1
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Pollenz RS, Barnhill K, Biggs A, Bland J, Carter V, Chase M, Clark H, Coleman C, Daffner M, Deam C, Finocchiaro A, Franco V, Fuller T, Pinera JG, Horne M, Howard Z, Kanahan O, Miklaszewski C, Miller S, Morgan R, Onalaja O, Otero L, Padhye S, Rainey E, Rasul F, Robichaux K, Rodier A, Schlosser S, Sciacchitano A, Stewart E, Thakkar R, Heller DM. A genome-wide cytotoxicity screen of cluster F1 mycobacteriophage Girr reveals novel inhibitors of Mycobacterium smegmatis growth. G3 (Bethesda) 2024; 14:jkae049. [PMID: 38456318 DOI: 10.1093/g3journal/jkae049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/09/2024]
Abstract
Over the past decade, thousands of bacteriophage genomes have been sequenced and annotated. A striking observation from this work is that known structural features and functions cannot be assigned for >65% of the encoded proteins. One approach to begin experimentally elucidating the function of these uncharacterized gene products is genome-wide screening to identify phage genes that confer phenotypes of interest like inhibition of host growth. This study describes the results of a screen evaluating the effects of overexpressing each gene encoded by the temperate Cluster F1 mycobacteriophage Girr on the growth of the host bacterium Mycobacterium smegmatis. Overexpression of 29 of the 102 Girr genes (~28% of the genome) resulted in mild to severe cytotoxicity. Of the 29 toxic genes described, 12 have no known function and are predominately small proteins of <125 amino acids. Overexpression of the majority of these 12 cytotoxic no known functions proteins resulted in moderate to severe growth reduction and represent novel antimicrobial products. The remaining 17 toxic genes have predicted functions, encoding products involved in phage structure, DNA replication/modification, DNA binding/gene regulation, or other enzymatic activity. Comparison of this dataset with prior genome-wide cytotoxicity screens of mycobacteriophages Waterfoul and Hammy reveals some common functional themes, though several of the predicted Girr functions associated with cytotoxicity in our report, including genes involved in lysogeny, have not been described previously. This study, completed as part of the HHMI-supported SEA-GENES project, highlights the power of parallel, genome-wide overexpression screens to identify novel interactions between phages and their hosts.
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Affiliation(s)
- Richard S Pollenz
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Kaylee Barnhill
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Abbigail Biggs
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Jackson Bland
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Victoria Carter
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Michael Chase
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Hayley Clark
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Caitlyn Coleman
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Marshall Daffner
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Caitlyn Deam
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Alyssa Finocchiaro
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Vanessa Franco
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Thomas Fuller
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Juan Gallardo Pinera
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Mae Horne
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Zoe Howard
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Olivia Kanahan
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | | | - Sydney Miller
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Ryan Morgan
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Oluwatobi Onalaja
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Louis Otero
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Shivani Padhye
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Emily Rainey
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Fareed Rasul
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Kobe Robichaux
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Alexandra Rodier
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Sydni Schlosser
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Ava Sciacchitano
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Emma Stewart
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Rajvi Thakkar
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Danielle M Heller
- Center for the Advancement of Science Leadership and Culture, Howard Hughes Medical Institute, Chevy Chase, MD 20185, USA
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2
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Bartlett HP, Dawson CC, Glickman CM, Osborn DW, Evans CR, Garcia BJ, Frost LC, Cummings JE, Whittel N, Slayden RA, Holder JW. Targeting intracellular nontuberculous mycobacteria and M. tuberculosis with a bactericidal enzymatic cocktail. Microbiol Spectr 2024; 12:e0353423. [PMID: 38534149 DOI: 10.1128/spectrum.03534-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
To address intracellular mycobacterial infections, we developed a cocktail of four enzymes that catalytically attack three layers of the mycobacterial envelope. This cocktail is delivered to macrophages, through a targeted liposome presented here as ENTX_001. Endolytix Cocktail 1 (EC1) leverages mycobacteriophage lysin enzymes LysA and LysB, while also including α-amylase and isoamylase for degradation of the mycobacterial envelope from outside of the cell. The LysA family of proteins from mycobacteriophages has been shown to cleave the peptidoglycan layer, whereas LysB is an esterase that hydrolyzes the linkage between arabinogalactan and mycolic acids of the mycomembrane. The challenge of gaining access to the substrates of LysA and LysB provided exogenously was addressed by adding amylase enzymes that degrade the extracellular capsule shown to be present in Mycobacterium tuberculosis. This enzybiotic approach avoids antimicrobial resistance, specific receptor-mediated binding, and intracellular DNA surveillance pathways that limit many bacteriophage applications. We show this cocktail of enzymes is bactericidal in vitro against both rapid- and slow-growing nontuberculous mycobacteria (NTM) as well as M. tuberculosis strains. The EC1 cocktail shows superior killing activity when compared to previously characterized LysB alone. EC1 is also powerfully synergistic with standard-of-care antibiotics. In addition to in vitro killing of NTM, ENTX_001 demonstrates the rescue of infected macrophages from necrotic death by Mycobacteroides abscessus and Mycobacterium avium. Here, we demonstrate shredding of mycobacterial cells by EC1 into cellular debris as a mechanism of bactericide.IMPORTANCEThe world needs entirely new forms of antibiotics as resistance to chemical antibiotics is a critical problem facing society. We addressed this need by developing a targeted enzyme therapy for a broad range of species and strains within mycobacteria and highly related genera including nontuberculous mycobacteria such as Mycobacteroides abscessus, Mycobacterium avium, Mycobacterium intracellulare, as well as Mycobacterium tuberculosis. One advantage of this approach is the ability to drive our lytic enzymes through encapsulation into macrophage-targeted liposomes resulting in attack of mycobacteria in the cells that harbor them where they hide from the adaptive immune system and grow. Furthermore, this approach shreds mycobacteria independent of cell physiology as the drug targets the mycobacterial envelope while sidestepping the host range limitations observed with phage therapy and resistance to chemical antibiotics.
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Affiliation(s)
| | | | | | | | | | | | | | - Jason E Cummings
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Nicholas Whittel
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Richard A Slayden
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
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3
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Abad L, Gauthier CH, Florian I, Jacobs-Sera D, Hatfull GF. The heterogenous and diverse population of prophages in Mycobacterium genomes. mSystems 2023; 8:e0044623. [PMID: 37791767 PMCID: PMC10654092 DOI: 10.1128/msystems.00446-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/18/2023] [Indexed: 10/05/2023] Open
Abstract
IMPORTANCE Mycobacterium species include several human pathogens and mycobacteriophages show potential for therapeutic use to control Mycobacterium infections. However, phage infection profiles vary greatly among Mycobacterium abscessus clinical isolates and phage therapies must be personalized for individual patients. Mycobacterium phage susceptibility is likely determined primarily by accessory parts of bacterial genomes, and we have identified the prophage and phage-related genomic regions across sequenced Mycobacterium strains. The prophages are numerous and diverse, especially in M. abscessus genomes, and provide a potentially rich reservoir of new viruses that can be propagated lytically and used to expand the repertoire of therapeutically useful phages.
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Affiliation(s)
- Lawrence Abad
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Christian H. Gauthier
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Isabella Florian
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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4
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Wetzel KS, Illouz M, Abad L, Aull HG, Russell DA, Garlena RA, Cristinziano M, Malmsheimer S, Chalut C, Hatfull GF, Kremer L. Therapeutically useful mycobacteriophages BPs and Muddy require trehalose polyphleates. Nat Microbiol 2023; 8:1717-1731. [PMID: 37644325 PMCID: PMC10465359 DOI: 10.1038/s41564-023-01451-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/17/2023] [Indexed: 08/31/2023]
Abstract
Mycobacteriophages show promise as therapeutic agents for non-tuberculous mycobacterium infections. However, little is known about phage recognition of Mycobacterium cell surfaces or mechanisms of phage resistance. We show here that trehalose polyphleates (TPPs)-high-molecular-weight, surface-exposed glycolipids found in some mycobacterial species-are required for infection of Mycobacterium abscessus and Mycobacterium smegmatis by clinically useful phages BPs and Muddy. TPP loss leads to defects in adsorption and infection and confers resistance. Transposon mutagenesis shows that TPP disruption is the primary mechanism for phage resistance. Spontaneous phage resistance occurs through TPP loss by mutation, and some M. abscessus clinical isolates are naturally phage-insensitive due to TPP synthesis gene mutations. Both BPs and Muddy become TPP-independent through single amino acid substitutions in their tail spike proteins, and M. abscessus mutants resistant to TPP-independent phages reveal additional resistance mechanisms. Clinical use of BPs and Muddy TPP-independent mutants should preempt phage resistance caused by TPP loss.
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Affiliation(s)
- Katherine S Wetzel
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Morgane Illouz
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Lawrence Abad
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Haley G Aull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Rebecca A Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Madison Cristinziano
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Silke Malmsheimer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Christian Chalut
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France.
- INSERM, IRIM, Montpellier, France.
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5
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Freeman KG, Robotham AC, Parks OB, Abad L, Jacobs-Sera D, Lauer MJ, Podgorski JM, Zhang Y, Williams JV, White SJ, Kelly JF, Hatfull GF, Pope WH. Virion glycosylation influences mycobacteriophage immune recognition. Cell Host Microbe 2023; 31:1216-1231.e6. [PMID: 37329881 PMCID: PMC10527164 DOI: 10.1016/j.chom.2023.05.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/19/2023] [Accepted: 05/25/2023] [Indexed: 06/19/2023]
Abstract
Glycosylation of eukaryotic virus particles is common and influences their uptake, trafficking, and immune recognition. In contrast, glycosylation of bacteriophage particles has not been reported; phage virions typically do not enter the cytoplasm upon infection, and they do not generally inhabit eukaryotic systems. We show here that several genomically distinct phages of Mycobacteria are modified with glycans attached to the C terminus of capsid and tail tube protein subunits. These O-linked glycans influence antibody production and recognition, shielding viral particles from antibody binding and reducing production of neutralizing antibodies. Glycosylation is mediated by phage-encoded glycosyltransferases, and genomic analysis suggests that they are relatively common among mycobacteriophages. Putative glycosyltransferases are also encoded by some Gordonia and Streptomyces phages, but there is little evidence of glycosylation among the broader phage population. The immune response to glycosylated phage virions in mice suggests that glycosylation may be an advantageous property for phage therapy of Mycobacterium infections.
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Affiliation(s)
- Krista G Freeman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Anna C Robotham
- Human Health Therapeutics, National Research Council of Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada
| | - Olivia B Parks
- UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Pediatrics and Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Lawrence Abad
- 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
| | - Michael J Lauer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Jennifer M Podgorski
- Biology/Physics Building, Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125, USA
| | - Yu Zhang
- UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Pediatrics and Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - John V Williams
- UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Pediatrics and Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Simon J White
- Biology/Physics Building, Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125, USA
| | - John F Kelly
- Human Health Therapeutics, National Research Council of Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Welkin H Pope
- Science Department, Chatham University, Pittsburgh, PA 15232, USA
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6
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Wang CL, Zhang LY, Ding XY, Sun YC. Identification of Toxic Proteins Encoded by Mycobacteriophage TM4 Using a Next-Generation Sequencing-Based Method. Microbiol Spectr 2023; 11:e0501522. [PMID: 37154774 PMCID: PMC10269906 DOI: 10.1128/spectrum.05015-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/13/2023] [Indexed: 05/10/2023] Open
Abstract
Mycobacteriophages are viruses that specifically infect mycobacteria and which, due to their diversity, represent a large gene pool. Characterization of the function of these genes should provide useful insights into host-phage interactions. Here, we describe a next-generation sequencing (NGS)-based, high-throughput screening approach for the identification of mycobacteriophage-encoded proteins that are toxic to mycobacteria. A plasmid-derived library representing the mycobacteriophage TM4 genome was constructed and transformed into Mycobacterium smegmatis. NGS and growth assays showed that the expression of TM4 gp43, gp77, -78, and -79, or gp85 was toxic to M. smegmatis. Although the genes associated with bacterial toxicity were expressed during phage infection, they were not required for lytic replication of mycobacteriophage TM4. In conclusion, we describe here an NGS-based approach which required significantly less time and resources than traditional methods and allowed the identification of novel mycobacteriophage gene products that are toxic to mycobacteria. IMPORTANCE The wide spread of drug-resistant Mycobacterium tuberculosis has brought an urgent need for new drug development. Mycobacteriophages are natural killers of M. tuberculosis, and their toxic gene products might provide potential anti-M. tuberculosis candidates. However, the enormous genetic diversity of mycobacteriophages poses challenges for the identification of these genes. Here, we used a simple and convenient screening method, based on next-generation sequencing, to identify mycobacteriophage genes encoding toxic products for mycobacteria. Using this approach, we screened and validated several toxic products encoded by mycobacteriophage TM4. In addition, we also found that the genes encoding these toxic products are nonessential for lytic replication of TM4. Our work describes a promising method for the identification of phage genes that encode proteins that are toxic to mycobacteria and which might facilitate the identification of novel antimicrobial molecules.
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Affiliation(s)
- Chun-Liang Wang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lan-Yue Zhang
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Xin-Yuan Ding
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yi-Cheng Sun
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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7
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Lang J, Zhen J, Li G, Li B, Xie J. Characterization and genome analysis of G1 sub-cluster mycobacteriophage Lang. Infect Genet Evol 2023; 109:105417. [PMID: 36804468 DOI: 10.1016/j.meegid.2023.105417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/08/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023]
Abstract
Phage therapy is revitalized as an alternative to antibiotics therapy against antimicrobials resistant pathogens. Mycobacteriophages are genetically diverse viruses that can specifically infect Mycobacterium genus including Mycobacterium tuberculosis and Mycobacterium smegmatis. Here, we isolated and annotated the genome of a mycobacteriophage Lang, a temperate mycobacteriophage isolated from the soil of Hohhot, Inner Mongolia, China, by using Mycolicibacterium smegmatis mc2 155 as the host. It belongs to the Siphoviridae family of Caudovirales as determined by transmission electron microscopy. The morphological characteristics and certain biological properties of the phage were considered in detail. Phage Lang genomes is 41,487 bp in length with 66.85% GC content and encodes 60 putative open reading frames and belongs to the G1 sub-cluster. Genome annotation indicated that genes for structure proteins, assembly proteins, replications/transcription and lysis of the host are present in function clucters. The genome sequence of phage Lang is more than 95% similar to that of mycobacteriophage Grizzly and Sweets, differing in substitutions, insertions and deletions in Lang. One-step growth curve revealed that Lang has a latent period of 30 min and a outbreak period of 90 min. The short latent period and rapid outbreak mark the unique properties of phage Lang, which can be another potential source for combating M. tuberculosis.
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Affiliation(s)
- Junying Lang
- Tuberculosis Department of Hohhot Second Hospital, Inner Mongolia, 010020, China; Hohhot Tuberculosis Prevention and Control Institute, Inner Mongolia, 010020, China
| | - Junfeng Zhen
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Guimei Li
- Tuberculosis Department of Hohhot Second Hospital, Inner Mongolia, 010020, China
| | - Bin Li
- Intensive Care Medicine Department of Hohhot First Hospital, Inner Mongolia, 010020, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China.
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8
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Abstract
Although more than 12,000 bacteriophages infecting mycobacteria (mycobacteriophages) have been isolated so far, there is a knowledge gap on their structure-function relationships. Here, we have explored the architecture of host-binding machineries from seven representative mycobacteriophages of the Siphoviridae family infecting Mycobacterium smegmatis, Mycobacterium abscessus, and Mycobacterium tuberculosis, using AlphaFold2 (AF2). AF2 enables confident structural analyses of large and flexible biological assemblies resistant to experimental methods, thereby opening new avenues to shed light on phage structure and function. Our results highlight the modularity and structural diversity of siphophage host-binding machineries that recognize host-specific receptors at the onset of viral infection. Interestingly, the studied mycobacteriophages' host-binding machineries present unique features compared with those of phages infecting other Gram-positive actinobacteria. Although they all assemble the classical Dit (distal tail), Tal (tail-associated lysin), and receptor-binding proteins, five of them contain two potential additional adhesion proteins. Moreover, we have identified brush-like domains formed of multiple polyglycine helices which expose hydrophobic residues as potential receptor-binding domains. These polyglycine-rich domains, which have been observed in only five native proteins, may be a hallmark of mycobacteriophages' host-binding machineries, and they may be more common in nature than expected. Altogether, the unique composition of mycobacteriophages' host-binding machineries indicate they might have evolved to bind to the peculiar mycobacterial cell envelope, which is rich in polysaccharides and mycolic acids. This work provides a rational framework to efficiently produce recombinant proteins or protein domains and test their host-binding function and, hence, to shed light on molecular mechanisms used by mycobacteriophages to infect their host. IMPORTANCE Mycobacteria include both saprophytes, such as the model system Mycobacterium smegmatis, and pathogens, such as Mycobacterium tuberculosis and Mycobacterium abscessus, that are poorly responsive to antibiotic treatments and pose a global public health problem. Mycobacteriophages have been collected at a very large scale over the last decade, and they have proven to be valuable tools for mycobacteria genetic manipulation, rapid diagnostics, and infection treatment. Yet, molecular mechanisms used by mycobacteriophages to infect their host remain poorly understood. Therefore, exploring the structural diversity of mycobacteriophages' host-binding machineries is important not only to better understand viral diversity and bacteriophage-host interactions, but also to rationally develop biotechnological tools. With the powerful protein structure prediction software AlphaFold2, which was publicly released a year ago, it is now possible to gain structural and functional insights on such challenging assemblies.
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Affiliation(s)
- Christian Cambillau
- School of Microbiology, University College Cork, Cork, Ireland
- AlphaGraphix, Formiguères, France
| | - Adeline Goulet
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie, Bioénergies et Biotechnologie, CNRS and Aix-Marseille Université, Marseille, France
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9
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Howell AA, Versoza CJ, Cerna G, Johnston T, Kakde S, Karuku K, Kowal M, Monahan J, Murray J, Nguyen T, Sanchez Carreon A, Streiff A, Su B, Youkhana F, Munig S, Patel Z, So M, Sy M, Weiss S, Pfeifer SP. Phylogenomic analyses and host range prediction of cluster P mycobacteriophages. G3 (Bethesda) 2022; 12:jkac244. [PMID: 36094333 PMCID: PMC9635641 DOI: 10.1093/g3journal/jkac244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
Bacteriophages, infecting bacterial hosts in every environment on our planet, are a driver of adaptive evolution in bacterial communities. At the same time, the host range of many bacteriophages-and thus one of the selective pressures acting on complex microbial systems in nature-remains poorly characterized. Here, we computationally inferred the putative host ranges of 40 cluster P mycobacteriophages, including members from 6 subclusters (P1-P6). A series of comparative genomic analyses revealed that mycobacteriophages of subcluster P1 are restricted to the Mycobacterium genus, whereas mycobacteriophages of subclusters P2-P6 are likely also able to infect other genera, several of which are commonly associated with human disease. Further genomic analysis highlighted that the majority of cluster P mycobacteriophages harbor a conserved integration-dependent immunity system, hypothesized to be the ancestral state of a genetic switch that controls the shift between lytic and lysogenic life cycles-a temperate characteristic that impedes their usage in antibacterial applications.
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Affiliation(s)
| | | | - Gabriella Cerna
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Tyler Johnston
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Shriya Kakde
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Keith Karuku
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Maria Kowal
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Jasmine Monahan
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Jillian Murray
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Teresa Nguyen
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Aurely Sanchez Carreon
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Abigail Streiff
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Blake Su
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- School of Politics and Global Studies, Arizona State University, Tempe, AZ 85281, USA
| | - Faith Youkhana
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Saige Munig
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Zeel Patel
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Minerva So
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Makena Sy
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Sarah Weiss
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Susanne P Pfeifer
- Corresponding author: Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA.
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10
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Heller D, Amaya I, Mohamed A, Ali I, Mavrodi D, Deighan P, Sivanathan V. Systematic overexpression of genes encoded by mycobacteriophage Waterfoul reveals novel inhibitors of mycobacterial growth. G3 (Bethesda) 2022; 12:jkac140. [PMID: 35727726 PMCID: PMC9339283 DOI: 10.1093/g3journal/jkac140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/14/2022] [Indexed: 01/21/2023]
Abstract
Bacteriophages represent an enormous reservoir of novel genes, many of which are unrelated to existing entries in public databases and cannot be assigned a predicted function. Characterization of these genes can provide important insights into the intricacies of phage-host interactions and may offer new strategies to manipulate bacterial growth and behavior. Overexpression is a useful tool in the study of gene-mediated effects, and we describe here the construction of a plasmid-based overexpression library of a complete set of genes for Waterfoul, a mycobacteriophage closely related to those infecting clinically important strains of Mycobacterium tuberculosis and/or Mycobacterium abscessus. The arrayed Waterfoul gene library was systematically screened in a plate-based cytotoxicity assay, identifying a diverse set of 32 Waterfoul gene products capable of inhibiting the growth of the host Mycobacterium smegmatis and providing a first look at the frequency and distribution of cytotoxic products encoded within a single mycobacteriophage genome. Several of these Waterfoul gene products were observed to confer potent anti-mycobacterial effects, making them interesting candidates for follow-up mechanistic studies.
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Affiliation(s)
- Danielle Heller
- Department of Science Education, Howard Hughes Medical Institute, Chevy Chase, MD 20185, USA
| | - Isabel Amaya
- Department of Science Education, Howard Hughes Medical Institute, Chevy Chase, MD 20185, USA
| | - Aleem Mohamed
- Department of Biology, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Ilzat Ali
- Department of Biology, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Dmitri Mavrodi
- Center for Molecular & Cellular Biosciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Padraig Deighan
- Department of Biology, Emmanuel College, Boston, MA 02115, USA
| | - Viknesh Sivanathan
- Department of Science Education, Howard Hughes Medical Institute, Chevy Chase, MD 20185, USA
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11
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Calcuttawala F, Shaw R, Sarbajna A, Dutta M, Sinha S, K. Das Gupta S. Apoptosis like symptoms associated with abortive infection of Mycobacterium smegmatis by mycobacteriophage D29. PLoS One 2022; 17:e0259480. [PMID: 35580120 PMCID: PMC9113562 DOI: 10.1371/journal.pone.0259480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 04/29/2022] [Indexed: 01/12/2023] Open
Abstract
Mycobacteriophages are phages that infect mycobacteria resulting in their killing. Although lysis is the primary mechanism by which mycobacteriophages cause cell death, others such as abortive infection may also be involved. We took recourse to perform immunofluorescence and electron microscopic studies using mycobacteriophage D29 infected Mycobacterium smegmatis cells to investigate this issue. We could observe the intricate details of the infection process using these techniques such as adsorption, the phage tail penetrating the thick mycolic acid layer, formation of membrane pores, membrane blebbing, and phage release. We observed a significant increase in DNA fragmentation and membrane depolarization using cell-biological techniques symptomatic of programmed cell death (PCD). As Toxin-Antitoxin (TA) systems mediate bacterial PCD, we measured their expression profiles with and without phage infection. Of the three TAs examined, MazEF, VapBC, and phd/doc, we found that in the case of VapBC, a significant decrease in the antitoxin (VapB): toxin (VapC) ratio was observed following phage infection, implying that high VapC may have a role to play in the induction of mycobacterial apoptotic cell death following phage infection. This study indicates that D29 infection causes mycobacteria to undergo morphological and molecular changes that are hallmarks of apoptotic cell death.
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Affiliation(s)
- Fatema Calcuttawala
- Department of Microbiology, Sister Nivedita University, Kolkata, India
- * E-mail:
| | - Rahul Shaw
- Department of Microbiology, Bose Institute, Kolkata, India
| | - Arpita Sarbajna
- Division of Electron Microscopy, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Moumita Dutta
- Division of Electron Microscopy, National Institute of Cholera and Enteric Diseases, Kolkata, India
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12
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Gauthier CH, Abad L, Venbakkam AK, Malnak J, Russell D, Hatfull G. OUP accepted manuscript. Nucleic Acids Res 2022; 50:e75. [PMID: 35451479 PMCID: PMC9303363 DOI: 10.1093/nar/gkac273] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/11/2022] [Accepted: 04/06/2022] [Indexed: 11/26/2022] Open
Abstract
Advances in genome sequencing have produced hundreds of thousands of bacterial genome sequences, many of which have integrated prophages derived from temperate bacteriophages. These prophages play key roles by influencing bacterial metabolism, pathogenicity, antibiotic resistance, and defense against viral attack. However, they vary considerably even among related bacterial strains, and they are challenging to identify computationally and to extract precisely for comparative genomic analyses. Here, we describe DEPhT, a multimodal tool for prophage discovery and extraction. It has three run modes that facilitate rapid screening of large numbers of bacterial genomes, precise extraction of prophage sequences, and prophage annotation. DEPhT uses genomic architectural features that discriminate between phage and bacterial sequences for efficient prophage discovery, and targeted homology searches for precise prophage extraction. DEPhT is designed for prophage discovery in Mycobacterium genomes but can be adapted broadly to other bacteria. We deploy DEPhT to demonstrate that prophages are prevalent in Mycobacterium strains but are absent not only from the few well-characterized Mycobacterium tuberculosis strains, but also are absent from all ∼30 000 sequenced M. tuberculosis strains.
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Affiliation(s)
| | | | - Ananya K Venbakkam
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Julia Malnak
- 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
| | - Graham F Hatfull
- To whom correspondence should be addressed. Tel: +1 412 624 6975;
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13
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Crane A, Versoza CJ, Hua T, Kapoor R, Lloyd L, Mehta R, Menolascino J, Morais A, Munig S, Patel Z, Sackett D, Schmit B, Sy M, Pfeifer SP. Phylogenetic relationships and codon usage bias amongst cluster K mycobacteriophages. G3 (Bethesda) 2021; 11:6353607. [PMID: 34849792 PMCID: PMC8527509 DOI: 10.1093/g3journal/jkab291] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/09/2021] [Indexed: 01/21/2023]
Abstract
Bacteriophages infecting pathogenic hosts play an important role in medical research, not only as potential treatments for antibiotic-resistant infections but also offering novel insights into pathogen genetics and evolution. A prominent example is cluster K mycobacteriophages infecting Mycobacterium tuberculosis, a causative agent of tuberculosis in humans. However, as handling M. tuberculosis as well as other pathogens in a laboratory remains challenging, alternative nonpathogenic relatives, such as Mycobacterium smegmatis, are frequently used as surrogates to discover therapeutically relevant bacteriophages in a safer environment. Consequently, the individual host ranges of the majority of cluster K mycobacteriophages identified to date remain poorly understood. Here, we characterized the complete genome of Stinson, a temperate subcluster K1 mycobacteriophage with a siphoviral morphology. A series of comparative genomic analyses revealed strong similarities with other cluster K mycobacteriophages, including the conservation of an immunity repressor gene and a toxin/antitoxin gene pair. Patterns of codon usage bias across the cluster offered important insights into putative host ranges in nature, highlighting that although all cluster K mycobacteriophages are able to infect M. tuberculosis, they are less likely to have shared an evolutionary infection history with Mycobacterium leprae (underlying leprosy) compared to the rest of the genus’ host species. Moreover, subcluster K1 mycobacteriophages are able to integrate into the genomes of Mycobacterium abscessus and Mycobacterium marinum—two bacteria causing pulmonary and cutaneous infections which are often difficult to treat due to their drug resistance.
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Affiliation(s)
- Adele Crane
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA
| | - Cyril J Versoza
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA
| | - Tiana Hua
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Rohan Kapoor
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Lillian Lloyd
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Rithik Mehta
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | | | - Abraham Morais
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Saige Munig
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Zeel Patel
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Daniel Sackett
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Brandon Schmit
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Makena Sy
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Susanne P Pfeifer
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA
- Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
- Corresponding author: School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85281, USA.
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14
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Guerrero-Bustamante CA, Dedrick RM, Garlena RA, Russell DA, Hatfull GF. Toward a Phage Cocktail for Tuberculosis: Susceptibility and Tuberculocidal Action of Mycobacteriophages against Diverse Mycobacterium tuberculosis Strains. mBio 2021; 12:e00973-21. [PMID: 34016711 PMCID: PMC8263002 DOI: 10.1128/mbio.00973-21] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 04/07/2021] [Indexed: 12/24/2022] Open
Abstract
The global health burden of human tuberculosis (TB) and the widespread antibiotic resistance of its causative agent Mycobacterium tuberculosis warrant new strategies for TB control. The successful use of a bacteriophage cocktail to treat a Mycobacterium abscessus infection suggests that phages could play a role in tuberculosis therapy. To assemble a phage cocktail with optimal therapeutic potential for tuberculosis, we have explored mycobacteriophage diversity to identify phages that demonstrate tuberculocidal activity and determined the phage infection profiles for a diverse set of strains spanning the major lineages of human-adapted strains of the Mycobacterium tuberculosis complex. Using a combination of genome engineering and bacteriophage genetics, we have assembled a five-phage cocktail that minimizes the emergence of phage resistance and cross-resistance to multiple phages, and which efficiently kills the M. tuberculosis strains tested. Furthermore, these phages function without antagonizing antibiotic effectiveness, and infect both isoniazid-resistant and -sensitive strains.IMPORTANCE Tuberculosis kills 1.5 million people each year, and resistance to commonly used antibiotics contributes to treatment failures. The therapeutic potential of bacteriophages against Mycobacterium tuberculosis offers prospects for shortening antibiotic regimens, provides new tools for treating multiple drug-resistant (MDR)-TB and extensively drug-resistant (XDR)-TB infections, and protects newly developed antibiotics against rapidly emerging resistance to them. Identifying a suitable suite of phages active against diverse M. tuberculosis isolates circumvents many of the barriers to initiating clinical evaluation of phages as part of the arsenal of antituberculosis therapeutics.
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Affiliation(s)
| | - Rebekah M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Rebecca A Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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15
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Suarez CA, Franceschelli JJ, Tasselli SE, Morbidoni HR. Weirdo19ES is a novel singleton mycobacteriophage that selects for glycolipid deficient phage-resistant M. smegmatis mutants. PLoS One 2020; 15:e0231881. [PMID: 32357186 PMCID: PMC7194413 DOI: 10.1371/journal.pone.0231881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 04/02/2020] [Indexed: 11/23/2022] Open
Abstract
The sequencing and bioinformatics analysis of bacteriophages infecting mycobacteria has yielded a large amount of information on their evolution, including that on their environmental propagation on other genera such as Gordonia, closely related to Mycobacterium. However, little is known on mycobacteriophages cell biology such as the nature of their receptor(s) or their replication cycle. As part of our on-going screening for novel mycobacteriophages, we herein report the isolation and genome bioinformatics analysis of Weirdo19ES, a singleton Siphoviridae temperate mycobacteriophage with a 70.19% GC content. Nucleotide and protein sequence comparison to actinobacteriophage databases revealed that Weirdo19ES shows low homology to Gordonia phage Ruthy and mycobacteriophages falling in clusters Q and G and to singleton DS6A.Weirdo19ES also displays uncommon features such as a very short Lysin A gene (with only one enzymatic domain) and two putative HNH endonucleases. Mycobacterium smegmatis mutants resistant to Weirdo19ES are cross- resistant to I3. In agreement with that phenotype, analysis of cell envelope of those mutants showed that Weirdo19ES shares receptors with the transducing mycobacteriophage I3.This singleton mycobacteriophage adds up to the uncommonness of local mycobacteriophages previously isolated by our group and helps understanding the nature of mycobacteriophage receptors.
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Affiliation(s)
- Cristian Alejandro Suarez
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Jorgelina Judith Franceschelli
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Sabrina Emilse Tasselli
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Héctor Ricardo Morbidoni
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
- * E-mail:
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16
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Singh S, Godavarthi S, Kumar A, Sen R. A mycobacteriophage genomics approach to identify novel mycobacteriophage proteins with mycobactericidal properties. Microbiology (Reading) 2019; 165:722-736. [PMID: 31091188 DOI: 10.1099/mic.0.000810] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mycobacteriophages that are specific to mycobacteria are sources of various effector proteins that are capable of eliciting bactericidal responses. We describe a genomics approach in combination with bioinformatics to identify mycobacteriophage proteins that are toxic to mycobacteria upon expression. A genomic library comprising phage genome collections was screened for clones capable of killing Mycobacterium smegmatis strain mc2155. We identified four unique clones: clones 45 and 12N (from the mycobacteriophage D29) and clones 66 and 85 (from the mycobacteriophage Che12). The gene products from clones 66 and 45 were identified as Gp49 of the Che12 phage and Gp34 of the D29 phage, respectively. The gene products of the other two clones, 85 and 12N, utilized novel open reading frames (ORFs) coding for synthetic proteins. These four clones (clones 45, 66, 85 and 12N) caused growth defects in M. smegmatis and Mycobacterium bovis upon expression. Clones with Gp49 and Gp34 also induced growth defects in Escherichia coli, indicating that they target conserved host machineries. Their expression induced various morphological changes, indicating that they affected DNA replication and cell division steps. We predicted that Gp34 is a Xis protein that is required in phage DNA excision from the bacterial chromosome. Gp49 is predicted to have an HTH motif with DNA-bending/twisting properties. We suggest that this methodology is useful to identify new phage proteins with the desired properties without laboriously characterizing the individual phages. It is universal and could be applied to other bacteria-phage systems. We speculate that the existence of a virtually unlimited number of phages with unique gene products could offer a cheaper and less hazardous alternative to explore new antimicrobial molecules.
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Affiliation(s)
- Shweta Singh
- Laboratory of Transcription, Center for DNA Fingerprinting and Diagnostics, Inner Ring Road, Uppal, Hyderabad-39, India
| | - Sapna Godavarthi
- Laboratory of Transcription, Center for DNA Fingerprinting and Diagnostics, Inner Ring Road, Uppal, Hyderabad-39, India
| | - Amit Kumar
- Laboratory of Transcription, Center for DNA Fingerprinting and Diagnostics, Inner Ring Road, Uppal, Hyderabad-39, India
| | - Ranjan Sen
- Laboratory of Transcription, Center for DNA Fingerprinting and Diagnostics, Inner Ring Road, Uppal, Hyderabad-39, India
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17
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Vilchèze C, Jacobs WR. The Isoniazid Paradigm of Killing, Resistance, and Persistence in Mycobacterium tuberculosis. J Mol Biol 2019; 431:3450-3461. [PMID: 30797860 PMCID: PMC6703971 DOI: 10.1016/j.jmb.2019.02.016] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/05/2019] [Accepted: 02/11/2019] [Indexed: 12/20/2022]
Abstract
Isoniazid (INH) was the first synthesized drug that mediated bactericidal killing of the bacterium Mycobacterium tuberculosis, a major clinical breakthrough. To this day, INH remains a cornerstone of modern tuberculosis (TB) chemotherapy. This review describes the serendipitous discovery of INH, its effectiveness on TB patients, and early studies to discover its mechanisms of bacteriocidal activity. Forty years after its introduction as a TB drug, the development of gene transfer in mycobacteria enabled the discovery of the genes encoding INH resistance, namely, the activator (katG) and the target (inhA) of INH. Further biochemical and x-ray crystallography studies on KatG and InhA proteins and mutants provided comprehensive understanding of INH mode of action and resistance mechanisms. Bacterial cultures can harbor subpopulations that are genetically or phenotypically resistant cells, the latter known as persisters. Treatment of exponentially growing cultures of M. tuberculosis with INH reproducibly kills 99% to 99.9% of cells in 3 days. Importantly, the surviving cells are slowly replicating or non-replicating cells expressing a unique stress response signature: these are the persisters. These persisters can be visualized using dual-reporter mycobacteriophages and their formation prevented using reducing compounds, such as N-acetylcysteine or vitamin C, that enhance M. tuberculosis' respiration. Altogether, this review portrays a detailed molecular analysis of INH killing and resistance mechanisms including persistence. The phenomenon of persistence is clearly the single greatest impediment to TB control, and research aimed at understanding persistence will provide new strategies to improve TB chemotherapy.
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Affiliation(s)
- Catherine Vilchèze
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA
| | - William R Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA.
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18
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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19
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Gigante AM, Hampton CM, Dillard RS, Gil F, Catalão MJ, Moniz-Pereira J, Wright ER, Pimentel M. The Ms6 Mycolyl-Arabinogalactan Esterase LysB is Essential for an Efficient Mycobacteriophage-Induced Lysis. Viruses 2017; 9:v9110343. [PMID: 29149017 PMCID: PMC5707550 DOI: 10.3390/v9110343] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 11/10/2017] [Accepted: 11/14/2017] [Indexed: 01/21/2023] Open
Abstract
All dsDNA phages encode two proteins involved in host lysis, an endolysin and a holin that target the peptidoglycan and cytoplasmic membrane, respectively. Bacteriophages that infect Gram-negative bacteria encode additional proteins, the spanins, involved in disruption of the outer membrane. Recently, a gene located in the lytic cassette was identified in the genomes of mycobacteriophages, which encodes a protein (LysB) with mycolyl-arabinogalactan esterase activity. Taking in consideration the complex mycobacterial cell envelope that mycobacteriophages encounter during their life cycle, it is valuable to evaluate the role of these proteins in lysis. In the present work, we constructed an Ms6 mutant defective on lysB and showed that Ms6 LysB has an important role in lysis. In the absence of LysB, lysis still occurs but the newly synthesized phage particles are deficiently released to the environment. Using cryo-electron microscopy and tomography to register the changes in the lysis phenotype, we show that at 150 min post-adsorption, mycobacteria cells are incompletely lysed and phage particles are retained inside the cell, while cells infected with Ms6wt are completely lysed. Our results confirm that Ms6 LysB is necessary for an efficient lysis of Mycobacterium smegmatis, acting, similarly to spanins, in the third step of the lysis process.
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Affiliation(s)
- Adriano M Gigante
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisbon, 1649-003, Portugal.
| | - Cheri M Hampton
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, GA, 30345, USA.
| | - Rebecca S Dillard
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, GA, 30345, USA.
| | - Filipa Gil
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisbon, 1649-003, Portugal.
| | - Maria João Catalão
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisbon, 1649-003, Portugal.
| | - José Moniz-Pereira
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisbon, 1649-003, Portugal.
| | - Elizabeth R Wright
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, GA, 30345, USA.
| | - Madalena Pimentel
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisbon, 1649-003, Portugal.
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20
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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: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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22
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Halleran A, Clamons S, Saha M. Transcriptomic Characterization of an Infection of Mycobacterium smegmatis by the Cluster A4 Mycobacteriophage Kampy. PLoS One 2015; 10:e0141100. [PMID: 26513661 PMCID: PMC4626039 DOI: 10.1371/journal.pone.0141100] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/04/2015] [Indexed: 01/29/2023] Open
Abstract
The mycobacteriophages, phages that infect the genus Mycobacterium, display profound genetic diversity and widespread geographical distribution, and possess significant medical and ecological importance. However, most of the majority of functions of mycobacteriophage proteins and the identity of most genetic regulatory elements remain unknown. We characterized the gene expression profile of Kampy, a cluster A4 mycobacteriophage, during infection of its host, Mycobacterium smegmatis, using RNA-Seq and mass spectrometry. We show that mycobacteriophage Kampy transcription occurs in roughly two phases, an early phase consisting of genes for metabolism, DNA synthesis, and gene regulation, and a late phase consisting of structural genes and lysis genes. Additionally, we identify the earliest genes transcribed during infection, along with several other possible regulatory units not obvious from inspection of Kampy's genomic structure. The transcriptional profile of Kampy appears similar to that of mycobacteriophage TM4 but unlike that of mycobacteriophage Giles, a result which further expands our understanding of the diversity of mycobacteriophage gene expression programs during infection.
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Affiliation(s)
- Andrew Halleran
- Department of Biology, College of William and Mary, Williamsburg, Virginia, United States of America
| | - Samuel Clamons
- Department of Biology, College of William and Mary, Williamsburg, Virginia, United States of America
| | - Margaret Saha
- Department of Biology, College of William and Mary, Williamsburg, Virginia, United States of America
- * E-mail:
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23
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Abstract
Temperate bacteriophages express transcription repressors that maintain lysogeny by down-regulating lytic promoters and confer superinfection immunity. Repressor regulation is critical to the outcome of infection—lysogenic or lytic growth—as well as prophage induction into lytic replication. Mycobacteriophage BPs and its relatives use an unusual integration-dependent immunity system in which the phage attachment site (attP) is located within the repressor gene (33) such that site-specific integration leads to synthesis of a prophage-encoded product (gp33103) that is 33 residues shorter at its C-terminus than the virally-encoded protein (gp33136). However, the shorter form of the repressor (gp33103) is stable and active in repression of the early lytic promoter PR, whereas the longer virally-encoded form (gp33136) is inactive due to targeted degradation via a C-terminal ssrA-like tag. We show here that both forms of the repressor bind similarly to the 33–34 intergenic regulatory region, and that BPs gp33103 is a tetramer in solution. The BPs gp33103 repressor binds to five regulatory regions spanning the BPs genome, and regulates four promoters including the early lytic promoter, PR. BPs gp33103 has a complex pattern of DNA recognition in which a full operator binding site contains two half sites separated by a variable spacer, and BPs gp33103 induces a DNA bend at the full operator site but not a half site. The operator site structure is unusual in that one half site corresponds to a 12 bp palindrome identified previously, but the other half site is a highly variable variant of the palindrome.
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Affiliation(s)
- Valerie M. Villanueva
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, United States of America
| | - Lauren M. Oldfield
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, United States of America
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, United States of America
- * E-mail:
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24
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Bhowmik P, Das Gupta SK. Biochemical Characterization of a Mycobacteriophage Derived DnaB Ortholog Reveals New Insight into the Evolutionary Origin of DnaB Helicases. PLoS One 2015; 10:e0134762. [PMID: 26237048 PMCID: PMC4523182 DOI: 10.1371/journal.pone.0134762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/13/2015] [Indexed: 11/23/2022] Open
Abstract
The bacterial replicative helicases known as DnaB are considered to be members of the RecA superfamily. All members of this superfamily, including DnaB, have a conserved C- terminal domain, known as the RecA core. We unearthed a series of mycobacteriophage encoded proteins in which the RecA core domain alone was present. These proteins were phylogenetically related to each other and formed a distinct clade within the RecA superfamily. A mycobacteriophage encoded protein, Wildcat Gp80 that roots deep in the DnaB family, was found to possess a core domain having significant sequence homology (Expect value < 10-5) with members of this novel cluster. This indicated that Wildcat Gp80, and by extrapolation, other members of the DnaB helicase family, may have evolved from a single domain RecA core polypeptide belonging to this novel group. Biochemical investigations confirmed that Wildcat Gp80 was a helicase. Surprisingly, our investigations also revealed that a thioredoxin tagged truncated version of the protein in which the N-terminal sequences were removed was fully capable of supporting helicase activity, although its ATP dependence properties were different. DnaB helicase activity is thus, primarily a function of the RecA core although additional N-terminal sequences may be necessary for fine tuning its activity and stability. Based on sequence comparison and biochemical studies we propose that DnaB helicases may have evolved from single domain RecA core proteins having helicase activities of their own, through the incorporation of additional N-terminal sequences.
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Affiliation(s)
- Priyanka Bhowmik
- Department of Microbiology, Bose Institute, P1/12 C.I.T. Scheme VIIM, Kolkata 700054, West Bengal, India
| | - Sujoy K. Das Gupta
- Department of Microbiology, Bose Institute, P1/12 C.I.T. Scheme VIIM, Kolkata 700054, West Bengal, India
- * E-mail:
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25
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Swift BMC, Gerrard ZE, Huxley JN, Rees CED. Factors affecting phage D29 infection: a tool to investigate different growth states of mycobacteria. PLoS One 2014; 9:e106690. [PMID: 25184428 PMCID: PMC4153674 DOI: 10.1371/journal.pone.0106690] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 07/31/2014] [Indexed: 01/15/2023] Open
Abstract
Bacteriophages D29 and TM4 are able to infect a wide range of mycobacteria, including pathogenic and non-pathogenic species. Successful phage infection of both fast- and slow-growing mycobacteria can be rapidly detected using the phage amplification assay. Using this method, the effect of oxygen limitation during culture of mycobacteria on the success of phage infection was studied. Both D29 and TM4 were able to infect cultures of M. smegmatis and Mycobacterium avium subspecies paratuberculosis (MAP) grown in liquid with aeration. However when cultures were grown under oxygen limiting conditions, only TM4 could productively infect the cells. Cell attachment assays showed that D29 could bind to the cells surface but did not complete the lytic cycle. The ability of D29 to productively infect the cells was rapidly recovered (within 1 day) when the cultures were returned to an aerobic environment and this recovery required de novo RNA synthesis. These results indicated that under oxygen limiting conditions the cells are entering a growth state which inhibits phage D29 replication, and this change in host cell biology which can be detected by using both phage D29 and TM4 in the phage amplification assay.
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Affiliation(s)
- Benjamin M. C. Swift
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
- * E-mail:
| | - Zara E. Gerrard
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Jonathan N. Huxley
- School of Veterinary and Medicine Science, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Catherine E. D. Rees
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
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26
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Pope WH, Jacobs-Sera D, Best AA, Broussard GW, Connerly PL, Dedrick RM, Kremer TA, Offner S, Ogiefo AH, Pizzorno MC, Rockenbach K, Russell DA, Stowe EL, Stukey J, Thibault SA, Conway JF, Hendrix RW, Hatfull GF. Cluster J mycobacteriophages: intron splicing in capsid and tail genes. PLoS One 2013; 8:e69273. [PMID: 23874930 PMCID: PMC3706429 DOI: 10.1371/journal.pone.0069273] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 06/06/2013] [Indexed: 11/18/2022] Open
Abstract
Bacteriophages isolated on Mycobacterium smegmatis mc2155 represent many distinct genomes sharing little or no DNA sequence similarity. The genomes are architecturally mosaic and are replete with genes of unknown function. A new group of genomes sharing substantial nucleotide sequences constitute Cluster J. The six mycobacteriophages forming Cluster J are morphologically members of the Siphoviridae, but have unusually long genomes ranging from 106.3 to 117 kbp. Reconstruction of the capsid by cryo-electron microscopy of mycobacteriophage BAKA reveals an icosahedral structure with a triangulation number of 13. All six phages are temperate and homoimmune, and prophage establishment involves integration into a tRNA-Leu gene not previously identified as a mycobacterial attB site for phage integration. The Cluster J genomes provide two examples of intron splicing within the virion structural genes, one in a major capsid subunit gene, and one in a tail gene. These genomes also contain numerous free-standing HNH homing endonuclease, and comparative analysis reveals how these could contribute to genome mosaicism. The unusual Cluster J genomes provide new insights into phage genome architecture, gene function, capsid structure, gene mobility, intron splicing, and evolution.
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Affiliation(s)
- Welkin H. Pope
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Aaron A. Best
- Department of Biology, Hope College, Holland, Michigan, United States of America
| | - Gregory W. Broussard
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Pamela L. Connerly
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, United States of America
| | - Rebekah M. Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Timothy A. Kremer
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, United States of America
| | - Susan Offner
- Lexington High School, Lexington, Massachusetts, United States of America
| | - Amenawon H. Ogiefo
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Marie C. Pizzorno
- Department of Biology, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Kate Rockenbach
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Daniel A. Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Emily L. Stowe
- Department of Biology, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Joseph Stukey
- Department of Biology, Hope College, Holland, Michigan, United States of America
| | - Sarah A. Thibault
- Department of Biology, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - James F. Conway
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Roger W. Hendrix
- 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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27
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Stella EJ, Franceschelli JJ, Tasselli SE, Morbidoni HR. Analysis of novel mycobacteriophages indicates the existence of different strategies for phage inheritance in mycobacteria. PLoS One 2013; 8:e56384. [PMID: 23468864 PMCID: PMC3585329 DOI: 10.1371/journal.pone.0056384] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 01/08/2013] [Indexed: 11/19/2022] Open
Abstract
Mycobacteriophages have been essential in the development of mycobacterial genetics through their use in the construction of tools for genetic manipulation. Due to the simplicity of their isolation and variety of exploitable molecular features, we searched for and isolated 18 novel mycobacteriophages from environmental samples collected from several geographic locations. Characterization of these phages did not differ from most of the previously described ones in the predominant physical features (virion size in the 100–400 nm, genome size in the 50–70 kbp, morphological features compatible with those corresponding to the Siphoviridae family), however novel characteristics for propagation were noticed. Although all the mycobacteriophages propagated at 30°C, eight of them failed to propagate at 37°C. Since some of our phages yielded pinpoint plaques, we improved plaque detection by including sub-inhibitory concentrations of isoniazid or ampicillin-sulbactam in the culture medium. Thus, searches for novel mycobacteriophages at low temperature and in the presence of these drugs would allow for the isolation of novel members that would otherwise not be detected. Importantly, while eight phages lysogenized Mycobacterium smegmatis, four of them were also capable of lysogenizing Mycobacterium tuberculosis. Analysis of the complete genome sequence obtained for twelve mycobacteriophages (the remaining six rendered partial genomic sequences) allowed for the identification of a new singleton. Surprisingly, sequence analysis revealed the presence of parA or parA/parB genes in 7/18 phages including four that behaved as temperate in M. tuberculosis. In summary, we report here the isolation and preliminary characterization of mycobacteriophages that bring new information to the field.
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Affiliation(s)
- Emma J. Stella
- Cátedra de Microbiología, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Jorgelina J. Franceschelli
- Cátedra de Microbiología, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Sabrina E. Tasselli
- Cátedra de Microbiología, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Héctor R. Morbidoni
- Cátedra de Microbiología, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
- * E-mail:
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28
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Pope WH, Ferreira CM, Jacobs-Sera D, Benjamin RC, Davis AJ, DeJong RJ, Elgin SCR, Guilfoile FR, Forsyth MH, Harris AD, Harvey SE, Hughes LE, Hynes PM, Jackson AS, Jalal MD, MacMurray EA, Manley CM, McDonough MJ, Mosier JL, Osterbann LJ, Rabinowitz HS, Rhyan CN, Russell DA, Saha MS, Shaffer CD, Simon SE, Sims EF, Tovar IG, Weisser EG, Wertz JT, Weston-Hafer KA, Williamson KE, Zhang B, Cresawn SG, Jain P, Piuri M, Jacobs WR, Hendrix RW, Hatfull GF. Cluster K mycobacteriophages: insights into the evolutionary origins of mycobacteriophage TM4. PLoS One 2011; 6:e26750. [PMID: 22053209 PMCID: PMC3203893 DOI: 10.1371/journal.pone.0026750] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 10/03/2011] [Indexed: 01/21/2023] Open
Abstract
Five newly isolated mycobacteriophages –Angelica, CrimD, Adephagia, Anaya, and Pixie – have similar genomic architectures to mycobacteriophage TM4, a previously characterized phage that is widely used in mycobacterial genetics. The nucleotide sequence similarities warrant grouping these into Cluster K, with subdivision into three subclusters: K1, K2, and K3. Although the overall genome architectures of these phages are similar, TM4 appears to have lost at least two segments of its genome, a central region containing the integration apparatus, and a segment at the right end. This suggests that TM4 is a recent derivative of a temperate parent, resolving a long-standing conundrum about its biology, in that it was reportedly recovered from a lysogenic strain of Mycobacterium avium, but it is not capable of forming lysogens in any mycobacterial host. Like TM4, all of the Cluster K phages infect both fast- and slow-growing mycobacteria, and all of them – with the exception of TM4 – form stable lysogens in both Mycobacterium smegmatis and Mycobacterium tuberculosis; immunity assays show that all five of these phages share the same immune specificity. TM4 infects these lysogens suggesting that it was either derived from a heteroimmune temperate parent or that it has acquired a virulent phenotype. We have also characterized a widely-used conditionally replicating derivative of TM4 and identified mutations conferring the temperature-sensitive phenotype. All of the Cluster K phages contain a series of well conserved 13 bp repeats associated with the translation initiation sites of a subset of the genes; approximately one half of these contain an additional sequence feature composed of imperfectly conserved 17 bp inverted repeats separated by a variable spacer. The K1 phages integrate into the host tmRNA and the Cluster K phages represent potential new tools for the genetics of M. tuberculosis and related species.
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Affiliation(s)
- Welkin H. Pope
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Christina M. Ferreira
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Deborah Jacobs-Sera
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Robert C. Benjamin
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Ariangela J. Davis
- Department of Biology, Calvin College, Grand Rapids , Michigan, United States of America
| | - Randall J. DeJong
- Department of Biology, Calvin College, Grand Rapids , Michigan, United States of America
| | - Sarah C. R. Elgin
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Forrest R. Guilfoile
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Mark H. Forsyth
- Department of Biology, College of William and Mary, Williamsburg, Virginia, United States of America
| | - Alexander D. Harris
- Department of Biology, Calvin College, Grand Rapids , Michigan, United States of America
| | - Samuel E. Harvey
- Department of Biology, College of William and Mary, Williamsburg, Virginia, United States of America
| | - Lee E. Hughes
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Peter M. Hynes
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Arrykka S. Jackson
- Department of Biology, College of William and Mary, Williamsburg, Virginia, United States of America
| | - Marilyn D. Jalal
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Elizabeth A. MacMurray
- Department of Biology, College of William and Mary, Williamsburg, Virginia, United States of America
| | - Coreen M. Manley
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Molly J. McDonough
- Department of Biology, College of William and Mary, Williamsburg, Virginia, United States of America
| | - Jordan L. Mosier
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Larissa J. Osterbann
- Department of Biology, Calvin College, Grand Rapids , Michigan, United States of America
| | - Hannah S. Rabinowitz
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Corwin N. Rhyan
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Daniel A. Russell
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Margaret S. Saha
- Department of Biology, College of William and Mary, Williamsburg, Virginia, United States of America
| | - Christopher D. Shaffer
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Stephanie E. Simon
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Erika F. Sims
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Isabel G. Tovar
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Emilie G. Weisser
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - John T. Wertz
- Department of Biology, Calvin College, Grand Rapids , Michigan, United States of America
| | | | - Kurt E. Williamson
- Department of Biology, College of William and Mary, Williamsburg, Virginia, United States of America
| | - Bo Zhang
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Steven G. Cresawn
- Department of Biology, James Madison University, Harrisonburg , Virginia, United States of America
| | - Paras Jain
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Mariana Piuri
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - William R. Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Roger W. Hendrix
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Graham F. Hatfull
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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29
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Catalão MJ, Milho C, Gil F, Moniz-Pereira J, Pimentel M. A second endolysin gene is fully embedded in-frame with the lysA gene of mycobacteriophage Ms6. PLoS One 2011; 6:e20515. [PMID: 21694774 PMCID: PMC3111421 DOI: 10.1371/journal.pone.0020515] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 05/02/2011] [Indexed: 11/24/2022] Open
Abstract
Mycobacteriophages are dsDNA viruses that infect mycobacterial hosts. The mycobacteriophage Ms6 accomplishes lysis by producing two cell wall hydrolytic enzymes, Lysin A (LysA) that possesses a central peptidoglycan recognition protein (PGRP) super-family conserved domain with the amidase catalytic site, that cleaves the amide bond between the N-acetylmuramic acid and L-alanine residues in the oligopeptide crosslinking chains of the peptidoglycan and Lysin B (LysB) a mycolylarabinogalactan esterase that hydrolyzes the mycolic acids from the mycolyl-arabinogalactan-peptidoglycan complex. Examination of the endolysin (lysA) DNA sequence revealed the existence of an embedded gene (lysA241) encoded in the same reading frame and preceded by a consensus ribosome-binding site. In the present work we show that, even though lysA is essential for Ms6 viability, phage mutants that express only the longer (Lysin384) or the shorter (Lysin241) endolysin are viable, but defective in the normal timing, progression and completion of host cell lysis. In addition, both endolysins have peptidoglycan hydrolase activity and demonstrated broad growth inhibition activity against various Gram-positive bacteria and mycobacteria.
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Affiliation(s)
- Maria João Catalão
- Centro de Patogénese Molecular, Unidade dos Retrovírus e Infecções Associadas, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Catarina Milho
- Centro de Patogénese Molecular, Unidade dos Retrovírus e Infecções Associadas, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Filipa Gil
- Centro de Patogénese Molecular, Unidade dos Retrovírus e Infecções Associadas, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - José Moniz-Pereira
- Centro de Patogénese Molecular, Unidade dos Retrovírus e Infecções Associadas, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Madalena Pimentel
- Centro de Patogénese Molecular, Unidade dos Retrovírus e Infecções Associadas, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
- * E-mail:
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Pope WH, Jacobs-Sera D, Russell DA, Peebles CL, Al-Atrache Z, Alcoser TA, Alexander LM, Alfano MB, Alford ST, Amy NE, Anderson MD, Anderson AG, Ang AAS, Ares M, Barber AJ, Barker LP, Barrett JM, Barshop WD, Bauerle CM, Bayles IM, Belfield KL, Best AA, Borjon A, Bowman CA, Boyer CA, Bradley KW, Bradley VA, Broadway LN, Budwal K, Busby KN, Campbell IW, Campbell AM, Carey A, Caruso SM, Chew RD, Cockburn CL, Cohen LB, Corajod JM, Cresawn SG, Davis KR, Deng L, Denver DR, Dixon BR, Ekram S, Elgin SCR, Engelsen AE, English BEV, Erb ML, Estrada C, Filliger LZ, Findley AM, Forbes L, Forsyth MH, Fox TM, Fritz MJ, Garcia R, George ZD, Georges AE, Gissendanner CR, Goff S, Goldstein R, Gordon KC, Green RD, Guerra SL, Guiney-Olsen KR, Guiza BG, Haghighat L, Hagopian GV, Harmon CJ, Harmson JS, Hartzog GA, Harvey SE, He S, He KJ, Healy KE, Higinbotham ER, Hildebrandt EN, Ho JH, Hogan GM, Hohenstein VG, Holz NA, Huang VJ, Hufford EL, Hynes PM, Jackson AS, Jansen EC, Jarvik J, Jasinto PG, Jordan TC, Kasza T, Katelyn MA, Kelsey JS, Kerrigan LA, Khaw D, Kim J, Knutter JZ, Ko CC, Larkin GV, Laroche JR, Latif A, Leuba KD, Leuba SI, Lewis LO, Loesser-Casey KE, Long CA, Lopez AJ, Lowery N, Lu TQ, Mac V, Masters IR, McCloud JJ, McDonough MJ, Medenbach AJ, Menon A, Miller R, Morgan BK, Ng PC, Nguyen E, Nguyen KT, Nguyen ET, Nicholson KM, Parnell LA, Peirce CE, Perz AM, Peterson LJ, Pferdehirt RE, Philip SV, Pogliano K, Pogliano J, Polley T, Puopolo EJ, Rabinowitz HS, Resiss MJ, Rhyan CN, Robinson YM, Rodriguez LL, Rose AC, Rubin JD, Ruby JA, Saha MS, Sandoz JW, Savitskaya J, Schipper DJ, Schnitzler CE, Schott AR, Segal JB, Shaffer CD, Sheldon KE, Shepard EM, Shepardson JW, Shroff MK, Simmons JM, Simms EF, Simpson BM, Sinclair KM, Sjoholm RL, Slette IJ, Spaulding BC, Straub CL, Stukey J, Sughrue T, Tang TY, Tatyana LM, Taylor SB, Taylor BJ, Temple LM, Thompson JV, Tokarz MP, Trapani SE, Troum AP, Tsay J, Tubbs AT, Walton JM, Wang DH, Wang H, Warner JR, Weisser EG, Wendler SC, Weston-Hafer KA, Whelan HM, Williamson KE, Willis AN, Wirtshafter HS, Wong TW, Wu P, Yang YJ, Yee BC, Zaidins DA, Zhang B, Zúniga MY, Hendrix RW, Hatfull GF. Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution. PLoS One 2011; 6:e16329. [PMID: 21298013 PMCID: PMC3029335 DOI: 10.1371/journal.pone.0016329] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 12/09/2010] [Indexed: 11/25/2022] Open
Abstract
Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists.
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Affiliation(s)
- Welkin H. Pope
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Daniel A. Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Craig L. Peebles
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Zein Al-Atrache
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Turi A. Alcoser
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Lisa M. Alexander
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Matthew B. Alfano
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Samantha T. Alford
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Nichols E. Amy
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Marie D. Anderson
- Department of Biology, Spelman College, Atlanta, Georgia, United States of America
| | - Alexander G. Anderson
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Andrew A. S. Ang
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Manuel Ares
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Amanda J. Barber
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Lucia P. Barker
- Howard Hughes Medical Institute, Science Education Alliance, Chevy Chase, Maryland United States of America
| | - Jonathan M. Barrett
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - William D. Barshop
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Cynthia M. Bauerle
- Department of Biology, Spelman College, Atlanta, Georgia, United States of America
| | - Ian M. Bayles
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Katherine L. Belfield
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Aaron A. Best
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Agustin Borjon
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Charles A. Bowman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Christine A. Boyer
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Kevin W. Bradley
- Howard Hughes Medical Institute, Science Education Alliance, Chevy Chase, Maryland United States of America
| | - Victoria A. Bradley
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Lauren N. Broadway
- Department of Biology, University of Louisiana at Monroe, Monroe, Louisiana, United States of America
| | - Keshav Budwal
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Kayla N. Busby
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Ian W. Campbell
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Anne M. Campbell
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Alyssa Carey
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Steven M. Caruso
- Department of Biological Sciences, University of Maryland, Baltimore, Maryland, United States of America
| | - Rebekah D. Chew
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Chelsea L. Cockburn
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Lianne B. Cohen
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Jeffrey M. Corajod
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Steven G. Cresawn
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Kimberly R. Davis
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Lisa Deng
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Dee R. Denver
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Breyon R. Dixon
- Department of Biology, Spelman College, Atlanta, Georgia, United States of America
| | - Sahrish Ekram
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Sarah C. R. Elgin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Angela E. Engelsen
- Department of Biology, University of Louisiana at Monroe, Monroe, Louisiana, United States of America
| | - Belle E. V. English
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Marcella L. Erb
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Crystal Estrada
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Laura Z. Filliger
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Ann M. Findley
- Department of Biology, University of Louisiana at Monroe, Monroe, Louisiana, United States of America
| | - Lauren Forbes
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Mark H. Forsyth
- Biology Department, College of William & Mary, Williamsburg, Virginia, United States of America
| | - Tyler M. Fox
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Melissa J. Fritz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Roberto Garcia
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Zindzi D. George
- Department of Biology, Spelman College, Atlanta, Georgia, United States of America
| | - Anne E. Georges
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | | | - Shannon Goff
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Rebecca Goldstein
- Department of Biological Sciences, University of Maryland, Baltimore, Maryland, United States of America
| | - Kobie C. Gordon
- Biology Department, College of William & Mary, Williamsburg, Virginia, United States of America
| | - Russell D. Green
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Stephanie L. Guerra
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Krysta R. Guiney-Olsen
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Bridget G. Guiza
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Leila Haghighat
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Garrett V. Hagopian
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Catherine J. Harmon
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Jeremy S. Harmson
- Department of Biology, University of Louisiana at Monroe, Monroe, Louisiana, United States of America
| | - Grant A. Hartzog
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Samuel E. Harvey
- Biology Department, College of William & Mary, Williamsburg, Virginia, United States of America
| | - Siping He
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Kevin J. He
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Kaitlin E. Healy
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Ellen R. Higinbotham
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Erin N. Hildebrandt
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Jason H. Ho
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Gina M. Hogan
- Department of Biology, University of Louisiana at Monroe, Monroe, Louisiana, United States of America
| | - Victoria G. Hohenstein
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Nathan A. Holz
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Vincent J. Huang
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Ericka L. Hufford
- Department of Biology, University of Louisiana at Monroe, Monroe, Louisiana, United States of America
| | - Peter M. Hynes
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Arrykka S. Jackson
- Biology Department, College of William & Mary, Williamsburg, Virginia, United States of America
| | - Erica C. Jansen
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Jonathan Jarvik
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Paul G. Jasinto
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Tuajuanda C. Jordan
- Howard Hughes Medical Institute, Science Education Alliance, Chevy Chase, Maryland United States of America
| | - Tomas Kasza
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Murray A. Katelyn
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Jessica S. Kelsey
- Department of Biological Sciences, University of Maryland, Baltimore, Maryland, United States of America
| | - Larisa A. Kerrigan
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Daryl Khaw
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Junghee Kim
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Justin Z. Knutter
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Ching-Chung Ko
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Gail V. Larkin
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Jennifer R. Laroche
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Asma Latif
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Kohana D. Leuba
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Sequoia I. Leuba
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Lynn O. Lewis
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Kathryn E. Loesser-Casey
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Courtney A. Long
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - A. Javier Lopez
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Nicholas Lowery
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Tina Q. Lu
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Victor Mac
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Isaac R. Masters
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Jazmyn J. McCloud
- Department of Biology, Spelman College, Atlanta, Georgia, United States of America
| | - Molly J. McDonough
- Biology Department, College of William & Mary, Williamsburg, Virginia, United States of America
| | - Andrew J. Medenbach
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Anjali Menon
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Rachel Miller
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Brandon K. Morgan
- Department of Biology, University of Louisiana at Monroe, Monroe, Louisiana, United States of America
| | - Patrick C. Ng
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Elvis Nguyen
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Katrina T. Nguyen
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Emilie T. Nguyen
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Kaylee M. Nicholson
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Lindsay A. Parnell
- Department of Biology, Spelman College, Atlanta, Georgia, United States of America
| | - Caitlin E. Peirce
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Allison M. Perz
- Biology Department, College of William & Mary, Williamsburg, Virginia, United States of America
| | - Luke J. Peterson
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Rachel E. Pferdehirt
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Seegren V. Philip
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Kit Pogliano
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Joe Pogliano
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Tamsen Polley
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Erica J. Puopolo
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Hannah S. Rabinowitz
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Michael J. Resiss
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Corwin N. Rhyan
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Yetta M. Robinson
- Department of Biology, Spelman College, Atlanta, Georgia, United States of America
| | - Lauren L. Rodriguez
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Andrew C. Rose
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Jeffrey D. Rubin
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jessica A. Ruby
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Margaret S. Saha
- Biology Department, College of William & Mary, Williamsburg, Virginia, United States of America
| | - James W. Sandoz
- Department of Biological Sciences, University of Maryland, Baltimore, Maryland, United States of America
| | - Judith Savitskaya
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Dale J. Schipper
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | | | - Amanda R. Schott
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - J. Bradley Segal
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Christopher D. Shaffer
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Kathryn E. Sheldon
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Erica M. Shepard
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jonathan W. Shepardson
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Madav K. Shroff
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Jessica M. Simmons
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Erika F. Simms
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Brandy M. Simpson
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Kathryn M. Sinclair
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Robert L. Sjoholm
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Ingrid J. Slette
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Blaire C. Spaulding
- Department of Biology, Spelman College, Atlanta, Georgia, United States of America
| | - Clark L. Straub
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Joseph Stukey
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Trevor Sughrue
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Tin-Yun Tang
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Lyons M. Tatyana
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Stephen B. Taylor
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Barbara J. Taylor
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Louise M. Temple
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Jasper V. Thompson
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Michael P. Tokarz
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Stephanie E. Trapani
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Alexander P. Troum
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Jonathan Tsay
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Anthony T. Tubbs
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Jillian M. Walton
- Biology Department, College of William & Mary, Williamsburg, Virginia, United States of America
| | - Danielle H. Wang
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Hannah Wang
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - John R. Warner
- Department of Biology, University of Louisiana at Monroe, Monroe, Louisiana, United States of America
| | - Emilie G. Weisser
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Samantha C. Wendler
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Kathleen A. Weston-Hafer
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Hilary M. Whelan
- Biology Department, College of William & Mary, Williamsburg, Virginia, United States of America
| | - Kurt E. Williamson
- Biology Department, College of William & Mary, Williamsburg, Virginia, United States of America
| | - Angelica N. Willis
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Hannah S. Wirtshafter
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Theresa W. Wong
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Phillip Wu
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Yun jeong Yang
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Brandon C. Yee
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - David A. Zaidins
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Bo Zhang
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Melina Y. Zúniga
- Department of Biology, Spelman College, Atlanta, Georgia, United States of America
| | - Roger W. Hendrix
- 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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Sampson T, Broussard GW, Marinelli LJ, Jacobs-Sera D, Ray M, Ko CC, Russell D, Hendrix RW, Hatfull GF. Mycobacteriophages BPs, Angel and Halo: comparative genomics reveals a novel class of ultra-small mobile genetic elements. Microbiology (Reading) 2009; 155:2962-2977. [PMID: 19556295 DOI: 10.1099/mic.0.030486-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mycobacteriophages BPs, Angel and Halo are closely related viruses isolated from Mycobacterium smegmatis, and possess the smallest known mycobacteriophage genomes, 41,901 bp, 42,289 bp and 41,441 bp, respectively. Comparative genome analysis reveals a novel class of ultra-small mobile genetic elements; BPs and Halo each contain an insertion of the proposed mobile elements MPME1 and MPME2, respectively, at different locations, while Angel contains neither. The close similarity of the genomes provides a comparison of the pre- and post-integration sequences, revealing an unusual 6 bp insertion at one end of the element and no target duplication. Nine additional copies of these mobile elements are identified in a variety of different contexts in other mycobacteriophage genomes. In addition, BPs, Angel and Halo have an unusual lysogeny module in which the repressor and integrase genes are closely linked. The attP site is located within the repressor-coding region, such that prophage formation results in expression of a C-terminally truncated, but active, form of the repressor.
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Affiliation(s)
- Timothy Sampson
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Gregory W Broussard
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Laura J Marinelli
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Deborah Jacobs-Sera
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Mondira Ray
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Ching-Chung Ko
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Daniel Russell
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Roger W Hendrix
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Graham F Hatfull
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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32
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Piuri M, Jacobs WR, Hatfull GF. Fluoromycobacteriophages for rapid, specific, and sensitive antibiotic susceptibility testing of Mycobacterium tuberculosis. PLoS One 2009; 4:e4870. [PMID: 19300517 PMCID: PMC2654538 DOI: 10.1371/journal.pone.0004870] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Accepted: 02/16/2009] [Indexed: 11/19/2022] Open
Abstract
Rapid antibiotic susceptibility testing of Mycobacterium tuberculosis is of paramount importance as multiple- and extensively- drug resistant strains of M. tuberculosis emerge and spread. We describe here a virus-based assay in which fluoromycobacteriophages are used to deliver a GFP or ZsYellow fluorescent marker gene to M. tuberculosis, which can then be monitored by fluorescent detection approaches including fluorescent microscopy and flow cytometry. Pre-clinical evaluations show that addition of either Rifampicin or Streptomycin at the time of phage addition obliterates fluorescence in susceptible cells but not in isogenic resistant bacteria enabling drug sensitivity determination in less than 24 hours. Detection requires no substrate addition, fewer than 100 cells can be identified, and resistant bacteria can be detected within mixed populations. Fluorescence withstands fixation by paraformaldehyde providing enhanced biosafety for testing MDR-TB and XDR-TB infections.
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Affiliation(s)
- Mariana Piuri
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - William R. Jacobs
- Howard Hughes Medical Institute, Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, 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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Abstract
The identification of essential genes is of major importance to mycobacterial research, and a number of essential genes have been identified in mycobacteria, however confirming essentiality is not straightforward, as deletion of essential genes results in a lethal phenotype. In this chapter, protocols are described that can be used to confirm gene essentiality using gene switching, following the construction of a delinquent strain. Because deletion mutants cannot be created for essential genes, a second gene copy is introduced via an integrating vector, which allows the chromosomal gene copy to be deleted. The integrated vector can then be replaced using the gene switching method; where no transformants are obtained, essentiality is confirmed. This technique can also be used to confirm functionality of gene homologues and to easily identify essential operon members.
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Affiliation(s)
- Amanda Claire Brown
- Institute of Cell and Molecular Science, Barts and the London, Queen Mary's School of Medicine and Dentistry, 4 Newark Street, Whitechapel, London E1 2AA, UK.
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34
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Stella EJ, de la Iglesia AI, Morbidoni HR. Mycobacteriophages as versatile tools for genetic manipulation of mycobacteria and development of simple methods for diagnosis of mycobacterial diseases. Rev Argent Microbiol 2009; 41:45-55. [PMID: 19391526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis, is responsible for over two million deaths per year worldwide. Due to its long doubling time (18 h), the microbiological detection of M. tuberculosis by conventional methods takes up to one month, unless the number of bacilli in the biological sample is high enough. Thus, drug resistance assessment requires at least one month for obtaining the primary culture and another month to determine its susceptibility to antimycobacterial drugs. Moreover, for a long time, the lack of genetic tools for mycobacteria has been a barrier for undertaking studies aimed at understanding the mechanisms of drug resistance and drug target identification, being all these topics of utmost importance considering the increase in the number of drug-resistant clones and the few therapeutic options available. Mycobacteriophages are promising as a novel source of genetic elements for mycobacteria manipulation, as well as for the development of versatile, simple, fast and cheap methods for drug resistance assessment of M. tuberculosis clinical isolates. We herein describe the background related to the use of mycobacteriophages, with emphasis placed on their utilization for drug resistance analysis in our country.
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Affiliation(s)
- E J Stella
- Cátedra de Microbiología, Virología y Parasitología, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Argentina
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Abstract
To increase science literacy and appreciation among nonscience majors, we offered a course in which 20 non-STEM (science, technology, engineering, math) undergraduates participated in a unique, two-semester research experience. Each student isolated and characterized his or her own bacteriophage from soil samples. One bacteriophage was selected for sequencing and together, the class annotated the genome of the newly sequenced bacteriophage. The class produced a group poster and gave PowerPoint presentations, and one student presented the joint work at a science symposium.
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Affiliation(s)
- Steven M Caruso
- Department of Biological Sciences, University of Maryland-Baltimore County, Baltimore, MD 21250, USA.
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36
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Kumar V, Loganathan P, Sivaramakrishnan G, Kriakov J, Dusthakeer A, Subramanyam B, Chan J, Jacobs WR, Paranji Rama N. Characterization of temperate phage Che12 and construction of a new tool for diagnosis of tuberculosis. Tuberculosis (Edinb) 2008; 88:616-23. [PMID: 18511339 DOI: 10.1016/j.tube.2008.02.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Revised: 02/08/2008] [Accepted: 02/14/2008] [Indexed: 11/18/2022]
Abstract
A temperate phage, Che12, able to infect Mycobacterium tuberculosis, was isolated from soil samples taken from tuberculosis sanatorium area in Chennai, India. The plaque morphology of this phage showed varying grades of turbidity on lawns of M. tuberculosis. The temperate nature of Che12 was established by super infection immunity. Phage integration into the host genomic DNA was confirmed by Southern hybridization using Che12 DNA as a probe. PCR amplification and sequencing of a part of the integrated phage genome in a M. tuberculosis lysogen also confirmed the temperate nature of Che12. The morphology of the phage particles was observed by electron microscopy, revealing similarities to other mycobacteriophages like L5, D29 and TM4. A luciferase reporter phage, phAETRC16, was constructed by cloning firefly luciferase gene into Che12. Infection of viable M. tuberculosis cells by phAETRC16 resulted in expression of luciferase leading to sustained light output. Che12, a true temperate phage infecting M. tuberculosis, is thus ideally suited for developing a diagnostic tool facilitating rapid diagnosis of M. tuberculosis.
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Affiliation(s)
- Vanaja Kumar
- Tuberculosis Research Centre (Indian Council of Medical Research), Bacteriology, Mayor V.R. Ramanathan Road, Chetput, Chennai 600 031, India.
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37
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Mandal P, Datta HJ, Sau S, Mandal NC. The delayed early gene G23 of temperate mycobacteriophage L1 regulates the expression of deoxyribonuclease, the product of another delayed early gene of the phage. Pol J Microbiol 2008; 57:113-119. [PMID: 18646398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
To get clues about the genes as well as the gene regulatory circuit controlling the lytic development of temperate mycobacteriophage L1, previously we screened several conditional lethal mutants of L1 and characterized some of them to an extent. One of the mutants, L1 G23ts23, was found defective in both growth and late gene transcription at 42 degrees C but not at 32 degrees C. Here we show that the above phage mutant is also defective in the expression of phage-coded deoxyribonuclease (DNase) at 42 degrees C but not at 32 degrees C. The G23 gene however does not code for the above enzyme. Further analyses using the L1 G23ts23 mutant suggest that synthesis of DNase is also not regulated by G23 at transcriptional level. Expression of functional DNase in fact requires de novo protein synthesis. Among the 25 revertants isolated from the L1 G23ts23 mutant, which are capable of growing at 42 degrees C (by overcoming the ts defect in late transcription), two, R4 and R22, have been shown to retain the ts defect in the expression of the above enzyme and R4, to retain also the G23ts23 mutation. This suggests that R4 (R22 was not tested for the presence of G23ts23 mutation) carries an extragenic suppressor of G23ts23 mutation in a different gene (we call this putative gene as Gx), which now helps bypass the requirement of G23 for late gene transcription. Possible role of G23 on the regulation of L1-coded Gx and deoxyribonuclease has been discussed at length.
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Affiliation(s)
- Prajna Mandal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
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38
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Abstract
Although substantial advances have been made in mycobacterial genetics over the past 15 yr, manipulation of mycobacterial genomes and Mycobacterium tuberculosis in particular, continues to be hindered by problems of relatively poor DNA uptake, slow growth rate, and high levels of illegitimate recombination. In Escherichia coli an effective approach to stimulating recombination frequencies has been developed called "recombineering," in which phage-encoded recombination functions are transiently expressed to promote efficient homologous recombination. Although homologs of these recombination proteins are rare among mycobacteriophages, we have identified one phage, Che9c, encoding relatives of both RecE and RecT of the E. coli rac prophage. Expression of the Che9c proteins from an inducible expression system in either slow- or fast-growing mycobacteria provides elevated recombination frequencies and facilitates simple allelic exchange using linear DNA substrates. Mycobacterial recombineering, therefore, offers a simple approach for constructing gene replacement mutants in M. smegmatis and M. tuberculosis.
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Affiliation(s)
- Julia C van Kessel
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
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39
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Pham TT, Jacobs-Sera D, Pedulla ML, Hendrix RW, Hatfull GF. Comparative genomic analysis of mycobacteriophage Tweety: evolutionary insights and construction of compatible site-specific integration vectors for mycobacteria. Microbiology (Reading) 2007; 153:2711-2723. [PMID: 17660435 PMCID: PMC2884959 DOI: 10.1099/mic.0.2007/008904-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Mycobacteriophage Tweety is a newly isolated phage of Mycobacterium smegmatis. It has a viral morphology with an isometric head and a long flexible tail, and forms turbid plaques from which stable lysogens can be isolated. The Tweety genome is 58 692 bp in length, contains 109 protein-coding genes, and shows significant but interrupted nucleotide sequence similarity with the previously described mycobacteriophages Llij, PMC and Che8. However, overall the genome possesses mosaic architecture, with gene products being related to other mycobacteriophages such as Che9d, Omega and Corndog. A gene encoding an integrase of the tyrosine-recombinase family is located close to the centre of the genome, and a putative attP site has been identified within a short intergenic region immediately upstream of int. This Tweety attP–int cassette was used to construct a new set of integration-proficient plasmid vectors that efficiently transform both fast- and slow-growing mycobacteria through plasmid integration at a chromosomal locus containing a tRNALys gene. These vectors are maintained well in the absence of selection and are completely compatible with integration vectors derived from mycobacteriophage L5, enabling the simple construction of complex recombinants with genes integrated simultaneously at different chromosomal positions.
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Affiliation(s)
- Thuy T. Pham
- Department of Biological Sciences and Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Deborah Jacobs-Sera
- Department of Biological Sciences and Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Marisa L. Pedulla
- Department of Biology, Montana Tech, University of Montana, Butte, MT 59701, USA
| | - Roger W. Hendrix
- Department of Biological Sciences and Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Graham F. Hatfull
- Department of Biological Sciences and Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA
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40
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Datta HJ, Mandal P, Bhattacharya R, Das N, Sau S, Mandal NC. The G23 and G25 Genes of Temperate Mycobacteriophage L1 Are Essential for The Transcription of Its Late Genes. BMB Rep 2007; 40:156-62. [PMID: 17394764 DOI: 10.5483/bmbrep.2007.40.2.156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two lysis-defective but DNA synthesis non-defective temperature-sensitive (ts) mutants of mycobacteriophage L1, L1G23ts23 and L1G25ts889 were found to be defective also in phage-specific RNA synthesis in the late period of their growth at 42 degrees C, each to the extent of 50% of that at 32 degrees C. The double mutant, L1G23ts23G25ts889 showed the ts defect in phage RNA synthesis that was nearly additive of those shown individually by the two single-mutant parents. Both G23 and G25 were shown to start functioning sometimes between 30 and 45 min after infection but the former gene might be dispensable after 45 min, while the latter was not. Northern analysis also shows that at 42 degrees C, L1G23ts23 affects RNA synthesis more strongly than L1G25ts889 from L1 DNA segments that serve as the template for late gene transcription. Among the 21 virion and 12 non-virion late proteins synthesized by L1, L1G23ts23 is defective in the synthesis of at least 9 virion and all of non-virion proteins at 42 degrees C. In contrast, L1G25ts889 is completely defective in synthesis of all the 33 late proteins. Possible roles of G23 and G25 in the positive regulation of transcription of different sets of late genes of L1 have been discussed.
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Affiliation(s)
- Hirock Jyoti Datta
- Department of Biochemistry, Bose Institute, P-1/12, CIT Scheme VII M, Calcutta 700 054, West Bengal, India.
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41
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Gomathi NS, Sameer H, Kumar V, Balaji S, Dustackeer VNA, Narayanan PR. In silico analysis of mycobacteriophage Che12 genome: characterization of genes required to lysogenise Mycobacterium tuberculosis. Comput Biol Chem 2007; 31:82-91. [PMID: 17379577 DOI: 10.1016/j.compbiolchem.2007.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Accepted: 02/14/2007] [Indexed: 11/23/2022]
Abstract
Che12 is a temperate Chennai phage infecting Mycobacterium tuberculosis. The nucleotide sequence of the 52,047 bp linear double stranded DNA genome has a GC content of 62.9% with 70 putative ORFs identified. Functions are assigned to 24 genes based on the similarity of the predicted products to known proteins. Che12 genome is highly similar to mycobacteriophage L5 and D29 genomes. The overall genome similarity of Che12 to L5 is 82.5% and D29 is 81.5%. The genes attributing to lysogeny such as integrase, excisionase and repressor protein are identified. The attachment site of Che12 genome attP is homologous to attB sites of Mycobacterium smegmatis and M. tuberculosis. Similarities between certain phage gene products are noted, in particular, the terminases, DNA primase and endonucleases. The complete sequence clarifies the overall transcription map of Che12 and the positions of elements involved in the maintenance of lysogeny.
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Affiliation(s)
- N S Gomathi
- Tuberculosis Research Centre (Indian Council of Medical Research), Mayor V.R. Ramanathan Road, Chetpet, Chennai 600031, India
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42
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Ranjan A, Vidyarthi AS, Poddar R. Evaluation of codon bias perspectives in phage therapy of Mycobacterium tuberculosis by multivariate analysis. In Silico Biol 2007; 7:423-431. [PMID: 18391235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
To reveal the relative synonymous codon usage and base composition variation in bacteriophages, six mycobacteriophages were used as a model system here and both parameters in these phages and their host bacteria, Mycobacterium tuberculosis, have been determined and compared. As expected for GC-rich genomes, there are predominantly G and C ending codons in all 6 phages. Both N_{c} plot and correspondence analysis on relative synonymous codon usage indicate that mutation bias and translation selection influences codon usage variation in the 6 phages. Further analysis indicates that among 6 Mycobacterium phages Che9c, Bxz1 and TM4 may be extremely virulent in nature as most of their genes have high translation efficiency. Based on our data we suggest that the genes of above three phages are expressed rapidly by host's translation machinery. The information might be used to select the extremely virulent Mycobacterium tuberculosis phages suitable for phage therapy.
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Affiliation(s)
- Ashutosh Ranjan
- Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi-835215, India
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43
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Abstract
Genetic dissection of M. tuberculosis is complicated by its slow growth and its high rate of illegitimate recombination relative to homologous DNA exchange. We report here the development of a facile allelic exchange system by identification and expression of mycobacteriophage-encoded recombination proteins, adapting a strategy developed previously for recombineering in Escherichia coli. Identifiable recombination proteins are rare in mycobacteriophages, and only 1 of 30 genomically characterized mycobacteriophages (Che9c) encodes homologs of both RecE and RecT. Expression and biochemical characterization show that Che9c gp60 and gp61 encode exonuclease and DNA-binding activities, respectively, and expression of these proteins substantially elevates recombination facilitating allelic exchange in both M. smegmatis and M. tuberculosis. Mycobacterial recombineering thus provides a simple approach for the construction of gene replacement mutants in both slow- and fast-growing mycobacteria.
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Affiliation(s)
- Julia C van Kessel
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, 376 Crawford Hall, 4249 Fifth Ave., University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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44
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Piuri M, Hatfull GF. A peptidoglycan hydrolase motif within the mycobacteriophage TM4 tape measure protein promotes efficient infection of stationary phase cells. Mol Microbiol 2006; 62:1569-85. [PMID: 17083467 PMCID: PMC1796659 DOI: 10.1111/j.1365-2958.2006.05473.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2006] [Indexed: 11/30/2022]
Abstract
The predominant morphotype of mycobacteriophage virions has a DNA-containing capsid attached to a long flexible non-contractile tail, features characteristic of the Siphoviridae. Within these phage genomes the tape measure protein (tmp) gene can be readily identified due to the well-established relationship between the length of the gene and the length of the phage tail--because these phages typically have long tails, the tmp gene is usually the largest gene in the genome. Many of these mycobacteriophage Tmp's contain small motifs with sequence similarity to host proteins. One of these motifs (motif 1) corresponds to the Rpf proteins that have lysozyme activity and function to stimulate growth of dormant bacteria, while the others (motifs 2 and 3) are related to proteins of unknown function, although some of the related proteins of the host are predicted to be involved in cell wall catabolism. We show here that motif 3-containing proteins have peptidoglycan-hydrolysing activity and that while this activity is not required for phage viability, it facilitates efficient infection and DNA injection into stationary phase cells. Tmp's of mycobacteriophages may thus have acquired these motifs in order to avoid a selective disadvantage that results from changes in peptidoglycan in non-growing cells.
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Affiliation(s)
- Mariana Piuri
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of PittsburghPittsburgh, PA 15260, USA
| | - Graham F Hatfull
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of PittsburghPittsburgh, PA 15260, USA
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45
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Pitcher RS, Tonkin LM, Daley JM, Palmbos PL, Green AJ, Velting TL, Brzostek A, Korycka-Machala M, Cresawn S, Dziadek J, Hatfull GF, Wilson TE, Doherty AJ. Mycobacteriophage exploit NHEJ to facilitate genome circularization. Mol Cell 2006; 23:743-8. [PMID: 16949369 DOI: 10.1016/j.molcel.2006.07.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2006] [Revised: 06/21/2006] [Accepted: 07/10/2006] [Indexed: 01/05/2023]
Abstract
Ku-dependent nonhomologous end joining (NHEJ) is a double-strand break repair process conserved in all branches of cellular life but has not previously been implicated in the DNA metabolic processes of viruses. We identified Ku homologs in Corndog and Omega, two related mycobacteriophages of Mycobacterium smegmatis. These proteins formed homodimers and bound DNA ends in a manner identical to other Ku's and stimulated joining of ends by the host NHEJ DNA ligase (LigD). Omega and Corndog are unusual in having short 4 base cos ends that would not be expected to self-anneal and would therefore require NHEJ during phage genome circularization. Consistently, M. smegmatis LigD null strains are entirely and selectively unable to support infection by Corndog or Omega, with concomitant failure of genome circularization. These results establish a new paradigm for sequestration of the host cell NHEJ process by bacteriophage and provide a framework for understanding similar transactions in eukaryotic viral infections.
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Affiliation(s)
- Robert S Pitcher
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK
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46
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Nkrumah LJ, Muhle RA, Moura PA, Ghosh P, Hatfull GF, Jacobs WR, Fidock DA. Efficient site-specific integration in Plasmodium falciparum chromosomes mediated by mycobacteriophage Bxb1 integrase. Nat Methods 2006; 3:615-21. [PMID: 16862136 PMCID: PMC2943413 DOI: 10.1038/nmeth904] [Citation(s) in RCA: 205] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2006] [Accepted: 06/19/2006] [Indexed: 01/03/2023]
Abstract
Here we report an efficient, site-specific system of genetic integration into Plasmodium falciparum malaria parasite chromosomes. This is mediated by mycobacteriophage Bxb1 integrase, which catalyzes recombination between an incoming attP and a chromosomal attB site. We developed P. falciparum lines with the attB site integrated into the glutaredoxin-like cg6 gene. Transfection of these attB(+) lines with a dual-plasmid system, expressing a transgene on an attP-containing plasmid together with a drug resistance gene and the integrase on a separate plasmid, produced recombinant parasites within 2 to 4 weeks that were genetically uniform for single-copy plasmid integration. Integrase-mediated recombination resulted in proper targeting of parasite proteins to intra-erythrocytic compartments, including the apicoplast, a plastid-like organelle. Recombinant attB x attP parasites were genetically stable in the absence of drug and were phenotypically homogeneous. This system can be exploited for rapid genetic integration and complementation analyses at any stage of the P. falciparum life cycle, and it illustrates the utility of Bxb1-based integrative recombination for genetic studies of intracellular eukaryotic organisms.
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Affiliation(s)
- Louis J Nkrumah
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
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47
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Ganguly T, Chanda PK, Bandhu A, Chattoraj P, Das M, Sau S. Effects of Physical, Ionic, and Structural Factors on the Binding of Repressor of Mycobacteriophage L1 to Its Cognate Operator DNA. Protein Pept Lett 2006; 13:793-8. [PMID: 17073724 DOI: 10.2174/092986606777841262] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To determine the factors influencing the binding of L1 repressor to its cognate operator DNA, several gel shift as well as bioinformatic analyses have been carried out. The data show that time, temperature, salt, and pH each greatly affect the binding. In order to achieve optimum operator binding of L1 repressor in Tris buffer, the minimum requirements of time, temperature, salt, and pH were estimated to be 1 min, 32 degrees C, NaCl (50 mM), and 7.9, respectively. Interestingly Na+ but not NH4+, K+, or Li+ was found to augment significantly the binding activity of CI protein above the basal level. Anions like Cl-, citrate-, acetate-, and H2PO4- do not alter the binding of L1 repressor to its operator. We also show that an in frame deletion mutant of L1 repressor which does not carry the putative HTH motif (at its N-terminal end) fails to bind to its cognate operator DNA even at very high concentrations. The putative HTH motif was found highly conserved and evolutionarily very close to that of regulatory proteins of Y. pestis, H. marismortui, A. tumefaciens, etc. Taken together we suggest that N-terminal end of L1 repressor carries a HTH motif. Further analysis of the putative secondary structures of mycobacteriophage repressors reveals that two common regions encompassing more than 90% of primary sequence are present in all the four repressor molecules studied here. The results suggest that these common regions are utilized for carrying out identical functions.
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Affiliation(s)
- Tridib Ganguly
- Department of Biochemistry, Bose Institute, P1/12 - CIT Scheme VII M, Calcutta 700 054, India
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Hatfull GF, Pedulla ML, Jacobs-Sera D, Cichon PM, Foley A, Ford ME, Gonda RM, Houtz JM, Hryckowian AJ, Kelchner VA, Namburi S, Pajcini KV, Popovich MG, Schleicher DT, Simanek BZ, Smith AL, Zdanowicz GM, Kumar V, Peebles CL, Jacobs WR, Lawrence JG, Hendrix RW. Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. PLoS Genet 2006; 2:e92. [PMID: 16789831 PMCID: PMC1475703 DOI: 10.1371/journal.pgen.0020092] [Citation(s) in RCA: 211] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2006] [Accepted: 05/04/2006] [Indexed: 01/18/2023] Open
Abstract
Bacteriophages are the most abundant forms of life in the biosphere and carry genomes characterized by high genetic diversity and mosaic architectures. The complete sequences of 30 mycobacteriophage genomes show them collectively to encode 101 tRNAs, three tmRNAs, and 3,357 proteins belonging to 1,536 "phamilies" of related sequences, and a statistical analysis predicts that these represent approximately 50% of the total number of phamilies in the mycobacteriophage population. These phamilies contain 2.19 proteins on average; more than half (774) of them contain just a single protein sequence. Only six phamilies have representatives in more than half of the 30 genomes, and only three-encoding tape-measure proteins, lysins, and minor tail proteins-are present in all 30 phages, although these phamilies are themselves highly modular, such that no single amino acid sequence element is present in all 30 mycobacteriophage genomes. Of the 1,536 phamilies, only 230 (15%) have amino acid sequence similarity to previously reported proteins, reflecting the enormous genetic diversity of the entire phage population. The abundance and diversity of phages, the simplicity of phage isolation, and the relatively small size of phage genomes support bacteriophage isolation and comparative genomic analysis as a highly suitable platform for discovery-based education.
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Affiliation(s)
- Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
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Gross L. A Novel Phage Protein Mediates the Virus's Removal from Bacterial Chromosomes. PLoS Biol 2006; 4:e213. [PMID: 20076596 PMCID: PMC1470462 DOI: 10.1371/journal.pbio.0040213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Galí N, Domínguez J, Blanco S, Prat C, Alcaide F, Coll P, Ausina V. Use of a mycobacteriophage-based assay for rapid assessment of susceptibilities of Mycobacterium tuberculosis isolates to isoniazid and influence of resistance level on assay performance. J Clin Microbiol 2006; 44:201-5. [PMID: 16390970 PMCID: PMC1351944 DOI: 10.1128/jcm.44.1.201-205.2006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We standardized and assessed the performance of an in-house microtiter assay for determining the susceptibilities of Mycobacterium tuberculosis clinical isolates to isoniazid based on mycobacteriophage amplification technology. Seventy isolates (43 resistant and 27 sensitive according to the BACTEC 460 radiometric method and MIC determination) were studied. The isoniazid resistance molecular mechanism was previously determined by sequencing the entire katG gene and the mabA-inhA regulatory region. The sensitivity of the mycobacteriophage-based assay in detecting isoniazid resistance was 86.1%, the specificity achieved was 92.6%, and the overall accuracy was 88.6%. In order to assess the possible influence of resistance levels on the mycobacteriophage-based-assay sensitivity, the results were analyzed according to the isoniazid MICs. All the isolates exhibiting high-level resistance (MIC > or = 2 microg/ml) were scored as resistant by the mycobacteriophage-based assay (100% concordance), and 95% showed mutations or deletions in the catalytic domain of the katG gene. In contrast, 26.1% of the low-level-resistance strains (MICs, 0.25 to 1 microg/ml) were misclassified, and 66.7% had alterations in the mabA-inhA regulatory region. The mycobacteriophage-based assay could be used as a rapid method to detect the isoniazid susceptibility pattern, although data from those areas with high rates of low-level-resistance strains should be interpreted with caution. The features of the assay make it suitable for widespread application due to its low technical demand and cost.
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Affiliation(s)
- N Galí
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Ctra. del Canyet, Badalona, Barcelona, Spain
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