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Genome Sequences of Microbacteriophages Zada and Ioannes. Microbiol Resour Announc 2020; 9:9/45/e01012-20. [PMID: 33154009 PMCID: PMC7645664 DOI: 10.1128/mra.01012-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Microbacteriophages Zada and Ioannes were isolated from soil and characterized. Genomes were then sequenced and annotated. This was done using the host bacterium Microbacterium foliorum. Zada and Ioannes are both lytic phages with a Siphoviridae morphotype. Microbacteriophages Zada and Ioannes were isolated from soil and characterized. Genomes were then sequenced and annotated. This was done using the host bacterium Microbacterium foliorum. Zada and Ioannes are both lytic phages with a Siphoviridae morphotype.
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52
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Mageeney CM, Mohammed HT, Dies M, Anbari S, Cudkevich N, Chen Y, Buceta J, Ware VC. Mycobacterium Phage Butters-Encoded Proteins Contribute to Host Defense against Viral Attack. mSystems 2020; 5:e00534-20. [PMID: 33024050 PMCID: PMC7542560 DOI: 10.1128/msystems.00534-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/15/2020] [Indexed: 01/21/2023] Open
Abstract
A diverse set of prophage-mediated mechanisms protecting bacterial hosts from infection has been recently uncovered within cluster N mycobacteriophages isolated on the host, Mycobacterium smegmatis mc2155. In that context, we unveil a novel defense mechanism in cluster N prophage Butters. By using bioinformatics analyses, phage plating efficiency experiments, microscopy, and immunoprecipitation assays, we show that Butters genes located in the central region of the genome play a key role in the defense against heterotypic viral attack. Our study suggests that a two-component system, articulated by interactions between protein products of genes 30 and 31, confers defense against heterotypic phage infection by PurpleHaze (cluster A/subcluster A3) or Alma (cluster A/subcluster A9) but is insufficient to confer defense against attack by the heterotypic phage Island3 (cluster I/subcluster I1). Therefore, based on heterotypic phage plating efficiencies on the Butters lysogen, additional prophage genes required for defense are implicated and further show specificity of prophage-encoded defense systems.IMPORTANCE Many sequenced bacterial genomes, including those of pathogenic bacteria, contain prophages. Some prophages encode defense systems that protect their bacterial host against heterotypic viral attack. Understanding the mechanisms undergirding these defense systems is crucial to appreciate the scope of bacterial immunity against viral infections and will be critical for better implementation of phage therapy that would require evasion of these defenses. Furthermore, such knowledge of prophage-encoded defense mechanisms may be useful for developing novel genetic tools for engineering phage-resistant bacteria of industrial importance.
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Affiliation(s)
- Catherine M Mageeney
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Hamidu T Mohammed
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Marta Dies
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Samira Anbari
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Netta Cudkevich
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Yanyan Chen
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Javier Buceta
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Vassie C Ware
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
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53
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Sørensen PE, Van Den Broeck W, Kiil K, Jasinskyte D, Moodley A, Garmyn A, Ingmer H, Butaye P. New insights into the biodiversity of coliphages in the intestine of poultry. Sci Rep 2020; 10:15220. [PMID: 32939020 PMCID: PMC7494930 DOI: 10.1038/s41598-020-72177-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/27/2020] [Indexed: 12/26/2022] Open
Abstract
Despite phages' ubiquitous presence and great importance in shaping microbial communities, little is known about the diversity of specific phages in different ecological niches. Here, we isolated, sequenced, and characterized 38 Escherichia coli-infecting phages (coliphages) from poultry faeces to gain a better understanding of the coliphage diversity in the poultry intestine. All phages belonged to either the Siphoviridae or Myoviridae family and their genomes ranged between 44,324 and 173,384 bp, with a G+C content between 35.5 and 46.4%. Phylogenetic analysis was performed based on single "marker" genes; the terminase large subunit, portal protein, and exonucleases, as well as the full draft genomes. Single gene analysis resulted in six distinct clusters. Only minor differences were observed between the different phylogenetic analyses, including branch lengths and additional duplicate or triplicate subclustering. Cluster formation was according to genome size, G+C content and phage subfamily. Phylogenetic analysis based on the full genomes supported these clusters. Moreover, several of our Siphoviridae phages might represent a novel unclassified phage genus. This study allowed for identification of several novel coliphages and provides new insights to the coliphage diversity in the intestine of poultry. Great diversity was observed amongst the phages, while they were isolated from an otherwise similar ecosystem.
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Affiliation(s)
- Patricia E Sørensen
- Department of Pathology, Bacteriology and Poultry Diseases, Ghent University, Merelbeke, Belgium.
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis.
| | | | - Kristoffer Kiil
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Dziuginta Jasinskyte
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Arshnee Moodley
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
- CGIAR Antimicrobial Resistance Hub, International Livestock Research Institute, Nairobi, Kenya
| | - An Garmyn
- Department of Pathology, Bacteriology and Poultry Diseases, Ghent University, Merelbeke, Belgium
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Patrick Butaye
- Department of Pathology, Bacteriology and Poultry Diseases, Ghent University, Merelbeke, Belgium
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
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54
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Olsen NS, Forero-Junco L, Kot W, Hansen LH. Exploring the Remarkable Diversity of Culturable Escherichia coli Phages in the Danish Wastewater Environment. Viruses 2020; 12:E986. [PMID: 32899836 PMCID: PMC7552041 DOI: 10.3390/v12090986] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/24/2020] [Accepted: 08/31/2020] [Indexed: 12/12/2022] Open
Abstract
Phages drive bacterial diversity, profoundly influencing microbial communities, from microbiomes to the drivers of global biogeochemical cycling. Aiming to broaden our understanding of Escherichiacoli (MG1655, K-12) phages, we screened 188 Danish wastewater samples and isolated 136 phages. Ninety-two of these have genomic sequences with less than 95% similarity to known phages, while most map to existing genera several represent novel lineages. The isolated phages are highly diverse, estimated to represent roughly one-third of the true diversity of culturable virulent dsDNA Escherichia phages in Danish wastewater, yet almost half (40%) are not represented in metagenomic databases, emphasising the importance of isolating phages to uncover diversity. Seven viral families, Myoviridae, Siphoviridae, Podoviridae,Drexlerviridae,Chaseviridae,Autographviridae, and Microviridae, are represented in the dataset. Their genomes vary drastically in length from 5.3 kb to 170.8 kb, with a guanine and cytosine (GC) content ranging from 35.3% to 60.0%. Hence, even for a model host bacterium, substantial diversity remains to be uncovered. These results expand and underline the range of coliphage diversity and demonstrate how far we are from fully disclosing phage diversity and ecology.
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Affiliation(s)
- Nikoline S. Olsen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark;
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark;
| | - Laura Forero-Junco
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark;
| | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark;
| | - Lars H. Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark;
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55
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Ko CC, Hatfull GF. Identification of mycobacteriophage toxic genes reveals new features of mycobacterial physiology and morphology. Sci Rep 2020; 10:14670. [PMID: 32887931 PMCID: PMC7474061 DOI: 10.1038/s41598-020-71588-5] [Citation(s) in RCA: 6] [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: 04/23/2020] [Accepted: 07/07/2020] [Indexed: 01/01/2023] Open
Abstract
Double-stranded DNA tailed bacteriophages typically code for 50-200 genes, of which 15-35 are involved in virion structure and assembly, DNA packaging, lysis, and DNA metabolism. However, vast numbers of other phage genes are small, are not required for lytic growth, and are of unknown function. The 1,885 sequenced mycobacteriophages encompass over 200,000 genes in 7,300 distinct protein 'phamilies', 77% of which are of unknown function. Gene toxicity provides potential insights into function, and here we screened 193 unrelated genes encoded by 13 different mycobacteriophages for their ability to impair the growth of Mycobacterium smegmatis. We identified 45 (23%) mycobacteriophage genes that are toxic when expressed. The impacts on M. smegmatis growth range from mild to severe, but many cause irreversible loss of viability. Expression of most of the severely toxic genes confers altered cellular morphologies, including filamentation, polar bulging, curving, and, surprisingly, loss of viability of one daughter cell at division, suggesting specific impairments of mycobacterial growth. Co-immunoprecipitation and mass spectrometry show that toxicity is frequently associated with interaction with host proteins and alteration or inactivation of their function. Mycobacteriophages thus present a massive reservoir of genes for identifying mycobacterial essential functions, identifying potential drug targets and for exploring mycobacteriophage physiology.
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Affiliation(s)
- Ching-Chung Ko
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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56
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Glickman C, Kammlade SM, Hasan NA, Epperson LE, Davidson RM, Strong M. Characterization of integrated prophages within diverse species of clinical nontuberculous mycobacteria. Virol J 2020; 17:124. [PMID: 32807206 PMCID: PMC7433156 DOI: 10.1186/s12985-020-01394-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/03/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Nontuberculous mycobacterial (NTM) infections are increasing in prevalence, with current estimates suggesting that over 100,000 people in the United States are affected each year. It is unclear how certain species of mycobacteria transition from environmental bacteria to clinical pathogens, or what genetic elements influence the differences in virulence among strains of the same species. A potential mechanism of genetic evolution and diversity within mycobacteria is the presence of integrated viruses called prophages in the host genome. Prophages may act as carriers of bacterial genes, with the potential of altering bacterial fitness through horizontal gene transfer. In this study, we quantify the frequency and composition of prophages within mycobacteria isolated from clinical samples and compare them against the composition of PhagesDB, an environmental mycobacteriophage database. METHODS Prophages were predicted by agreement between two discovery tools, VirSorter and Phaster, and the frequencies of integrated prophages were compared by growth rate. Prophages were assigned to PhagesDB lettered clusters. Bacterial virulence gene frequency was calculated using a combination of the Virulence Factor Database (VFDB) and the Pathosystems Resource Integration Center virulence database (Patric-VF) within the gene annotation software Prokka. CRISPR elements were discovered using CRT. ARAGORN was used to quantify tRNAs. RESULTS Rapidly growing mycobacteria (RGM) were more likely to contain prophage than slowly growing mycobacteria (SGM). CRISPR elements were not associated with prophage abundance in mycobacteria. The abundance of tRNAs was enriched in SGM compared to RGM. We compared the abundance of bacterial virulence genes within prophage genomes from clinical isolates to mycobacteriophages from PhagesDB. Our data suggests that prophages from clinical mycobacteria are enriched for bacterial virulence genes relative to environmental mycobacteriophage from PhagesDB. CONCLUSION Prophages are present in clinical NTM isolates. Prophages are more likely to be present in RGM compared to SGM genomes. The mechanism and selective advantage of this enrichment by growth rate remain unclear. In addition, the frequency of bacterial virulence genes in prophages from clinical NTM is enriched relative to the PhagesDB environmental proxy. This suggests prophages may act as a reservoir of genetic elements bacteria could use to thrive within a clinical environment.
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Affiliation(s)
- Cody Glickman
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA.
- Computational Bioscience Program, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA.
| | - Sara M Kammlade
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Nabeeh A Hasan
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - L Elaine Epperson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Rebecca M Davidson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Michael Strong
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
- Computational Bioscience Program, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
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57
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Abstract
The antibiotic resistance crisis has led to renewed interest in phage therapy as an alternative means of treating infection. However, conventional methods for isolating pathogen-specific phage are slow, labor-intensive, and frequently unsuccessful. We have demonstrated that computationally identified prophages carried by near-neighbor bacteria can serve as starting material for production of engineered phages that kill the target pathogen. Our approach and technology platform offer new opportunity for rapid development of phage therapies against most, if not all, bacterial pathogens, a foundational advance for use of phage in treating infectious disease. New therapies are necessary to combat increasingly antibiotic-resistant bacterial pathogens. We have developed a technology platform of computational, molecular biology, and microbiology tools which together enable on-demand production of phages that target virtually any given bacterial isolate. Two complementary computational tools that identify and precisely map prophages and other integrative genetic elements in bacterial genomes are used to identify prophage-laden bacteria that are close relatives of the target strain. Phage genomes are engineered to disable lysogeny, through use of long amplicon PCR and Gibson assembly. Finally, the engineered phage genomes are introduced into host bacteria for phage production. As an initial demonstration, we used this approach to produce a phage cocktail against the opportunistic pathogen Pseudomonas aeruginosa PAO1. Two prophage-laden P. aeruginosa strains closely related to PAO1 were identified, ATCC 39324 and ATCC 27853. Deep sequencing revealed that mitomycin C treatment of these strains induced seven phages that grow on P. aeruginosa PAO1. The most diverse five phages were engineered for nonlysogeny by deleting the integrase gene (int), which is readily identifiable and typically conveniently located at one end of the prophage. The Δint phages, individually and in cocktails, killed P. aeruginosa PAO1 in liquid culture as well as in a waxworm (Galleria mellonella) model of infection. IMPORTANCE The antibiotic resistance crisis has led to renewed interest in phage therapy as an alternative means of treating infection. However, conventional methods for isolating pathogen-specific phage are slow, labor-intensive, and frequently unsuccessful. We have demonstrated that computationally identified prophages carried by near-neighbor bacteria can serve as starting material for production of engineered phages that kill the target pathogen. Our approach and technology platform offer new opportunity for rapid development of phage therapies against most, if not all, bacterial pathogens, a foundational advance for use of phage in treating infectious disease.
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58
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Abstract
We report the discovery of the novel bacteriophage Donny, a Siphoviridae virus that infects Mycobacterium smegmatis mc2155. Donny has a genome length of 69,691 bp and a G+C content of 68.5%. Donny shares 99% and 93% nucleotide identity with bacteriophages Acadian and Baee, respectively. We report the discovery of the novel bacteriophage Donny, a Siphoviridae virus that infects Mycobacterium smegmatis mc2155. Donny has a genome length of 69,691 bp and a G+C content of 68.5%. Donny shares 99% and 93% nucleotide identity with bacteriophages Acadian and Baee, respectively.
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59
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de Melo AG, Rousseau GM, Tremblay DM, Labrie SJ, Moineau S. DNA tandem repeats contribute to the genetic diversity of Brevibacterium aurantiacum phages. Environ Microbiol 2020; 22:3413-3428. [PMID: 32510858 DOI: 10.1111/1462-2920.15113] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/23/2020] [Accepted: 06/02/2020] [Indexed: 12/16/2022]
Abstract
This report presents the characterization of the first virulent phages infecting Brevibacterium aurantiacum, a bacterial species used during the manufacture of surface-ripened cheeses. These phages were also responsible for flavour and colour defects in surface-ripened cheeses. Sixteen phages (out of 62 isolates) were selected for genome sequencing and comparative analyses. These cos-type phages with a long non-contractile tail currently belong to the Siphoviridae family (Caudovirales order). Their genome sizes vary from 35,637 to 36,825 bp and, similar to their host, have a high GC content (~61%). Genes encoding for an immunity repressor, an excisionase and a truncated integrase were found, suggesting that these virulent phages may be derived from a prophage. Their genomic organization is highly conserved, with most of the diversity coming from the presence of long (198 bp) DNA tandem repeats (TRs) within an open reading frame coding for a protein of unknown function. We categorized these phages into seven genomic groups according to their number of TR, which ranged from two to eight. Moreover, we showed that TRs are widespread in phage genomes, found in more than 85% of the genomes available in public databases.
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Affiliation(s)
- Alessandra G de Melo
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Québec City, Canada.,Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, Québec City, Canada
| | - Geneviève M Rousseau
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, Québec City, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de Médecine Dentaire, Université Laval, Québec, Québec City, Canada
| | - Denise M Tremblay
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, Québec City, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de Médecine Dentaire, Université Laval, Québec, Québec City, Canada
| | | | - Sylvain Moineau
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Québec City, Canada.,Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, Québec City, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de Médecine Dentaire, Université Laval, Québec, Québec City, Canada
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60
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Furfaro LL, Payne MS, Chang BJ. Host range, morphological and genomic characterisation of bacteriophages with activity against clinical Streptococcus agalactiae isolates. PLoS One 2020; 15:e0235002. [PMID: 32574197 PMCID: PMC7310703 DOI: 10.1371/journal.pone.0235002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/06/2020] [Indexed: 01/21/2023] Open
Abstract
Streptococcus agalactiae or Group B Streptococcus (GBS) is a leading cause of sepsis in neonates. As a preventative measure prophylactic antibiotic administration is common in pregnant women colonised with GBS, but antibiotic-resistance and adverse effects on neonatal microbiomes may result. Use of bacteriophages (phages) is one option for targeted therapy. To this end, four phages (LF1 –LF4) were isolated from wastewater. They displayed lytic activity in vitro against S. agalactiae isolates collected from pregnant women and neonates, with 190/246 isolates (77.2%) and 10/10 (100%) isolates susceptible to at least one phage, respectively. Phage genomes ranged from 32,205–44,768 bp and all phages were members of the Siphoviridae family. High nucleotide identity (99.9%) was observed between LF1 and LF4, which were closely related to a putative prophage of S. agalactiae. The genome organisation of LF2 differed, and it showed similarity to a different S. agalactiae prophage, while LF3 was more closely related to a Streptococcus pyogenes phage. Lysogenic gene presence (integrase, repressor and regulatory modules), was suggestive of temperate phages. In a therapeutic context, temperate phages are not ideal candidates, however, the broad host range activity of these phages observed on clinical isolates in vitro is promising for future therapeutic approaches including bioengineered phage or lysin applications.
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Affiliation(s)
- Lucy L. Furfaro
- The School of Medicine, Division of Obstetrics and Gynaecology, The University of Western Australia, Crawley, Australia
- * E-mail:
| | - Matthew S. Payne
- The School of Medicine, Division of Obstetrics and Gynaecology, The University of Western Australia, Crawley, Australia
| | - Barbara J. Chang
- The School of Biomedical Sciences, The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Crawley, Australia
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61
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Jacobs-Sera D, Abad LA, Alvey RM, Anders KR, Aull HG, Bhalla SS, Blumer LS, Bollivar DW, Bonilla JA, Butela KA, Coomans RJ, Cresawn SG, D'Elia T, Diaz A, Divens AM, Edgington NP, Frederick GD, Gainey MD, Garlena RA, Grant KW, Gurney SMR, Hendrickson HL, Hughes LE, Kenna MA, Klyczek KK, Kotturi H, Mavrich TN, McKinney AL, Merkhofer EC, Moberg Parker J, Molloy SD, Monti DL, Pape-Zambito DA, Pollenz RS, Pope WH, Reyna NS, Rinehart CA, Russell DA, Shaffer CD, Sivanathan V, Stoner TH, Stukey J, Sunnen CN, Tolsma SS, Tsourkas PK, Wallen JR, Ware VC, Warner MH, Washington JM, Westover KM, Whitefleet-Smith JL, Wiersma-Koch HI, Williams DC, Zack KM, Hatfull GF. Genomic diversity of bacteriophages infecting Microbacterium spp. PLoS One 2020; 15:e0234636. [PMID: 32555720 PMCID: PMC7302621 DOI: 10.1371/journal.pone.0234636] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 05/29/2020] [Indexed: 11/19/2022] Open
Abstract
The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, and their G+C% content ranges from 51.4% to 71.4%, compared to ~67% for their Microbacterium hosts. The phages were isolated on five different Microbacterium species, but typically do not efficiently infect strains beyond the one on which they were isolated. These Microbacterium phages contain many novel features, including very large viral genes (13.5 kbp) and unusual fusions of structural proteins, including a fusion of VIP2 toxin and a MuF-like protein into a single gene. These phages and their genetic components such as integration systems, recombineering tools, and phage-mediated delivery systems, will be useful resources for advancing Microbacterium genetics.
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Affiliation(s)
- Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Lawrence A. Abad
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Richard M. Alvey
- Department of Biology, Illinois Wesleyan University, Bloomington, Illinois, United States of America
| | - Kirk R. Anders
- Department of Biology, Gonzaga University, Spokane, Washington, United States of America
| | - Haley G. Aull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Suparna S. Bhalla
- Department of Natural Sciences, Mount Saint Mary College, Newburgh, New York, United States of America
| | - Lawrence S. Blumer
- Department of Biology, Morehouse College, Atlanta, Georgia, United States of America
| | - David W. Bollivar
- Department of Biology, Illinois Wesleyan University, Bloomington, Illinois, United States of America
| | - J. Alfred Bonilla
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Kristen A. Butela
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Roy J. Coomans
- Department of Biology, North Carolina A&T State University, Greensboro, North Carolina, United States of America
| | - Steven G. Cresawn
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Tom D'Elia
- Department of Biological Sciences, Indian River State College, Fort Pierce, Florida, United States of America
| | - Arturo Diaz
- Department of Biology, La Sierra University, Riverside, California, United States of America
| | - Ashley M. Divens
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Nicholas P. Edgington
- Department of Biology, Southern Connecticut State University, New Haven, Connecticut, United States of America
| | - Gregory D. Frederick
- Department of Biology and Kinesiology, LeTourneau University, Longview, Texas, United States of America
| | - Maria D. Gainey
- Department of Chemistry & Physics, Western Carolina University, Cullowhee, North Carolina, United States of America
| | - Rebecca A. Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kenneth W. Grant
- Department of Pathology, Wake Forest Baptist Health, Winston-Salem, North Carolina, United States of America
| | - Susan M. R. Gurney
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | | | - Lee E. Hughes
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Margaret A. Kenna
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Karen K. Klyczek
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Hari Kotturi
- Department of Biology, University of Central Oklahoma, Edmond, Oklahoma, United States of America
| | - Travis N. Mavrich
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Angela L. McKinney
- Department of Biology, Nebraska Wesleyan University, Lincoln, Nebraska, United States of America
| | - Evan C. Merkhofer
- Department of Natural Sciences, Mount Saint Mary College, Newburgh, New York, United States of America
| | - Jordan Moberg Parker
- Department of Microbiology, Immunology, & Molecular Genetics, University of California, Los Angeles, California, United States of America
| | - Sally D. Molloy
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, United States of America
| | - Denise L. Monti
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Dana A. Pape-Zambito
- Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Richard S. Pollenz
- Department Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida, United States of America
| | - Welkin H. Pope
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Nathan S. Reyna
- Department of Biology, Ouachita Baptist University, Arkadelphia, Arkansas, United States of America
| | - Claire A. Rinehart
- Department of Biology, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Daniel A. Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Christopher D. Shaffer
- Department of Biology, University of Washington in St. Louis, St. Louis, Missouri, United States of America
| | - Viknesh Sivanathan
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Ty H. Stoner
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Joseph Stukey
- Biology Department, Hope College, Holland, Michigan, United States of America
| | - C. Nicole Sunnen
- Department of Biological Sciences, University of the Sciences, Philadelphia, Pennsylvania, United States of America
| | - Sara S. Tolsma
- Biology Department, Northwestern College, Orange City, Iowa, United States of America
| | - Philippos K. Tsourkas
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, United States of America
| | - Jamie R. Wallen
- Department of Chemistry & Physics, Western Carolina University, Cullowhee, North Carolina, United States of America
| | - Vassie C. Ware
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Marcie H. Warner
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | | | - Kristi M. Westover
- Department of Biology, Winthrop University, Rock Hill, South Carolina, United States of America
| | - JoAnn L. Whitefleet-Smith
- Department of Biology & Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Helen I. Wiersma-Koch
- Department of Biological Sciences, Indian River State College, Fort Pierce, Florida, United States of America
| | - Daniel C. Williams
- Department of Biology, Coastal Carolina University, Conway, South Carolina, United States of America
| | - Kira M. Zack
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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62
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Complete Genome Sequences of Cluster G Mycobacteriophage Darionha, Cluster A Mycobacteriophage Salz, and Cluster J Mycobacteriophage ThreeRngTarjay. Microbiol Resour Announc 2020; 9:9/20/e00160-20. [PMID: 32409529 PMCID: PMC7225528 DOI: 10.1128/mra.00160-20] [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] [Indexed: 11/20/2022] Open
Abstract
Mycobacteriophages Darionha, Salz, and ThreeRngTarjay are mycobacteriophages isolated using the host Mycobacterium smegmatis mc2155. Following isolation from soil samples, all three siphoviridae phages were characterized, and their genomes were sequenced and annotated. Mycobacteriophages Darionha, Salz, and ThreeRngTarjay are mycobacteriophages isolated using the host Mycobacterium smegmatis mc2155. Following isolation from soil samples, all three siphoviridae phages were characterized, and their genomes were sequenced and annotated.
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63
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Abstract
Bacteriophages are the most abundant biological entities in the biosphere and are a source of uncharacterized biological mechanisms and genetic tools. Here, we identify segments of phage genomes that are used for stable extrachromosomal replication in the prophage state. Autonomous replication of some of these phages requires a RepA-like protein, although most lack repA and use RNA-based systems for replication initiation. We describe a suite of plasmids based on these prophage replication functions that vary in copy number, stability, host range, and compatibility. These plasmids expand the toolbox available for genetic manipulation of Mycobacterium and other Actinobacteria, including Gordonia terrae. Temperate bacteriophages are common and establish lysogens of their bacterial hosts in which the prophage is stably inherited. It is typical for such prophages to be integrated into the bacterial chromosome, but extrachromosomally replicating prophages have been described also, with the best characterized being the Escherichia coli phage P1 system. Among the large collection of sequenced mycobacteriophages, more than half are temperate or predicted to be temperate, most of which code for a tyrosine or serine integrase that promotes site-specific prophage integration. However, within the large group of 621 cluster A temperate phages, ∼20% lack an integration cassette, which is replaced with a parABS partitioning system. A subset of these phages carry genes coding for a RepA-like protein (RepA phages), which we show here is necessary and sufficient for autonomous extrachromosomal replication. The non-RepA phages appear to replicate using an RNA-based system, as a parABS-proximal region expressing a noncoding RNA is required for replication. Both RepA and non-RepA phage-based plasmids replicate at one or two copies per cell, transform both Mycobacterium smegmatis and Mycobacterium tuberculosis, and are compatible with pAL5000-derived oriM and integration-proficient plasmid vectors. Characterization of these phage-based plasmids offers insights into the variability of lysogenic maintenance systems and provides a large suite of plasmids for actinobacterial genetics that vary in stability, copy number, compatibility, and host range.
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64
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Podgorski J, Calabrese J, Alexandrescu L, Jacobs-Sera D, Pope W, Hatfull G, White S. Structures of Three Actinobacteriophage Capsids: Roles of Symmetry and Accessory Proteins. Viruses 2020; 12:v12030294. [PMID: 32182721 PMCID: PMC7150772 DOI: 10.3390/v12030294] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 02/07/2023] Open
Abstract
Here, we describe the structure of three actinobacteriophage capsids that infect Mycobacterium smegmatis. The capsid structures were resolved to approximately six angstroms, which allowed confirmation that each bacteriophage uses the HK97-fold to form their capsid. One bacteriophage, Rosebush, may have a novel variation of the HK97-fold. Four novel accessory proteins that form the capsid head along with the major capsid protein were identified. Two of the accessory proteins were minor capsid proteins and showed some homology, based on bioinformatic analysis, to the TW1 bacteriophage. The remaining two accessory proteins are decoration proteins that are located on the outside of the capsid and do not resemble any previously described bacteriophage decoration protein. SDS-PAGE and mass spectrometry was used to identify the accessory proteins and bioinformatic analysis of the accessory proteins suggest they are used in many actinobacteriophage capsids.
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Affiliation(s)
- Jennifer Podgorski
- Biology/Physics Building, Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125. Storrs, CT 06269-3125, USA; (J.P.); (J.C.); (L.A.)
| | - Joshua Calabrese
- Biology/Physics Building, Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125. Storrs, CT 06269-3125, USA; (J.P.); (J.C.); (L.A.)
| | - Lauren Alexandrescu
- Biology/Physics Building, Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125. Storrs, CT 06269-3125, USA; (J.P.); (J.C.); (L.A.)
| | - Deborah Jacobs-Sera
- Clapp Hall, Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA; (D.J.-S.); (W.P.); (G.H.)
| | - Welkin Pope
- Clapp Hall, Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA; (D.J.-S.); (W.P.); (G.H.)
| | - Graham Hatfull
- Clapp Hall, Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA; (D.J.-S.); (W.P.); (G.H.)
| | - Simon White
- Biology/Physics Building, Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125. Storrs, CT 06269-3125, USA; (J.P.); (J.C.); (L.A.)
- Correspondence:
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65
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A Novel Genus of Actinobacterial Tectiviridae. Viruses 2019; 11:v11121134. [PMID: 31817897 PMCID: PMC6950372 DOI: 10.3390/v11121134] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 01/31/2023] Open
Abstract
Streptomyces phages WheeHeim and Forthebois are two novel members of the Tectiviridae family. These phages were isolated on cultures of the plant pathogen Streptomyces scabiei, known for its worldwide economic impact on potato crops. Transmission electron microscopy showed viral particles with double-layered icosahedral capsids, and frequent instances of protruding nanotubes harboring a collar-like structure. Mass-spectrometry confirmed the presence of lipids in the virion, and serial purification of colonies from turbid plaques and immunity testing revealed that both phages are temperate. Streptomycesphages WheeHeim and Forthebois have linear dsDNA chromosomes (18,266 bp and 18,251 bp long, respectively) with the characteristic two-segment architecture of the Tectiviridae. Both genomes encode homologs of the canonical tectiviral proteins (major capsid protein, packaging ATPase and DNA polymerase), as well as PRD1-type virion-associated transglycosylase and membrane DNA delivery proteins. Comparative genomics and phylogenetic analyses firmly establish that these two phages, together with Rhodococcusphage Toil, form a new genus within the Tectiviridae, which we have tentatively named Deltatectivirus. The identification of a cohesive clade of Actinobacteria-infecting tectiviruses with conserved genome structure but with scant sequence similarity to members of other tectiviral genera confirms that the Tectiviridae are an ancient lineage infecting a broad range of bacterial hosts.
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66
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Prophylaxis of Mycobacterium tuberculosis H37Rv Infection in a Preclinical Mouse Model via Inhalation of Nebulized Bacteriophage D29. Antimicrob Agents Chemother 2019:AAC.00871-19. [PMID: 31527037 DOI: 10.1128/aac.00871-19] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Globally, more people die annually from tuberculosis than from any other single infectious agent. Unfortunately, there is no commercially-available vaccine that is sufficiently effective at preventing acquisition of pulmonary tuberculosis in adults. In this study, pre-exposure prophylactic pulmonary delivery of active aerosolized anti-tuberculosis bacteriophage D29 was evaluated as an option for protection against Mycobacterium tuberculosis infection. An average bacteriophage concentration of approximately 1 PFU/alveolus was achieved in the lungs of mice using a nose-only inhalation device optimized with a dose simulation technique and adapted for use with a vibrating mesh nebulizer. Within 30 minutes of bacteriophage delivery, the mice received either a low dose (∼50-100 CFU), or an ultra-low dose (∼5-10 CFU), of M. tuberculosis H37Rv aerosol to the lungs. A prophylactic effect was observed with bacteriophage aerosol pre-treatment significantly decreasing M. tuberculosis burden in mouse lungs 24 hours and 3 weeks post-challenge (p < 0.05). These novel results indicate that a sufficient dose of nebulized mycobacteriophage aerosol to the lungs may be a valuable intervention to provide extra protection to health care professionals and other individuals at risk of exposure to M. tuberculosis.
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67
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Salisbury A, Tsourkas PK. A Method for Improving the Accuracy and Efficiency of Bacteriophage Genome Annotation. Int J Mol Sci 2019; 20:E3391. [PMID: 31295925 PMCID: PMC6678273 DOI: 10.3390/ijms20143391] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/02/2019] [Accepted: 07/09/2019] [Indexed: 12/31/2022] Open
Abstract
Bacteriophages are the most numerous entities on Earth. The number of sequenced phage genomes is approximately 8000 and increasing rapidly. Sequencing of a genome is followed by annotation, where genes, start codons, and functions are putatively identified. The mainstays of phage genome annotation are auto-annotation programs such as Glimmer and GeneMark. Due to the relatively small size of phage genomes, many groups choose to manually curate auto-annotation results to increase accuracy. An additional benefit of manual curation of auto-annotated phage genomes is that the process is amenable to be performed by students, and has been shown to improve student recruitment to the sciences. However, despite its greater accuracy and pedagogical value, manual curation suffers from high labor cost, lack of standardization and a degree of subjectivity in decision making, and susceptibility to mistakes. Here, we present a method developed in our lab that is designed to produce accurate annotations while reducing subjectivity and providing a degree of standardization in decision-making. We show that our method produces genome annotations more accurate than auto-annotation programs while retaining the pedagogical benefits of manual genome curation.
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Affiliation(s)
- Alicia Salisbury
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Philippos K Tsourkas
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA.
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68
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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: 0.6] [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.
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69
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Dedrick RM, Guerrero-Bustamante CA, Garlena RA, Russell DA, Ford K, Harris K, Gilmour KC, Soothill J, Jacobs-Sera D, Schooley RT, Hatfull GF, Spencer H. Engineered bacteriophages for treatment of a patient with a disseminated drug-resistant Mycobacterium abscessus. Nat Med 2019; 25:730-733. [PMID: 31068712 PMCID: PMC6557439 DOI: 10.1038/s41591-019-0437-z] [Citation(s) in RCA: 753] [Impact Index Per Article: 150.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/27/2019] [Indexed: 12/17/2022]
Abstract
A 15-year-old patient with cystic fibrosis with a disseminated Mycobacterium abscessus infection was treated with a three-phage cocktail following bilateral lung transplantation. Effective lytic phage derivatives that efficiently kill the infectious M. abscessus strain were developed by genome engineering and forward genetics. Intravenous phage treatment was well tolerated and associated with objective clinical improvement, including sternal wound closure, improved liver function, and substantial resolution of infected skin nodules.
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Affiliation(s)
- Rebekah M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Rebecca A Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | | | | | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert T Schooley
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
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70
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Cebriá-Mendoza M, Sanjuán R, Domingo-Calap P. Directed Evolution of a Mycobacteriophage. Antibiotics (Basel) 2019; 8:antibiotics8020046. [PMID: 31027152 PMCID: PMC6627502 DOI: 10.3390/antibiotics8020046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 12/03/2022] Open
Abstract
Bacteriophages represent an alternative strategy to combat pathogenic bacteria. Currently, Mycobacterium tuberculosis infections constitute a major public health problem due to extensive antibiotic resistance in some strains. Using a non-pathogenic species of the same genus as an experimental model, Mycobacterium smegmatis, here we have set up a basic methodology for mycobacteriophage growth and we have explored directed evolution as a tool for increasing phage infectivity and lytic activity. We demonstrate mycobacteriophage adaptation to its host under different conditions. Directed evolution could be used for the development of future phage therapy applications against mycobacteria.
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Affiliation(s)
- María Cebriá-Mendoza
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46980 Paterna, Valencia, Spain.
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46980 Paterna, Valencia, Spain.
- Department of Genetics, Universitat de València, 46100 Burjassot, Valencia, Spain.
| | - Pilar Domingo-Calap
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46980 Paterna, Valencia, Spain.
- Department of Genetics, Universitat de València, 46100 Burjassot, Valencia, Spain.
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71
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More Evidence of Collusion: a New Prophage-Mediated Viral Defense System Encoded by Mycobacteriophage Sbash. mBio 2019; 10:mBio.00196-19. [PMID: 30890613 PMCID: PMC6426596 DOI: 10.1128/mbio.00196-19] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The arms race between bacteria and their bacteriophages profoundly influences microbial evolution. With an estimated 1023 phage infections occurring per second, there is strong selection for both bacterial survival and phage coevolution for continued propagation. Many phage resistance systems, including restriction-modification systems, clustered regularly interspaced short palindromic repeat-Cas (CRISPR-Cas) systems, a variety of abortive infection systems, and many others that are not yet mechanistically defined, have been described. Temperate bacteriophages are common and form stable lysogens that are immune to superinfection by the same or closely related phages. However, temperate phages collude with their hosts to confer defense against genomically distinct phages, to the mutual benefit of the bacterial host and the prophage. Prophage-mediated viral systems have been described in Mycobacterium phages and Pseudomonas phages but are predicted to be widespread throughout the microbial world. Here we describe a new viral defense system in which the mycobacteriophage Sbash prophage colludes with its Mycobacterium smegmatis host to confer highly specific defense against infection by the unrelated mycobacteriophage Crossroads. Sbash genes 30 and 31 are lysogenically expressed and are necessary and sufficient to confer defense against Crossroads but do not defend against any of the closely related phages grouped in subcluster L2. The mapping of Crossroads defense escape mutants shows that genes 132 and 141 are involved in recognition by the Sbash defense system and are proposed to activate a loss in membrane potential mediated by Sbash gp30 and gp31.IMPORTANCE Viral infection is an ongoing challenge to bacterial survival, and there is strong selection for development or acquisition of defense systems that promote survival when bacteria are attacked by bacteriophages. Temperate phages play central roles in these dynamics through lysogenic expression of genes that defend against phage attack, including those unrelated to the prophage. Few prophage-mediated viral defense systems have been characterized, but they are likely widespread both in phage genomes and in the prophages integrated in bacterial chromosomes.
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72
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Alam CM, Iqbal A, Sharma A, Schulman AH, Ali S. Microsatellite Diversity, Complexity, and Host Range of Mycobacteriophage Genomes of the Siphoviridae Family. Front Genet 2019; 10:207. [PMID: 30923537 PMCID: PMC6426759 DOI: 10.3389/fgene.2019.00207] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 02/26/2019] [Indexed: 01/21/2023] Open
Abstract
The incidence, distribution, and variation of simple sequence repeats (SSRs) in viruses is instrumental in understanding the functional and evolutionary aspects of repeat sequences. Full-length genome sequences retrieved from NCBI were used for extraction and analysis of repeat sequences using IMEx software. We have also developed two MATLAB-based tools for extraction of gene locations from GenBank in tabular format and simulation of this data with SSR incidence data. Present study encompassing 147 Mycobacteriophage genomes revealed 25,284 SSRs and 1,127 compound SSRs (cSSRs) through IMEx. Mono- to hexa-nucleotide motifs were present. The SSR count per genome ranged from 78 (M100) to 342 (M58) while cSSRs incidence ranged from 1 (M138) to 17 (M28, M73). Though cSSRs were present in all the genomes, their frequency and SSR to cSSR conversion percentage varied from 1.08 (M138 with 93 SSRs) to 8.33 (M116 with 96 SSRs). In terms of localization, the SSRs were predominantly localized to coding regions (∼78%). Interestingly, genomes of around 50 kb contained a similar number of SSRs/cSSRs to that in a 110 kb genome, suggesting functional relevance for SSRs which was substantiated by variation in motif constitution between species with different host range. The three species with broad host range (M97, M100, M116) have around 90% of their mono-nucleotide repeat motifs composed of G or C and only M16 has both A and T mononucleotide motifs. Around 20% of the di-nucleotide repeat motifs in the genomes exhibiting a broad host range were CT/TC, which were either absent or represented to a much lesser extent in the other genomes.
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Affiliation(s)
- Chaudhary Mashhood Alam
- Luke/BI Plant Genome Dynamics Lab, Institute of Biotechnology and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Ingenious e-Brain Solutions, Gurugram, India
| | - Asif Iqbal
- PIRO Technologies Private Limited, New Delhi, India
| | - Anjana Sharma
- Department of Biomedical Sciences, SRCASW, University of Delhi, New Delhi, India
| | - Alan H Schulman
- Luke/BI Plant Genome Dynamics Lab, Institute of Biotechnology and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Safdar Ali
- Department of Biomedical Sciences, SRCASW, University of Delhi, New Delhi, India.,Department of Biological Sciences, Aliah University, Kolkata, India
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73
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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.
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74
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Wilson K, Ely B. Analyses of four new Caulobacter Phicbkviruses indicate independent lineages. J Gen Virol 2019; 100:321-331. [PMID: 30657445 DOI: 10.1099/jgv.0.001218] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteriophages with genomes larger than 200 kbp are considered giant phages, and the giant Phicbkviruses are the most frequently isolated Caulobacter crescentus phages. In this study, we compare six bacteriophage genomes that differ from the genomes of the majority of Phicbkviruses. Four of these genomes are much larger than those of the rest of the Phicbkviruses, with genome sizes that are more than 250 kbp. A comparison of 16 Phicbkvirus genomes identified a 'core genome' of 69 genes that is present in all of these Phicbkvirus genomes, as well as shared accessory genes and genes that are unique for each phage. Most of the core genes are clustered into the regions coding for structural proteins or those involved in DNA replication. A phylogenetic analysis indicated that these 16 CaulobacterPhicbkvirus genomes are related, but they represent four distinct branches of the Phicbkvirus genomic tree with distantly related branches sharing little nucleotide homology. In contrast, pairwise comparisons within each branch of the phylogenetic tree showed that more than 80 % of the entire genome is shared among phages within a group. This conservation of the genomes within each branch indicates that horizontal gene transfer events between the groups are rare. Therefore, the Phicbkvirus genus consists of at least four different phylogenetic branches that are evolving independently from one another. One of these branches contains a 27-gene inversion relative to the other three branches. Also, an analysis of the tRNA genes showed that they are relatively mobile within the Phicbkvirus genus.
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Affiliation(s)
- Kiesha Wilson
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Bert Ely
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
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75
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Dedrick RM, Guerrero Bustamante CA, Garlena RA, Pinches RS, Cornely K, Hatfull GF. Mycobacteriophage ZoeJ: A broad host-range close relative of mycobacteriophage TM4. Tuberculosis (Edinb) 2019; 115:14-23. [PMID: 30948168 DOI: 10.1016/j.tube.2019.01.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/09/2019] [Accepted: 01/13/2019] [Indexed: 10/27/2022]
Abstract
A collection of over 1600 sequenced bacteriophages isolated on a single host strain, Mycobacterium smegmatis mc2155, can be grouped into over two dozen types that have little or no nucleotide sequence similarity to each other. One group, Cluster K, can be divided into several subclusters, and the well-characterized and much exploited phage TM4 lies in Subcluster K2. Many of the Cluster K phages have broad host ranges and infect both fast- and slow-growing mycobacterial strains. Here we describe phage ZoeJ, a new Subcluster K2 member, which infects a broad spectrum of mycobacterial hosts including M. smegmatis, Mycobacterium tuberculosis, and Mycobacterium avium. ZoeJ has extensive sequence similarity to TM4, and comparative analysis reveals the precise deletion conferring the lytic phenotype of TM4. The ZoeJ immunity repressor was identified as gene 45, which is prophage-expressed, is required for lysogeny, and is sufficient to confer superinfection immunity to ZoeJ. ZoeJ gp45 also confers immunity to Subcluster K2 phage Milly, and Subcluster K1 phages Adephagia and CrimD, but surprisingly not to TM4. RNAseq analysis reveals the temporal pattern of early and late gene expressions in ZoeJ lytic growth and suggests a role for the ESAS motifs for gene regulation.
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Affiliation(s)
- Rebekah M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | | | - Rebecca A Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - R Seth Pinches
- Department of Chemistry and Biochemistry, Providence College, Providence, RI 02918, USA
| | - Kathleen Cornely
- Department of Chemistry and Biochemistry, Providence College, Providence, RI 02918, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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76
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Marinelli LJ, Piuri M, Hatfull GF. Genetic Manipulation of Lytic Bacteriophages with BRED: Bacteriophage Recombineering of Electroporated DNA. Methods Mol Biol 2019; 1898:69-80. [PMID: 30570724 DOI: 10.1007/978-1-4939-8940-9_6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We describe a recombineering-based method for the genetic manipulation of lytically replicating bacteriophages, focusing on mycobacteriophages. The approach utilizes recombineering-proficient strains of Mycobacterium smegmatis and employs a cotransformation strategy with purified phage genomic DNA and a mutagenic substrate, which selects for only those cells that are competent to take up DNA. The cotransformation method, combined with the high rates of recombination obtained in M. smegmatis recombineering strains, allows for the efficient and rapid generation of bacteriophage mutants.
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Affiliation(s)
- Laura J Marinelli
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina
- Laboratorio "Bacteriófagos y Aplicaciones Biotecnológicas", Departamento de Química Biológica, FCEyN, UBA, Ciudad Universitaria, Ciudad Autónoma de Buenos Aires, Argentina
| | - Graham F Hatfull
- Department of Biological Sciences and Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, PA, USA
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Complete Genome Sequences of Six BI Cluster Streptomyces Bacteriophages, HotFries, Moozy, Rainydai, RavenPuff, Scap1, and SenditCS. Microbiol Resour Announc 2018; 7:MRA00993-18. [PMID: 30533665 PMCID: PMC6256688 DOI: 10.1128/mra.00993-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 08/30/2018] [Indexed: 11/20/2022] Open
Abstract
Six double-stranded DNA Streptomyces bacteriophages, HotFries, Moozy, RavenPuff, Scap1, Rainydai, and SenditCS, were isolated using the phytopathogen Streptomyces scabiei as a host. These phages have been identified as Siphoviridae and members of cluster BI by genomic analysis.
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78
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Catalão MJ, Pimentel M. Mycobacteriophage Lysis Enzymes: Targeting the Mycobacterial Cell Envelope. Viruses 2018; 10:E428. [PMID: 30110929 PMCID: PMC6116114 DOI: 10.3390/v10080428] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 08/07/2018] [Accepted: 08/12/2018] [Indexed: 01/18/2023] Open
Abstract
Mycobacteriophages are viruses that specifically infect mycobacteria, which ultimately culminate in host cell death. Dedicated enzymes targeting the complex mycobacterial cell envelope arrangement have been identified in mycobacteriophage genomes, thus being potential candidates as antibacterial agents. These comprise lipolytic enzymes that target the mycolic acid-containing outer membrane and peptidoglycan hydrolases responsive to the atypical mycobacterial peptidoglycan layer. In the recent years, a remarkable progress has been made, particularly on the comprehension of the mechanisms of bacteriophage lysis proteins activity and regulation. Notwithstanding, information about mycobacteriophages lysis strategies is limited and is mainly represented by the studies performed with mycobacteriophage Ms6. Since mycobacteriophages target a specific group of bacteria, which include Mycobacterium tuberculosis responsible for one of the leading causes of death worldwide, exploitation of the use of these lytic enzymes demands a special attention, as they may be an alternative to tackle multidrug resistant tuberculosis. This review focuses on the current knowledge of the function of lysis proteins encoded by mycobacteriophages and their potential applications, which may contribute to increasing the effectiveness of antimycobacterial therapy.
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Affiliation(s)
- Maria João Catalão
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal.
| | - Madalena Pimentel
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal.
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79
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Wong HC, Wang TY, Yang CW, Tang CT, Ying C, Wang CH, Chang WH. Characterization of a lytic vibriophage VP06 of Vibrio parahaemolyticus. Res Microbiol 2018; 170:13-23. [PMID: 30077624 DOI: 10.1016/j.resmic.2018.07.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 07/06/2018] [Accepted: 07/09/2018] [Indexed: 01/21/2023]
Abstract
Vibrio parahaemolyticus is a human enteropathogenic bacterium and is also pathogenic to shrimp and finfish. In a search for a biocontrol agent for V. parahaemolyticus and other pathogenic Vibrio species, a lytic phage VP06 was isolated from oyster using V. parahaemolyticus as the host. VP06 is a Siphoviridae phage with a polyhedral head and a long tail. The genome sequence of VP06 was 75,893 nucleotides in length and the G + C content was 49%; a total of 101 CDSs were identified in VP06, of which 39 exhibited functional domains/motifs. The genomic sequence of VP06 is similar to those of a lytic Vibrio vulnificus phage SSP002 and a temperate V. parahaemolyticus phage vB_VpaS_MAR10, although VP06 has distinct features in the CDS arrangement and 14 unique CDSs. Phylogenetic analysis revealed that VP06, SSP002 and vB_VpaS_MAR10 belong to a novel genus cluster of Siphoviridae phages. This phage lysed 28.1% of various Vibrio strains, and the efficiency of plating method revealed that VP06 was highly effective in lysing strains of Vibrio alginolyticus, Vibrio azureus, Vibrio harveyi and V. parahaemolyticus. The properties of VP06, including its broad range of hosts and resistance to environmental stresses, indicate that it may be a candidate biocontrol agent.
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Affiliation(s)
- Hin-Chung Wong
- Department of Microbiology, Soochow University, Taipei, 111, Taiwan, ROC.
| | - Tzu-Yun Wang
- Department of Microbiology, Soochow University, Taipei, 111, Taiwan, ROC.
| | - Chu-Wen Yang
- Department of Microbiology, Soochow University, Taipei, 111, Taiwan, ROC.
| | - Chung-Tao Tang
- Department of Microbiology, Soochow University, Taipei, 111, Taiwan, ROC.
| | - Chingwen Ying
- Department of Microbiology, Soochow University, Taipei, 111, Taiwan, ROC.
| | - Chun-Hsiung Wang
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan, ROC.
| | - Wei-Hau Chang
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan, ROC.
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80
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Arens DK, Brady TS, Carter JL, Pape JA, Robinson DM, Russell KA, Staley LA, Stettler JM, Tateoka OB, Townsend MH, Whitley KV, Wienclaw TM, Williamson TL, Johnson SM, Grose JH. Characterization of two related Erwinia myoviruses that are distant relatives of the PhiKZ-like Jumbo phages. PLoS One 2018; 13:e0200202. [PMID: 29979759 PMCID: PMC6034870 DOI: 10.1371/journal.pone.0200202] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 06/21/2018] [Indexed: 12/25/2022] Open
Abstract
Bacteriophages are a major force in the evolution of bacteria due to their sheer abundance as well as their ability to infect and kill their hosts and to transfer genetic material. Bacteriophages that infect the Enterobacteriaceae family are of particular interest because this bacterial family contains dangerous animal and plant pathogens. Herein we report the isolation and characterization of two jumbo myovirus Erwinia phages, RisingSun and Joad, collected from apple trees. These two genomes are nearly identical with Joad harboring two additional putative gene products. Despite mass spectrometry data that support the putative annotation, 43% of their gene products have no significant BLASTP hit. These phages are also more closely related to Pseudomonas and Vibrio phages than to published Enterobacteriaceae phages. Of the 140 gene products with a BLASTP hit, 81% and 63% of the closest hits correspond to gene products from Pseudomonas and Vibrio phages, respectively. This relatedness may reflect their ecological niche, rather than the evolutionary history of their host. Despite the presence of over 800 Enterobacteriaceae phages on NCBI, the uniqueness of these two phages highlights the diversity of Enterobacteriaceae phages still to be discovered.
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Affiliation(s)
- Daniel K. Arens
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - T. Scott Brady
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - John L. Carter
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - Jenny A. Pape
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - David M. Robinson
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - Kerri A. Russell
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - Lyndsay A. Staley
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - Jason M. Stettler
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, United States of America
| | - Olivia B. Tateoka
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - Michelle H. Townsend
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - Kiara V. Whitley
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - Trevor M. Wienclaw
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - Taryn L. Williamson
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, United States of America
| | - Steven M. Johnson
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - Julianne H. Grose
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
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81
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Rational Design of Biosafety Level 2-Approved, Multidrug-Resistant Strains of Mycobacterium tuberculosis through Nutrient Auxotrophy. mBio 2018; 9:mBio.00938-18. [PMID: 29844114 PMCID: PMC5974470 DOI: 10.1128/mbio.00938-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Multidrug-resistant (MDR) tuberculosis, defined as tuberculosis resistant to the two first-line drugs isoniazid and rifampin, poses a serious problem for global tuberculosis control strategies. Lack of a safe and convenient model organism hampers progress in combating the spread of MDR strains of Mycobacterium tuberculosis. We reasoned that auxotrophic MDR mutants of M. tuberculosis would provide a safe means for studying MDR M. tuberculosis without the need for a biosafety level 3 (BSL3) laboratory. Two different sets of triple auxotrophic mutants of M. tuberculosis were generated, which were auxotrophic for the nutrients leucine, pantothenate, and arginine or for leucine, pantothenate, and methionine. These triple auxotrophic strains retained their acid-fastness, their ability to generate both a drug persistence phenotype and drug-resistant mutants, and their susceptibility to plaque-forming mycobacterial phages. MDR triple auxotrophic mutants were obtained in a two-step fashion, selecting first for solely isoniazid-resistant or rifampin-resistant mutants. Interestingly, selection for isoniazid-resistant mutants of the methionine auxotroph generated isolates with single point mutations in katG, which encodes an isoniazid-activating enzyme, whereas similar selection using the arginine auxotroph yielded isoniazid-resistant mutants with large deletions in the chromosomal region containing katG. These M. tuberculosis MDR strains were readily sterilized by second-line tuberculosis drugs and failed to kill immunocompromised mice. These strains provide attractive candidates for M. tuberculosis biology studies and drug screening outside the BSL3 facility. Elimination of Mycobacterium tuberculosis, the bacterium causing tuberculosis, requires enhanced understanding of its biology in order to identify new drugs against drug-susceptible and drug-resistant M. tuberculosis as well as uncovering novel pathways that lead to M. tuberculosis death. To circumvent the need for a biosafety level 3 (BSL3) laboratory when conducting research on M. tuberculosis, we have generated drug-susceptible and drug-resistant triple auxotrophic strains of M. tuberculosis suitable for use in a BSL2 laboratory. These strains originate from a double auxotrophic M. tuberculosis strain, H37Rv ΔpanCD ΔleuCD, which was reclassified as a BSL2 strain based on its lack of lethality in immunocompromised and immunocompetent mice. A third auxotrophy (methionine or arginine) was introduced via deletion of metA or argB, respectively, since M. tuberculosis ΔmetA and M. tuberculosis ΔargB are unable to survive amino acid auxotrophy and infect their host. The resulting triple auxotrophic M. tuberculosis strains retained characteristics of M. tuberculosis relevant for most types of investigations.
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82
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Ko CC, Hatfull GF. Mycobacteriophage Fruitloop gp52 inactivates Wag31 (DivIVA) to prevent heterotypic superinfection. Mol Microbiol 2018; 108:443-460. [PMID: 29488662 DOI: 10.1111/mmi.13946] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2018] [Indexed: 01/04/2023]
Abstract
Bacteriophages engage in complex dynamic interactions with their bacterial hosts and with each other. Bacteria have numerous mechanisms to resist phage infection, and phages must co-evolve by overcoming bacterial resistance or by choosing an alternative host. Phages also compete with each other, both during lysogeny by prophage-mediated defense against viral attack and by superinfection exclusion during lytic replication. Phages are enormously diverse genetically and are replete with small genes of unknown function, many of which are not required for lytic growth, but which may modulate these bacteria-phage and phage-phage dynamics. Using cellular toxicity of phage gene overexpression as an assay, we identified the 93-residue protein gp52 encoded by Cluster F mycobacteriophage Fruitloop. The toxicity of Fruitloop gp52 overexpression results from interaction with and inactivation of Wag31 (DivIVA), an essential Mycobacterium smegmatis protein organizing cell wall biosynthesis at the growing cellular poles. Fruitloop gene 52 is expressed early in lytic growth and is not required for normal Fruitloop lytic replication but interferes with Subcluster B2 phages such as Hedgerow and Rosebush. We conclude that Hedgerow and Rosebush are Wag31-dependent phages and that Fruitloop gp52 confers heterotypic superinfection exclusion by inactivating Wag31.
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Affiliation(s)
- Ching-Chung Ko
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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83
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Abstract
Bacteriophages are the most abundant and diverse biological entities on the planet, and new phage genomes are being discovered at a rapid pace. As more phage genomes are published, new methods are needed for placing these genomes in an ecological and evolutionary context. Phages are difficult to study by phylogenetic methods, because they exchange genes regularly, and no single gene is conserved across all phages. Here, we demonstrate how gene-level networks can provide a high-resolution view of phage genetic diversity and offer a novel perspective on virus ecology. We focus our analyses on virus host range and show how network topology corresponds to host relatedness, how to find groups of genes with the strongest host-specific signatures, and how this perspective can complement phage host prediction tools. We discuss extensions of gene network analysis to predicting the emergence of phages on new hosts, as well as applications to features of phage biology beyond host range. Bacteriophages (phages) are viruses that infect bacteria, and they are critical drivers of bacterial evolution and community structure. It is generally difficult to study phages by using tree-based methods, because gene exchange is common, and no single gene is shared among all phages. Instead, networks offer a means to compare phages while placing them in a broader ecological and evolutionary context. In this work, we build a network that summarizes gene sharing across phages and test how a key constraint on phage ecology, host range, corresponds to the structure of the network. We find that the network reflects the relatedness among phage hosts, and phages with genes that are closer in the network are likelier to infect similar hosts. This approach can also be used to identify genes that affect host range, and we discuss possible extensions to analyze other aspects of viral ecology.
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84
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Recovery of mycobacteriophages from archival stocks stored for approximately 50 years in Japan. Arch Virol 2018; 163:1915-1919. [PMID: 29511830 DOI: 10.1007/s00705-018-3788-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/09/2018] [Indexed: 10/17/2022]
Abstract
Mycobacteriophage archival stocks have been kept for ca. 20-50 years in Japan. In this study, we attempted to recover mycobacteriophages from 50 archival stocks and briefly analyzed the recovered phages. The phages were recovered from 72.2% (13/18) of the lyophilized stocks that had been stored for 47-56 years. Moreover, the analysis of 12 representative recovered phages led to their classification as belonging to the family Siphoviridae, and seven of them were typed by polymerase chain reaction (PCR) targeting the gene that encodes the tape measure protein. Considering these results, lyophilization seems to be suitable for phage archival storage.
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85
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Cheng L, Marinelli LJ, Grosset N, Fitz-Gibbon ST, Bowman CA, Dang BQ, Russell DA, Jacobs-Sera D, Shi B, Pellegrini M, Miller JF, Gautier M, Hatfull GF, Modlin RL. Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages. BMC Microbiol 2018; 18:19. [PMID: 29490612 PMCID: PMC5831693 DOI: 10.1186/s12866-018-1159-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 02/15/2018] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND A remarkable exception to the large genetic diversity often observed for bacteriophages infecting a specific bacterial host was found for the Cutibacterium acnes (formerly Propionibacterium acnes) phages, which are highly homogeneous. Phages infecting the related species, which is also a member of the Propionibacteriaceae family, Propionibacterium freudenreichii, a bacterium used in production of Swiss-type cheeses, have also been described and are common contaminants of the cheese manufacturing process. However, little is known about their genetic composition and diversity. RESULTS We obtained seven independently isolated bacteriophages that infect P. freudenreichii from Swiss-type cheese samples, and determined their complete genome sequences. These data revealed that all seven phage isolates are of similar genomic length and GC% content, but their genomes are highly diverse, including genes encoding the capsid, tape measure, and tail proteins. In contrast to C. acnes phages, all P. freudenreichii phage genomes encode a putative integrase protein, suggesting they are capable of lysogenic growth. This is supported by the finding of related prophages in some P. freudenreichii strains. The seven phages could further be distinguished as belonging to two distinct genomic types, or 'clusters', based on nucleotide sequences, and host range analyses conducted on a collection of P. freudenreichii strains show a higher degree of host specificity than is observed for the C. acnes phages. CONCLUSIONS Overall, our data demonstrate P. freudenreichii bacteriophages are distinct from C. acnes phages, as evidenced by their higher genetic diversity, potential for lysogenic growth, and more restricted host ranges. This suggests substantial differences in the evolution of these related species from the Propionibacteriaceae family and their phages, which is potentially related to their distinct environmental niches.
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Affiliation(s)
- Lucy Cheng
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90095 CA USA
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Laura J. Marinelli
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90095 CA USA
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Noël Grosset
- Equipe Microbiologie de l’œuf et des Ovoproduits (MICOV), Agrocampus Ouest, INRA, (UMR1253) Science et Technologie du Lait et de l’Œuf, Rennes, France
| | - Sorel T. Fitz-Gibbon
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Charles A. Bowman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Brian Q. Dang
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Daniel A. Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Baochen Shi
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Jeff F. Miller
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095 USA
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Michel Gautier
- Equipe Microbiologie de l’œuf et des Ovoproduits (MICOV), Agrocampus Ouest, INRA, (UMR1253) Science et Technologie du Lait et de l’Œuf, Rennes, France
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Robert L. Modlin
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90095 CA USA
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095 USA
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86
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Genome Sequence of a Newly Isolated F2 Subcluster Mycobacteriophage from the Black Belt Geological Region of Western Alabama. GENOME ANNOUNCEMENTS 2018; 6:6/4/e01555-17. [PMID: 29371367 PMCID: PMC5786693 DOI: 10.1128/genomea.01555-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The bacteriophage Demsculpinboyz was discovered in a soil sample from the Black Belt region of Alabama using Mycobacterium smegmatis mc2155 as its host. The genome is 57,437 bp long and contains 116 protein-coding genes. It belongs to the F2 subcluster, which has only five other members.
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87
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Abstract
While taxonomy is an often-unappreciated branch of science it serves very important roles. Bacteriophage taxonomy has evolved from a mainly morphology-based discipline, characterized by the work of David Bradley and Hans-Wolfgang Ackermann, to the holistic approach that is taken today. The Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) takes a comprehensive approach to classifying prokaryote viruses measuring overall DNA and protein identity and phylogeny before making decisions about the taxonomic position of a new virus. The huge number of complete genomes being deposited with NCBI and other public databases has resulted in a reassessment of the taxonomy of many viruses, and the future will see the introduction of new viral families and higher orders.
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Affiliation(s)
- Igor Tolstoy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Andrew M Kropinski
- Department of Food Science, University of Guelph, Guelph, ON, Canada, N1G 2W1.
- Department of Molecular & Cellular Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1.
- Department of Pathobiology, University of Guelph, 6 Mayfield Ave, Guelph, ON, Canada, N1G 2W1.
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
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88
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Dedrick RM, Mavrich TN, Ng WL, Hatfull GF. Expression and evolutionary patterns of mycobacteriophage D29 and its temperate close relatives. BMC Microbiol 2017; 17:225. [PMID: 29197343 PMCID: PMC5712189 DOI: 10.1186/s12866-017-1131-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 11/16/2017] [Indexed: 11/17/2022] Open
Abstract
Background Mycobacteriophages are viruses that infect Mycobacterium hosts. A large collection of phages known to infect the same bacterial host strain – Mycobacterium smegmatis mc2155 – exhibit substantial diversity and characteristically mosaic architectures. The well-studied lytic mycobacteriophage D29 appears to be a deletion derivative of a putative temperate parent, although its parent has yet to be identified. Results Here we describe three newly-isolated temperate phages – Kerberos, Pomar16 and StarStuff – that are related to D29, and are predicted to be very close relatives of its putative temperate parent, revealing the repressor and additional genes that are lost in D29. Transcriptional profiles show the patterns of both lysogenic and lytic gene expression and identify highly-expressed, abundant, stable, small non-coding transcripts made from the Pleft early lytic promoter, and which are toxic to M. smegmatis. Conclusions Comparative genomics of phages D29, Kerberos, Pomar16 and StarStuff provide insights into bacteriophage evolution, and comparative transcriptomics identifies the pattern of lysogenic and lytic expression with unusual features including highly expressed, small, non-coding RNAs. Electronic supplementary material The online version of this article (10.1186/s12866-017-1131-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rebekah M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Travis N Mavrich
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Wei L Ng
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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89
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Virus-host protein-protein interactions of mycobacteriophage Giles. Sci Rep 2017; 7:16514. [PMID: 29184079 PMCID: PMC5705681 DOI: 10.1038/s41598-017-16303-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 10/31/2017] [Indexed: 01/21/2023] Open
Abstract
Mycobacteriophage are viruses that infect mycobacteria. More than 1,400 mycobacteriophage genomes have been sequenced, coding for over one hundred thousand proteins of unknown functions. Here we investigate mycobacteriophage Giles-host protein-protein interactions (PPIs) using yeast two-hybrid screening (Y2H). A total of 25 reproducible PPIs were found for a selected set of 10 Giles proteins, including a putative virion assembly protein (gp17), the phage integrase (gp29), the endolysin (gp31), the phage repressor (gp47), and six proteins of unknown function (gp34, gp35, gp54, gp56, gp64, and gp65). We note that overexpression of the proteins is toxic to M. smegmatis, although whether this toxicity and the associated changes in cellular morphology are related to the putative interactions revealed in the Y2H screen is unclear.
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90
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Genome Sequences of Chancellor, Mitti, and Wintermute, Three Subcluster K4 Phages Isolated Using Mycobacterium smegmatis mc
2
155. GENOME ANNOUNCEMENTS 2017; 5:5/45/e01070-17. [PMID: 29122858 PMCID: PMC5679791 DOI: 10.1128/genomea.01070-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Mycobacteriophages Chancellor, Mitti, and Wintermute infect Mycobacterium smegmatis mc2155 and are closely related to phages Cheetobro and Fionnbharth in subcluster K4. Genome sizes range from 57,697 bp to 58,046 bp. Phages are predicted to be temperate and to infect the pathogen Mycobacterium tuberculosis.
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91
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Abstract
The global bacteriophage population is large, dynamic, old, and highly diverse genetically. Many phages are tailed and contain double-stranded DNA, but these remain poorly characterized genomically. A collection of over 1,000 phages infecting Mycobacterium smegmatis reveals the diversity of phages of a common bacterial host, but their relationships to phages of phylogenetically proximal hosts are not known. Comparative sequence analysis of 79 phages isolated on Gordonia shows these also to be diverse and that the phages can be grouped into 14 clusters of related genomes, with an additional 14 phages that are “singletons” with no closely related genomes. One group of six phages is closely related to Cluster A mycobacteriophages, but the other Gordonia phages are distant relatives and share only 10% of their genes with the mycobacteriophages. The Gordonia phage genomes vary in genome length (17.1 to 103.4 kb), percentage of GC content (47 to 68.8%), and genome architecture and contain a variety of features not seen in other phage genomes. Like the mycobacteriophages, the highly mosaic Gordonia phages demonstrate a spectrum of genetic relationships. We show this is a general property of bacteriophages and suggest that any barriers to genetic exchange are soft and readily violable. Despite the numerical dominance of bacteriophages in the biosphere, there is a dearth of complete genomic sequences. Current genomic information reveals that phages are highly diverse genomically and have mosaic architectures formed by extensive horizontal genetic exchange. Comparative analysis of 79 phages of Gordonia shows them to not only be highly diverse, but to present a spectrum of relatedness. Most are distantly related to phages of the phylogenetically proximal host Mycobacterium smegmatis, although one group of Gordonia phages is more closely related to mycobacteriophages than to the other Gordonia phages. Phage genome sequence space remains largely unexplored, but further isolation and genomic comparison of phages targeted at related groups of hosts promise to reveal pathways of bacteriophage evolution.
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92
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Genome Sequences of Mycobacteriophages Kerberos, Pomar16, and StarStuff. GENOME ANNOUNCEMENTS 2017; 5:5/32/e00690-17. [PMID: 28798169 PMCID: PMC5552978 DOI: 10.1128/genomea.00690-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We describe the genome sequences of three closely related mycobacteriophages, Kerberos, Pomar16, and StarStuff, isolated at similar times but from geographically distinct regions. All three genomes are similar to those of other subcluster A2 phages, such as L5 and D29, are temperate, and have siphoviral virion morphologies.
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93
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Abatángelo V, Peressutti Bacci N, Boncompain CA, Amadio AA, Carrasco S, Suárez CA, Morbidoni HR. Broad-range lytic bacteriophages that kill Staphylococcus aureus local field strains. PLoS One 2017; 12:e0181671. [PMID: 28742812 PMCID: PMC5526547 DOI: 10.1371/journal.pone.0181671] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 07/05/2017] [Indexed: 01/08/2023] Open
Abstract
Staphylococcus aureus is a very successful opportunistic pathogen capable of causing a variety of diseases ranging from mild skin infections to life-threatening sepsis, meningitis and pneumonia. Its ability to display numerous virulence mechanisms matches its skill to display resistance to several antibiotics, including β-lactams, underscoring the fact that new anti-S. aureus drugs are urgently required. In this scenario, the utilization of lytic bacteriophages that kill bacteria in a genus -or even species- specific way, has become an attractive field of study. In this report, we describe the isolation, characterization and sequencing of phages capable of killing S. aureus including methicillin resistant (MRSA) and multi-drug resistant S. aureus local strains from environmental, animal and human origin. Genome sequencing and bio-informatics analysis showed the absence of genes encoding virulence factors, toxins or antibiotic resistance determinants. Of note, there was a high similarity between our set of phages to others described in the literature such as phage K. Considering that reported phages were obtained in different continents, it seems plausible that there is a commonality of genetic features that are needed for optimum, broad host range anti-staphylococcal activity of these related phages. Importantly, the high activity and broad host range of one of our phages underscores its promising value to control the presence of S. aureus in fomites, industry and hospital environments and eventually on animal and human skin. The development of a cocktail of the reported lytic phages active against S. aureus–currently under way- is thus, a sensible strategy against this pathogen.
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Affiliation(s)
- Virginia Abatángelo
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Natalia Peressutti Bacci
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Carina A. Boncompain
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Ariel A. Amadio
- EEA Rafaela, Instituto Nacional de Tecnología Agropecuaria (INTA), Rafaela, Santa Fe, Argentina
| | - Soledad Carrasco
- Bioinformatics Program, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Cristian A. Suárez
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
- * E-mail: (HRM); (CAS)
| | - Héctor R. Morbidoni
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
- * E-mail: (HRM); (CAS)
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94
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Bacteriophage evolution differs by host, lifestyle and genome. Nat Microbiol 2017; 2:17112. [PMID: 28692019 PMCID: PMC5540316 DOI: 10.1038/nmicrobiol.2017.112] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/09/2017] [Indexed: 01/21/2023]
Abstract
Bacteriophages play key roles in microbial evolution1,2, marine nutrient cycling3 and human disease4. Phages are genetically diverse, and their genome architectures are characteristically mosaic, driven by horizontal gene transfer with other phages and host genomes5. As a consequence, phage evolution is complex and their genomes are composed of genes with distinct and varied evolutionary histories6,7. However, there are conflicting perspectives on the roles of mosaicism and the extent to which it generates a spectrum of genome diversity8 or genetically discrete populations9,10. Here, we show that bacteriophages evolve within two general evolutionary modes that differ in the extent of horizontal gene transfer by an order of magnitude. Temperate phages distribute into high and low gene flux modes, whereas lytic phages share only the lower gene flux mode. The evolutionary modes are also a function of the bacterial host and different proportions of temperate and lytic phages are distributed in either mode depending on the host phylum. Groups of genetically related phages fall into either the high or low gene flux modes, suggesting there are genetic as well as ecological drivers of horizontal gene transfer rates. Consequently, genome mosaicism varies depending on the host, lifestyle and genetic constitution of phages.
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95
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Kalatzis PG, Rørbo NI, Castillo D, Mauritzen JJ, Jørgensen J, Kokkari C, Zhang F, Katharios P, Middelboe M. Stumbling across the Same Phage: Comparative Genomics of Widespread Temperate Phages Infecting the Fish Pathogen Vibrio anguillarum. Viruses 2017; 9:E122. [PMID: 28531104 PMCID: PMC5454434 DOI: 10.3390/v9050122] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/12/2017] [Accepted: 05/12/2017] [Indexed: 01/03/2023] Open
Abstract
Nineteen Vibrio anguillarum-specific temperate bacteriophages isolated across Europe and Chile from aquaculture and environmental sites were genome sequenced and analyzed for host range, morphology and life cycle characteristics. The phages were classified as Siphoviridae with genome sizes between 46,006 and 54,201 bp. All 19 phages showed high genetic similarity, and 13 phages were genetically identical. Apart from sporadically distributed single nucleotide polymorphisms (SNPs), genetic diversifications were located in three variable regions (VR1, VR2 and VR3) in six of the phage genomes. Identification of specific genes, such as N6-adenine methyltransferase and lambda like repressor, as well as the presence of a tRNAArg, suggested a both mutualistic and parasitic interaction between phages and hosts. During short term phage exposure experiments, 28% of a V. anguillarum host population was lysogenized by the temperate phages and a genomic analysis of a collection of 31 virulent V. anguillarum showed that the isolated phages were present as prophages in >50% of the strains covering large geographical distances. Further, phage sequences were widely distributed among CRISPR-Cas arrays of publicly available sequenced Vibrios. The observed distribution of these specific temperate Vibriophages across large geographical scales may be explained by efficient dispersal of phages and bacteria in the marine environment combined with a mutualistic interaction between temperate phages and their hosts which selects for co-existence rather than arms race dynamics.
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Affiliation(s)
- Panos G Kalatzis
- Marine Biological Section, University of Copenhagen, DK-3000 Helsingør, Denmark.
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Crete, 71500, Greece.
| | - Nanna Iben Rørbo
- Marine Biological Section, University of Copenhagen, DK-3000 Helsingør, Denmark.
| | - Daniel Castillo
- Marine Biological Section, University of Copenhagen, DK-3000 Helsingør, Denmark.
| | | | - Jóhanna Jørgensen
- Marine Biological Section, University of Copenhagen, DK-3000 Helsingør, Denmark.
| | - Constantina Kokkari
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Crete, 71500, Greece.
| | - Faxing Zhang
- Beijing Genomics Institute (BGI) Park, No.21 Hongan 3rd Street, Building NO. 7, Yantian District, Shenzhen 518083, China.
| | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Crete, 71500, Greece.
| | - Mathias Middelboe
- Marine Biological Section, University of Copenhagen, DK-3000 Helsingør, Denmark.
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96
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Chung CH, Walter MH, Yang L, Chen SCG, Winston V, Thomas MA. Predicting genome terminus sequences of Bacillus cereus-group bacteriophage using next generation sequencing data. BMC Genomics 2017; 18:350. [PMID: 28472946 PMCID: PMC5418689 DOI: 10.1186/s12864-017-3744-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/28/2017] [Indexed: 11/10/2022] Open
Abstract
Background Most tailed bacteriophages (phages) feature linear dsDNA genomes. Characterizing novel phages requires an understanding of complete genome sequences, including the definition of genome physical ends. Result We sequenced 48 Bacillus cereus phage isolates and analyzed Next-generation sequencing (NGS) data to resolve the genome configuration of these novel phages. Most assembled contigs featured reads that mapped to both contig ends and formed circularized contigs. Independent assemblies of 31 nearly identical I48-like Bacillus phage isolates allowed us to observe that the assembly programs tended to produce random cleavage on circularized contigs. However, currently available assemblers were not capable of reporting the underlying phage genome configuration from sequence data. To identify the genome configuration of sequenced phage in silico, a terminus prediction method was developed by means of ‘neighboring coverage ratios’ and ‘read edge frequencies’ from read alignment files. Termini were confirmed by primer walking and supported by phylogenetic inference of large DNA terminase protein sequences. Conclusions The Terminus package using phage NGS data along with the contig circularity could efficiently identify the proximal positions of phage genome terminus. Complete phage genome sequences allow a proposed characterization of the potential packaging mechanisms and more precise genome annotation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3744-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cheng-Han Chung
- Department of Biological Sciences, Idaho State University, 921 South 8th Avenue, Pocatello, ID, 83209-8007, USA.
| | - Michael H Walter
- Department of Biology, University of Northern Iowa, 144 McCollum Science Hall, Cedar Falls, IA, 50614-0421, USA
| | - Luobin Yang
- Department of Biological Sciences, Idaho State University, 921 South 8th Avenue, Pocatello, ID, 83209-8007, USA
| | - Shu-Chuan Grace Chen
- Department of Mathematics and Statistics, Idaho State University, 921 South 8th Avenue, Pocatello, ID, 83209-8085, USA
| | - Vern Winston
- Department of Biological Sciences, Idaho State University, 921 South 8th Avenue, Pocatello, ID, 83209-8007, USA
| | - Michael A Thomas
- Department of Biological Sciences, Idaho State University, 921 South 8th Avenue, Pocatello, ID, 83209-8007, USA
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97
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Dedrick RM, Jacobs-Sera D, Guerrero Bustamante CA, Garlena RA, Mavrich TN, Pope WH, Reyes JCC, Russell DA, Adair T, Alvey R, Bonilla JA, Bricker JS, Brown BR, Byrnes D, Cresawn SG, Davis WB, Dickson LA, Edgington NP, Findley AM, Golebiewska U, Grose JH, Hayes CF, Hughes LE, Hutchison KW, Isern S, Johnson AA, Kenna MA, Klyczek KK, Mageeney CM, Michael SF, Molloy SD, Montgomery MT, Neitzel J, Page ST, Pizzorno MC, Poxleitner MK, Rinehart CA, Robinson CJ, Rubin MR, Teyim JN, Vazquez E, Ware VC, Washington J, Hatfull GF. Prophage-mediated defence against viral attack and viral counter-defence. Nat Microbiol 2017; 2:16251. [PMID: 28067906 PMCID: PMC5508108 DOI: 10.1038/nmicrobiol.2016.251] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 11/09/2016] [Indexed: 01/22/2023]
Abstract
Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defence promotes phage co-evolution.
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Affiliation(s)
- Rebekah M. Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | | | - Rebecca A. Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Travis N. Mavrich
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Welkin H. Pope
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | | | - Daniel A. Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Tamarah Adair
- Department of Biology, Baylor University, Waco, TX 76798
| | - Richard Alvey
- Biology Department, Illinois-Wesleyan University, Bloomington, IL 61702
| | - J. Alfred Bonilla
- Biology Department University of Wisconsin-River Falls, River Falls, WI 54016
| | | | - Bryony R. Brown
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Deanna Byrnes
- Biology Department, Carthage College, Kenosha, WI53140
| | - Steven G. Cresawn
- Biology Department, James Madison University, Harrisonburg, VA 22807
| | - William B. Davis
- School of Molecular Biosciences, Washington State University Pullman, WA 99164
| | - Leon A. Dickson
- Department of Biology, Howard University, Washington, DC 20059
| | | | - Ann M. Findley
- Biology, School of Sciences, University of Louisiana at Monroe, Monroe, LA 71209
| | - Urszula Golebiewska
- Biological Sciences and Geology, Queensborough Community College, Bayside, NY 11364
| | | | - Cory F. Hayes
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Lee E. Hughes
- Biological Sciences, University of North Texas, Denton, TX 76203
| | - Keith W. Hutchison
- Molecular and Biomedical Sciences, University of Maine, Honors College, Orono, ME 04469
| | - Sharon Isern
- Dept. of Biological Sciences, Florida Gulf Coast University, Fort Myers, FL 33965
| | - Allison A. Johnson
- Biology Department, Virginia Commonwealth University, Richmond, VA 23284
| | | | - Karen K. Klyczek
- Biology Department University of Wisconsin-River Falls, River Falls, WI 54016
| | | | - Scott F. Michael
- Dept. of Biological Sciences, Florida Gulf Coast University, Fort Myers, FL 33965
| | - Sally D. Molloy
- Molecular and Biomedical Sciences, University of Maine, Honors College, Orono, ME 04469
| | | | - James Neitzel
- Biology Department, The Evergreen State College, Olympia, WA 98502
| | - Shallee T. Page
- Division of Environmental and, Biological Sciences, University of Maine-Machias, Machias, ME 04654
| | | | | | - Claire A. Rinehart
- Biology Department, Western Kentucky University, Bowling Green, KY 42101
| | | | - Michael R. Rubin
- Biology Department, University of Puerto Rico-Cayey, Cayey, PR 00736
| | | | - Edwin Vazquez
- Biology Department, University of Puerto Rico-Cayey, Cayey, PR 00736
| | - Vassie C. Ware
- Biological Sciences, Lehigh University, Bethlehem, PA 18015
| | | | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
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98
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Fluorescent Reporter DS6A Mycobacteriophages Reveal Unique Variations in Infectibility and Phage Production in Mycobacteria. J Bacteriol 2016; 198:3220-3232. [PMID: 27672191 DOI: 10.1128/jb.00592-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 09/13/2016] [Indexed: 12/22/2022] Open
Abstract
Mycobacteriophage DS6A is unique among the more than 8,000 isolated mycobacteriophages due to its ability to form plaques exclusively on mycobacteria belonging to the Mycobacterium tuberculosis complex (MTBC). Speculation surrounding this specificity has led to unsupported assertions in published studies and patents that nontuberculous mycobacteria (NTM) are wholly resistant to DS6A infection. In this study, we identified two independent nonessential regions in the DS6A genome and replaced them with an mVenus-expressing plasmid to generate fluorescent reporter phages Φ2GFP12 and Φ2GFP13. We show that even though DS6A is able to form plaques only on MTBC bacteria, infection of various NTM results in mVenus expression in transduced cells. The efficiency of DS6A in delivering DNA varied between NTM species. Additionally, we saw a striking difference in the efficiency of DNA delivery between the closely related members of the Mycobacterium abscessus complex, M. abscessus and Mycobacterium massiliense We also demonstrated that TM4 and DS6A, two phages that do not form plaques on M. massiliense, differ in their ability to deliver DNA, suggesting that there is a phage-specific restriction between mycobacterial species. Phylogenetic analysis reveals that the DS6A genome has a characteristically mosaic structure but provided few insights into the basis for the specificity for MTBC hosts. This study demonstrates that the inability of the MTBC-specific phage DS6A to form plaques on NTM is more complex than previously thought. Moreover, the DS6A-derived fluorophages provide important new tools for the study of mycobacterial biology. IMPORTANCE The coevolution of bacteria and their infecting phages involves a constant arms race for bacteria to prevent phage infection and phage to overcome these preventions. Although a diverse array of phage defense systems is well characterized in bacteria, very few phage restriction systems are known in mycobacteria. The DS6A mycobacteriophage is unique in the mycobacterial world in that it forms plaques only on members of the Mycobacterium tuberculosis complex. However, the novel DS6A reporter phages developed in this work demonstrate that DS6A can infect nontuberculous mycobacteria at various efficiencies. By comparing the abilities of DS6A and another phage, TM4, to infect and form plaques on various mycobacterial species, we can begin to discern new phage restriction systems employed within the genus.
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99
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Esposito LA, Gupta S, Streiter F, Prasad A, Dennehy JJ. Evolutionary interpretations of mycobacteriophage biodiversity and host-range through the analysis of codon usage bias. Microb Genom 2016; 2:e000079. [PMID: 28348827 PMCID: PMC5359403 DOI: 10.1099/mgen.0.000079] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/18/2016] [Indexed: 12/31/2022] Open
Abstract
In an genomics course sponsored by the Howard Hughes Medical Institute (HHMI), undergraduate students have isolated and sequenced the genomes of more than 1,150 mycobacteriophages, creating the largest database of sequenced bacteriophages able to infect a single host, Mycobacterium smegmatis, a soil bacterium. Genomic analysis indicates that these mycobacteriophages can be grouped into 26 clusters based on genetic similarity. These clusters span a continuum of genetic diversity, with extensive genomic mosaicism among phages in different clusters. However, little is known regarding the primary hosts of these mycobacteriophages in their natural habitats, nor of their broader host ranges. As such, it is possible that the primary host of many newly isolated mycobacteriophages is not M. smegmatis, but instead a range of closely related bacterial species. However, determining mycobacteriophage host range presents difficulties associated with mycobacterial cultivability, pathogenicity and growth. Another way to gain insight into mycobacteriophage host range and ecology is through bioinformatic analysis of their genomic sequences. To this end, we examined the correlations between the codon usage biases of 199 different mycobacteriophages and those of several fully sequenced mycobacterial species in order to gain insight into the natural host range of these mycobacteriophages. We find that UPGMA clustering tends to match, but not consistently, clustering by shared nucleotide sequence identify. In addition, analysis of GC content, tRNA usage and correlations between mycobacteriophage and mycobacterial codon usage bias suggests that the preferred host of many clustered mycobacteriophages is not M. smegmatis but other, as yet unknown, members of the mycobacteria complex or closely allied bacterial species.
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Affiliation(s)
| | - Swati Gupta
- Biology Department, Queens College, Queens, NY 11367, USA
| | | | - Ashley Prasad
- Biology Department, Queens College, Queens, NY 11367, USA
| | - John J. Dennehy
- Biology Department, Queens College, Queens, NY 11367, USA
- Biology PhD Program, The Graduate Center of the City University of New York, New York, NY 10016, USA
- Correspondence John J. Dennehy ()
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100
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Abstract
Inteins are self-splicing protein elements that are mobile at the DNA level and are sporadically distributed across microbial genomes. Inteins appear to be horizontally transferred, and it has been speculated that phages may play a role in intein distribution. Our attention turns to mycobacteriophages, which infect mycobacteria, where both phage and host harbor inteins. Using bioinformatics, mycobacteriophage genomes were mined for inteins. This study reveals that these mobile elements are present across multiple mycobacteriophage clusters and are pervasive in certain genes, like the large terminase subunit TerL and a RecB-like nuclease, with the majority of intein-containing genes being phage specific. Strikingly, despite this phage specificity, inteins localize to functional motifs shared with bacteria, such that intein-containing genes have similar roles, like hydrolase activity and nucleic acid binding, indicating a global commonality among intein-hosting proteins. Additionally, there are multiple insertion points within active centers, implying independent invasion events, with regulatory implications. Several phage inteins were shown to be splicing competent and to encode functional homing endonucleases, important for mobility. Further, bioinformatic analysis supports the potential for phages as facilitators of intein movement among mycobacteria and related genera. Analysis of catalytic intein residues finds the highly conserved penultimate histidine inconsistently maintained among mycobacteriophages. Biochemical characterization of a noncanonical phage intein shows that this residue influences precursor accumulation, suggesting that splicing has been tuned in phages to modulate generation of important proteins. Together, this work expands our understanding of phage-based intein dissemination and evolution and implies that phages provide a context for evolution of splicing-based regulation. Inteins are mobile protein splicing elements found in critical genes across all domains of life. Mycobacterial inteins are of particular interest because of their occurrence in pathogenic species, such as Mycobacterium tuberculosis and Mycobacterium leprae, which harbor inteins in important proteins. We have discovered a similarity in activities of intein-containing proteins among mycobacteriophages and their intein-rich actinobacterial hosts, with implications for both posttranslational regulation by inteins and phages participating in horizontal intein transfer. Our demonstration of multiple insertion points within active centers of phage proteins implies independent invasion events, indicating the importance of intein maintenance at specific functional sites. The variable conservation of a catalytic splicing residue, leading to profoundly altered splicing rates, points to the regulatory potential of inteins and to mycobacteriophages playing a role in intein evolution. Collectively, these results suggest inteins as posttranslational regulators and mycobacteriophages as both vehicles for intein distribution and incubators for intein evolution.
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