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Cingolani G, Iglesias S, Hou CF, Lemire S, Soriaga A, Kyme P. Cryo-EM analysis of Pseudomonas phage Pa193 structural components. RESEARCH SQUARE 2024:rs.3.rs-4189479. [PMID: 38659960 PMCID: PMC11042391 DOI: 10.21203/rs.3.rs-4189479/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The World Health Organization has designated Pseudomonas aeruginosa as a critical pathogen for the development of new antimicrobials. Bacterial viruses, or bacteriophages, have been used in various clinical settings, commonly called phage therapy, to address this growing public health crisis. Here, we describe a high-resolution structural atlas of a therapeutic, contractile-tailed Pseudomonas phage, Pa193. We used bioinformatics, proteomics, and cryogenic electron microscopy single particle analysis to identify, annotate, and build atomic models for 21 distinct structural polypeptide chains forming the icosahedral capsid, neck, contractile tail, and baseplate. We identified a putative scaffolding protein stabilizing the interior of the capsid 5-fold vertex. We also visualized a large portion of Pa193 ~ 500 Å long tail fibers and resolved the interface between the baseplate and tail fibers. The work presented here provides a framework to support a better understanding of phages as biomedicines for phage therapy and inform engineering opportunities.
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Nair G, Jain V. An intramolecular cross-talk in D29 mycobacteriophage endolysin governs the lytic cycle and phage-host population dynamics. SCIENCE ADVANCES 2024; 10:eadh9812. [PMID: 38335296 PMCID: PMC10857449 DOI: 10.1126/sciadv.adh9812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 01/10/2024] [Indexed: 02/12/2024]
Abstract
D29 mycobacteriophage encodes LysA endolysin, which mediates mycobacterial host cell lysis by targeting its peptidoglycan layer, thus projecting itself as a potential therapeutic. However, the regulatory mechanism of LysA during the phage lytic cycle remains ill defined. Here, we show that during D29 lytic cycle, structural and functional regulation of LysA not only orchestrates host cell lysis but also is critical for maintaining phage-host population dynamics by governing various phases of lytic cycle. We report that LysA exists in two conformations, of which only one is active, and the protein undergoes a host peptidoglycan-dependent conformational switch to become active for carrying out endogenous host cell lysis. D29 maintains a pool of inactive LysA, allowing complete assembly of phage progeny, thus helping avoid premature host lysis. In addition, we show that the switch reverses after lysis, thus preventing exogenous targeting of bystanders, which otherwise negatively affects phage propagation in the environment.
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Affiliation(s)
- Gokul Nair
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462066, Madhya Pradesh, India
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3
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Behera M, Singh G, Vats A, Parmanand, Roshan M, Gautam D, Rana C, Kesharwani RK, De S, Ghorai SM. Expression and characterization of novel chimeric endolysin CHAPk-SH3bk against biofilm-forming methicillin-resistant Staphylococcus aureus. Int J Biol Macromol 2024; 254:127969. [PMID: 37944719 DOI: 10.1016/j.ijbiomac.2023.127969] [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: 07/31/2023] [Revised: 10/27/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023]
Abstract
The continuous evolution of antibiotic resistance in methicillin-resistant Staphylococcus aureus (MRSA) due to the misuse of antibiotics lays out the need for the development of new antimicrobials with higher activity and lower resistance. In this study, we have expressed novel chimeric endolysin CHAPk-SH3bk derived from LysK to investigate its antibacterial activity against planktonic and biofilm-forming MRSA. The molecular docking and MD simulation results identified critical amino acids (ASP47, ASP56, ARG71, and Gly74) of CHAPk domain responsible for its catalytic activity. Chimeric endolysin CHAPk-SH3bk showed an effective binding to peptidoglycan fragment using 14 hydrogen bonds. The in-vitro antibacterial assays displayed higher activity of CHAPk against planktonic MRSA with 2-log10 reduction in 2 h. Both CHAPk and CHAPk-SH3bk displayed bactericidal activity against MRSA with ∼4log10 and ∼3.5log10 reduction in 24 h. Biofilm reduction activity displayed CHAPk-SH3bk reduced 33 % and 60 % of hospital-associated ATCC®BAA-44™ and bovine origin SA1 respectively. The CHAPk treatment reduced 47 % of the preformed biofilm formed by bovine-origin MRSA SA1. This study indicates an effective reduction of preformed MRSA biofilms of human and animal origin using novel chimeric construct CHAPk-SH3bk. Stating that the combination and shuffling of different domains of phage endolysin potentially increase its bacteriolytic effectiveness against MRSA.
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Affiliation(s)
- Manisha Behera
- Department of Zoology, Hindu College, University of Delhi, Delhi 110007, India; National Dairy Research Institute (NDRI), Animal Biotechnology Centre, Animal Genomics Lab, Karnal 132001, Haryana, India
| | - Gagandeep Singh
- Section of Microbiology, Central Ayurveda Research Institute, Jhansi, Uttar Pradesh, India; Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
| | - Ashutosh Vats
- National Dairy Research Institute (NDRI), Animal Biotechnology Centre, Animal Genomics Lab, Karnal 132001, Haryana, India
| | - Parmanand
- National Dairy Research Institute (NDRI), Animal Biotechnology Centre, Animal Genomics Lab, Karnal 132001, Haryana, India
| | - Mayank Roshan
- National Dairy Research Institute (NDRI), Animal Biotechnology Centre, Animal Genomics Lab, Karnal 132001, Haryana, India
| | - Devika Gautam
- National Dairy Research Institute (NDRI), Animal Biotechnology Centre, Animal Genomics Lab, Karnal 132001, Haryana, India
| | - Chanchal Rana
- National Dairy Research Institute (NDRI), Animal Biotechnology Centre, Animal Genomics Lab, Karnal 132001, Haryana, India
| | - Rajesh Kumar Kesharwani
- Department of Computer Application, Nehru Gram Bharati (Deemed to be University), Prayagraj, India
| | - Sachinandan De
- National Dairy Research Institute (NDRI), Animal Biotechnology Centre, Animal Genomics Lab, Karnal 132001, Haryana, India.
| | - Soma M Ghorai
- Department of Zoology, Hindu College, University of Delhi, Delhi 110007, India.
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Cui JQ, Liu WH, Zhang C, Zou L, Ren HY. Genomic characterization of three bacteriophages infecting donkey-derived Escherichia coli. Virus Genes 2023; 59:752-762. [PMID: 37322310 DOI: 10.1007/s11262-023-02008-9] [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: 03/04/2023] [Accepted: 05/13/2023] [Indexed: 06/17/2023]
Abstract
Bacteriophages are an important source of novel genetic diversity. Sequencing of phage genomes can reveal new proteins with potential uses in phage therapy and help unravel the diversity of biological mechanisms by which phages take over the machinery of the host during infection. To expand the available collection of phage genomes, we have isolated, sequenced, and assembled the genome sequences of three phages that infect three pathogenic Escherichia coli strains: vB_EcoM_DE15, vB_EcoM_DE16, and vB_EcoM_DE17. Morphological characterization and genomic analysis indicated that all three phages were strictly lytic and free from integrases, virulence factors, toxins, and antimicrobial resistance genes. All three phages contained tRNAs, and especially, vB_EcoM_DE17 contained 25 tRNAs. The genomic features of these phages indicate that natural phages are capable of lysing pathogenic E.coli and have great potential in the biocontrol of bacteria.
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Affiliation(s)
- Jia-Qi Cui
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Wen-Hua Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Can Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Ling Zou
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Hui-Ying Ren
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China.
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5
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Opperman CJ, Wojno J, Goosen W, Warren R. Phages for the treatment of Mycobacterium species. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 201:41-92. [PMID: 37770176 DOI: 10.1016/bs.pmbts.2023.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Highly drug-resistant strains are not uncommon among the Mycobacterium genus, with patients requiring lengthy antibiotic treatment regimens with multiple drugs and harmful side effects. This alarming increase in antibiotic resistance globally has renewed the interest in mycobacteriophage therapy for both Mycobacterium tuberculosis complex and non-tuberculosis mycobacteria. With the increasing number of genetically well-characterized mycobacteriophages and robust engineering tools to convert temperate phages to obligate lytic phages, the phage cache against extensive drug-resistant mycobacteria is constantly expanding. Synergistic effects between phages and TB drugs are also a promising avenue to research, with mycobacteriophages having several additional advantages compared to traditional antibiotics due to their different modes of action. These advantages include less side effects, a narrow host spectrum, biofilm penetration, self-replication at the site of infection and the potential to be manufactured on a large scale. In addition, mycobacteriophage enzymes, not yet in clinical use, warrant further studies with their additional benefits for rupturing host bacteria thereby limiting resistance development as well as showing promise in vitro to act synergistically with TB drugs. Before mycobacteriophage therapy can be envisioned as part of routine care, several obstacles must be overcome to translate in vitro work into clinical practice. Strategies to target intracellular bacteria and selecting phage cocktails to limit cross-resistance remain important avenues to explore. However, insight into pathophysiological host-phage interactions on a molecular level and innovative solutions to transcend mycobacteriophage therapy impediments, offer sufficient encouragement to explore phage therapy. Recently, the first successful clinical studies were performed using a mycobacteriophage-constructed cocktail to treat non-tuberculosis mycobacteria, providing substantial insight into lessons learned and potential pitfalls to avoid in order to ensure favorable outcomes. However, due to mycobacterium strain variation, mycobacteriophage therapy remains personalized, only being utilized in compassionate care cases until there is further regulatory approval. Therefore, identifying the determinants that influence clinical outcomes that can expand the repertoire of mycobacteriophages for therapeutic benefit, remains key for their future application.
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Affiliation(s)
- Christoffel Johannes Opperman
- National Health Laboratory Service, Green Point TB-Laboratory, Cape Town, South Africa; DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa; Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa.
| | - Justyna Wojno
- Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa; Lancet Laboratories, Cape Town, South Africa
| | - Wynand Goosen
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
| | - Rob Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
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6
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Alrafaie AM, Stafford GP. Enterococcal bacteriophage: A survey of the tail associated lysin landscape. Virus Res 2023; 327:199073. [PMID: 36787848 DOI: 10.1016/j.virusres.2023.199073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 02/05/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023]
Abstract
Bacteriophages are viruses that exclusively infect bacteria which require local degradation of cell barriers. This degradation is accomplished by various lysins located mainly within the phage tail structure. In this paper we surveyed and analysed the genomes of 506 isolated bacteriophage and prophage infecting or harboured within the genomes of the medically important Enterococcus faecalis and faecium. We highlight and characterise the major features of the genomes of phage in the morphological groups podovirus, siphovirus and myovirus, and explore their categorisation according to the new ICTV classifications, with a focus on putative extracellular lysins chiefly within tail modules. Our analysis reveals a range of potential cell-wall targeting enzyme domains that are part of tail, tape measure or other predicted base structures of these phages or prophages. These largely fall into protein domains targeting pentapeptide or glycosidic linkages within peptidoglycan but also potentially the enterococcal polysaccharide antigen (EPA) and wall teichoic acids of these species (i.e., Pectinesterases and Phosphodiesterases). Notably, there is a great variety of domain architectures that reveal the diversity of evolutionary solutions to attack the Enterococcus cell wall. Despite this variety, most phage and prophage possess a putative endopeptidase (70%), reflecting the ubiquity of this cell surface barrier. We also identified a predicted lytic transglycosylase domain belonging to the glycosyl hydrolase (GH) family 23 and present exclusively within tape measure proteins. Our data also reveal distinct features of the genomes of podo-, sipho- and myo-type viruses that most likely relate to their size and complexity. Overall, we lay a foundation for expression of recombinant TAL proteins and engineering of enterococcal and other phage that will be invaluable for researchers in this field.
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Affiliation(s)
- Alhassan M Alrafaie
- Integrated BioSciences, School of Clinical Dentistry, University of Sheffield, Sheffield, United Kingdom; Department of Medical Laboratory Sciences, College of Applied Medical Sciences in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia.
| | - Graham P Stafford
- Integrated BioSciences, School of Clinical Dentistry, University of Sheffield, Sheffield, United Kingdom.
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Cui JQ, Liu WH, Zang YX, Zhang C, Zou L, Sun HZ, Pan Q, Ren HY. Characterization and complete genome analysis of a bacteriophage vB_EcoM_DE7 infecting donkey-derived Escherichia coli. Virus Res 2022; 321:198913. [PMID: 36064043 DOI: 10.1016/j.virusres.2022.198913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 12/24/2022]
Abstract
A lytic bacteriophage vB_EcoM_DE7 (hereafter designated DE7) that could infect donkey-derived Escherichia coli was isolated. The bacteriophage was examined by transmission electron microscopy, and the result showed that DE7 belonged to the family Myoviridae. The microbiological characterization revealed that DE7 was stable over a broad range of pHs (3 ∼10) at 40-50 °C. The latent period was 10 min, and the burst size was 43 PFUs/infected cell. The whole-genome sequencing showed that DE7 was a dsDNA virus and had a genome of 86,130 bp. The genome contained 124 predicted open reading frames (ORFs), 35 of which had known functions, including DNA replication and modification, transcriptional regulation, structural and packaging proteins, and host cell lysis. Twenty tRNA genes were identified, but no genes associated with bacterial pathogenicity, lysogeny and drug resistance were identified. BLASTN analysis revealed that phage DE7 had a high sequence identity (96%) with Salmonella phage vB_SPuM_SP116, but it could not lyse any Salmonella strain tested in this study. DE7 was classified as a Felix O1-like virus based on its general characterization and genomic information. Since phage DE7 exhibited high efficacy in lysing E. coli and lacked genes associated with bacterial virulence, antimicrobial resistance and lysogeny, it could be potentially used to control foal diarrhoea caused by E. coli.
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Affiliation(s)
- Jia-Qi Cui
- College of Veterinary medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Wen-Hua Liu
- College of Veterinary medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Ya-Xin Zang
- College of Veterinary medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Can Zhang
- College of Veterinary medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Ling Zou
- College of Veterinary medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Hu-Zhi Sun
- Qingdao Phagepharm Bio-tech Co, Ltd, Qingdao, Shandong, China
| | - Qiang Pan
- Qingdao Phagepharm Bio-tech Co, Ltd, Qingdao, Shandong, China
| | - Hui-Ying Ren
- College of Veterinary medicine, Qingdao Agricultural University, Qingdao, Shandong, China.
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8
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Gonzales MF, Piya DK, Koehler B, Zhang K, Yu Z, Zeng L, Gill JJ. New Insights into the Structure and Assembly of Bacteriophage P1. Viruses 2022; 14:v14040678. [PMID: 35458408 PMCID: PMC9024508 DOI: 10.3390/v14040678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/10/2022] [Accepted: 03/16/2022] [Indexed: 12/10/2022] Open
Abstract
Bacteriophage P1 is the premier transducing phage of E. coli. Despite its prominence in advancing E. coli genetics, modern molecular techniques have not been applied to thoroughly understand P1 structure. Here, we report the proteome of the P1 virion as determined by liquid chromatography tandem mass-spectrometry. Additionally, a library of single-gene knockouts identified the following five previously unknown essential genes: pmgA, pmgB, pmgC, pmgG, and pmgR. In addition, proteolytic processing of the major capsid protein is a known feature of P1 morphogenesis, and we identified the processing site by N-terminal sequencing to be between E120 and S121, producing a 448-residue, 49.3 kDa mature peptide. Furthermore, the P1 defense against restriction (Dar) system consists of six known proteins that are incorporated into the virion during morphogenesis. The largest of these, DarB, is a 250 kDa protein that is believed to translocate into the cell during infection. DarB deletions indicated the presence of an N-terminal packaging signal, and the N-terminal 30 residues of DarB are shown to be sufficient for directing a heterologous reporter protein to the capsid. Taken together, the data expand on essential structural P1 proteins as well as introduces P1 as a nanomachine for cellular delivery.
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Affiliation(s)
- Miguel F. Gonzales
- Center for Phage Technology, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA; (M.F.G.); (D.K.P.); (K.Z.); (Z.Y.); (L.Z.)
- Interdisciplinary Program in Genetics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA
| | - Denish K. Piya
- Center for Phage Technology, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA; (M.F.G.); (D.K.P.); (K.Z.); (Z.Y.); (L.Z.)
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA;
| | - Brian Koehler
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA;
| | - Kailun Zhang
- Center for Phage Technology, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA; (M.F.G.); (D.K.P.); (K.Z.); (Z.Y.); (L.Z.)
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA;
| | - Zihao Yu
- Center for Phage Technology, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA; (M.F.G.); (D.K.P.); (K.Z.); (Z.Y.); (L.Z.)
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA;
| | - Lanying Zeng
- Center for Phage Technology, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA; (M.F.G.); (D.K.P.); (K.Z.); (Z.Y.); (L.Z.)
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA;
| | - Jason J. Gill
- Center for Phage Technology, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA; (M.F.G.); (D.K.P.); (K.Z.); (Z.Y.); (L.Z.)
- Interdisciplinary Program in Genetics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA
- Department of Animal Science, Texas A&M University, 2471 TAMU, College Station, TX 77843, USA
- Correspondence: ; Tel.: +1-979-458-6368
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Gp29 LysA of mycobacteriophage TM4 can hydrolyze peptidoglycan through an N-acetyl-muramoyl-L-alanine amidase activity. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140745. [PMID: 34906734 DOI: 10.1016/j.bbapap.2021.140745] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 01/09/2023]
Abstract
Bacteriophage endolysins are crucial for progeny release at the end of the lytic cycle. Mycobacteriophage's genomes carry a lysin A essential gene, whose product cleaves the peptidoglycan (PG) layer and a lysin B, coding for an esterase, that cleaves the linkage between the mycolic acids and the arabinogalactan-PG complex. Lysin A mycobacteriophage proteins are highly modular and in gp29 (LysA) of phage TM4 three distinctive domains were identified. By bioinformatics analysis the central module was previously found to be similar to an amidase-2 domain family with an N-acetylmuramoyl -L-alanine amidase activity. We demonstrated experimentally that purified LysA is able to lyse a suspension of Micrococcus lysodeikticus and can promote cell lysis when expressed in E. coli and Mycobacterium smegmatis. After incubation of LysA with MDP (Muramyl dipeptide, N-acetyl-muramyl-L-alanyl-D-isoglutamine) we detected the presence of N-acetylmuramic acid (NAcMur) and L-Ala- D- isoGlutamine (L-Ala-D-isoGln) corroborating the proposed muramidase activity of this enzyme. This protein was stabilized at acidic pH in the presence of Zn consistent with the increase of the enzymatic activity under these conditions. By homology modeling, we predicted that the Zn ion is coordinated by His 226, His 335, and Asp 347 and we also identified the amino acid Glu 290 as the catalytic residue. LysA activity was completely abolished in derived mutants on these key residues, suggesting that the PG hydrolysis solely relies on the central domain of the protein.
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Comparative Genomics of Three Novel Jumbo Bacteriophages Infecting Staphylococcus aureus. J Virol 2021; 95:e0239120. [PMID: 34287047 DOI: 10.1128/jvi.02391-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The majority of previously described Staphylococcus aureus bacteriophages belong to three major groups: P68-like podophages, Twort-like or K-like myophages, and a more diverse group of temperate siphophages. Here we present three novel S. aureus "jumbo" phages: MarsHill, Madawaska, and Machias. These phages were isolated from swine production environments in the United States and represent a novel clade of S. aureus myophage. The average genome size for these phages is ∼269 kb with each genome encoding ∼263 predicted protein-coding genes. Phage genome organization and content is similar to known jumbo phages of Bacillus, including AR9 and vB_BpuM-BpSp. All three phages possess genes encoding complete virion and non-virion RNA polymerases, multiple homing endonucleases, and a retron-like reverse transcriptase. Like AR9, all of these phages are presumed to have uracil-substituted DNA which interferes with DNA sequencing. These phages are also able to transduce host plasmids, which is significant as these phages were found circulating in swine production environments and can also infect human S. aureus isolates. Importance of work: This study describes the comparative genomics of three novel S. aureus jumbo phages: MarsHill, Madawaska, and Machias. These three S. aureus myophages represent an emerging class of S. aureus phage. These genomes contain abundant introns which show a pattern consistent with repeated acquisition rather than vertical inheritance, suggesting intron acquisition and loss is an active process in the evolution of these phages. These phages have presumably hypermodified DNA which inhibits sequencing by several different common platforms. Therefore, these phages also represent potential genomic diversity that has been missed due to the limitations of standard sequencing techniques. In particular, such hypermodified genomes may be missed by metagenomic studies due to their resistance to standard sequencing techniques. Phage MarsHill was found to be able to transduce host DNA at levels comparable to that found for other transducing S. aureus phages, making them a potential vector for horizontal gene transfer in the environment.
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Seul A, Brasilès S, Petitpas I, Lurz R, Campanacci V, Cambillau C, Weise F, Zairi M, Tavares P, Auzat I. Biogenesis of a Bacteriophage Long Non-Contractile Tail. J Mol Biol 2021; 433:167112. [PMID: 34153288 DOI: 10.1016/j.jmb.2021.167112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/22/2021] [Accepted: 06/15/2021] [Indexed: 10/21/2022]
Abstract
Siphoviruses are main killers of bacteria. They use a long non-contractile tail to recognize the host cell and to deliver the genome from the viral capsid to the bacterial cytoplasm. Here, we define the molecular organization of the Bacillus subtilis bacteriophage SPP1 ~ 6.8 MDa tail and uncover its biogenesis mechanisms. A complex between gp21 and the tail distal protein (Dit) gp19.1 is assembled first to build the tail cap (gp19.1-gp21Nter) connected by a flexible hinge to the tail fiber (gp21Cter). The tip of the gp21Cter fiber is loosely associated to gp22. The cap provides a platform where tail tube proteins (TTPs) initiate polymerization around the tape measure protein gp18 (TMP), a reaction dependent on the non-structural tail assembly chaperones gp17.5 and gp17.5* (TACs). Gp17.5 is essential for stability of gp18 in the cell. Helical polymerization stops at a precise tube length followed by binding of proteins gp16.1 (TCP) and gp17 (THJP) to build the tail interface for attachment to the capsid portal system. This finding uncovers the function of the extensively conserved gp16.1-homologs in assembly of long tails. All SPP1 tail components, apart from gp22, share homology to conserved proteins whose coding genes' synteny is broadly maintained in siphoviruses. They conceivably represent the minimal essential protein set necessary to build functional long tails. Proteins homologous to SPP1 tail building blocks feature a variety of add-on modules that diversify extensively the tail core structure, expanding its capability to bind host cells and to deliver the viral genome to the bacterial cytoplasm.
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Affiliation(s)
- Anait Seul
- Unité de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS UPR 3296 and IFR115, CNRS, Gif-sur-Yvette, France
| | - Sandrine Brasilès
- Unité de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS UPR 3296 and IFR115, CNRS, Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Isabelle Petitpas
- Unité de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS UPR 3296 and IFR115, CNRS, Gif-sur-Yvette, France
| | - Rudi Lurz
- Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
| | - Valérie Campanacci
- Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS and Universités d'Aix-Marseille I & II, Campus de Luminy, Marseille, France
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS and Universités d'Aix-Marseille I & II, Campus de Luminy, Marseille, France
| | - Frank Weise
- Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
| | - Mohamed Zairi
- Unité de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS UPR 3296 and IFR115, CNRS, Gif-sur-Yvette, France
| | - Paulo Tavares
- Unité de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS UPR 3296 and IFR115, CNRS, Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France.
| | - Isabelle Auzat
- Unité de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS UPR 3296 and IFR115, CNRS, Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France.
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12
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Goswami A, Sharma PR, Agarwal R. Combatting intracellular pathogens using bacteriophage delivery. Crit Rev Microbiol 2021; 47:461-478. [PMID: 33818246 DOI: 10.1080/1040841x.2021.1902266] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Intracellular pathogens reside in specialised compartments within the host cells restricting the access of antibiotics. Insufficient intracellular delivery of antibiotics along with several other resistance mechanisms weaken the efficacy of current therapies. An alternative to antibiotic therapy could be bacteriophage (phage) therapy. Although phage therapy has been in practice for a century against various bacterial infections, the efficacy of phages against intracellular bacteria is still being explored. In this review, we will discuss the advancement and challenges in phage therapy, particularly against intracellular bacterial pathogens. Finally, we will highlight the uptake mechanisms and approaches to overcome the challenges to phage therapy against intracellular bacteria.
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Affiliation(s)
- Avijit Goswami
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru, India
| | - Pallavi Raj Sharma
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru, India
| | - Rachit Agarwal
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru, India
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13
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The Pup-Proteasome System Protects Mycobacteria from Antimicrobial Antifolates. Antimicrob Agents Chemother 2021; 65:AAC.01967-20. [PMID: 33468462 DOI: 10.1128/aac.01967-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/30/2020] [Indexed: 12/21/2022] Open
Abstract
Protein turnover via the Pup-proteasome system (PPS) is essential for nitric oxide resistance and virulence of Mycobacterium tuberculosis, the causative agent of tuberculosis. Our study revealed components of PPS as novel determinants of intrinsic antifolate resistance in both M. tuberculosis and nonpathogenic M. smegmatis The lack of expression of the prokaryotic ubiquitin-like protein (Pup) or the ligase, PafA, responsible for ligating Pup to its protein targets, enhanced antifolate susceptibility in M. smegmatis Cross-species expression of M. tuberculosis homologs restored wild-type resistance to M. smegmatis proteasomal mutants. Targeted deletion of prcA and prcB, encoding the structural components of the PPS proteolytic core, similarly resulted in reduced antifolate resistance. Furthermore, sulfonamides were synergistic with acidified nitrite, and the synergy against mycobacteria was enhanced in the absence of proteasomal activity. In M. tuberculosis, targeted mutagenesis followed by genetic complementation of mpa, encoding the regulatory subunit responsible for translocating pupylated proteins to the proteolytic core, demonstrated a similar function of PPS in antifolate resistance. The overexpression of dihydrofolate reductase, responsible for the reduction of dihydrofolate to tetrahydrofolate, or disruption of the Lonely Guy gene, responsible for PPS-controlled production of cytokinins, abolished PPS-mediated antifolate sensitivity. Together, our results show that PPS protects mycobacteria from antimicrobial antifolates via regulating both folate reduction and cytokinin production.
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14
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Kalapala YC, Sharma PR, Agarwal R. Antimycobacterial Potential of Mycobacteriophage Under Disease-Mimicking Conditions. Front Microbiol 2020; 11:583661. [PMID: 33381088 PMCID: PMC7767895 DOI: 10.3389/fmicb.2020.583661] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/16/2020] [Indexed: 01/05/2023] Open
Abstract
Antibiotic resistance continues to be a major global health risk with an increase in multi-drug resistant infections seen across nearly all bacterial diseases. Mycobacterial infections such as Tuberculosis (TB) and Non-Tuberculosis infections have seen a significant increase in the incidence of multi-drug resistant and extensively drug-resistant infections. With this increase in drug-resistant Mycobacteria, mycobacteriophage therapy offers a promising alternative. However, a comprehensive study on the infection dynamics of mycobacteriophage against their host bacteria and the evolution of bacteriophage (phage) resistance in the bacteria remains elusive. We aim to study the infection dynamics of a phage cocktail against Mycobacteria under various pathophysiological conditions such as low pH, low growth rate and hypoxia. We show that mycobacteriophages are effective against M. smegmatis under various conditions and the phage cocktail prevents emergence of resistance for long durations. Although the phages are able to amplify after infection, the initial multiplicity of infection plays an important role in reducing the bacterial growth and prolonging efficacy. Mycobacteriophages are effective against antibiotic-resistant strains of Mycobacterium and show synergy with antibiotics such as rifampicin and isoniazid. Finally, we also show that mycobacteriophages are efficient against M. tuberculosis both under lag and log phase for several weeks. These findings have important implications for developing phage therapy for Mycobacterium.
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Affiliation(s)
| | | | - Rachit Agarwal
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru, India
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15
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Gong Z, Lv X, Li C, Gu Y, Fan X, Sun Q, Tong Y, Zhao F, Xing S, Pei G, Li Q, Xie L, Xie J. Genomic and proteomic portrait of a novel mycobacteriophage SWU2 isolated from China. INFECTION GENETICS AND EVOLUTION 2020; 87:104665. [PMID: 33279716 DOI: 10.1016/j.meegid.2020.104665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/22/2020] [Accepted: 12/01/2020] [Indexed: 11/30/2022]
Abstract
Phage therapy, especially combination with antibiotics, was revitalized to control the antibiotics resistance. Mycobacteriophage, the phage of mycobacterium with the most notorious Mycobacterium tuberculosis (M. tuberculosis), was intensively explored. A novel mycobacteriophage SWU2 was isolated from a soil sample collected at Nanchang city, Jiangxi province, China, by using Mycolicibacterium smegmatis (M. smegmatis) mc2 155 as the host. Phage morphology and biology were characterized. Phage structure proteins were analyzed by LC-MS/MS. The putative functions of phage proteins and multi-genome comparison were performed with bioinformatics. The transmission electron microscopy result indicated that this phage belongs to Siphoviridae of Caudovirales. Plaques of SWU2 appeared clear but small. In a one-step growth test, we demonstrated that SWU2 had a latent period of 30 min and a logarithmic phase of 120 min. Among the 76 predicted Open Reading Frames (ORFs), 9 ORFs were identified as phage structure proteins of SWU2. The assembled phage genome size is 50,013 bp, with 62.7% of G + C content. SWU2 genome sequence shares 88% identity with Mycobacterium phages HINdeR and Timshel, differing in substitutions, insertions and deletions in SWU2. Phylogenetic tree revealed that SWU2 is grouped into A7 sub-cluster. There are several substitutions, insertions and deletions in SWU2 genome in comparison with close cousin phages HINdeR and Timshel. The new phage adds another dimension of abundance to the mycobacteriophages.
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Affiliation(s)
- Zhen Gong
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Xi Lv
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Chunyan Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Yinzhong Gu
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Xiangyu Fan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China; School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Qingyu Sun
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Feiyang Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Shaozhen Xing
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Guangqian Pei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Qiming Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Longxiang Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, 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 Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China.
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16
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Identification of Uncharacterized Components of Prokaryotic Immune Systems and Their Diverse Eukaryotic Reformulations. J Bacteriol 2020; 202:JB.00365-20. [PMID: 32868406 DOI: 10.1128/jb.00365-20] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/25/2020] [Indexed: 12/19/2022] Open
Abstract
Nucleotide-activated effector deployment, prototyped by interferon-dependent immunity, is a common mechanistic theme shared by immune systems of several animals and prokaryotes. Prokaryotic versions include CRISPR-Cas with the CRISPR polymerase domain, their minimal variants, and systems with second messenger oligonucleotide or dinucleotide synthetase (SMODS). Cyclic or linear oligonucleotide signals in these systems help set a threshold for the activation of potentially deleterious downstream effectors in response to invader detection. We establish such a regulatory mechanism to be a more general principle of immune systems, which can also operate independently of such messengers. Using sensitive sequence analysis and comparative genomics, we identify 12 new prokaryotic immune systems, which we unify by this principle of threshold-dependent effector activation. These display regulatory mechanisms paralleling physiological signaling based on 3'-5' cyclic mononucleotides, NAD+-derived messengers, two- and one-component signaling that includes histidine kinase-based signaling, and proteolytic activation. Furthermore, these systems allowed the identification of multiple new sensory signal sensory components, such as a tetratricopeptide repeat (TPR) scaffold predicted to recognize NAD+-derived signals, unreported versions of the STING domain, prokaryotic YEATS domains, and a predicted nucleotide sensor related to receiver domains. We also identify previously unrecognized invader detection components and effector components, such as prokaryotic versions of the Wnt domain. Finally, we show that there have been multiple acquisitions of unidentified STING domains in eukaryotes, while the TPR scaffold was incorporated into the animal immunity/apoptosis signal-regulating kinase (ASK) signalosome.IMPORTANCE Both prokaryotic and eukaryotic immune systems face the dangers of premature activation of effectors and degradation of self-molecules in the absence of an invader. To mitigate this, they have evolved threshold-setting regulatory mechanisms for the triggering of effectors only upon the detection of a sufficiently strong invader signal. This work defines general templates for such regulation in effector-based immune systems. Using this, we identify several previously uncharacterized prokaryotic immune mechanisms that accomplish the regulation of downstream effector deployment by using nucleotide, NAD+-derived, two-component, and one-component signals paralleling physiological homeostasis. This study has also helped identify several previously unknown sensor and effector modules in these systems. Our findings also augment the growing evidence for the emergence of key animal immunity and chromatin regulatory components from prokaryotic progenitors.
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17
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Fluckiger A, Daillère R, Sassi M, Sixt BS, Liu P, Loos F, Richard C, Rabu C, Alou MT, Goubet AG, Lemaitre F, Ferrere G, Derosa L, Duong CPM, Messaoudene M, Gagné A, Joubert P, De Sordi L, Debarbieux L, Simon S, Scarlata CM, Ayyoub M, Palermo B, Facciolo F, Boidot R, Wheeler R, Boneca IG, Sztupinszki Z, Papp K, Csabai I, Pasolli E, Segata N, Lopez-Otin C, Szallasi Z, Andre F, Iebba V, Quiniou V, Klatzmann D, Boukhalil J, Khelaifia S, Raoult D, Albiges L, Escudier B, Eggermont A, Mami-Chouaib F, Nistico P, Ghiringhelli F, Routy B, Labarrière N, Cattoir V, Kroemer G, Zitvogel L. Cross-reactivity between tumor MHC class I-restricted antigens and an enterococcal bacteriophage. Science 2020; 369:936-942. [PMID: 32820119 DOI: 10.1126/science.aax0701] [Citation(s) in RCA: 206] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 02/28/2020] [Accepted: 06/23/2020] [Indexed: 12/28/2022]
Abstract
Intestinal microbiota have been proposed to induce commensal-specific memory T cells that cross-react with tumor-associated antigens. We identified major histocompatibility complex (MHC) class I-binding epitopes in the tail length tape measure protein (TMP) of a prophage found in the genome of the bacteriophage Enterococcus hirae Mice bearing E. hirae harboring this prophage mounted a TMP-specific H-2Kb-restricted CD8+ T lymphocyte response upon immunotherapy with cyclophosphamide or anti-PD-1 antibodies. Administration of bacterial strains engineered to express the TMP epitope improved immunotherapy in mice. In renal and lung cancer patients, the presence of the enterococcal prophage in stools and expression of a TMP-cross-reactive antigen by tumors correlated with long-term benefit of PD-1 blockade therapy. In melanoma patients, T cell clones recognizing naturally processed cancer antigens that are cross-reactive with microbial peptides were detected.
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Affiliation(s)
- Aurélie Fluckiger
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, U1015, Institut Gustave Roussy, Villejuif, France
| | - Romain Daillère
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, U1015, Institut Gustave Roussy, Villejuif, France.,everImmune, Gustave Roussy Cancer Center, Villejuif, France
| | - Mohamed Sassi
- Université Rennes 1, Laboratoire de Biochimie Pharmaceutique, Inserm U1230 - UPRES EA 2311, Rennes, France
| | - Barbara Susanne Sixt
- Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Department of Molecular Biology, Umeå University, 90187, Umeå, Sweden.,Cell Biology and Metabolomics Platforms, Gustave Roussy Cancer Campus, Villejuif, France.,Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,INSERM U1138, Paris, France.,Université de Paris, Paris, France.,Sorbonne Université, Paris, France
| | - Peng Liu
- Cell Biology and Metabolomics Platforms, Gustave Roussy Cancer Campus, Villejuif, France.,Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,INSERM U1138, Paris, France.,Université de Paris, Paris, France.,Sorbonne Université, Paris, France
| | - Friedemann Loos
- Cell Biology and Metabolomics Platforms, Gustave Roussy Cancer Campus, Villejuif, France.,Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,INSERM U1138, Paris, France.,Université de Paris, Paris, France.,Sorbonne Université, Paris, France
| | - Corentin Richard
- Research Platform in Biological Oncology, Dijon, France.,GIMI Genetic and Immunology Medical Institute, Dijon, France.,University of Burgundy-Franche Comté, Dijon, France
| | - Catherine Rabu
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | - Maryam Tidjani Alou
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, U1015, Institut Gustave Roussy, Villejuif, France.,UMR MEPHI, Aix-Marseille Université, IRD, AP-HM, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Anne-Gaëlle Goubet
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, U1015, Institut Gustave Roussy, Villejuif, France
| | - Fabien Lemaitre
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,everImmune, Gustave Roussy Cancer Center, Villejuif, France
| | - Gladys Ferrere
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, U1015, Institut Gustave Roussy, Villejuif, France
| | - Lisa Derosa
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, U1015, Institut Gustave Roussy, Villejuif, France.,Université Paris-Saclay, Villejuif, F-94805, France
| | - Connie P M Duong
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, U1015, Institut Gustave Roussy, Villejuif, France
| | - Meriem Messaoudene
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Research Center and Department of Cytology and Pathology, Québec City, Québec, Canada
| | - Andréanne Gagné
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Research Center and Department of Cytology and Pathology, Québec City, Québec, Canada
| | - Philippe Joubert
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Research Center and Department of Cytology and Pathology, Québec City, Québec, Canada
| | - Luisa De Sordi
- Bacteriophage, Bacterium, Host Laboratory, Institut Pasteur, F-75015 Paris, France.,Sorbonne Université, Centre de Recherche Saint Antoine, INSERM UMRS_938, Paris, France
| | - Laurent Debarbieux
- Bacteriophage, Bacterium, Host Laboratory, Institut Pasteur, F-75015 Paris, France
| | - Sylvain Simon
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | - Clara-Maria Scarlata
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France
| | - Maha Ayyoub
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France
| | - Belinda Palermo
- Unit of Tumor Immunology and Immunotherapy, Department of Research, Advanced Diagnostics and Technological Innovation, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Francesco Facciolo
- Thoracic Surgery Unit, Department of Surgical Oncology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Romain Boidot
- Unit of Molecular Biology, Department of Biology and Pathology of Tumors, Georges-François Leclerc Anticancer Center, UNICANCER, Dijon, France
| | - Richard Wheeler
- Institut Pasteur, Unit Biology and Genetics of the Bacterial Cell Wall, Paris, France
| | - Ivo Gomperts Boneca
- Institut Pasteur, Unit Biology and Genetics of the Bacterial Cell Wall, Paris, France
| | - Zsofia Sztupinszki
- Computational Health Informatics Program (CHIP), Boston Children's Hospital, Boston, MA, USA
| | - Krisztian Papp
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Istvan Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Carlos Lopez-Otin
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,INSERM U1138, Paris, France.,Université de Paris, Paris, France.,Sorbonne Université, Paris, France.,Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Zoltan Szallasi
- Computational Health Informatics Program (CHIP), Boston Children's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Danish Cancer Society Research Center, Copenhagen, Denmark.,MTA-SE-NAP, Brain Metastasis Research Group, 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Fabrice Andre
- Department of Cancer Medicine, Breast Cancer Committee, Gustave Roussy, Villejuif, France.,INSERM Unit 981, Gustave Roussy, Villejuif, France
| | - Valerio Iebba
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, U1015, Institut Gustave Roussy, Villejuif, France.,Department of Medical Sciences, University of Trieste, 34137 Trieste, Italy
| | - Valentin Quiniou
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center in Biotherapy (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), F-75651, Paris, France.,Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), F-75651, Paris, France
| | - David Klatzmann
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center in Biotherapy (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), F-75651, Paris, France.,Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), F-75651, Paris, France
| | - Jacques Boukhalil
- UMR MEPHI, Aix-Marseille Université, IRD, AP-HM, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Saber Khelaifia
- UMR MEPHI, Aix-Marseille Université, IRD, AP-HM, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Didier Raoult
- UMR MEPHI, Aix-Marseille Université, IRD, AP-HM, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Laurence Albiges
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Bernard Escudier
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Department of Medical Oncology, Gustave Roussy, Villejuif, France.,INSERM U981, GRCC, Villejuif, France
| | - Alexander Eggermont
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Princess Maxima Center, CS 3584 Utrecht, the Netherlands
| | - Fathia Mami-Chouaib
- INSERM UMR 1186, Integrative Tumor Immunology and Immunotherapy, Gustave Roussy, Fac. de Médecine - Univ. Paris-Sud, Université Paris-Saclay, 94805, Villejuif, France
| | - Paola Nistico
- Unit of Tumor Immunology and Immunotherapy, Department of Research, Advanced Diagnostics and Technological Innovation, IRCCS Regina Elena National Cancer Institute, Rome, Italy.,Thoracic Surgery Unit, Department of Surgical Oncology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | | | - Bertrand Routy
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Research Center and Department of Cytology and Pathology, Québec City, Québec, Canada.,Division d'Hémato-Oncologie, Département de Médicine, Centre Hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
| | - Nathalie Labarrière
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | - Vincent Cattoir
- Université Rennes 1, Laboratoire de Biochimie Pharmaceutique, Inserm U1230 - UPRES EA 2311, Rennes, France.,CHU de Rennes - Hôpital Ponchaillou, Service de Bactériologie-Hygiène Hospitalière, Rennes, France.,CNR de la Résistance aux Antibiotiques (laboratoire associé 'Entérocoques'), Rennes, France
| | - Guido Kroemer
- Cell Biology and Metabolomics Platforms, Gustave Roussy Cancer Campus, Villejuif, France. .,Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,INSERM U1138, Paris, France.,Université de Paris, Paris, France.,Sorbonne Université, Paris, France.,Pôle de Biologie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France.,Department of Women's and Children's Health, Karolinska University Hospital, 1 Stockholm, Sweden.,Suzhou Institute for Systems Biology, Chinese Academy of Medical Sciences, Suzhou, China.,Institut Universitaire de France, Paris, France
| | - Laurence Zitvogel
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France. .,Institut National de la Santé et de la Recherche Médicale, U1015, Institut Gustave Roussy, Villejuif, France.,Université Paris-Saclay, Villejuif, F-94805, France.,Suzhou Institute for Systems Biology, Chinese Academy of Medical Sciences, Suzhou, China
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18
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Gunathilake KMD, Halmillawewa AP, MacKenzie KD, Perry BJ, Yost CK, Hynes MF. A bacteriophage infecting Mesorhizobium species has a prolate capsid and shows similarities to a family of Caulobacter crescentus phages. Can J Microbiol 2020; 67:147-160. [PMID: 32905709 DOI: 10.1139/cjm-2020-0281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mesorhizobium phage vB_MloS_Cp1R7A-A1 was isolated from soil planted with chickpea in Saskatchewan. It is dissimilar in sequence and morphology to previously described rhizobiophages. It is a B3 morphotype virus with a distinct prolate capsid and belongs to the tailed phage family Siphoviridae. Its genome has a GC content of 60.3% and 238 predicted genes. Putative functions were predicted for 57 genes, which include 27 tRNA genes with anticodons corresponding to 18 amino acids. This represents the highest number of tRNA genes reported yet in a rhizobiophage. The gene arrangement shows a partially modular organization. Most of the structural genes are found in one module, whereas tRNA genes are in another. Genes for replication, recombination, and nucleotide metabolism form the third module. The arrangement of the replication module resembles the replication module of Enterobacteria phage T5, raising the possibility that it uses a recombination-based replication mechanism, but there is also a suggestion that a T7-like replication mechanism could be used. Phage termini appear to be long direct repeats of just over 12 kb in length. Phylogenetic analysis revealed that Cp1R7A-A1 is more closely related to PhiCbK-like Caulobacter phages and other B3 morphotype phages than to other rhizobiophages sequenced thus far.
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Affiliation(s)
| | - Anupama P Halmillawewa
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.,Department of Microbiology, University of Kelaniya, Sri Lanka
| | - Keith D MacKenzie
- Biology Department, University of Regina, Regina Saskatchewan, Canada
| | - Benjamin J Perry
- Biology Department, University of Regina, Regina Saskatchewan, Canada.,Department of Microbiology, University of Otago, Dunedin, New Zealand
| | | | - Michael F Hynes
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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19
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Maitra A, Munshi T, Healy J, Martin LT, Vollmer W, Keep NH, Bhakta S. Cell wall peptidoglycan in Mycobacterium tuberculosis: An Achilles' heel for the TB-causing pathogen. FEMS Microbiol Rev 2020; 43:548-575. [PMID: 31183501 PMCID: PMC6736417 DOI: 10.1093/femsre/fuz016] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/07/2019] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis (TB), caused by the intracellular pathogen Mycobacterium tuberculosis, remains one of the leading causes of mortality across the world. There is an urgent requirement to build a robust arsenal of effective antimicrobials, targeting novel molecular mechanisms to overcome the challenges posed by the increase of antibiotic resistance in TB. Mycobacterium tuberculosis has a unique cell envelope structure and composition, containing a peptidoglycan layer that is essential for maintaining cellular integrity and for virulence. The enzymes involved in the biosynthesis, degradation, remodelling and recycling of peptidoglycan have resurfaced as attractive targets for anti-infective drug discovery. Here, we review the importance of peptidoglycan, including the structure, function and regulation of key enzymes involved in its metabolism. We also discuss known inhibitors of ATP-dependent Mur ligases, and discuss the potential for the development of pan-enzyme inhibitors targeting multiple Mur ligases.
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Affiliation(s)
- Arundhati Maitra
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Tulika Munshi
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Jess Healy
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Liam T Martin
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Waldemar Vollmer
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Nicholas H Keep
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
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20
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Gustine JN, Au MB, Haserick JR, Hett EC, Rubin EJ, Gibson FC, Deng LL. Cell Wall Hydrolytic Enzymes Enhance Antimicrobial Drug Activity Against Mycobacterium. Curr Microbiol 2019; 76:398-409. [PMID: 30603964 DOI: 10.1007/s00284-018-1620-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 12/19/2018] [Indexed: 01/09/2023]
Abstract
Cell wall hydrolases are enzymes that cleave bacterial cell walls by hydrolyzing specific bonds within peptidoglycan and other portions of the envelope. Two major sources of hydrolases in nature are from hosts and microbes. This study specifically investigated whether cell wall hydrolytic enzymes could be employed as exogenous reagents to augment the efficacy of antimicrobial agents against mycobacteria. Mycobacterium smegmatis cultures were treated with ten conventional antibiotics and six anti-tuberculosis drugs-alone or in combination with cell wall hydrolases. Culture turbidity, colony-forming units (CFUs), vital staining, and oxygen consumption were all monitored. The majority of antimicrobial agents tested alone only had minimal inhibitory effects on bacterial growth. However, the combination of cell wall hydrolases and most of the antimicrobial agents tested, revealed a synergistic effect that resulted in significant enhancement of bactericidal activity. Vital staining showed increased cellular damage when M. smegmatis and Mycobacterium bovis bacillus Calmette-Guérin (M. bovis BCG) were treated with both drug and lysozyme. Respiration analysis revealed stress responses when cells were treated with lysozyme and drugs individually, and an acute increase in oxygen consumption when treated with both drug and lysozyme. Similar trends were also observed for the other three enzymes (hydrolase-30, RipA-His6 and RpfE-His6) evaluated. These findings demonstrated that cell wall hydrolytic enzymes, as a group of biological agents, have the capability to improve the potency of many current antimicrobial drugs and render ineffective antibiotics effective in killing mycobacteria. This combinatorial approach may represent an important strategy to eliminate drug-resistant bacteria.
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Affiliation(s)
- Joshua N Gustine
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Matthew B Au
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - John R Haserick
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Erik C Hett
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA.,Merck, Exploratory Science Center, Chemical Biology, Cambridge, MA, USA
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Frank C Gibson
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Lingyi L Deng
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
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21
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Marinelli LJ, Piuri M, Hatfull GF. Genetic Manipulation of Lytic Bacteriophages with BRED: Bacteriophage Recombineering of Electroporated DNA. Methods Mol Biol 2019; 1898:69-80. [PMID: 30570724 DOI: 10.1007/978-1-4939-8940-9_6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We describe a recombineering-based method for the genetic manipulation of lytically replicating bacteriophages, focusing on mycobacteriophages. The approach utilizes recombineering-proficient strains of Mycobacterium smegmatis and employs a cotransformation strategy with purified phage genomic DNA and a mutagenic substrate, which selects for only those cells that are competent to take up DNA. The cotransformation method, combined with the high rates of recombination obtained in M. smegmatis recombineering strains, allows for the efficient and rapid generation of bacteriophage mutants.
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Affiliation(s)
- Laura J Marinelli
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina
- Laboratorio "Bacteriófagos y Aplicaciones Biotecnológicas", Departamento de Química Biológica, FCEyN, UBA, Ciudad Universitaria, Ciudad Autónoma de Buenos Aires, Argentina
| | - Graham F Hatfull
- Department of Biological Sciences and Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, PA, USA
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22
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Biodiversity of Streptococcus thermophilus Phages in Global Dairy Fermentations. Viruses 2018; 10:v10100577. [PMID: 30360457 PMCID: PMC6213268 DOI: 10.3390/v10100577] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 12/26/2022] Open
Abstract
Streptococcus thermophilus strains are among the most widely employed starter cultures in dairy fermentations, second only to those of Lactococcus lactis. The extensive application of this species provides considerable opportunity for the proliferation of its infecting (bacterio)phages. Until recently, dairy streptococcal phages were classified into two groups (cos and pac groups), while more recently, two additional groups have been identified (5093 and 987 groups). This highlights the requirement for consistent monitoring of phage populations in the industry. Here, we report a survey of 35 samples of whey derived from 27 dairy fermentation facilities in ten countries against a panel of S. thermophilus strains. This culminated in the identification of 172 plaque isolates, which were characterized by multiplex PCR, restriction fragment length polymorphism analysis, and host range profiling. Based on this characterisation, 39 distinct isolates representing all four phage groups were selected for genome sequencing. Genetic diversity was observed among the cos isolates and correlations between receptor binding protein phylogeny and host range were also clear within this phage group. The 987 phages isolated within this study shared high levels of sequence similarity, yet displayed reduced levels of similarity to those identified in previous studies, indicating that they are subject to ongoing genetic diversification.
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23
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Catalão MJ, Pimentel M. Mycobacteriophage Lysis Enzymes: Targeting the Mycobacterial Cell Envelope. Viruses 2018; 10:E428. [PMID: 30110929 PMCID: PMC6116114 DOI: 10.3390/v10080428] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 08/07/2018] [Accepted: 08/12/2018] [Indexed: 01/18/2023] Open
Abstract
Mycobacteriophages are viruses that specifically infect mycobacteria, which ultimately culminate in host cell death. Dedicated enzymes targeting the complex mycobacterial cell envelope arrangement have been identified in mycobacteriophage genomes, thus being potential candidates as antibacterial agents. These comprise lipolytic enzymes that target the mycolic acid-containing outer membrane and peptidoglycan hydrolases responsive to the atypical mycobacterial peptidoglycan layer. In the recent years, a remarkable progress has been made, particularly on the comprehension of the mechanisms of bacteriophage lysis proteins activity and regulation. Notwithstanding, information about mycobacteriophages lysis strategies is limited and is mainly represented by the studies performed with mycobacteriophage Ms6. Since mycobacteriophages target a specific group of bacteria, which include Mycobacterium tuberculosis responsible for one of the leading causes of death worldwide, exploitation of the use of these lytic enzymes demands a special attention, as they may be an alternative to tackle multidrug resistant tuberculosis. This review focuses on the current knowledge of the function of lysis proteins encoded by mycobacteriophages and their potential applications, which may contribute to increasing the effectiveness of antimycobacterial therapy.
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Affiliation(s)
- Maria João Catalão
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal.
| | - Madalena Pimentel
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal.
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24
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25
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Enzymes and Mechanisms Employed by Tailed Bacteriophages to Breach the Bacterial Cell Barriers. Viruses 2018; 10:v10080396. [PMID: 30060520 PMCID: PMC6116005 DOI: 10.3390/v10080396] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/23/2018] [Accepted: 07/26/2018] [Indexed: 01/07/2023] Open
Abstract
Monoderm bacteria possess a cell envelope made of a cytoplasmic membrane and a cell wall, whereas diderm bacteria have and extra lipid layer, the outer membrane, covering the cell wall. Both cell types can also produce extracellular protective coats composed of polymeric substances like, for example, polysaccharidic capsules. Many of these structures form a tight physical barrier impenetrable by phage virus particles. Tailed phages evolved strategies/functions to overcome the different layers of the bacterial cell envelope, first to deliver the genetic material to the host cell cytoplasm for virus multiplication, and then to release the virion offspring at the end of the reproductive cycle. There is however a major difference between these two crucial steps of the phage infection cycle: virus entry cannot compromise cell viability, whereas effective virion progeny release requires host cell lysis. Here we present an overview of the viral structures, key protein players and mechanisms underlying phage DNA entry to bacteria, and then escape of the newly-formed virus particles from infected hosts. Understanding the biological context and mode of action of the phage-derived enzymes that compromise the bacterial cell envelope may provide valuable information for their application as antimicrobials.
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26
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Abstract
In a view of growing interest in bacteriophages as the most abundant members of microbial communities and as antibacterial agents, reliable methods for bacteriophage long-term preservation, that warrant the access to original or mutant stocks of unchanged properties, have become of crucial importance. A storage method that retains the infectivity of any kind of bacteriophage virions, either in a cell lysate or in a purified suspension, does not exist, due to the enormous diversity of bacteriophages and hence the differentiation of their sensitivity to various storage conditions. Here, we describe a method of long-term bacteriophage preservation, which is based on freezing of freshly infected susceptible bacteria at early stages of bacteriophage development. The infected bacteria release mature bacteriophages upon melting enabling the recovery of bacteriophage virions with high efficiency. The only limitation of this method is the sensitivity of bacteriophage host to deep-freezing, and thus it can be used for the long-term preservation of the vast majority of bacteriophages.
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Affiliation(s)
- Małgorzata B Łobocka
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Pawińskiego 5A, Warsaw, 02-106, Poland.
- Faculty of Agriculture and Biology, Autonomous Department of Microbial Biology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, Warsaw, 02-776, Poland.
| | - Aleksandra Głowacka
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Pawińskiego 5A, Warsaw, 02-106, Poland
| | - Piotr Golec
- Laboratory of Molecular Biology (affiliated with the University of Gdańsk), Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Pawińskiego 5A, Gdańsk, 02-106, Poland
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27
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Khakhum N, Yordpratum U, Boonmee A, Tattawasart U, Rodrigues JLM, Sermswan RW. Cloning, expression, and characterization of a peptidoglycan hydrolase from the Burkholderia pseudomallei phage ST79. AMB Express 2016; 6:77. [PMID: 27637947 PMCID: PMC5025407 DOI: 10.1186/s13568-016-0251-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 09/08/2016] [Indexed: 01/28/2023] Open
Abstract
The lytic phage ST79 of Burkholderia pseudomallei can lyse a broad range of its host including antibiotic resistant isolates from within using a set of proteins, holin, lysB, lysC and endolysin, a peptidoglycan (PG) hydrolase enzyme. The phage ST79 endolysin gene identified as peptidase M15A was cloned, expressed and purified to evaluate its potential to lyse pathogenic bacteria. The molecular size of the purified enzyme is approximately 18 kDa and the in silico study cited here indicated the presence of a zinc-binding domain predicted to be a member of the subfamily A of a metallopeptidase. Its activity, however, was reduced by the presence of Zn2+. When Escherichia coli PG was used as a substrate and subjected to digestion for 5 min with 3 μg/ml of enzyme, the peptidase M15A showed 2 times higher in lysis efficiency when compared to the commercial lysozyme. The enzyme works in a broad alkaligenic pH range of 7.5–9.0 and temperatures from 25 to 42 °C. The enzyme was able to lyse 18 Gram-negative bacteria in which the outer membrane was permeabilized by chloroform treatment. Interestingly, it also lysed Enterococcus sp., but not other Gram-positive bacteria. In general, endolysin cannot lyse Gram-negative bacteria from outside, however, the cationic amphipathic C-terminal in some endolysins showed permeability to Gram-negative outer membranes. Genetically engineered ST79 peptidase M15A that showed a broad spectrum against Gram-negative bacterial PG or, in combination with an antibiotic the same way as combined drug methodology, could facilitate an effective treatment of severe or antibiotic resistant cases.
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28
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Mahony J, Alqarni M, Stockdale S, Spinelli S, Feyereisen M, Cambillau C, Sinderen DV. Functional and structural dissection of the tape measure protein of lactococcal phage TP901-1. Sci Rep 2016; 6:36667. [PMID: 27824135 PMCID: PMC5099701 DOI: 10.1038/srep36667] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/18/2016] [Indexed: 01/22/2023] Open
Abstract
The tail tape measure protein (TMP) of tailed bacteriophages (also called phages) dictates the tail length and facilitates DNA transit to the cell cytoplasm during infection. Here, a thorough mutational analysis of the TMP from lactococcal phage TP901-1 (TMPTP901-1) was undertaken. We generated 56 mutants aimed at defining TMPTP901-1 domains that are essential for tail assembly and successful infection. Through analysis of the derived mutants, we determined that TP901-1 infectivity requires the N-terminal 154 aa residues, the C-terminal 60 residues and the first predicted hydrophobic region of TMPTP901-1 as a minimum. Furthermore, the role of TMPTP901-1 in tail length determination was visualized by electron microscopic imaging of TMP-deletion mutants. The inverse linear correlation between the extent of TMPTP901-1-encoding gene deletions and tail length of the corresponding virion provides an estimate of TMPTP901-1 regions interacting with the connector or involved in initiator complex formation. This study represents the most thorough characterisation of a TMP from a Gram-positive host-infecting phage and provides essential advances to understanding its role in virion assembly, morphology and infection.
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Affiliation(s)
- Jennifer Mahony
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Mona Alqarni
- School of Microbiology, University College Cork, Cork, Ireland
| | - Stephen Stockdale
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Silvia Spinelli
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Marseille, France.,Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, Marseille, France
| | | | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Marseille, France.,Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, Marseille, France
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
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29
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van Wyk N, Drancourt M, Henrissat B, Kremer L. Current perspectives on the families of glycoside hydrolases ofMycobacterium tuberculosis: their importance and prospects for assigning function to unknowns. Glycobiology 2016; 27:112-122. [DOI: 10.1093/glycob/cww099] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 08/28/2016] [Accepted: 09/26/2016] [Indexed: 11/14/2022] Open
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30
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Abstract
The complex cell envelope is a hallmark of mycobacteria and is anchored by the peptidoglycan layer, which is similar to that of Escherichia coli and a number of other bacteria but with modifications to the monomeric units and other structural complexities that are likely related to a role for the peptidoglycan in stabilizing the mycolyl-arabinogalactan-peptidoglycan complex (MAPc). In this article, we will review the genetics of several aspects of peptidoglycan biosynthesis in mycobacteria, including the production of monomeric precursors in the cytoplasm, assembly of the monomers into the mature wall, cell wall turnover, and cell division. Finally, we will touch upon the resistance of mycobacteria to β-lactam antibiotics, an important class of drugs that, until recently, have not been extensively exploited as potential antimycobacterial agents. We will also note areas of research where there are still unanswered questions.
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31
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Korol N, Van den Bossche A, Romaniuk L, Noben JP, Lavigne R, Tovkach F. Experimental evidence for proteins constituting virion components and particle morphogenesis of bacteriophage ZF40. FEMS Microbiol Lett 2016; 363:fnw042. [PMID: 26887841 DOI: 10.1093/femsle/fnw042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2016] [Indexed: 11/13/2022] Open
Abstract
Bacteriophage ZF40 is the only currently available, temperate Myoviridae phage infecting the potato pathogen Pectobacterium carotovorum subsp. carotovorum. Despite its unusual tail morphology, its major tail sheath and tube proteins remained uncharacterized after the initial genome annotation. Using ESI tandem mass-spectrometry, 24 structural proteins of the ZF40 virion were identified, with a sequence coverage ranging between 15.8% and 87.8%. The putative function of 16 proteins could be elucidated based on secondary structure analysis and conservative domain searches. The experimental annotation of 35% of the encoded gene products within the structural region of the genome represents a complete view of the virion structure, which can serve as the basis for future structural analysis as a model phage.
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Affiliation(s)
- Natalia Korol
- Department of Bacteriophage Molecular Genetics, D. K. Zabolotny Institute of Microbiology and Virology, NAS of Ukraine, D03680 Kyiv, Ukraine
| | - An Van den Bossche
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium Division of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Liudmyla Romaniuk
- Department of Bacteriophage Molecular Genetics, D. K. Zabolotny Institute of Microbiology and Virology, NAS of Ukraine, D03680 Kyiv, Ukraine
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnationale Universiteit Limburg, School of Life Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
| | - Fedor Tovkach
- Department of Bacteriophage Molecular Genetics, D. K. Zabolotny Institute of Microbiology and Virology, NAS of Ukraine, D03680 Kyiv, Ukraine
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32
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Dynamics of Mycobacteriophage-Mycobacterial Host Interaction: Evidence for Secondary Mechanisms for Host Lethality. Appl Environ Microbiol 2015; 82:124-33. [PMID: 26475112 DOI: 10.1128/aem.02700-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 10/12/2015] [Indexed: 12/15/2022] Open
Abstract
Mycobacteriophages infect mycobacteria, resulting in their death. Therefore, the possibility of using them as therapeutic agents against the deadly mycobacterial disease tuberculosis (TB) is of great interest. To obtain better insight into the dynamics of mycobacterial inactivation by mycobacteriophages, this study was initiated using mycobacteriophage D29 and Mycobacterium smegmatis as the phage-host system. Here, we implemented a goal-oriented iterative cycle of experiments on one hand and mathematical modeling combined with Monte Carlo simulations on the other. This integrative approach lends valuable insight into the detailed kinetics of bacterium-phage interactions. We measured time-dependent changes in host viability during the growth of phage D29 in M. smegmatis at different multiplicities of infection (MOI). The predictions emerging out of theoretical analyses were further examined using biochemical and cell biological assays. In a phage-host interaction system where multiple rounds of infection are allowed to take place, cell counts drop more rapidly than expected if cell lysis is considered the only mechanism for cell death. The phenomenon could be explained by considering a secondary factor for cell death in addition to lysis. Further investigations reveal that phage infection leads to the increased production of superoxide radicals, which appears to be the secondary factor. Therefore, mycobacteriophage D29 can function as an effective antimycobacterial agent, the killing potential of which may be amplified through secondary mechanisms.
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33
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van der Merwe RG, van Helden PD, Warren RM, Sampson SL, Gey van Pittius NC. Phage-based detection of bacterial pathogens. Analyst 2015; 139:2617-26. [PMID: 24658771 DOI: 10.1039/c4an00208c] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bacterial pathogens cause significant morbidity and mortality annually to both humans and animals. With the rampant spread of drug resistance and the diminishing effectiveness of current antibiotics, there is a pressing need for effective diagnostics for detection of bacterial pathogens and their drug resistances. Bacteriophages offer several unique opportunities for bacterial detection. This review highlights the means by which bacteriophages have been utilized to achieve and facilitate specific bacterial detection.
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Affiliation(s)
- R G van der Merwe
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
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34
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EC300: a phage-based, bacteriolysin-like protein with enhanced antibacterial activity against Enterococcus faecalis. Appl Microbiol Biotechnol 2015; 99:5137-49. [DOI: 10.1007/s00253-015-6483-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 10/23/2022]
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35
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Ehebauer MT, Zimmermann M, Jakobi AJ, Noens EE, Laubitz D, Cichocki B, Marrakchi H, Lanéelle MA, Daffé M, Sachse C, Dziembowski A, Sauer U, Wilmanns M. Characterization of the mycobacterial acyl-CoA carboxylase holo complexes reveals their functional expansion into amino acid catabolism. PLoS Pathog 2015; 11:e1004623. [PMID: 25695631 PMCID: PMC4347857 DOI: 10.1371/journal.ppat.1004623] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 12/11/2014] [Indexed: 01/22/2023] Open
Abstract
Biotin-mediated carboxylation of short-chain fatty acid coenzyme A esters is a key
step in lipid biosynthesis that is carried out by multienzyme complexes to extend
fatty acids by one methylene group. Pathogenic mycobacteria have an unusually high
redundancy of carboxyltransferase genes and biotin carboxylase genes, creating
multiple combinations of protein/protein complexes of unknown overall composition and
functional readout. By combining pull-down assays with mass spectrometry, we
identified nine binary protein/protein interactions and four validated holo
acyl-coenzyme A carboxylase complexes. We investigated one of these - the AccD1-AccA1
complex from Mycobacterium tuberculosis with hitherto unknown
physiological function. Using genetics, metabolomics and biochemistry we found that
this complex is involved in branched amino-acid catabolism with methylcrotonyl
coenzyme A as the substrate. We then determined its overall architecture by electron
microscopy and found it to be a four-layered dodecameric arrangement that matches the
overall dimensions of a distantly related methylcrotonyl coenzyme A holo complex. Our
data argue in favor of distinct structural requirements for biotin-mediated
γ-carboxylation of α−β unsaturated acid esters and will
advance the categorization of acyl-coenzyme A carboxylase complexes. Knowledge about
the underlying structural/functional relationships will be crucial to make the target
category amenable for future biomedical applications. Tuberculosis is deadly human disease caused by infection with the bacterium
Mycobacterium tuberculosis. This pathogen has a complex
metabolism with many genes required for the synthesis of components of its unique
cell envelope. We have investigated a family of closely related genes coding for
different acyl CoA carboxylase enzyme complexes with previously unexplained genetic
redundancy that have been thought to have an involvement in the synthesis of these
cell envelope components. We identified five functional multienzyme complexes. Of the
two complexes with hitherto unknown function we chose to investigate, one
specifically and to our surprise it is required for the degradation of the amino acid
leucine. To our knowledge this is the first demonstration that mycobacteria have a
specific pathway for leucine degradation and thus broaden the functional diversity
associated with acyl CoA carboxylase coding genes.
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Affiliation(s)
| | | | - Arjen J. Jakobi
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg,
Germany
- European Molecular Biology Laboratory, Structural Biology and Computational
Biology Programme, Heidelberg, Germany
| | - Elke E. Noens
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg,
Germany
| | - Daniel Laubitz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw,
Poland
- Department of Genetics & Biotechnology, Warsaw University, Warsaw,
Poland
| | - Bogdan Cichocki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw,
Poland
- Department of Genetics & Biotechnology, Warsaw University, Warsaw,
Poland
| | - Hedia Marrakchi
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de
Biologie Structurale, Tuberculosis & Infection Biology Department, Toulouse,
France; Université Paul Sabatier, Toulouse, France
| | - Marie-Antoinette Lanéelle
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de
Biologie Structurale, Tuberculosis & Infection Biology Department, Toulouse,
France; Université Paul Sabatier, Toulouse, France
| | - Mamadou Daffé
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de
Biologie Structurale, Tuberculosis & Infection Biology Department, Toulouse,
France; Université Paul Sabatier, Toulouse, France
| | - Carsten Sachse
- European Molecular Biology Laboratory, Structural Biology and Computational
Biology Programme, Heidelberg, Germany
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw,
Poland
- Department of Genetics & Biotechnology, Warsaw University, Warsaw,
Poland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich,
Switzerland
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg,
Germany
- Center for Structural Systems Biology, Hamburg, Germany
- * E-mail:
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36
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Gan Y, Yao Y, Guo S. The dormant cells of Mycobacterium tuberculosis may be resuscitated by targeting-expression system of recombinant mycobacteriophage-Rpf: implication of shorter course of TB chemotherapy in the future. Med Hypotheses 2015; 84:477-80. [PMID: 25691378 DOI: 10.1016/j.mehy.2015.01.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 01/30/2015] [Indexed: 11/24/2022]
Abstract
Here we hypothesized that dormant cells of Mycobacterium tuberculosis (M. tuberculosis) may be resuscitated by a new expression system of recombinant mycobacteriophage-resuscitation-promoting factor (Rpf). In this system, gene of targeted Rpf was cloned into mycobacteriophage genome, since mycobacteriophages possess several characteristics, including automatic identification and specific infection of M. tuberculosis. Thus the targeted delivery and endogenous expression of Rpf to the infected area of M. tuberculosis can be realized, followed by resuscitating the dormant cells of M. tuberculosis. Finally, these resuscitated M. tuberculosis can be thoroughly killed by a strong short-term subsequent chemotherapy, which makes the course of TB chemotherapy much shorter in the future compared to simple chemotherapy. Early studies have confirmed that dormant cells of M. tuberculosis can be resuscitated by Rpf in vitro, but so far, there is no report that Rpf can succeed in resuscitating dormant cells of M. tuberculosis in vivo, the reason may be that it is difficult for purified Rpf to remain active in vivo, especially to achieve targeted delivery of exogenous Rpf to the infected area of dormant cells of M. tuberculosis. Mycobacteriophage is a virus, capable of specifically identifying and infecting mycobacterium, such as M. tuberculosis. Several studies show that motif 3-containing proteins have peptidoglycan-hydrolysing activity and that while this activity is not required for mycobacteriophage viability, it facilitates efficient infection and DNA injection of mycobacteriophage (including motif 3 protein) into stationary phase cells. Thus this expression system can achieve targeted delivery and endogenous expression of Rpf to infected area of dormant cells of M. tuberculosis. Finally, we discuss the implication of this recombinant expression system for shortening the course of TB chemotherapy.
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Affiliation(s)
- Yiling Gan
- Department of Respiratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Yiyong Yao
- Department of Respiratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Shuliang Guo
- Department of Respiratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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37
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Marinelli LJ, Hatfull GF, Piuri M. Recombineering: A powerful tool for modification of bacteriophage genomes. BACTERIOPHAGE 2014; 2:5-14. [PMID: 22666652 PMCID: PMC3357384 DOI: 10.4161/bact.18778] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Recombineering, a recently developed technique for efficient genetic manipulation of bacteria, is facilitated by phage-derived recombination proteins and has the advantage of using DNA substrates with short regions of homology. This system was first developed in E. coli but has since been adapted for use in other bacteria. It is now widely used in a number of different systems for a variety of purposes, and the construction of chromosomal gene knockouts, deletions, insertions, point mutations, as well as in vivo cloning, mutagenesis of bacterial artificial chromosomes and phasmids, and the construction of genomic libraries has been reported. However, these methods also can be effectively applied to the genetic modification of bacteriophage genomes, in both their prophage and lytically growing states. The ever-growing collection of fully sequenced bacteriophages raises more questions than they answer, including the unknown functions of vast numbers of genes with no known homologs and of unknown function. Recombineering of phage genomes is central to addressing these questions, enabling the simple construction of mutants, determination of gene essentiality, and elucidation of gene function. In turn, advances in our understanding of phage genomics should present similar recombineering tools for dissecting a multitude of other genetically naïve bacterial systems.
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38
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Wittmann J, Gartemann KH, Eichenlaub R, Dreiseikelmann B. Genomic and molecular analysis of phage CMP1 from Clavibacter michiganensis subspecies michiganensis. BACTERIOPHAGE 2014; 1:6-14. [PMID: 21687530 DOI: 10.4161/bact.1.1.13873] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 09/30/2010] [Accepted: 10/04/2010] [Indexed: 11/19/2022]
Abstract
Bacteriophage CMP1 is a member of the Siphoviridae family that infects specifically the plant-pathogen Clavibacter michiganensis subsp. michiganensis. The linear double- stranded DNA is terminally redundant and not circularly permuted. The complete nucleotide sequence of the bacteriophage CMP1 genome consists of 58,652 bp including the terminal redundant ends of 791 bp. The G+C content of the phage (57%) is significantly lower than that of its host (72.66%). 74 potential open reading frames were identified and annotated by different bioinformatic tools. Two large clusters which encode the early and the late functions could be identified which are divergently transcribed. There are only a few hypothetical gene products with conserved domains and significant similarity to sequences from the databases. Functional analyses confirmed the activity of four gene products, an endonuclease, an exonuclease, a single-stranded DNA binding protein and a thymidylate synthase. Partial genomic sequences of CN77, a phage of Clavibacter michiganensis subsp. nebraskensis, revealed a similar genome structure and significant similarities on the level of deduced amino acid sequences. An endolysin with peptidase activity has been identified for both phages, which may be good tools for disease control of tomato plants against Clavibacter infections.
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Affiliation(s)
- Johannes Wittmann
- Department of Microbiology/Genetechnology; Faculty of Biology; University of Bielefeld Universitaetsstr; Bielefeld, Germany
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39
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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] [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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40
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Controlling strategy of dormant Mycobacterium tuberculosis. Chin Med J (Engl) 2014. [DOI: 10.1097/00029330-201409200-00022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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41
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Chandra G, Chater KF. Developmental biology of Streptomyces from the perspective of 100 actinobacterial genome sequences. FEMS Microbiol Rev 2014; 38:345-79. [PMID: 24164321 PMCID: PMC4255298 DOI: 10.1111/1574-6976.12047] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 08/06/2013] [Accepted: 08/20/2013] [Indexed: 12/22/2022] Open
Abstract
To illuminate the evolution and mechanisms of actinobacterial complexity, we evaluate the distribution and origins of known Streptomyces developmental genes and the developmental significance of actinobacteria-specific genes. As an aid, we developed the Actinoblast database of reciprocal blastp best hits between the Streptomyces coelicolor genome and more than 100 other actinobacterial genomes (http://streptomyces.org.uk/actinoblast/). We suggest that the emergence of morphological complexity was underpinned by special features of early actinobacteria, such as polar growth and the coupled participation of regulatory Wbl proteins and the redox-protecting thiol mycothiol in transducing a transient nitric oxide signal generated during physiologically stressful growth transitions. It seems that some cell growth and division proteins of early actinobacteria have acquired greater importance for sporulation of complex actinobacteria than for mycelial growth, in which septa are infrequent and not associated with complete cell separation. The acquisition of extracellular proteins with structural roles, a highly regulated extracellular protease cascade, and additional regulatory genes allowed early actinobacterial stationary phase processes to be redeployed in the emergence of aerial hyphae from mycelial mats and in the formation of spore chains. These extracellular proteins may have contributed to speciation. Simpler members of morphologically diverse clades have lost some developmental genes.
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42
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Gutiérrez D, Adriaenssens EM, Martínez B, Rodríguez A, Lavigne R, Kropinski AM, García P. Three proposed new bacteriophage genera of staphylococcal phages: "3alikevirus", "77likevirus" and "Phietalikevirus". Arch Virol 2014; 159:389-98. [PMID: 24022640 DOI: 10.1007/s00705-013-1833-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 07/16/2013] [Indexed: 10/26/2022]
Abstract
To date, most members of the Siphoviridae family of bacteriophages remain unclassified, including the 46 staphylococcal phages for which the complete genome sequences have been deposited in public databases. Comparative nucleotide and protein sequence analysis, in addition to available data on phage morphology, allowed us to propose three new phage genera within the family Siphoviridae: "3alikevirus", "77likevirus" and "Phietalikevirus", which include related phages infecting Staphylococcus aureus and Staphylococcus epidermidis. However, six phages infecting S. aureus, Staphylococcus pasteuri, Staphylococcus hominis and Staphylococcus capitis strains remain to be classified (orphan phages). Overall, the former phages share morphological features and genome organization. The three groups have conserved domains containing peptidoglycan hydrolytic activities clearly identified as part of tape measure proteins ("3alikevirus" and "77likevirus") or as individual virionassociated proteins ("Phietalikevirus"). In addition, bacteriophages belonging to the genus "3alikevirus" share closely related DNA-processing and packaging proteins, while bacteriophages included in the genus "Phietalikevirus" encode specific tail proteins for host interaction. These properties are considered distinctive for these genera. Orphan phages seem to have a more divergent organization, but they share some properties with members of these proposed genera.
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Abstract
ABSTRACT
Mycobacteriophages have provided numerous essential tools for mycobacterial genetics, including delivery systems for transposons, reporter genes, and allelic exchange substrates, and components for plasmid vectors and mutagenesis. Their genetically diverse genomes also reveal insights into the broader nature of the phage population and the evolutionary mechanisms that give rise to it. The substantial advances in our understanding of the biology of mycobacteriophages including a large collection of completely sequenced genomes indicates a rich potential for further contributions in tuberculosis genetics and beyond.
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44
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Hatfull GF. Molecular Genetics of Mycobacteriophages. Microbiol Spectr 2014; 2:1-36. [PMID: 25328854 PMCID: PMC4199240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023] Open
Abstract
Mycobacteriophages have provided numerous essential tools for mycobacterial genetics, including delivery systems for transposons, reporter genes, and allelic exchange substrates, and components for plasmid vectors and mutagenesis. Their genetically diverse genomes also reveal insights into the broader nature of the phage population and the evolutionary mechanisms that give rise to it. The substantial advances in our understanding of the biology of mycobacteriophages including a large collection of completely sequenced genomes indicates a rich potential for further contributions in tuberculosis genetics and beyond.
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Affiliation(s)
- Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
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45
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Chaperone-protein interactions that mediate assembly of the bacteriophage lambda tail to the correct length. J Mol Biol 2013; 426:1004-18. [PMID: 23911548 DOI: 10.1016/j.jmb.2013.06.040] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 06/21/2013] [Accepted: 06/30/2013] [Indexed: 11/22/2022]
Abstract
Bacteriophage λ makes two proteins with overlapping amino acid sequences that are essential for tail assembly. These two proteins, gpG and gpGT, are related by a programmed translational frameshift that is conserved among diverse phages and functions in λ to ensure that gpG and the frameshift product gpGT are made in a molar ratio of approximately 30:1. Although both proteins are required and must be present in the correct ratio for assembly of functional tails, neither is present in mature tails. During λ tail assembly, major tail protein gpV polymerizes to form a long tube whose length is controlled by the tape measure protein gpH. We show that the "G" domains of gpG and gpGT bind to all or parts of tail length tape measure protein gpH and that the "T" domain of gpGT binds to major tail shaft subunit gpV, and present a model for how gpG and gpGT chaperone gpH and direct the polymerization of gpV to form a tail of the correct length.
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46
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The peptidoglycan hydrolase of Staphylococcus aureus bacteriophage 11 plays a structural role in the viral particle. Appl Environ Microbiol 2013; 79:6187-90. [PMID: 23892745 DOI: 10.1128/aem.01388-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The role of virion-associated peptidoglycan hydrolases (VAPGHs) in the phage infection cycle is not clear. gp49, the VAPGH from Staphylococcus aureus phage 11, is not essential for phage growth but stabilizes the viral particles. 11Δ49 phages showed a reduced burst size and delayed host lysis. Complementation of gp49 with HydH5 from bacteriophage vB_SauS-phiIPLA88 restored the wild-type phenotype.
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47
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Generation of affinity-tagged fluoromycobacteriophages by mixed assembly of phage capsids. Appl Environ Microbiol 2013. [PMID: 23851082 DOI: 10.1128/aem.01016-13; 10.1128/aem.01016-13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Addition of affinity tags to bacteriophage particles facilitates a variety of applications, including vaccine construction and diagnosis of bacterial infections. Addition of tags to phage capsids is desirable, as modification of the tails can lead to poor adsorption and loss of infectivity. Although tags can readily be included as fusions to head decoration proteins, many phages do not have decoration proteins as virion components. The addition of a small (10-amino-acid) Strep-tag II (STAG II) to the mycobacteriophage TM4 capsid subunit, gp9, was not tolerated as a genetically homogenous recombinant phage but could be incorporated into the head by growth of wild-type phage on a host expressing the capsid-STAG fusion. Particles with capsids composed of wild-type and STAG-tagged subunit mixtures could be grown to high titers, showed good infectivities, and could be used to isolate phage-bacterium complexes. Preparation of a STAG-labeled fluoromycobacteriophage enabled capture of bacterial complexes and identification of infected bacteria by fluorescence.
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48
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Generation of affinity-tagged fluoromycobacteriophages by mixed assembly of phage capsids. Appl Environ Microbiol 2013; 79:5608-15. [PMID: 23851082 DOI: 10.1128/aem.01016-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Addition of affinity tags to bacteriophage particles facilitates a variety of applications, including vaccine construction and diagnosis of bacterial infections. Addition of tags to phage capsids is desirable, as modification of the tails can lead to poor adsorption and loss of infectivity. Although tags can readily be included as fusions to head decoration proteins, many phages do not have decoration proteins as virion components. The addition of a small (10-amino-acid) Strep-tag II (STAG II) to the mycobacteriophage TM4 capsid subunit, gp9, was not tolerated as a genetically homogenous recombinant phage but could be incorporated into the head by growth of wild-type phage on a host expressing the capsid-STAG fusion. Particles with capsids composed of wild-type and STAG-tagged subunit mixtures could be grown to high titers, showed good infectivities, and could be used to isolate phage-bacterium complexes. Preparation of a STAG-labeled fluoromycobacteriophage enabled capture of bacterial complexes and identification of infected bacteria by fluorescence.
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49
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Abstract
The study of mycobacteriophages provides insights into viral diversity and evolution, as well as the genetics and physiology of their pathogenic hosts. Genomic characterization of 80 mycobacteriophages reveals a high degree of genetic diversity and an especially rich reservoir of interesting genes. These include a vast number of genes of unknown function that do not match known database entries and many genes whose functions can be predicted but which are not typically found as components of phage genomes. Thus many mysteries surround these genomes, such as why the genes are there, what do they do, how are they expressed and regulated, how do they influence the physiology of the host bacterium, and what forces of evolution directed them to their genomic homes? Although the genetic diversity and novelty of these phages is full of intrigue, it is a godsend for the mycobacterial geneticist, presenting an abundantly rich toolbox that can be exploited to devise new and effective ways for understanding the genetics and physiology of human tuberculosis. As the number of sequenced genomes continues to grow, their mysteries continue to thicken, and the time has come to learn more about the secret lives of mycobacteriophages.
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Affiliation(s)
- Graham F Hatfull
- Department of Biological Sciences, Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, Pennslyvania, USA
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50
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Klumpp J, Fouts DE, Sozhamannan S. Bacteriophage functional genomics and its role in bacterial pathogen detection. Brief Funct Genomics 2013; 12:354-65. [DOI: 10.1093/bfgp/elt009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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