 624 4350
| |
Collapse
|
38
|
Sampson T, Broussard GW, Marinelli LJ, Jacobs-Sera D, Ray M, Ko CC, Russell D, Hendrix RW, Hatfull GF. Mycobacteriophages BPs, Angel and Halo: comparative genomics reveals a novel class of ultra-small mobile genetic elements. MICROBIOLOGY-SGM 2009; 155:2962-2977. [PMID: 19556295 DOI: 10.1099/mic.0.030486-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mycobacteriophages BPs, Angel and Halo are closely related viruses isolated from Mycobacterium smegmatis, and possess the smallest known mycobacteriophage genomes, 41,901 bp, 42,289 bp and 41,441 bp, respectively. Comparative genome analysis reveals a novel class of ultra-small mobile genetic elements; BPs and Halo each contain an insertion of the proposed mobile elements MPME1 and MPME2, respectively, at different locations, while Angel contains neither. The close similarity of the genomes provides a comparison of the pre- and post-integration sequences, revealing an unusual 6 bp insertion at one end of the element and no target duplication. Nine additional copies of these mobile elements are identified in a variety of different contexts in other mycobacteriophage genomes. In addition, BPs, Angel and Halo have an unusual lysogeny module in which the repressor and integrase genes are closely linked. The attP site is located within the repressor-coding region, such that prophage formation results in expression of a C-terminally truncated, but active, form of the repressor.
Collapse
Affiliation(s)
- Timothy Sampson
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Gregory W Broussard
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Laura J Marinelli
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Deborah Jacobs-Sera
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Mondira Ray
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Ching-Chung Ko
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Daniel Russell
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Roger W Hendrix
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Graham F Hatfull
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| |
Collapse
|
39
|
Kumar V, Loganathan P, Sivaramakrishnan G, Kriakov J, Dusthakeer A, Subramanyam B, Chan J, Jacobs WR, Paranji Rama N. Characterization of temperate phage Che12 and construction of a new tool for diagnosis of tuberculosis. Tuberculosis (Edinb) 2008; 88:616-23. [PMID: 18511339 DOI: 10.1016/j.tube.2008.02.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Revised: 02/08/2008] [Accepted: 02/14/2008] [Indexed: 11/18/2022]
Abstract
A temperate phage, Che12, able to infect Mycobacterium tuberculosis, was isolated from soil samples taken from tuberculosis sanatorium area in Chennai, India. The plaque morphology of this phage showed varying grades of turbidity on lawns of M. tuberculosis. The temperate nature of Che12 was established by super infection immunity. Phage integration into the host genomic DNA was confirmed by Southern hybridization using Che12 DNA as a probe. PCR amplification and sequencing of a part of the integrated phage genome in a M. tuberculosis lysogen also confirmed the temperate nature of Che12. The morphology of the phage particles was observed by electron microscopy, revealing similarities to other mycobacteriophages like L5, D29 and TM4. A luciferase reporter phage, phAETRC16, was constructed by cloning firefly luciferase gene into Che12. Infection of viable M. tuberculosis cells by phAETRC16 resulted in expression of luciferase leading to sustained light output. Che12, a true temperate phage infecting M. tuberculosis, is thus ideally suited for developing a diagnostic tool facilitating rapid diagnosis of M. tuberculosis.
Collapse
Affiliation(s)
- Vanaja Kumar
- Tuberculosis Research Centre (Indian Council of Medical Research), Bacteriology, Mayor V.R. Ramanathan Road, Chetput, Chennai 600 031, India.
| | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Two-step site selection for serine-integrase-mediated excision: DNA-directed integrase conformation and central dinucleotide proofreading. Proc Natl Acad Sci U S A 2008; 105:3238-43. [PMID: 18299577 DOI: 10.1073/pnas.0711649105] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteriophage-encoded serine-integrases are members of the large family of serine-recombinases and catalyze site-specific integrative recombination between a phage attP site and a bacterial attB site to form an integrated prophage. Prophage excision involves a second site-specific recombination event, in which the sites generated by integration, attL and attR, are used as substrates to regenerate attP and attB. Excision is catalyzed by integrase but also requires a phage-encoded recombination directionality factor (RDF). The Bxb1 recombination sites, attP and attB, are small (<50 bp), different in sequence, and quasisymmetrical, and they give rise to attL- and attR-recombinant products that are asymmetric but similar to each other, each being composed of B- and P-type half-sites. We show here that the determination of correct excision products is a two-step process, with a presynaptic RDF-dependent step that aligns attL and attR in the correct orientation and a postsynaptic step in which the nonpalindromic central dinucleotide confers identity to attL and attR and prevents each from recombining with itself.
Collapse
|
41
|
Zhou Y, Wang YJ, Wang Y. [Application prospect of new site-specific recombination systems in gene transformation and gene stacking]. YI CHUAN = HEREDITAS 2008; 30:149-154. [PMID: 18244918 DOI: 10.3724/sp.j.1005.2008.00149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Site-specific recombination technology provides an important means for regulating transgene expression and improving efficiency of gene transformation. This technique can lead to the translocation, inversion, deletion, and integration, and the expression of the affected genes can be manipulated in different tissues and organs at different developmental periods. Using site-specific recombination system in gene transformation, we can not only acquire plenty of transformants with precise structural fidelity and faithful expression, but also understand the function of new genes efficiently. Gene stacking technology based on the site-specific recombination can produce transgenic crops with good complex traits, which will accelerate the process of research and development of elite cultivars and provide technical support for the exploration of transgenic crops in China.
Collapse
Affiliation(s)
- Yin Zhou
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
| | | | | |
Collapse
|
42
|
Genomic characterization of mycobacteriophage Giles: evidence for phage acquisition of host DNA by illegitimate recombination. J Bacteriol 2008; 190:2172-82. [PMID: 18178732 DOI: 10.1128/jb.01657-07] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A characteristic feature of bacteriophage genomes is that they are architecturally mosaic, with each individual genome representing a unique assemblage of individual exchangeable modules. Plausible mechanisms for generating mosaicism include homologous recombination at shared boundary sequences of module junctions, illegitimate recombination in a non-sequence-directed process, and site-specific recombination. Analysis of the novel mycobacteriophage Giles genome not only extends our current perspective on bacteriophage genetic diversity, with more than 60% of the genes unrelated to other mycobacteriophages, but offers novel insights into how mosaic genomes are created. In one example, the integration/excision cassette is atypically situated within the structural gene operon and could have moved there either by illegitimate recombination or more plausibly via integrase-mediated site-specific recombination. In a second example, a DNA segment has been recently acquired from the host bacterial chromosome by illegitimate recombination, providing further evidence that phage genomic mosaicism is generated by nontargeted recombination processes.
Collapse
|
43
|
Ventura M, Canchaya C, Tauch A, Chandra G, Fitzgerald GF, Chater KF, van Sinderen D. Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol Mol Biol Rev 2007; 71:495-548. [PMID: 17804669 PMCID: PMC2168647 DOI: 10.1128/mmbr.00005-07] [Citation(s) in RCA: 634] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Actinobacteria constitute one of the largest phyla among bacteria and represent gram-positive bacteria with a high G+C content in their DNA. This bacterial group includes microorganisms exhibiting a wide spectrum of morphologies, from coccoid to fragmenting hyphal forms, as well as possessing highly variable physiological and metabolic properties. Furthermore, Actinobacteria members have adopted different lifestyles, and can be pathogens (e.g., Corynebacterium, Mycobacterium, Nocardia, Tropheryma, and Propionibacterium), soil inhabitants (Streptomyces), plant commensals (Leifsonia), or gastrointestinal commensals (Bifidobacterium). The divergence of Actinobacteria from other bacteria is ancient, making it impossible to identify the phylogenetically closest bacterial group to Actinobacteria. Genome sequence analysis has revolutionized every aspect of bacterial biology by enhancing the understanding of the genetics, physiology, and evolutionary development of bacteria. Various actinobacterial genomes have been sequenced, revealing a wide genomic heterogeneity probably as a reflection of their biodiversity. This review provides an account of the recent explosion of actinobacterial genomics data and an attempt to place this in a biological and evolutionary context.
Collapse
Affiliation(s)
- Marco Ventura
- Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, parco Area delle Scienze 11a, 43100 Parma, Italy.
| | | | | | | | | | | | | |
Collapse
|
44
|
Ackermann HW, Kropinski AM. Curated list of prokaryote viruses with fully sequenced genomes. Res Microbiol 2007; 158:555-66. [PMID: 17889511 DOI: 10.1016/j.resmic.2007.07.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2007] [Revised: 07/18/2007] [Accepted: 07/18/2007] [Indexed: 11/19/2022]
Abstract
Genome sequencing is of enormous importance for classification of prokaryote viruses and for understanding the evolution of these viruses. This survey covers 284 sequenced viruses for which a full description has been published and for which the morphology is known. This corresponds to 219 (4%) of tailed and 75 (36%) of tailless viruses of prokaryotes. The number of sequenced tailless viruses almost doubles if viruses of unknown morphology are counted. The sequences are from representatives of 15 virus families and three groups without family status, including eight taxa of archaeal viruses. Tailed phages, especially those with large genomes and hosts other than enterobacteria or lactococci, mycobacteria and pseudomonads, are vastly under investigated.
Collapse
Affiliation(s)
- Hans-W Ackermann
- Felix d'Herelle Reference Center for Bacterial Viruses, Department of Medical Biology, Faculty of Medicine, Laval University, Québec, QC G1K 7P4, Canada.
| | | |
Collapse
|
45
|
Farrar MD, Howson KM, Bojar RA, West D, Towler JC, Parry J, Pelton K, Holland KT. Genome sequence and analysis of a Propionibacterium acnes bacteriophage. J Bacteriol 2007; 189:4161-7. [PMID: 17400737 PMCID: PMC1913406 DOI: 10.1128/jb.00106-07] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cutaneous propionibacteria are important commensals of human skin and are implicated in a wide range of opportunistic infections. Propionibacterium acnes is also associated with inflammatory acne vulgaris. Bacteriophage PA6 is the first phage of P. acnes to be sequenced and demonstrates a high degree of similarity to many mycobacteriophages both morphologically and genetically. PA6 possesses an icosahedreal head and long noncontractile tail characteristic of the Siphoviridae. The overall genome organization of PA6 resembled that of the temperate mycobacteriophages, although the genome was much smaller, 29,739 bp (48 predicted genes), compared to, for example, 50,550 bp (86 predicted genes) for the Bxb1 genome. PA6 infected only P. acnes and produced clear plaques with turbid centers, but it lacked any obvious genes for lysogeny. The host range of PA6 was restricted to P. acnes, but the phage was able to infect and lyse all P. acnes isolates tested. Sequencing of the PA6 genome makes an important contribution to the study of phage evolution and propionibacterial genetics.
Collapse
Affiliation(s)
- Mark D Farrar
- Skin Research Centre, Institute of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Hatfull GF, Pedulla ML, Jacobs-Sera D, Cichon PM, Foley A, Ford ME, Gonda RM, Houtz JM, Hryckowian AJ, Kelchner VA, Namburi S, Pajcini KV, Popovich MG, Schleicher DT, Simanek BZ, Smith AL, Zdanowicz GM, Kumar V, Peebles CL, Jacobs WR, Lawrence JG, Hendrix RW. Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. PLoS Genet 2006; 2:e92. [PMID: 16789831 PMCID: PMC1475703 DOI: 10.1371/journal.pgen.0020092] [Citation(s) in RCA: 203] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2006] [Accepted: 05/04/2006] [Indexed: 01/18/2023] Open
Abstract
Bacteriophages are the most abundant forms of life in the biosphere and carry genomes characterized by high genetic diversity and mosaic architectures. The complete sequences of 30 mycobacteriophage genomes show them collectively to encode 101 tRNAs, three tmRNAs, and 3,357 proteins belonging to 1,536 "phamilies" of related sequences, and a statistical analysis predicts that these represent approximately 50% of the total number of phamilies in the mycobacteriophage population. These phamilies contain 2.19 proteins on average; more than half (774) of them contain just a single protein sequence. Only six phamilies have representatives in more than half of the 30 genomes, and only three-encoding tape-measure proteins, lysins, and minor tail proteins-are present in all 30 phages, although these phamilies are themselves highly modular, such that no single amino acid sequence element is present in all 30 mycobacteriophage genomes. Of the 1,536 phamilies, only 230 (15%) have amino acid sequence similarity to previously reported proteins, reflecting the enormous genetic diversity of the entire phage population. The abundance and diversity of phages, the simplicity of phage isolation, and the relatively small size of phage genomes support bacteriophage isolation and comparative genomic analysis as a highly suitable platform for discovery-based education.
Collapse
Affiliation(s)
- Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Keravala A, Groth AC, Jarrahian S, Thyagarajan B, Hoyt JJ, Kirby PJ, Calos MP. A diversity of serine phage integrases mediate site-specific recombination in mammalian cells. Mol Genet Genomics 2006; 276:135-46. [PMID: 16699779 DOI: 10.1007/s00438-006-0129-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2006] [Accepted: 04/09/2006] [Indexed: 12/12/2022]
Abstract
This study evaluated the ability of five serine phage integrases, from phages A118, U153, Bxb1, phiFC1, and phiRV1, to mediate recombination in mammalian cells. Two types of recombination were investigated, including the ability of an integrase to mediate recombination between its own phage att sites in the context of a mammalian cell and the ability of an integrase to perform genomic integration pairing a phage att site with an endogenous mammalian sequence. We demonstrated that the A118 integrase mediated precise intra-molecular recombination of a plasmid containing its attB and attP sites at a frequency of approximately 50% in human cells. The closely related U153 integrase also performed efficient recombination in human cells on a plasmid containing the attB and attP sites of A118. The integrases from phages Bxb1, phiFC1, and phiRV1 carried out such recombination at their attB and attP sites at frequencies ranging from 11 to 75%. Furthermore, the A118 integrase mediated recombination between its attP site on a plasmid and pseudo attB sites in the human genome, i.e. native sequences with partial identity to attB. Fifteen such A118 pseudo att sites were analyzed, and a consensus recognition site was identified. The other integrases did not mediate integration at genomic sequences at a frequency above background. These site-specific integrases represent valuable new tools for manipulating eukaryotic genomes.
Collapse
Affiliation(s)
- Annahita Keravala
- Department of Genetics, M-334, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305-5120, USA
| | | | | | | | | | | | | |
Collapse
|
48
|
Ojha A, Anand M, Bhatt A, Kremer L, Jacobs WR, Hatfull GF. GroEL1: a dedicated chaperone involved in mycolic acid biosynthesis during biofilm formation in mycobacteria. Cell 2006; 123:861-73. [PMID: 16325580 DOI: 10.1016/j.cell.2005.09.012] [Citation(s) in RCA: 297] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Revised: 07/27/2005] [Accepted: 09/07/2005] [Indexed: 11/20/2022]
Abstract
Mycobacteria are unusual in encoding two GroEL paralogs, GroEL1 and GroEL2. GroEL2 is essential--presumably providing the housekeeping chaperone functions--while groEL1 is nonessential, contains the attB site for phage Bxb1 integration, and encodes a putative chaperone with unusual structural features. Inactivation of the Mycobacterium smegmatis groEL1 gene by phage Bxb1 integration allows normal planktonic growth but prevents the formation of mature biofilms. GroEL1 modulates synthesis of mycolates--long-chain fatty acid components of the mycobacterial cell wall--specifically during biofilm formation and physically associates with KasA, a key component of the type II Fatty Acid Synthase involved in mycolic acid synthesis. Biofilm formation is associated with elevated synthesis of short-chain (C56-C68) fatty acids, and strains with altered mycolate profiles--including an InhA mutant resistant to the antituberculosis drug isoniazid and a strain overexpressing KasA--are defective in biofilm formation.
Collapse
Affiliation(s)
- Anil Ojha
- Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | | | | | | | | | | |
Collapse
|
49
|
Thomson JG, Ow DW. Site-specific recombination systems for the genetic manipulation of eukaryotic genomes. Genesis 2006; 44:465-76. [PMID: 16981199 DOI: 10.1002/dvg.20237] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Site-specific recombination systems, such as the bacteriophage Cre-lox and yeast FLP-FRT systems, have become valuable tools for the rearrangement of DNA in higher eukaryotes. As a first step to expanding the repertoire of recombination tools, we screened recombination systems derived from the resolvase/invertase family for site-specific recombinase activity in the fission yeast Schizosaccharomyces pombe. Here, we report that seven recombination systems, four from the small serine resolvase subfamily (CinH, ParA, Tn1721, and Tn5053) and three from the large serine resolvase subfamily (Bxb1, TP901-1, and U153), can catalyze site-specific deletion in S. pombe. Those from the large serine resolvase subfamily were also capable of site-specific integration and inversion. In all cases, the recombination events were precise. Functional operation of these recombination systems in the fission yeast holds promise that they may be further developed as recombination tools for the site-specific rearrangement of plant and animal genomes.
Collapse
Affiliation(s)
- James G Thomson
- Plant Gene Expression Center, USDA, Albany, California 94710, USA
| | | |
Collapse
|
50
|
Affiliation(s)
- R McNerney
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
| | | |
Collapse
|