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Liu Y, Liang Z, Yu S, Ye Y, Lin Z. CRISPR RNA-Guided Transposases Facilitate Dispensable Gene Study in Phage. Viruses 2024; 16:422. [PMID: 38543787 PMCID: PMC10974960 DOI: 10.3390/v16030422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 05/23/2024] Open
Abstract
Phages provide a potential therapy for multi-drug-resistant (MDR) bacteria. However, a significant portion of viral genes often remains unknown, posing potential dangers. The identification of non-essential genes helps dissect and simplify phage genomes, but current methods have various limitations. In this study, we present an in vivo two-plasmid transposon insertion system to assess the importance of phage genes, which is based on the V. cholerae transposon Tn6677, encoding a nuclease-deficient type I-F CRISPR-Cas system. We first validated the system in Pseudomonas aeruginosa PAO1 and its phage S1. We then used the selection marker AcrVA1 to protect transposon-inserted phages from CRISPR-Cas12a and enriched the transposon-inserted phages. For a pool of selected 10 open-reading frames (2 known functional protein genes and 8 hypothetical protein genes) of phage S1, we identified 5 (2 known functional protein genes and 3 hypothetical protein genes) as indispensable genes and the remaining 5 (all hypothetical protein genes) as dispensable genes. This approach offers a convenient, site-specific method that does not depend on homologous arms and double-strand breaks (DSBs), holding promise for future applications across a broader range of phages and facilitating the identification of the importance of phage genes and the insertion of genetic cargos.
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Affiliation(s)
- Yanmei Liu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (Y.L.); (Z.L.); (S.Y.)
| | - Zizhen Liang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (Y.L.); (Z.L.); (S.Y.)
| | - Shuting Yu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (Y.L.); (Z.L.); (S.Y.)
| | - Yanrui Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (Y.L.); (Z.L.); (S.Y.)
| | - Zhanglin Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (Y.L.); (Z.L.); (S.Y.)
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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2
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Yutin N, Rayko M, Antipov D, Mutz P, Wolf YI, Krupovic M, Koonin EV. Varidnaviruses in the Human Gut: A Major Expansion of the Order Vinavirales. Viruses 2022; 14:1842. [PMID: 36146653 PMCID: PMC9502842 DOI: 10.3390/v14091842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/19/2022] [Accepted: 08/20/2022] [Indexed: 11/29/2022] Open
Abstract
Bacteriophages play key roles in the dynamics of the human microbiome. By far the most abundant components of the human gut virome are tailed bacteriophages of the realm Duplodnaviria, in particular, crAss-like phages. However, apart from duplodnaviruses, the gut virome has not been dissected in detail. Here we report a comprehensive census of a minor component of the gut virome, the tailless bacteriophages of the realm Varidnaviria. Tailless phages are primarily represented in the gut by prophages, that are mostly integrated in genomes of Alphaproteobacteria and Verrucomicrobia and belong to the order Vinavirales, which currently consists of the families Corticoviridae and Autolykiviridae. Phylogenetic analysis of the major capsid proteins (MCP) suggests that at least three new families should be established within Vinavirales to accommodate the diversity of prophages from the human gut virome. Previously, only the MCP and packaging ATPase genes were reported as conserved core genes of Vinavirales. Here we report an extended core set of 12 proteins, including MCP, packaging ATPase, and previously undetected lysis enzymes, that are shared by most of these viruses. We further demonstrate that replication system components are frequently replaced in the genomes of Vinavirales, suggestive of selective pressure for escape from yet unknown host defenses or avoidance of incompatibility with coinfecting related viruses. The results of this analysis show that, in a sharp contrast to marine viromes, varidnaviruses are a minor component of the human gut virome. Moreover, they are primarily represented by prophages, as indicated by the analysis of the flanking genes, suggesting that there are few, if any, lytic varidnavirus infections in the gut at any given time. These findings complement the existing knowledge of the human gut virome by exploring a group of viruses that has been virtually overlooked in previous work.
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Affiliation(s)
- Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Mike Rayko
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, 199004 St. Petersburg, Russia
| | - Dmitry Antipov
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, 199004 St. Petersburg, Russia
| | - Pascal Mutz
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université Paris Cité, CNRS UMR6047, F-75015 Paris, France
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
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3
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Willcocks SJ, Stabler RA, Atkins HS, Oyston PF, Wren BW. High-throughput analysis of Yersinia pseudotuberculosis gene essentiality in optimised in vitro conditions, and implications for the speciation of Yersinia pestis. BMC Microbiol 2018; 18:46. [PMID: 29855259 PMCID: PMC5984423 DOI: 10.1186/s12866-018-1189-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 05/18/2018] [Indexed: 12/12/2022] Open
Abstract
Background Yersinia pseudotuberculosis is a zoonotic pathogen, causing mild gastrointestinal infection in humans. From this comparatively benign pathogenic species emerged the highly virulent plague bacillus, Yersinia pestis, which has experienced significant genetic divergence in a relatively short time span. Much of our knowledge of Yersinia spp. evolution stems from genomic comparison and gene expression studies. Here we apply transposon-directed insertion site sequencing (TraDIS) to describe the essential gene set of Y. pseudotuberculosis IP32953 in optimised in vitro growth conditions, and contrast these with the published essential genes of Y. pestis. Results The essential genes of an organism are the core genetic elements required for basic survival processes in a given growth condition, and are therefore attractive targets for antimicrobials. One such gene we identified is yptb3665, which encodes a peptide deformylase, and here we report for the first time, the sensitivity of Y. pseudotuberculosis to actinonin, a deformylase inhibitor. Comparison of the essential genes of Y. pseudotuberculosis with those of Y. pestis revealed the genes whose importance are shared by both species, as well as genes that were differentially required for growth. In particular, we find that the two species uniquely rely upon different iron acquisition and respiratory metabolic pathways under similar in vitro conditions. Conclusions The discovery of uniquely essential genes between the closely related Yersinia spp. represent some of the fundamental, species-defining points of divergence that arose during the evolution of Y. pestis from its ancestor. Furthermore, the shared essential genes represent ideal candidates for the development of novel antimicrobials against both species. Electronic supplementary material The online version of this article (10.1186/s12866-018-1189-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Samuel J Willcocks
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Richard A Stabler
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Helen S Atkins
- Microbiology, CBR Division, DSTL Porton Down, Salisbury, SP4 0JQ, UK
| | - Petra F Oyston
- Microbiology, CBR Division, DSTL Porton Down, Salisbury, SP4 0JQ, UK
| | - Brendan W Wren
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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Philippe C, Krupovic M, Jaomanjaka F, Claisse O, Petrel M, le Marrec C. Bacteriophage GC1, a Novel Tectivirus Infecting Gluconobacter Cerinus, an Acetic Acid Bacterium Associated with Wine-Making. Viruses 2018; 10:v10010039. [PMID: 29337868 PMCID: PMC5795452 DOI: 10.3390/v10010039] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/05/2018] [Accepted: 01/12/2018] [Indexed: 12/22/2022] Open
Abstract
The Gluconobacter phage GC1 is a novel member of the Tectiviridae family isolated from a juice sample collected during dry white wine making. The bacteriophage infects Gluconobacter cerinus, an acetic acid bacterium which represents a spoilage microorganism during wine making, mainly because it is able to produce ethyl alcohol and transform it into acetic acid. Transmission electron microscopy revealed tail-less icosahedral particles with a diameter of ~78 nm. The linear double-stranded DNA genome of GC1 (16,523 base pairs) contains terminal inverted repeats and carries 36 open reading frames, only a handful of which could be functionally annotated. These encode for the key proteins involved in DNA replication (protein-primed family B DNA polymerase) as well as in virion structure and assembly (major capsid protein, genome packaging ATPase (adenosine triphosphatase) and several minor capsid proteins). GC1 is the first tectivirus infecting an alphaproteobacterial host and is thus far the only temperate tectivirus of gram-negative bacteria. Based on distinctive sequence and life-style features, we propose that GC1 represents a new genus within the Tectiviridae, which we tentatively named “Gammatectivirus”. Furthermore, GC1 helps to bridge the gap in the sequence space between alphatectiviruses and betatectiviruses.
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Affiliation(s)
- Cécile Philippe
- Institut des Sciences de la Vigne et du Vin (ISVV), University Bordeaux, Equipe d'Accueil 4577, Unité de Recherche Oenologie, 33882 Villenave d'Ornon, France.
| | - Mart Krupovic
- Department of Microbiology, Institut Pasteur, 75015 Paris, France.
| | - Fety Jaomanjaka
- Institut des Sciences de la Vigne et du Vin (ISVV), University Bordeaux, Equipe d'Accueil 4577, Unité de Recherche Oenologie, 33882 Villenave d'Ornon, France.
| | - Olivier Claisse
- Institut des Sciences de la Vigne et du Vin (ISVV), University Bordeaux, Equipe d'Accueil 4577, Unité de Recherche Oenologie, 33882 Villenave d'Ornon, France.
- Institut National de la Recherche Agronomique (INRA), ISVV, Unité Sous Contrat 1366 Oenologie, 33882 Villenave d'Ornon, France.
| | - Melina Petrel
- Bordeaux Imaging Center, University Bordeaux, Unité Mixte de Service 3420 CNRS-Unité de Service 4, Institut National de la Santé et de la Recherche Médicale, 33076 Bordeaux, France.
| | - Claire le Marrec
- Institut des Sciences de la Vigne et du Vin (ISVV), University Bordeaux, Equipe d'Accueil 4577, Unité de Recherche Oenologie, 33882 Villenave d'Ornon, France.
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Applications of the Bacteriophage Mu In Vitro Transposition Reaction and Genome Manipulation via Electroporation of DNA Transposition Complexes. Methods Mol Biol 2018; 1681:279-286. [PMID: 29134602 DOI: 10.1007/978-1-4939-7343-9_20] [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] [Indexed: 02/06/2023]
Abstract
The capacity of transposable elements to insert into the genomes has been harnessed during the past decades to various in vitro and in vivo applications. This chapter describes in detail the general protocols and principles applicable for the Mu in vitro transposition reaction as well as the assembly of DNA transposition complexes that can be electroporated into bacterial cells to accomplish efficient gene delivery. These techniques with their modifications potentiate various gene and genome modification applications, which are discussed briefly here, and the reader is referred to the original publications for further details.
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6
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Pulkkinen E, Haapa-Paananen S, Turakainen H, Savilahti H. A set of mini-Mu transposons for versatile cloning of circular DNA and novel dual-transposon strategy for increased efficiency. Plasmid 2016; 86:46-53. [PMID: 27387339 DOI: 10.1016/j.plasmid.2016.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 06/29/2016] [Accepted: 07/02/2016] [Indexed: 12/22/2022]
Abstract
Mu transposition-based cloning of DNA circles employs in vitro transposition reaction to deliver both the plasmid origin of replication and a selectable marker into the target DNA of interest. We report here the construction of a platform for the purpose that contains ten mini-Mu transposons with five different replication origins, enabling a variety of research approaches for the discovery and study of circular DNA. We also demonstrate that the simultaneous use of two transposons, one with the origin of replication and the other with selectable marker, is beneficial as it improves the cloning efficiency by reducing the fraction of autointegration-derived plasmid clones. The constructed transposons now provide a set of new tools for the studies on DNA circles and widen the applicability of Mu transposition based approaches to clone circular DNA from various sources.
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Affiliation(s)
- Elsi Pulkkinen
- Division of Genetics and Physiology, Department of Biology, University of Turku, Vesilinnantie 5, FI-20500 Turku, Finland
| | - Saija Haapa-Paananen
- Division of Genetics and Physiology, Department of Biology, University of Turku, Vesilinnantie 5, FI-20500 Turku, Finland
| | - Hilkka Turakainen
- Institute of Biotechnology, Viikki Biocenter, P.O. Box 56, Viikinkaari 9, FI-00014, University of Helsinki, Helsinki, Finland
| | - Harri Savilahti
- Division of Genetics and Physiology, Department of Biology, University of Turku, Vesilinnantie 5, FI-20500 Turku, Finland; Institute of Biotechnology, Viikki Biocenter, P.O. Box 56, Viikinkaari 9, FI-00014, University of Helsinki, Helsinki, Finland.
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7
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MuA-mediated in vitro cloning of circular DNA: transpositional autointegration and the effect of MuB. Mol Genet Genomics 2016; 291:1181-91. [DOI: 10.1007/s00438-016-1175-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 01/21/2016] [Indexed: 11/26/2022]
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8
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Kiljunen S, Pajunen MI, Dilks K, Storf S, Pohlschroder M, Savilahti H. Generation of comprehensive transposon insertion mutant library for the model archaeon, Haloferax volcanii, and its use for gene discovery. BMC Biol 2014; 12:103. [PMID: 25488358 PMCID: PMC4300041 DOI: 10.1186/s12915-014-0103-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 11/26/2014] [Indexed: 12/04/2022] Open
Abstract
Background Archaea share fundamental properties with bacteria and eukaryotes. Yet, they also possess unique attributes, which largely remain poorly characterized. Haloferax volcanii is an aerobic, moderately halophilic archaeon that can be grown in defined media. It serves as an excellent archaeal model organism to study the molecular mechanisms of biological processes and cellular responses to changes in the environment. Studies on haloarchaea have been impeded by the lack of efficient genetic screens that would facilitate the identification of protein functions and respective metabolic pathways. Results Here, we devised an insertion mutagenesis strategy that combined Mu in vitro DNA transposition and homologous-recombination-based gene targeting in H. volcanii. We generated an insertion mutant library, in which the clones contained a single genomic insertion. From the library, we isolated pigmentation-defective and auxotrophic mutants, and the respective insertions pinpointed a number of genes previously known to be involved in carotenoid and amino acid biosynthesis pathways, thus validating the performance of the methodologies used. We also identified mutants that had a transposon insertion in a gene encoding a protein of unknown or putative function, demonstrating that novel roles for non-annotated genes could be assigned. Conclusions We have generated, for the first time, a random genomic insertion mutant library for a halophilic archaeon and used it for efficient gene discovery. The library will facilitate the identification of non-essential genes behind any specific biochemical pathway. It represents a significant step towards achieving a more complete understanding of the unique characteristics of halophilic archaea. Electronic supplementary material The online version of this article (doi:10.1186/s12915-014-0103-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Saija Kiljunen
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland.
| | - Maria I Pajunen
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland. .,Current address: Department of Biosciences, Division of Biochemistry and Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Kieran Dilks
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Stefanie Storf
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
| | | | - Harri Savilahti
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland.
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9
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Pulkkinen E, Haapa-Paananen S, Savilahti H. An assay to monitor the activity of DNA transposition complexes yields a general quality control measure for transpositional recombination reactions. Mob Genet Elements 2014; 4:1-8. [PMID: 26442171 PMCID: PMC4590003 DOI: 10.4161/21592543.2014.969576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 08/22/2014] [Accepted: 09/01/2014] [Indexed: 12/20/2022] Open
Abstract
Transposon-based technologies have many applications in molecular biology and can be used for gene delivery into prokaryotic and eukaryotic cells. Common transpositional activity measurement assays suitable for many types of transposons would be beneficial, as diverse transposon systems could be compared for their performance attributes. Therefore, we developed a general-purpose assay to enable and standardize the activity measurement for DNA transposition complexes (transpososomes), using phage Mu transposition as a test platform. This assay quantifies transpositional recombination efficiency and is based on an in vitro transposition reaction with a target plasmid carrying a lethal ccdB gene. If transposition targets ccdB, this gene becomes inactivated, enabling plasmid-receiving Escherichia coli cells to survive and to be scored as colonies on selection plates. The assay was validated with 3 mini-Mu transposons varying in size and differing in their marker gene constitution. Tests with different amounts of transposon DNA provided a linear response and yielded a 10-fold operational range for the assay. The colony formation capacity was linearly correlated with the competence status of the E.coli cells, enabling normalization of experimental data obtained with different batches of recipient cells. The developed assay can now be used to directly compare transpososome activities with all types of mini-Mu transposons, regardless of their aimed use. Furthermore, the assay should be directly applicable to other transposition-based systems with a functional in vitro reaction, and it provides a dependable quality control measure that previously has been lacking but is highly important for the evaluation of current and emerging transposon-based applications.
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Affiliation(s)
- Elsi Pulkkinen
- Division of Genetics and Physiology; Department of Biology; University of Turku; Turku, Finland
| | - Saija Haapa-Paananen
- Division of Genetics and Physiology; Department of Biology; University of Turku; Turku, Finland
| | - Harri Savilahti
- Division of Genetics and Physiology; Department of Biology; University of Turku; Turku, Finland
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10
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Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses. Curr Opin Virol 2013; 3:578-86. [PMID: 23850154 DOI: 10.1016/j.coviro.2013.06.010] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 06/13/2013] [Accepted: 06/17/2013] [Indexed: 11/22/2022]
Abstract
Viruses with single-stranded (ss) DNA genomes infect hosts from all three domains of life and are present in all imaginable environments. Many new ssDNA viruses have been recently isolated, including those infecting algae, fungi, insects and even archaea. In parallel, culture-independent metagenomic approaches have illuminated the tremendous genetic diversity of these viruses, yielding valuable insights into their evolution. Here, I integrate this knowledge to propose a scenario in which certain groups of ssDNA viruses (including Geminiviridae, Circoviridae, Parvoviridae and Microviridae) have originated from plasmids via acquisition of jelly-roll capsid protein genes from ssRNA viruses. This scenario places structurally related viruses with DNA and RNA genomes into an evolutionary continuum and highlights general evolutionary trends in the virosphere.
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11
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Archaeal virus with exceptional virion architecture and the largest single-stranded DNA genome. Proc Natl Acad Sci U S A 2012; 109:13386-91. [PMID: 22826255 DOI: 10.1073/pnas.1203668109] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Known viruses build their particles using a restricted number of redundant structural solutions. Here, we describe the Aeropyrum coil-shaped virus (ACV), of the hyperthermophilic archaeon Aeropyrum pernix, with a virion architecture not previously observed in the viral world. The nonenveloped, hollow, cylindrical virion is formed from a coiling fiber, which consists of two intertwining halves of a single circular nucleoprotein. The virus ACV is also exceptional for its genomic properties. It is the only virus with a single-stranded (ss) DNA genome among the known hyperthermophilic archaeal viruses. Moreover, the size of its circular genome, 24,893 nt, is double that of the largest known ssDNA genome, suggesting an efficient solution for keeping ssDNA intact at 90-95 °C, the optimal temperature range of A. pernix growth. The genome content of ACV is in line with its unique morphology and confirms that ACV is not closely related to any known virus.
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12
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Rasila TS, Vihinen M, Paulin L, Haapa-Paananen S, Savilahti H. Flexibility in MuA transposase family protein structures: functional mapping with scanning mutagenesis and sequence alignment of protein homologues. PLoS One 2012; 7:e37922. [PMID: 22666413 PMCID: PMC3362531 DOI: 10.1371/journal.pone.0037922] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 04/26/2012] [Indexed: 12/13/2022] Open
Abstract
MuA transposase protein is a member of the retroviral integrase superfamily (RISF). It catalyzes DNA cleavage and joining reactions via an initial assembly and subsequent structural transitions of a protein-DNA complex, known as the Mu transpososome, ultimately attaching transposon DNA to non-specific target DNA. The transpososome functions as a molecular DNA-modifying machine and has been used in a wide variety of molecular biology and genetics/genomics applications. To analyze structure-function relationships in MuA action, a comprehensive pentapeptide insertion mutagenesis was carried out for the protein. A total of 233 unique insertion variants were generated, and their activity was analyzed using a quantitative in vivo DNA transposition assay. The results were then correlated with the known MuA structures, and the data were evaluated with regard to the protein domain function and transpososome development. To complement the analysis with an evolutionary component, a protein sequence alignment was produced for 44 members of MuA family transposases. Altogether, the results pinpointed those regions, in which insertions can be tolerated, and those where insertions are harmful. Most insertions within the subdomains Iγ, IIα, IIβ, and IIIα completely destroyed the transposase function, yet insertions into certain loop/linker regions of these subdomains increased the protein activity. Subdomains Iα and IIIβ were largely insertion-tolerant. The comprehensive structure-function data set will be useful for designing MuA transposase variants with improved properties for biotechnology/genomics applications, and is informative with regard to the function of RISF proteins in general.
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Affiliation(s)
- Tiina S. Rasila
- Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Mauno Vihinen
- Institute of Biomedical Technology, University of Tampere, Tampere, Finland
- BioMediTech, Tampere, Finland
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Lars Paulin
- Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Saija Haapa-Paananen
- Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Harri Savilahti
- Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland
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13
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Krupovic M, Prangishvili D, Hendrix RW, Bamford DH. Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere. Microbiol Mol Biol Rev 2011; 75:610-35. [PMID: 22126996 PMCID: PMC3232739 DOI: 10.1128/mmbr.00011-11] [Citation(s) in RCA: 158] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Prokaryotes, bacteria and archaea, are the most abundant cellular organisms among those sharing the planet Earth with human beings (among others). However, numerous ecological studies have revealed that it is actually prokaryotic viruses that predominate on our planet and outnumber their hosts by at least an order of magnitude. An understanding of how this viral domain is organized and what are the mechanisms governing its evolution is therefore of great interest and importance. The vast majority of characterized prokaryotic viruses belong to the order Caudovirales, double-stranded DNA (dsDNA) bacteriophages with tails. Consequently, these viruses have been studied (and reviewed) extensively from both genomic and functional perspectives. However, albeit numerous, tailed phages represent only a minor fraction of the prokaryotic virus diversity. Therefore, the knowledge which has been generated for this viral system does not offer a comprehensive view of the prokaryotic virosphere. In this review, we discuss all families of bacterial and archaeal viruses that contain more than one characterized member and for which evolutionary conclusions can be attempted by use of comparative genomic analysis. We focus on the molecular mechanisms of their genome evolution as well as on the relationships between different viral groups and plasmids. It becomes clear that evolutionary mechanisms shaping the genomes of prokaryotic viruses vary between different families and depend on the type of the nucleic acid, characteristics of the virion structure, as well as the mode of the life cycle. We also point out that horizontal gene transfer is not equally prevalent in different virus families and is not uniformly unrestricted for diverse viral functions.
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Affiliation(s)
- Mart Krupovic
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, 25 rue du Dr. Roux, 75015 Paris, France.
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14
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Calcium ion-dependent entry of the membrane-containing bacteriophage PM2 into its Pseudoalteromonas host. Virology 2010; 405:120-8. [PMID: 20646729 DOI: 10.1016/j.virol.2010.05.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 05/09/2010] [Accepted: 05/19/2010] [Indexed: 11/22/2022]
Abstract
Marine bacteriophage PM2 infects gram-negative Pseudoalteromonas species and is currently the only assigned member of the Corticoviridae family. The icosahedral protein shell covers an internal protein-rich phage membrane that encloses the highly supercoiled dsDNA genome. In this study we investigated PM2 entry into the host. Our results indicate that PM2 adsorption to the host is dependent on the intracellular ATP concentration, while genome penetration through the cytoplasmic membrane depends on the presence of millimolar concentrations of calcium ions in the medium. In the absence of Ca(2+) the infection is arrested at the entry stage but can be rescued by the addition of Ca(2+). Interestingly, PM2 entry induces abrupt cell lysis if the host outer membrane is not stabilized by divalent cations. Experimental data described in this study in combination with results obtained previously allowed us to propose a sequential model describing the entry of bacteriophage PM2 into the host cells.
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Wu Z, Xuanyuan Z, Li R, Jiang D, Li C, Xu H, Bai Y, Zhang X, Turakainen H, Saris P, Savilahti H, Qiao M. Mu transposition complex mutagenesis inLactococcus lactis- identification of genes affecting nisin production. J Appl Microbiol 2009; 106:41-8. [DOI: 10.1111/j.1365-2672.2008.03962.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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High-resolution metagenomics targets specific functional types in complex microbial communities. Nat Biotechnol 2008; 26:1029-34. [PMID: 18711340 DOI: 10.1038/nbt.1488] [Citation(s) in RCA: 168] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Accepted: 07/21/2008] [Indexed: 11/08/2022]
Abstract
Most microbes in the biosphere remain unculturable. Whole genome shotgun (WGS) sequencing of environmental DNA (metagenomics) can be used to study the genetic and metabolic properties of natural microbial communities. However, in communities of high complexity, metagenomics fails to link specific microbes to specific ecological functions. To overcome this limitation, we developed a method to target microbial subpopulations by labeling DNA through stable isotope probing (SIP), followed by WGS sequencing. Metagenome analysis of microbes from Lake Washington in Seattle that oxidize single-carbon (C1) compounds shows specific sequence enrichments in response to different C1 substrates, revealing the ecological roles of individual phylotypes. We also demonstrate the utility of our approach by extracting a nearly complete genome of a novel methylotroph, Methylotenera mobilis, reconstructing its metabolism and conducting genome-wide analyses. This high-resolution, targeted metagenomics approach may be applicable to a wide variety of ecosystems.
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Paatero AO, Turakainen H, Happonen LJ, Olsson C, Palomäki T, Pajunen MI, Meng X, Otonkoski T, Tuuri T, Berry C, Malani N, Frilander MJ, Bushman FD, Savilahti H. Bacteriophage Mu integration in yeast and mammalian genomes. Nucleic Acids Res 2008; 36:e148. [PMID: 18953026 PMCID: PMC2602771 DOI: 10.1093/nar/gkn801] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 10/09/2008] [Accepted: 10/10/2008] [Indexed: 11/14/2022] Open
Abstract
Genomic parasites have evolved distinctive lifestyles to optimize replication in the context of the genomes they inhabit. Here, we introduced new DNA into eukaryotic cells using bacteriophage Mu DNA transposition complexes, termed 'transpososomes'. Following electroporation of transpososomes and selection for marker gene expression, efficient integration was verified in yeast, mouse and human genomes. Although Mu has evolved in prokaryotes, strong biases were seen in the target site distributions in eukaryotic genomes, and these biases differed between yeast and mammals. In Saccharomyces cerevisiae transposons accumulated outside of genes, consistent with selection against gene disruption. In mouse and human cells, transposons accumulated within genes, which previous work suggests is a favorable location for efficient expression of selectable markers. Naturally occurring transposons and viruses in yeast and mammals show related, but more extreme, targeting biases, suggesting that they are responding to the same pressures. These data help clarify the constraints exerted by genome structure on genomic parasites, and illustrate the wide utility of the Mu transpososome technology for gene transfer in eukaryotic cells.
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Affiliation(s)
- Anja O. Paatero
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Hilkka Turakainen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Lotta J. Happonen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Cia Olsson
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Tiina Palomäki
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Maria I. Pajunen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Xiaojuan Meng
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Timo Otonkoski
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Timo Tuuri
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Charles Berry
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Nirav Malani
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Mikko J. Frilander
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Frederic D. Bushman
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Harri Savilahti
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
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Krupovič M, Cvirkaitė-Krupovič V, Bamford DH. Identification and functional analysis of the Rz/Rz1-like accessory lysis genes in the membrane-containing bacteriophage PRD1. Mol Microbiol 2008; 68:492-503. [DOI: 10.1111/j.1365-2958.2008.06165.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Genetics for Pseudoalteromonas provides tools to manipulate marine bacterial virus PM2. J Bacteriol 2007; 190:1298-307. [PMID: 18083813 DOI: 10.1128/jb.01639-07] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The genetic manipulation of marine double-stranded DNA (dsDNA) bacteriophage PM2 (Corticoviridae) has been limited so far. The isolation of an autonomously replicating DNA element of Pseudoalteromonas haloplanktis TAC125 and construction of a shuttle vector replicating in both Escherichia coli and Pseudoalteromonas enabled us to design a set of conjugative shuttle plasmids encoding tRNA suppressors for amber mutations. Using a host strain carrying a suppressor plasmid allows the introduction and analysis of nonsense mutations in PM2. Here, we describe the isolation and characterization of a suppressor-sensitive PM2 sus2 mutant deficient in the structural protein P10. To infect and replicate, PM2 delivers its 10-kbp genome across the cell envelopes of two gram-negative Pseudoalteromonas species. The events leading to the internalization of the circular supercoiled dsDNA are puzzling. In a poorly understood process that follows receptor recognition, the virion capsid disassembles and the internal membrane fuses with the host outer membrane. While beginning to unravel the mechanism of this process, we found that protein P10 plays an essential role in the host cell penetration.
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Krupovic M, Daugelavicius R, Bamford DH. A novel lysis system in PM2, a lipid-containing marine double-stranded DNA bacteriophage. Mol Microbiol 2007; 64:1635-48. [PMID: 17555443 DOI: 10.1111/j.1365-2958.2007.05769.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In this study we investigated the lysis system of the lipid-containing double-stranded DNA bacteriophage PM2 infecting Gram-negative marine Pseudoalteromonas species. We analysed wt and lysis-deficient phage-induced changes in the host physiology and ascribed functions to two PM2 gene products (gp) involved in lysis. We show that bacteriophage PM2 uses a novel system to disrupt the infected cell. The novelty is based on the following findings: (i) gp k is needed for the permeabilization of the cytoplasmic membrane and appears to play the role of a typical holin. However, its unique primary structure [53 aa, 1 transmembrane domain (TMD)] places it into a new class of holins. (ii) We have proposed that, unlike other bacteriophages studied, PM2 relies on lytic factors of the cellular origin for digestion of the peptidoglycan. (iii) gp l (51 aa, no TMDs) is needed for disruption of the outer membrane, which is highly rigidified by the divalent cations abundant in the marine environment. The gp l has no precedent in other phage lytic systems studied so far. However, the presence of open reading frame l-like genes in genomes of other bacterial viruses suggests that the same system might be used by other phages and is not unique to PM2.
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Affiliation(s)
- Mart Krupovic
- Department of Biological and Environmental Sciences and Institute of Biotechnology, Biocenter 2, PO Box 56 (Viikinkaari 5), 00014 University of Helsinki, Finland
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Putative prophages related to lytic tailless marine dsDNA phage PM2 are widespread in the genomes of aquatic bacteria. BMC Genomics 2007; 8:236. [PMID: 17634101 PMCID: PMC1950889 DOI: 10.1186/1471-2164-8-236] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Accepted: 07/16/2007] [Indexed: 02/08/2023] Open
Abstract
Background The origin and evolution of viruses is currently a heavily discussed issue. One element in this discussion is the innate viral "self" concept, which suggests that viral structures and functions can be divided into two categories. The first category consists of genetic determinants that are inherited from a viral ancestor and encode the viral "self". The second group consists of another set of structures and functions, the "nonself", which is interchangeable between different viruses and can be obtained via lateral gene transfer. Comparing the structures and sequences of the "self" elements, we have proposed that viruses can be grouped into lineages regardless of which domain of life (bacteria, archaea, eukarya) they infect. It has also been suggested that viruses are ancient and possibly predate modern cells. Results Here we identified thirteen putative prophages (viral genomes integrated into bacterial chromosome) closely related to the virulent icosahedral tailless lipid-containing bacteriophage PM2. Using the comparative genomics approach, we present evidence to support the viral "self" hypothesis and divide genes of the bacteriophage PM2 and related prophages into "self" and "nonself" categories. Conclusion We show here that the previously proposed most conserved viral "self" determinants, the major coat protein and the packaging ATPase, were the only proteins that could be recognized in all detected corticoviral elements. We also argue here that the genes needed for viral genome replication, as well as for host cell lysis, belong to the "nonself" category of genes. Furthermore, we suggest that abundance of PM2-like viruses in the aquatic environment as well as their importance in the ecology of aquatic microorganisms might have been underestimated.
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