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Raman SK, Siva Reddy DV, Jain V, Bajpai U, Misra A, Singh AK. Mycobacteriophages: therapeutic approach for mycobacterial infections. Drug Discov Today 2024; 29:104049. [PMID: 38830505 DOI: 10.1016/j.drudis.2024.104049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 05/07/2024] [Accepted: 05/29/2024] [Indexed: 06/05/2024]
Abstract
Tuberculosis (TB) is a significant global health threat, and cases of infection with non-tuberculous mycobacteria (NTM) causing lung disease (NTM-LD) are rising. Bacteriophages and their gene products have garnered interest as potential therapeutic options for bacterial infections. Here, we have compiled information on bacteriophages and their products that can kill Mycobacterium tuberculosis or NTM. We summarize the mechanisms whereby viable phages can access macrophage-resident bacteria and not elicit immune responses, review methodologies of pharmaceutical product development containing mycobacteriophages and their gene products, mainly lysins, in the context of drug regulatory requirements and we discuss industrially relevant methods for producing pharmaceutical products comprising mycobacteriophages, emphasizing delivery of mycobacteriophages to the lungs. We conclude with an outline of some recent case studies on mycobacteriophage therapy.
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Affiliation(s)
- Sunil Kumar Raman
- Pharmaceutics and Pharmacokinetics Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - D V Siva Reddy
- Pharmaceutics and Pharmacokinetics Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Vikas Jain
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India
| | - Urmi Bajpai
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji , New Delhi 110019, India
| | - Amit Misra
- Pharmaceutics and Pharmacokinetics Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Amit Kumar Singh
- Experimental Animal Facility, ICMR-National JALMA Institute for Leprosy & Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra 282004, Uttar Pradesh, India.
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2
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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, MD.) 2024; 14:jkae049. [PMID: 38456318 PMCID: PMC11075535 DOI: 10.1093/g3journal/jkae049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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3
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Amaya I, Edwards K, Wise BM, Bhattacharyya A, Pablo CHD, Mushrush E, Coats AN, Dao S, Dittmar G, Gore T, Jarva TM, Kenkebashvili G, Rathan-Kumar S, Reyes GM, Watts GL, Watts VK, Dubrow D, Lewis G, Stone BH, Xue B, Cresawn SG, Mavrodi D, Sivanathan V, Heller D. A genome-wide overexpression screen reveals Mycobacterium smegmatis growth inhibitors encoded by mycobacteriophage Hammy. G3 (BETHESDA, MD.) 2023; 13:jkad240. [PMID: 37934806 PMCID: PMC10700055 DOI: 10.1093/g3journal/jkad240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/06/2023] [Indexed: 11/09/2023]
Abstract
During infection, bacteriophages produce diverse gene products to overcome bacterial antiphage defenses, to outcompete other phages, and to take over cellular processes. Even in the best-studied model phages, the roles of most phage-encoded gene products are unknown, and the phage population represents a largely untapped reservoir of novel gene functions. Considering the sheer size of this population, experimental screening methods are needed to sort through the enormous collection of available sequences and identify gene products that can modulate bacterial behavior for downstream functional characterization. Here, we describe the construction of a plasmid-based overexpression library of 94 genes encoded by Hammy, a Cluster K mycobacteriophage closely related to those infecting clinically important mycobacteria. The arrayed library was systematically screened in a plate-based cytotoxicity assay, identifying a diverse set of 24 gene products (representing ∼25% of the Hammy genome) capable of inhibiting growth of the host bacterium Mycobacterium smegmatis. Half of these are related to growth inhibitors previously identified in related phage Waterfoul, supporting their functional conservation; the other genes represent novel additions to the list of known antimycobacterial growth inhibitors. This work, conducted as part of the HHMI-supported Science Education Alliance Gene-function Exploration by a Network of Emerging Scientists (SEA-GENES) project, highlights the value of parallel, comprehensive overexpression screens in exploring genome-wide patterns of phage gene function and novel interactions between phages and their hosts.
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Affiliation(s)
- Isabel Amaya
- Center for the Advancement of Science Leadership and Culture, Howard Hughes Medical Institute, Chevy Chase, MD 20185, USA
| | - Kaylia Edwards
- Center for the Advancement of Science Leadership and Culture, Howard Hughes Medical Institute, Chevy Chase, MD 20185, USA
| | - Bethany M Wise
- Center for the Advancement of Science Leadership and Culture, Howard Hughes Medical Institute, Chevy Chase, MD 20185, USA
| | - Ankita Bhattacharyya
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Clint H D Pablo
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Ember Mushrush
- Department of Biology, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Amber N Coats
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Sara Dao
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Grace Dittmar
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Taylor Gore
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Taiya M Jarva
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Giorgi Kenkebashvili
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Sudiksha Rathan-Kumar
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Gabriella M Reyes
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Garrett L Watts
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Victoria Kalene Watts
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Deena Dubrow
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Gabrielle Lewis
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Benjamin H Stone
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Bingjie Xue
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Steven G Cresawn
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Dmitri Mavrodi
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Viknesh Sivanathan
- Center for the Advancement of Science Leadership and Culture, Howard Hughes Medical Institute, Chevy Chase, MD 20185, USA
| | - Danielle Heller
- Center for the Advancement of Science Leadership and Culture, Howard Hughes Medical Institute, Chevy Chase, MD 20185, USA
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4
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Binsabaan SA, Freeman KG, Hatfull GF, VanDemark AP. The Cytotoxic Mycobacteriophage Protein Phaedrus gp82 Interacts with and Modulates the Activity of the Host ATPase, MoxR. J Mol Biol 2023; 435:168261. [PMID: 37678706 PMCID: PMC10593117 DOI: 10.1016/j.jmb.2023.168261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/09/2023]
Abstract
Approximately 70% of bacteriophage-encoded proteins are of unknown function. Elucidating these protein functions represents opportunities to discover new phage-host interactions and mechanisms by which the phages modulate host activities. Here, we describe a pipeline for prioritizing phage-encoded proteins for structural analysis and characterize the gp82 protein encoded by mycobacteriophage Phaedrus. Structural and solution studies of gp82 show it is a trimeric protein containing two domains. Co-precipitation studies with the host Mycobacterium smegmatis identified the ATPase MoxR as an interacting partner protein. Phaedrus gp82-MoxR interaction requires the presence of a loop sequence within gp82 that is highly exposed and disordered in the crystallographic structure. We show that Phaedrus gp82 overexpression in M. smegmatis retards the growth of M. smegmatis on solid medium, resulting in a small colony phenotype. Overexpression of gp82 containing a mutant disordered loop or the overexpression of MoxR both rescue this phenotype. Lastly, we show that recombinant gp82 reduces levels of MoxR-mediated ATPase activity in vitro that is required for its chaperone function, and that the disordered loop plays an important role in this phenotype. We conclude that Phaedrus gp82 binds to and reduces mycobacterial MoxR activity, leading to reduced function of host proteins that require MoxR chaperone activity for their normal activity.
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Affiliation(s)
- Saeed A Binsabaan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260, USA
| | - Krista G Freeman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260, USA
| | - Andrew P VanDemark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260, USA; Department of Chemistry, University of Pittsburgh, Pittsburgh PA 15260, USA.
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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] [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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6
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Genome Sequence of the Cluster CD
Gordonia
Phage Widow. Microbiol Resour Announc 2022; 11:e0069522. [PMID: 36066262 PMCID: PMC9583811 DOI: 10.1128/mra.00695-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Widow is a novel cluster CD bacteriophage isolated from a soil sample using the bacterial host Gordonia terrae. The Widow genome is 43,656 bp in length and encodes 64 protein-coding genes and no tRNAs. The genome shares 52 to 92% gene content with other cluster CD members.
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7
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Heller D, Sivanathan V. Publishing student-led discoveries in genetics. G3 (BETHESDA, MD.) 2022; 12:jkac141. [PMID: 35727730 PMCID: PMC9339278 DOI: 10.1093/g3journal/jkac141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Danielle Heller
- Department of Science Education, Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Viknesh Sivanathan
- Corresponding author: Department of Science Education, Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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