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Ji Y, Xi H, Chen C, Sun C, Feng X, Lei L, Han W, Gu J. The pig intestinal phageome is an important reservoir and transfer vector for virulence genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170076. [PMID: 38220020 DOI: 10.1016/j.scitotenv.2024.170076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/16/2024]
Abstract
Bacteriophages (phages) can significantly influence the composition and functions of their host communities, and enhance host pathogenicity via the transport of phage-encoded virulence genes. Phages are the main component of animal gut viruses, however, there are few reports on the piglet gut phageome and its contribution to virulence genes. Here, a total of 185 virulence genes from 59,955 predicted genes of gut phages in weaned piglets were identified, with 0.688 % of the phage contigs coding for at least one virulence gene. The virulence gene pblA was the most abundant, with various virulence genes significantly correlated with gut phages and their encoded mobile gene element (MGE) genes. Importantly, multiple virulence genes and MGE genes coexist in some phage sequences, and up to 12 virulence genes were detected in a single phage sequence, greatly increasing the risk of phage-mediated transmission of virulence genes into the bacterial genome. In addition, diarrhoea has driven changes in the composition and structure of phage and bacterial communities in the intestinal tract of weaned piglets, significantly increasing the abundance of phage contigs encoding both virulence genes and MGE genes in faecal samples, which potentially increases the risk of phage-mediated virulence genes being transfected into the gut bacterial genome. In summary, this study expands our understanding of the gut microbiome of piglets, advances our understanding of the potential role of phages in driving host pathogenesis in the gut system, and provides new insights into the sources of virulence genes and genetic evolution of bacteria in pig farm environments.
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Affiliation(s)
- Yalu Ji
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Hengyu Xi
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Chong Chen
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Changjiang Sun
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xin Feng
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Liancheng Lei
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Wenyu Han
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jingmin Gu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China.
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2
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Putzeys L, Wicke L, Boon M, van Noort V, Vogel J, Lavigne R. Refining the transcriptional landscapes for distinct clades of virulent phages infecting Pseudomonas aeruginosa. MICROLIFE 2024; 5:uqae002. [PMID: 38444699 PMCID: PMC10914365 DOI: 10.1093/femsml/uqae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/24/2024] [Accepted: 02/27/2024] [Indexed: 03/07/2024]
Abstract
The introduction of high-throughput sequencing has resulted in a surge of available bacteriophage genomes, unveiling their tremendous genomic diversity. However, our current understanding of the complex transcriptional mechanisms that dictate their gene expression during infection is limited to a handful of model phages. Here, we applied ONT-cappable-seq to reveal the transcriptional architecture of six different clades of virulent phages infecting Pseudomonas aeruginosa. This long-read microbial transcriptomics approach is tailored to globally map transcription start and termination sites, transcription units, and putative RNA-based regulators on dense phage genomes. Specifically, the full-length transcriptomes of LUZ19, LUZ24, 14-1, YuA, PAK_P3, and giant phage phiKZ during early, middle, and late infection were collectively charted. Beyond pinpointing traditional promoter and terminator elements and transcription units, these transcriptional profiles provide insights in transcriptional attenuation and splicing events and allow straightforward validation of Group I intron activity. In addition, ONT-cappable-seq data can guide genome-wide discovery of novel regulatory element candidates, including noncoding RNAs and riboswitches. This work substantially expands the number of annotated phage-encoded transcriptional elements identified to date, shedding light on the intricate and diverse gene expression regulation mechanisms in Pseudomonas phages, which can ultimately be sourced as tools for biotechnological applications in phage and bacterial engineering.
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Affiliation(s)
- Leena Putzeys
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
| | - Laura Wicke
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
| | - Vera van Noort
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Jörg Vogel
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
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3
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Silva MD, Melo LDR. Phage-Host Interaction Analysis Using Flow Cytometry. Methods Mol Biol 2024; 2734:133-140. [PMID: 38066366 DOI: 10.1007/978-1-0716-3523-0_8] [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] [Indexed: 12/18/2023]
Abstract
Phage-host interactions are commonly evaluated by culture-based methods. However, these techniques are very laborious and time-consuming. Therefore, other time-efficient, not labor-intensive, and cost-effective methods have been developed.This chapter describes the methodology used to assess the susceptibility of planktonic cultures of bacteria to phage infection and to study their interactions over time by flow cytometry.
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Affiliation(s)
- Maria Daniela Silva
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga & Guimarães, Portugal
| | - Luís D R Melo
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal.
- LABBELS - Associate Laboratory, Braga & Guimarães, Portugal.
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4
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Phothichaisri W, Phetruen T, Chankhamhaengdecha S, Janvilisri T, Ounjai P, Fagan RP, Chanarat S. Unraveling Physical Interactions of Clostridioides difficile with Phage and Phage-Derived Proteins Using In Vitro and Whole-Cell Assays. Methods Mol Biol 2024; 2738:245-262. [PMID: 37966604 DOI: 10.1007/978-1-0716-3549-0_16] [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] [Indexed: 11/16/2023]
Abstract
Physical interactions between bacteria and phages provide valuable insights into the mechanisms of phage infection and may provide information on the use of phages as a therapeutic approach. In this study, we employed a combination of in vitro and whole-cell assays to examine the interactions between Clostridioides difficile and phages and phage-derived proteins. These techniques can also be adapted for studying the physical interactions between other bacterial species and their associated phages.
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Affiliation(s)
- Wichuda Phothichaisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Tanaporn Phetruen
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
- Laboratory of Molecular Cell Biology, Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Puey Ounjai
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Robert P Fagan
- School of Biosciences, Florey Institute, University of Sheffield, Sheffield, UK
| | - Sittinan Chanarat
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand.
- Laboratory of Molecular Cell Biology, Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand.
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5
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Schroven K, Putzeys L, Kerremans A, Ceyssens PJ, Vallino M, Paeshuyse J, Haque F, Yusuf A, Koch MD, Lavigne R. The phage-encoded PIT4 protein affects multiple two-component systems of Pseudomonas aeruginosa. Microbiol Spectr 2023; 11:e0237223. [PMID: 37962408 PMCID: PMC10714779 DOI: 10.1128/spectrum.02372-23] [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: 06/08/2023] [Accepted: 10/04/2023] [Indexed: 11/15/2023] Open
Abstract
IMPORTANCE More and more Pseudomonas aeruginosa isolates have become resistant to antibiotics like carbapenem. As a consequence, P. aeruginosa ranks in the top three of pathogens for which the development of novel antibiotics is the most crucial. The pathogen causes both acute and chronic infections, especially in patients who are the most vulnerable. Therefore, efforts are urgently needed to develop alternative therapies. One path explored in this article is the use of bacteriophages and, more specifically, phage-derived proteins. In this study, a phage-derived protein was studied that impacts key virulence factors of the pathogen via interaction with multiple histidine kinases of TCSs. The fundamental insights gained for this protein can therefore serve as inspiration for the development of an anti-virulence compound that targets the bacterial TCS.
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Affiliation(s)
- Kaat Schroven
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Leena Putzeys
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | | | | | - Marta Vallino
- Institute of Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| | - Jan Paeshuyse
- Host and Pathogen Interactions, KU Leuven, Leuven, Belgium
| | - Farhana Haque
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Ahmed Yusuf
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Matthias D. Koch
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
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6
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Schroven K, Putzeys L, Swinnen AL, Hendrix H, Paeshuyse J, Lavigne R. The phage-encoded protein PIT2 impacts Pseudomonas aeruginosa quorum sensing by direct interaction with LasR. iScience 2023; 26:107745. [PMID: 37736037 PMCID: PMC10509696 DOI: 10.1016/j.isci.2023.107745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/07/2023] [Accepted: 08/24/2023] [Indexed: 09/23/2023] Open
Abstract
In recent decades, there has been a notable increase in antibiotic-resistant Pseudomonas aeruginosa isolates, necessitating the development of innovative treatments to combat this pathogen. This manuscript explores the potential of different phage proteins to attenuate virulence factors of P. aeruginosa, particularly the type II secretion system (T2SS). PIT2, a protein derived from the lytic Pseudomonas phage LMA2 inhibits the T2SS effectors PrpL and LasA and attenuates the bacterial virulence toward HeLa cells and Galleria mellonella. Using RNAseq-based differential gene expression analysis, PIT2's impact on the LasR regulatory network is revealed, which plays a key role in bacterial quorum sensing. This discovery expands our knowledge on phage-encoded modulators of the bacterial metabolism and offers a promising anti-virulence target in P. aeruginosa. As such, it lays the foundation for a new phage-inspired anti-virulence strategy to combat multidrug resistant pathogens and opens the door for SynBio applications.
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Affiliation(s)
- Kaat Schroven
- Laboratory of Gene Technology, KU Leuven, 3000 Heverlee, Belgium
| | - Leena Putzeys
- Laboratory of Gene Technology, KU Leuven, 3000 Heverlee, Belgium
| | | | - Hanne Hendrix
- Laboratory of Gene Technology, KU Leuven, 3000 Heverlee, Belgium
| | - Jan Paeshuyse
- Laboratory for Host Pathogen Interactions in Livestock, KU Leuven, 3000 Heverlee, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, 3000 Heverlee, Belgium
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7
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Loganathan K, Viswanathan B. Genome editing for phage design and uses for therapeutic applications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 201:203-224. [PMID: 37770172 DOI: 10.1016/bs.pmbts.2023.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
The over usage of antibiotics leads to antibiotic abuse which in turn eventually raises resistance mechanisms among wide range of pathogens. Due to lack of experimental data of efficacy of phages as potential antimicrobial and therapeutic agent and also more specific and cumbersome isolation process against specific pathogens makes it not so feasible technology to be looked as an alternative therapy. But, recent developments in genome editing techniques enables programmed nuclease enzymes that has effectively improvised our methodology to make accurate changes in the genomes of prokaryote as well as eukaryote cells. It is already strengthening our ability to improvise genetic engineering to disease identification by facilitating the creation of more precise models to identify the root cause. The present chapter discusses on improvisation of phage therapy using recent genome editing tools and also shares data on the methods of usage of phages and their derivatives like proteins and enzymes such as lysins and depolymerases, as a potential therapeutic or prophylaxis agent. Methods involved in recombinant based techniques were also discussed in this chapter. Combination of traditional approach with modern tools has led to a potential development of phage-based therapeutics in near future.
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8
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Jia HJ, Jia PP, Yin S, Bu LK, Yang G, Pei DS. Engineering bacteriophages for enhanced host range and efficacy: insights from bacteriophage-bacteria interactions. Front Microbiol 2023; 14:1172635. [PMID: 37323893 PMCID: PMC10264812 DOI: 10.3389/fmicb.2023.1172635] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/10/2023] [Indexed: 06/17/2023] Open
Abstract
Bacteriophages, the most abundant organisms on earth, have the potential to address the rise of multidrug-resistant bacteria resulting from the overuse of antibiotics. However, their high specificity and limited host range can hinder their effectiveness. Phage engineering, through the use of gene editing techniques, offers a means to enhance the host range of bacteria, improve phage efficacy, and facilitate efficient cell-free production of phage drugs. To engineer phages effectively, it is necessary to understand the interaction between phages and host bacteria. Understanding the interaction between the receptor recognition protein of bacteriophages and host receptors can serve as a valuable guide for modifying or replacing these proteins, thereby altering the receptor range of the bacteriophage. Research and development focused on the CRISPR-Cas bacterial immune system against bacteriophage nucleic acids can provide the necessary tools to promote recombination and counter-selection in engineered bacteriophage programs. Additionally, studying the transcription and assembly functions of bacteriophages in host bacteria can facilitate the engineered assembly of bacteriophage genomes in non-host environments. This review highlights a comprehensive summary of phage engineering methods, including in-host and out-of-host engineering, and the use of high-throughput methods to understand their role. The main aim of these techniques is to harness the intricate interactions between bacteriophages and hosts to inform and guide the engineering of bacteriophages, particularly in the context of studying and manipulating the host range of bacteriophages. By employing advanced high-throughput methods to identify specific bacteriophage receptor recognition genes, and subsequently introducing modifications or performing gene swapping through in-host recombination or out-of-host synthesis, it becomes possible to strategically alter the host range of bacteriophages. This capability holds immense significance for leveraging bacteriophages as a promising therapeutic approach against antibiotic-resistant bacteria.
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Affiliation(s)
- Huang-Jie Jia
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Pan-Pan Jia
- School of Public Health, Chongqing Medical University, Chongqing, China
| | - Supei Yin
- Urinary Nephropathy Center, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ling-Kang Bu
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Guan Yang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - De-Sheng Pei
- School of Public Health, Chongqing Medical University, Chongqing, China
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9
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Timoshina OY, Kasimova AA, Shneider MM, Matyuta IO, Nikolaeva AY, Evseev PV, Arbatsky NP, Shashkov AS, Chizhov AO, Shelenkov AA, Mikhaylova YV, Slukin PV, Volozhantsev NV, Boyko KM, Knirel YA, Miroshnikov KA, Popova AV. Friunavirus Phage-Encoded Depolymerases Specific to Different Capsular Types of Acinetobacter baumannii. Int J Mol Sci 2023; 24:ijms24109100. [PMID: 37240444 DOI: 10.3390/ijms24109100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/06/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Acinetobacter baumannii is a critical priority nosocomial pathogen that produces a variety of capsular polysaccharides (CPSs), the primary receptors for specific depolymerase-carrying phages. In this study, the tailspike depolymerases (TSDs) encoded in genomes of six novel Friunaviruses, APK09, APK14, APK16, APK86, APK127v, APK128, and one previously described Friunavirus phage, APK37.1, were characterized. For all TSDs, the mechanism of specific cleavage of corresponding A. baumannii capsular polysaccharides (CPSs) was established. The structures of oligosaccharide fragments derived from K9, K14, K16, K37/K3-v1, K86, K127, and K128 CPSs degradation by the recombinant depolymerases have been determined. The crystal structures of three of the studied TSDs were obtained. A significant reduction in mortality of Galleria mellonella larvae infected with A. baumannii of K9 capsular type was shown in the example of recombinant TSD APK09_gp48. The data obtained will provide a better understanding of the interaction of phage-bacterial host systems and will contribute to the formation of principles of rational usage of lytic phages and phage-derived enzymes as antibacterial agents.
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Affiliation(s)
- Olga Y Timoshina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
| | - Anastasia A Kasimova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Mikhail M Shneider
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Ilya O Matyuta
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Alena Y Nikolaeva
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", 123182 Moscow, Russia
| | - Peter V Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Nikolay P Arbatsky
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander S Shashkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander O Chizhov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Andrey A Shelenkov
- Central Scientific Research Institute of Epidemiology, 111123 Moscow, Russia
| | - Yulia V Mikhaylova
- Central Scientific Research Institute of Epidemiology, 111123 Moscow, Russia
| | - Pavel V Slukin
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
| | - Nikolay V Volozhantsev
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
| | - Konstantin M Boyko
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Yuriy A Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Konstantin A Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Anastasia V Popova
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
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10
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The application of adaptively evolved thermostable bacteriophage ΦYMFM0293 to control spp. in poultry skin. Food Res Int 2023; 167:112665. [PMID: 37087250 DOI: 10.1016/j.foodres.2023.112665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/02/2023] [Accepted: 03/05/2023] [Indexed: 03/12/2023]
Abstract
Bacteriophages, bacterial viruses, are now being re-highlighted as one of the promising alternative antimicrobial agents to control bacterial pathogens in various fields, including the food industry. However, wild-type (WT) phages isolated from nature are vulnerable to external stresses such as heat, limiting the usability of phages in thermal processing. Here, we applied an adaptive laboratory evolution approach to improving the heat stability of newly isolated Salmonella-infecting lytic phage ΦYMFM0293 and examined its application in the poultry scalding process. After 15 cycles of exposure to sub-lethal temperature, the obtained adaptively evolved (AE) phages maintained approximately 3-log more infectious particles at 73 or 74 °C than the WT and non-heat-treated control phages. Missense mutations mainly concentrated in the genes related to the phage tail module were identified from the independently obtained heat-challenged phages, regardless of host Salmonella's heat-shock protein chaperone induction. These results demonstrated the necessity and sufficiency of the phage exposures to heat for thermal adaptation and suggested the involvement of the phage tail in heat stability. No significant physiological or morphological changes except the mutually offsetting phage replication parameters were observed in the AE phages. Accordingly, hot water supplemented with the AE phages significantly reduced the number of artificially contaminated Salmonella cells on chicken and duck skin in the mimicked scalding process. The AE strategy used here could be applied to other WT phages to improve their usability as more feasible antimicrobials for food safety.
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11
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Aggarwal S, Dhall A, Patiyal S, Choudhury S, Arora A, Raghava GPS. An ensemble method for prediction of phage-based therapy against bacterial infections. Front Microbiol 2023; 14:1148579. [PMID: 37032893 PMCID: PMC10076811 DOI: 10.3389/fmicb.2023.1148579] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/06/2023] [Indexed: 04/11/2023] Open
Abstract
Phage therapy is a viable alternative to antibiotics for treating microbial infections, particularly managing drug-resistant strains of bacteria. One of the major challenges in designing phage-based therapy is to identify the most appropriate potential phage candidate to treat bacterial infections. In this study, an attempt has been made to predict phage-host interactions with high accuracy to identify the potential bacteriophage that can be used for treating a bacterial infection. The developed models have been created using a training dataset containing 826 phage- host interactions, and have been evaluated on a validation dataset comprising 1,201 phage-host interactions. Firstly, alignment-based models have been developed using similarity between phage-phage (BLASTPhage), host-host (BLASTHost) and phage-CRISPR (CRISPRPred), where we achieved accuracy between 42.4-66.2% for BLASTPhage, 55-78.4% for BLASTHost, and 43.7-80.2% for CRISPRPred across five taxonomic levels. Secondly, alignment free models have been developed using machine learning techniques. Thirdly, hybrid models have been developed by integrating the alignment-free models and the similarity-scores where we achieved maximum performance of (60.6-93.5%). Finally, an ensemble model has been developed that combines the hybrid and alignment-based models. Our ensemble model achieved highest accuracy of 67.9, 80.6, 85.5, 90, and 93.5% at Genus, Family, Order, Class, and Phylum levels on validation dataset. In order to serve the scientific community, we have also developed a webserver named PhageTB and provided a standalone software package (https://webs.iiitd.edu.in/raghava/phagetb/) for the same.
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Affiliation(s)
- Suchet Aggarwal
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology, New Delhi, India
| | - Anjali Dhall
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Sumeet Patiyal
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Shubham Choudhury
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Akanksha Arora
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Gajendra P. S. Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
- *Correspondence: Gajendra P. S. Raghava,
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12
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A Cyanophage MarR-Type Transcription Factor Regulates Host RNase E Expression during Infection. Microorganisms 2022; 10:microorganisms10112245. [DOI: 10.3390/microorganisms10112245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/04/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
The marine picocyanobacterium Prochlorococcus contributes significantly to global primary production, and its abundance and diversity is shaped in part by viral infection. Here, we identified a cyanophage-encoded MarR-type transcription factor that induces the gene expression of host Prochlorococcus MED4 endoribonuclease (RNase) E during phage infection. The increase in rne transcript levels relies on the phage (p)MarR-mediated activation of an alternative promoter that gives rise to a truncated yet enzymatically fully functional RNase E isoform. In this study, we demonstrate that pMarR binds to an atypical activator site downstream of the transcriptional start site and that binding is enhanced in the presence of Ca2+ ions. Furthermore, we show that dimeric pMarR interacts with the α subunit of RNA polymerase, and we identified amino acid residues S66, R67, and G106, which are important for Ca2+ binding, DNA binding, and dimerization of pMarR, respectively.
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13
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Abeysekera GS, Love MJ, Manners SH, Billington C, Dobson RCJ. Bacteriophage-encoded lethal membrane disruptors: Advances in understanding and potential applications. Front Microbiol 2022; 13:1044143. [PMID: 36345304 PMCID: PMC9636201 DOI: 10.3389/fmicb.2022.1044143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 10/10/2022] [Indexed: 09/09/2023] Open
Abstract
Holins and spanins are bacteriophage-encoded membrane proteins that control bacterial cell lysis in the final stage of the bacteriophage reproductive cycle. Due to their efficient mechanisms for lethal membrane disruption, these proteins are gaining interest in many fields, including the medical, food, biotechnological, and pharmaceutical fields. However, investigating these lethal proteins is challenging due to their toxicity in bacterial expression systems and the resultant low protein yields have hindered their analysis compared to other cell lytic proteins. Therefore, the structural and dynamic properties of holins and spanins in their native environment are not well-understood. In this article we describe recent advances in the classification, purification, and analysis of holin and spanin proteins, which are beginning to overcome the technical barriers to understanding these lethal membrane disrupting proteins, and through this, unlock many potential biotechnological applications.
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Affiliation(s)
- Gayan S. Abeysekera
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Michael J. Love
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Health and Environment Group, Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Sarah H. Manners
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Craig Billington
- Health and Environment Group, Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, VIC, Australia
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14
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Igler C. Phenotypic flux: The role of physiology in explaining the conundrum of bacterial persistence amid phage attack. Virus Evol 2022; 8:veac086. [PMID: 36225237 PMCID: PMC9547521 DOI: 10.1093/ve/veac086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 08/11/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022] Open
Abstract
Bacteriophages, the viruses of bacteria, have been studied for over a century. They were not only instrumental in laying the foundations of molecular biology, but they are also likely to play crucial roles in shaping our biosphere and may offer a solution to the control of drug-resistant bacterial infections. However, it remains challenging to predict the conditions for bacterial eradication by phage predation, sometimes even under well-defined laboratory conditions, and, most curiously, if the majority of surviving cells are genetically phage-susceptible. Here, I propose that even clonal phage and bacterial populations are generally in a state of continuous 'phenotypic flux', which is caused by transient and nongenetic variation in phage and bacterial physiology. Phenotypic flux can shape phage infection dynamics by reducing the force of infection to an extent that allows for coexistence between phages and susceptible bacteria. Understanding the mechanisms and impact of phenotypic flux may be key to providing a complete picture of phage-bacteria coexistence. I review the empirical evidence for phenotypic variation in phage and bacterial physiology together with the ways they have been modeled and discuss the potential implications of phenotypic flux for ecological and evolutionary dynamics between phages and bacteria, as well as for phage therapy.
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Affiliation(s)
- Claudia Igler
- Department of Environmental Systems Science, ETH Zürich, Institute of Integrative Biology, Universitätstrasse 16, Zurich 8092, Switzerland
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15
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Tabib-Salazar A, Wigneshweraraj S. RNA Management During T7 Infection. PHAGE (NEW ROCHELLE, N.Y.) 2022; 3:136-140. [PMID: 36793551 PMCID: PMC9917321 DOI: 10.1089/phage.2022.0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Post-transcriptional regulation (PTR) determines the fate of RNA in the cell and represents an important control point in the flow of genetic information and thus underpins many, if not all, aspects of cell function. Host takeover by phages through misappropriation of the bacterial transcription machinery is a relatively advanced area of research. However, several phages encode small regulatory RNAs, which are major mediators of PTR, and produce specific proteins to manipulate bacterial enzymes involved in RNA degradation.1-4 However, PTR during phage development still represents an understudied area of phage-bacteria interaction biology. In this study, we discuss the potential role PTR could play in determining the fate of RNA during the lifecycle of the prototypic phage T7 in Escherichia coli.
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Affiliation(s)
- Aline Tabib-Salazar
- Section of Molecular Microbiology, Department of Infectious Disease, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Sivaramesh Wigneshweraraj
- Section of Molecular Microbiology, Department of Infectious Disease, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
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16
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Liu S, Feng J, Sun T, Xu B, Zhang J, Li G, Zhou J, Jiang J. The Synthesis and Assembly of a Truncated Cyanophage Genome and Its Expression in a Heterogenous Host. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081234. [PMID: 36013413 PMCID: PMC9410186 DOI: 10.3390/life12081234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022]
Abstract
Cyanophages play an important role in regulating the dynamics of cyanobacteria communities in the hydrosphere, representing a promising biological control strategy for cyanobacterial blooms. Nevertheless, most cyanophages are host-specific, making it difficult to control blooming cyanobacteria via single or multiple cyanophages. In order to address the issue, we explore the interaction between cyanophages and their heterologous hosts, with the aim of revealing the principles of designing and constructing an artificial cyanophage genome towards multiple cyanobacterial hosts. In the present study, we use synthetic biological approaches to assess the impact of introducing a fragment of cyanophage genome into a heterologous cyanobacterium under a variety of environmental conditions. Based on a natural cyanophage A-4L genome (41,750 bp), a truncated cyanophage genome Syn-A-4-8 is synthesized and assembled in Saccharomyces cerevisiae. We found that a 351-15,930 bp area of the A-4L genome has a fragment that is lethal to Escherichia coli during the process of attempting to assemble the full-length A-4L genome. Syn-A-4-8 was successfully introduced into E. coli and then transferred into the model cyanobacterium Synechococcus elongatus PCC 7942 (Syn7942) via conjugation. Although no significant phenotypes of Syn7942 carrying Syn-A-4-8 (LS-02) could be observed under normal conditions, its growth exhibited a prolonged lag phase compared to that of the control strain under 290-millimolar NaCl stress. Finally, the mechanisms of altered salt tolerance in LS-02 were revealed through comparative transcriptomics, and ORF25 and ORF26 on Syn-A-4-8 turned out to be the key genes causing the phenotype. Our research represents an important attempt in designing artificial cyanophages towards multiple hosts, and offers new future insights into the control of cyanobacterial blooms.
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Affiliation(s)
- Shujing Liu
- School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Jia Feng
- School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Tao Sun
- School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, China
| | - Bonan Xu
- School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Jiabao Zhang
- School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Guorui Li
- School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Jianting Zhou
- School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
- Correspondence: (J.Z.); (J.J.)
| | - Jianlan Jiang
- School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
- Correspondence: (J.Z.); (J.J.)
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17
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Shehreen S, Birkholz N, Fineran P, Brown C. Widespread repression of anti-CRISPR production by anti-CRISPR-associated proteins. Nucleic Acids Res 2022; 50:8615-8625. [PMID: 35947749 PMCID: PMC9410906 DOI: 10.1093/nar/gkac674] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/06/2022] [Accepted: 07/25/2022] [Indexed: 12/24/2022] Open
Abstract
Many bacteria use CRISPR-Cas systems to defend against invasive mobile genetic elements (MGEs). In response, MGEs have developed strategies to resist CRISPR-Cas, including the use of anti-CRISPR (Acr) proteins. Known acr genes may be followed in an operon by a putative regulatory Acr-associated gene (aca), suggesting the importance of regulation. Although ten families of helix-turn-helix (HTH) motif containing Aca proteins have been identified (Aca1-10), only three have been tested and shown to be transcriptional repressors of acr-aca expression. The AcrIIA1 protein (a Cas9 inhibitor) also contains a functionally similar HTH containing repressor domain. Here, we identified and analysed Aca and AcrIIA1 homologs across all bacterial genomes. Using HMM models we found aca-like genes are widely distributed in bacteria, both with and without known acr genes. The putative promoter regions of acr-aca operons were analysed and members of each family of bacterial Aca tested for regulatory function. For each Aca family, we predicted a conserved inverted repeat binding site within a core promoter. Promoters containing these sites directed reporter expression in E. coli and were repressed by the cognate Aca protein. These data demonstrate that acr repression by Aca proteins is widely conserved in nature.
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Affiliation(s)
- Saadlee Shehreen
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand,Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Nils Birkholz
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand,Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand,Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin 9054, New Zealand,Genetics Otago, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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18
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Visnapuu A, Van der Gucht M, Wagemans J, Lavigne R. Deconstructing the Phage-Bacterial Biofilm Interaction as a Basis to Establish New Antibiofilm Strategies. Viruses 2022; 14:v14051057. [PMID: 35632801 PMCID: PMC9145820 DOI: 10.3390/v14051057] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 05/11/2022] [Accepted: 05/11/2022] [Indexed: 12/19/2022] Open
Abstract
The bacterial biofilm constitutes a complex environment that endows the bacterial community within with an ability to cope with biotic and abiotic stresses. Considering the interaction with bacterial viruses, these biofilms contain intrinsic defense mechanisms that protect against phage predation; these mechanisms are driven by physical, structural, and metabolic properties or governed by environment-induced mutations and bacterial diversity. In this regard, horizontal gene transfer can also be a driver of biofilm diversity and some (pro)phages can function as temporary allies in biofilm development. Conversely, as bacterial predators, phages have developed counter mechanisms to overcome the biofilm barrier. We highlight how these natural systems have previously inspired new antibiofilm design strategies, e.g., by utilizing exopolysaccharide degrading enzymes and peptidoglycan hydrolases. Next, we propose new potential approaches including phage-encoded DNases to target extracellular DNA, as well as phage-mediated inhibitors of cellular communication; these examples illustrate the relevance and importance of research aiming to elucidate novel antibiofilm mechanisms contained within the vast set of unknown ORFs from phages.
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19
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Gao L, Ouyang M, Li Y, Zhang H, Zheng XF, Li HX, Rao SQ, Yang ZQ, Gao S. Isolation and Characterization of a Lytic Vibriophage OY1 and Its Biocontrol Effects Against Vibrio spp. Front Microbiol 2022; 13:830692. [PMID: 35464931 PMCID: PMC9022663 DOI: 10.3389/fmicb.2022.830692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/15/2022] [Indexed: 01/22/2023] Open
Abstract
Vibrio species are important pathogens of marine animals and aquaculture populations and some of them can cause serious infections in humans through consumption of contaminated seafood and aquaculture products. Lytic bacteriophages can potentially alleviate Vibrio contamination in the aquaculture organisms and in the processing of aquatic products and have gained significant scientific attention in recent years. In the present study, bacteriophages were isolated from sewage of local aquatic products markets and grown using Vibrio mimicus CICC 21613 as host cells. The lytic vibriophage OY1 belonging to the newly proposed family Autographiviridae and the genus Maculvirus was identified by observation under electron microscope and comparative genomic analysis. The phage OY1 showed lytic activity against 24 among 32 tested strains belonging to eight Vibrio species. The complete phage OY1 genome consists of a single circular double-stranded DNA of 43,479 bp with a total GC content of 49.27% and was predicted to encode 40 open reading frames (ORFs). To evaluate its potential against vibrios, the one-step growth curve, thermal and pH stability, host range, and lytic activity of the OY1 phage against Vibrio species were evaluated. The results showed that phage OY1 had a range of thermal and pH tolerance, and exhibited a significant inhibitory effect on the growth of tested Vibrio species. Bacterial growth in the fish muscle extract juice (FMEJ) inoculated with Vibrio mimicus CICC 21613, Vibrio parahaemolyticus CICC 21617, Vibrio alginolyticus VJ14, and the mixed bacterial culture was reduced by 2.65 log CFU/ml, 2.42 log CFU/ml, 1.93 log CFU/ml, and 2.01 log CFU/ml, respectively, by incubation with phage OY1 at 25°C for 36 h. Phage OY1 also showed a strong ability to prevent biofilm formation and destroy formed Vibrio species biofilms. These results indicate that phage OY1 is a potential biocontrol agent against Vibrio species in the aquaculture industry and in food safety control.
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Affiliation(s)
- Lu Gao
- College of Food Science and Engineering, Yangzhou University, Yangzhou, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture, Yangzhou, China
| | - Min Ouyang
- College of Food Science and Engineering, Yangzhou University, Yangzhou, China
| | - Yi Li
- College of Food Science and Engineering, Yangzhou University, Yangzhou, China
| | - Hui Zhang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, China
| | - Xiang-Feng Zheng
- College of Food Science and Engineering, Yangzhou University, Yangzhou, China
| | - Hua-Xiang Li
- College of Food Science and Engineering, Yangzhou University, Yangzhou, China
| | - Sheng-Qi Rao
- College of Food Science and Engineering, Yangzhou University, Yangzhou, China
| | - Zhen-Quan Yang
- College of Food Science and Engineering, Yangzhou University, Yangzhou, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture, Yangzhou, China
| | - Song Gao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
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20
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Temporal Transcriptional Responses of a Vibrio alginolyticus Strain to
Podoviridae
Phage HH109 Revealed by RNA-Seq. mSystems 2022; 7:e0010622. [PMID: 35400200 PMCID: PMC9040624 DOI: 10.1128/msystems.00106-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio alginolyticus
is a common opportunistic pathogen that causes mass mortality in cultured marine animals. Phage HH109 lyses pathogenic
V. alginolyticus
strain E110 with high efficiency and thus serves as a useful model to understand the dynamic interplay of a phage and its host.
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21
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Regulation of Gene Expression of phiEco32-like Bacteriophage 7-11. Viruses 2022; 14:v14030555. [PMID: 35336962 PMCID: PMC8948821 DOI: 10.3390/v14030555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 02/05/2023] Open
Abstract
Salmonella enterica serovar Newport bacteriophage 7-11 shares 41 homologous ORFs with Escherichia coli phage phiEco32, and both phages encode a protein similar to bacterial RNA polymerase promoter specificity σ subunit. Here, we investigated the temporal pattern of 7-11 gene expression during infection and compared it to the previously determined transcription strategy of phiEco32. Using primer extension and in vitro transcription assays, we identified eight promoters recognized by host RNA polymerase holoenzyme containing 7-11 σ subunit SaPh711_gp47. These promoters are characterized by a bipartite consensus, GTAAtg-(16)-aCTA, and are located upstream of late phage genes. While dissimilar from single-element middle and late promoters of phiEco32 recognized by holoenzymes formed by the phi32_gp36 σ factor, the 7-11 late promoters are located at genome positions similar to those of phiEco32 middle and late promoters. Two early 7-11 promoters are recognized by the RNA polymerase holoenzyme containing the host primary σ70 factor. Unlike the case of phiEco32, no shut-off of σ70-dependent transcription is observed during 7-11 infection and there are no middle promoters. These differences can be explained by the fact that phage 7-11 does not encode a homologue of phi32_gp79, an inhibitor of host and early phage transcription and an activator of transcription by the phi32_gp36-holoenzyme.
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22
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Hendrix H, Zimmermann-Kogadeeva M, Zimmermann M, Sauer U, De Smet J, Muchez L, Lissens M, Staes I, Voet M, Wagemans J, Ceyssens PJ, Noben JP, Aertsen A, Lavigne R. Metabolic reprogramming of Pseudomonas aeruginosa by phage-based quorum sensing modulation. Cell Rep 2022; 38:110372. [PMID: 35172131 DOI: 10.1016/j.celrep.2022.110372] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/29/2021] [Accepted: 01/21/2022] [Indexed: 12/31/2022] Open
Abstract
The Pseudomonas quinolone signal (PQS) is a multifunctional quorum sensing molecule of key importance to P. aeruginosa. Here, we report that the lytic Pseudomonas bacterial virus LUZ19 targets this population density-dependent signaling system by expressing quorum sensing targeting protein (Qst) early during infection. We demonstrate that Qst interacts with PqsD, a key host quinolone signal biosynthesis pathway enzyme, resulting in decreased levels of PQS and its precursor 2-heptyl-4(1H)-quinolone. The lack of a functional PqsD enzyme impairs LUZ19 infection but is restored by external supplementation of 2-heptyl-4(1H)-quinolone, suggesting that LUZ19 exploits the PQS system for successful infection. We establish a broad functional interaction network of Qst, which includes enzymes of cofactor biosynthesis pathways (CoaC/ThiD) and a non-ribosomal peptide synthetase pathway (PA1217). Qst therefore represents an exquisite example of intricate reprogramming of the bacterium by a phage, which may be further exploited as tool to combat antibiotic resistant bacterial pathogens.
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Affiliation(s)
- Hanne Hendrix
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium
| | | | - Michael Zimmermann
- Institute of Molecular Systems Biology, ETH Zurich, 8092 Zürich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, 8092 Zürich, Switzerland
| | - Jeroen De Smet
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium
| | - Laurens Muchez
- Centre for Surface Chemistry and Catalysis, Department of Microbial and Molecular Systems, KU Leuven, 3001 Heverlee, Belgium
| | - Maries Lissens
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium
| | - Ines Staes
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, KU Leuven, 3001 Heverlee, Belgium
| | - Marleen Voet
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium
| | - Jeroen Wagemans
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium
| | - Pieter-Jan Ceyssens
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, School of Life Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Abram Aertsen
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, KU Leuven, 3001 Heverlee, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium.
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23
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Dakheel KH, Abdul Rahim R, Al-Obaidi JR, Neela VK, Hun TG, Mat Isa MN, Razali N, Yusoff K. Proteomic analysis revealed the biofilm-degradation abilities of the bacteriophage UPMK_1 and UPMK_2 against Methicillin-resistant Staphylococcus aureus. Biotechnol Lett 2022; 44:513-522. [PMID: 35122191 DOI: 10.1007/s10529-022-03229-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/26/2022] [Indexed: 11/02/2022]
Abstract
OBJECTIVE The degradation activity of two bacteriophages UPMK_1 and UPMK_2 against methicillin-resistant Staphylococcus aureus phages were examined using gel zymography. METHODS The analysis was done using BLASTP to detect peptides catalytic domains. Many peptides that are related to several phage proteins were revealed. RESULTS UPMK_1 and UPMK_2 custom sequence database were used for peptide identification. The biofilm-degrading proteins in the bacteriophage UPMK_2 revealed the same lytic activity towards polysaccharide intercellular adhesin-dependent and independent of Methicillin-resistant Staphylococcus aureus (MRSA) biofilm producers in comparison to UPMK_1, which had lytic activity restricted solely to its host. CONCLUSION Both bacteriophage enzymes were involved in MRSA biofilm degradation during phage infection and they have promising enzybiotics properties against MRSA biofilm formation.
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Affiliation(s)
- Khulood Hamid Dakheel
- Department of Biology, College of Science, Mustansiriyah University, Palestine Street, PO Box 14022, Baghdad, Iraq
| | - Raha Abdul Rahim
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.,Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Jameel R Al-Obaidi
- Department of Biology, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, 35900, Tanjong Malim, Perak, Malaysia.
| | - Vasantha Kumari Neela
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Tan Geok Hun
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Mohd Noor Mat Isa
- Malaysia Genome Institute (MGI), Jalan Bangi, 43000, Kajang, Selangor, Malaysia
| | - Nurhanani Razali
- Membranology Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1, Tancha, Onna-son, Kunigami-kun, Okinawa, 904-0495, Japan
| | - Khatijah Yusoff
- Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.,Department of Microbiology, Faculty of Biotechnology & Biomolecular Science, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
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24
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Musin EV, Kim AL, Dubrovskii AV, Ariskina EV, Kudryashova EB, Tikhonenko SA. The Pathways to Create Containers for Bacteriophage Delivery. Polymers (Basel) 2022; 14:polym14030613. [PMID: 35160602 PMCID: PMC8840248 DOI: 10.3390/polym14030613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 12/10/2022] Open
Abstract
Antimicrobial resistance is a global public health threat. One of the possible ways to solve this problem is phage therapy, but the instability of bacteriophages hinders the development of this approach. A bacteriophage delivery system that stabilizes the phage is one of the possible solutions to this problem. This study is dedicated to exploring methods to create encapsulated forms of bacteriophages for delivery. We studied the effect of proteolytic enzymes on the destruction of the polyelectrolyte microcapsule shell and revealed that protease from Streptomyces griseus was able to destroy the membrane of the microcapsule (dextran sulfate/polyarginine)3 ((DS/PArg)3). In addition, the protease decreased the activity of the bacteriophage in the second hour of incubation, and the phage lost activity after 16 h. It was found that a medium with pH 9.02 did not affect the survival of the bacteriophage or E. coli. The bacteriophages were encapsulated into polyelectrolyte microcapsules (DS/PArg)3. It was established that it is impossible to use microcapsules as a means of delivering bacteriophages since the bacteriophages are inactivated. When bacteriophages were included inside a CaCO3 core, it was demonstrated that the phage retained activity before and after the dissolution of the CaCO3 particle. From the results of this study, we recommend using CaCO3 microparticles as a container for bacteriophage delivery through the acidic stomach barrier.
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Affiliation(s)
- Egor V. Musin
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, Institutskaya St., 3, 142290 Puschino, Moscow Region, Russia; (E.V.M.); (A.L.K.); (A.V.D.)
| | - Aleksandr L. Kim
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, Institutskaya St., 3, 142290 Puschino, Moscow Region, Russia; (E.V.M.); (A.L.K.); (A.V.D.)
| | - Alexey V. Dubrovskii
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, Institutskaya St., 3, 142290 Puschino, Moscow Region, Russia; (E.V.M.); (A.L.K.); (A.V.D.)
| | - Elena V. Ariskina
- All-Russian Collection of Microorganisms (VKM), G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Prospect Nauki 5, 142290 Pushchino, Moscow Region, Russia; (E.B.K.); (E.V.A.)
| | - Ekaterina B. Kudryashova
- All-Russian Collection of Microorganisms (VKM), G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Prospect Nauki 5, 142290 Pushchino, Moscow Region, Russia; (E.B.K.); (E.V.A.)
| | - Sergey A. Tikhonenko
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, Institutskaya St., 3, 142290 Puschino, Moscow Region, Russia; (E.V.M.); (A.L.K.); (A.V.D.)
- Correspondence:
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Melo LDR, Monteiro R, Pires DP, Azeredo J. Phage-Host Interaction Analysis by Flow Cytometry Allows for Rapid and Efficient Screening of Phages. Antibiotics (Basel) 2022; 11:antibiotics11020164. [PMID: 35203767 PMCID: PMC8868278 DOI: 10.3390/antibiotics11020164] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 01/27/2023] Open
Abstract
Recently, phages have become popular as an alternative to antibiotics. This increased demand for phage therapy needs rapid and efficient methods to screen phages infecting specific hosts. Existing methods are time-consuming, and for clinical purposes, novel, quick, and reliable screening methods are highly needed. Flow cytometry (FC) allows a quick differentiation and enumeration of bacterial cell populations and has been used to assess in vitro the activity of antimicrobial compounds. In this work, we propose FC as a rapid and reliable method to assess the susceptibility of a bacterial population to phage infection. For that, the interaction of phages vB_PaeM_CEB_DP1 and vB_PaeP_PE3 with Pseudomonas aeruginosa PAO1 was characterized by FC. Synchronous infection assays were performed, and samples were collected at different time points and stained with SYTO BC and PI before analysis. Part of the collected samples was used to characterize the expression of early, middle, and late genes by qPCR. Both FC and qPCR results were correlated with phage propagation assays. Results showed that SYTO BC median fluorescence intensity (MFI) values increased in the first 25 min of PE3 and DP1 infection. The increase of fluorescence is due to the expression of phage genes observed by qPCR. Since SYTO BC MFI values increase with gene expression, it allows the determination of host susceptibility to a phage in a short period of time, avoiding false positives caused by lysis from without. In conclusion, this method may allow for a quick and high-throughput real-time screening of different phages to a specific host, which can be crucial for a quick phage selection in clinical practice.
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Affiliation(s)
- Luís D. R. Melo
- LIBRO—Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, Campus de Gualtar, University of Minho, 4700-057 Braga, Portugal; (R.M.); (D.P.P.)
- LABBELS—Associate Laboratory, Braga, 4800-122 Guimarães, Portugal
- Correspondence: (L.D.R.M.); (J.A.); Tel.: +351-253-601-989 (L.D.R.M.); +351-253-604-414 (J.A.)
| | - Rodrigo Monteiro
- LIBRO—Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, Campus de Gualtar, University of Minho, 4700-057 Braga, Portugal; (R.M.); (D.P.P.)
- LABBELS—Associate Laboratory, Braga, 4800-122 Guimarães, Portugal
| | - Diana P. Pires
- LIBRO—Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, Campus de Gualtar, University of Minho, 4700-057 Braga, Portugal; (R.M.); (D.P.P.)
- LABBELS—Associate Laboratory, Braga, 4800-122 Guimarães, Portugal
| | - Joana Azeredo
- LIBRO—Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, Campus de Gualtar, University of Minho, 4700-057 Braga, Portugal; (R.M.); (D.P.P.)
- LABBELS—Associate Laboratory, Braga, 4800-122 Guimarães, Portugal
- Correspondence: (L.D.R.M.); (J.A.); Tel.: +351-253-601-989 (L.D.R.M.); +351-253-604-414 (J.A.)
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Oliveira H, Domingues R, Evans B, Sutton JM, Adriaenssens EM, Turner D. Genomic Diversity of Bacteriophages Infecting the Genus Acinetobacter. Viruses 2022; 14:v14020181. [PMID: 35215775 PMCID: PMC8878043 DOI: 10.3390/v14020181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 01/21/2023] Open
Abstract
The number of sequenced Acinetobacter phage genomes in the International Nucleotide Sequence Database Collaboration has increased significantly in recent years, from 37 in 2017 to a total of 139 as of January 2021 with genome sizes ranging from 31 to 378 kb. Here, we explored the genetic diversity of the Acinetobacter phages using comparative genomics approaches that included assessment of nucleotide similarity, shared gene content, single gene phylogeny, and the network-based classification tool vConTACT2. Phages infecting Acinetobacter sp. are genetically diverse and can be grouped into 8 clusters (subfamilies) and 46 sub-clusters (genera), of which 8 represent genomic singletons (additional genera). We propose the creation of five new subfamilies and suggest a reorganisation of the genus Obolenskvirus. These results provide an updated view of the viruses infecting Acinetobacter species, providing insights into their diversity.
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Affiliation(s)
- Hugo Oliveira
- Centre of Biological Engineering, University of Minho, Campus de Gualtar Braga, 4710-057 Braga, Portugal; (H.O.); (R.D.)
| | - Rita Domingues
- Centre of Biological Engineering, University of Minho, Campus de Gualtar Braga, 4710-057 Braga, Portugal; (H.O.); (R.D.)
| | - Benjamin Evans
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK;
| | - J. Mark Sutton
- United Kingdom Health Security Agency, Research and Evaluation, Porton Down, Salisbury SP4 OJG, UK;
| | | | - Dann Turner
- Department of Applied Sciences, Faculty of Health and Applied Sciences, University of the West of England, Bristol BS16 1QY, UK
- Correspondence:
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Expression of a phage-encoded Gp21 protein protects Pseudomonas aeruginosa against phage infection. J Virol 2022; 96:e0176921. [PMID: 35020473 DOI: 10.1128/jvi.01769-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
There is a continuously expanding gap between predicted phage gene sequences and their corresponding functions, which largely hampered the development of phage therapy. Previous studies reported several phage proteins that could interfere with the intracellular processes of the host to obtain efficient infection. But few phage proteins that protect host against phage infection has been identified and characterized in detail. Here, we isolate a phage vB_Pae_QDWS capable of infecting Pseudomonas aeruginosa PAO1, and report its encoded Gp21 protein protects PAO1 against phage infection. Expressing of Gp21 regulate bacterial quorum sensing with an inhibitory effect in low cell density and activation effect in high cell density. By testing the TFPs-mediated twitching motility and transmission electron microscopy analysis, Gp21 was found decreased the pilus synthesis. Further constructing the TFPs synthesis gene pilB mutant and performing adsorption and phage resistance assay, we demonstrated Gp21 protein could block phage infection via decreasing the TFPs-mediated phage adsorption. Gp21 is a novel protein that inhibit phage efficacy against bacteria. The study deepens our understanding of phage-host interactions. Importance The majority of the annotated phage genes are currently deposited as "hypothetical protein" with unknown function. Researches revealed that some phage proteins serve to inhibit or redirect the host intracellular processes for phage infection. Differently, we report a phage encoded protein Gp21 that protect the host against phage infection. The pathways that Gp21 involved in anti-phage defense in Pseudomonas aeruginosa PAO1 are interfering with quorum sensing and decreasing the type IV pilus-mediated phage adsorption. Gp21 is a novel protein with a low sequence homology with other reported twitching inhibitory proteins. As a lytic phage derived protein, Gp21 expression protects P. aeruginosa PAO1 from reinfection by phage vB_Pae_QDWS, which may explain the well-known pseudolysogeny caused by virulent phages. Our discoveries provide valuable new insight into the phage-host evolutionary dynamics.
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Wójcicki M, Średnicka P, Błażejak S, Gientka I, Kowalczyk M, Emanowicz P, Świder O, Sokołowska B, Juszczuk-Kubiak E. Characterization and Genome Study of Novel Lytic Bacteriophages against Prevailing Saprophytic Bacterial Microflora of Minimally Processed Plant-Based Food Products. Int J Mol Sci 2021; 22:12460. [PMID: 34830335 PMCID: PMC8624825 DOI: 10.3390/ijms222212460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 12/13/2022] Open
Abstract
The food industry is still searching for novel solutions to effectively ensure the microbiological safety of food, especially fresh and minimally processed food products. Nowadays, the use of bacteriophages as potential biological control agents in microbiological food safety and preservation is a promising strategy. The aim of the study was the isolation and comprehensive characterization of novel bacteriophages with lytic activity against saprophytic bacterial microflora of minimally processed plant-based food products, such as mixed leaf salads. From 43 phages isolated from municipal sewage, four phages, namely Enterobacter phage KKP 3263, Citrobacter phage KKP 3664, Enterobacter phage KKP 3262, and Serratia phage KKP 3264 have lytic activity against Enterobacter ludwigii KKP 3083, Citrobacter freundii KKP 3655, Enterobacter cloacae KKP 3082, and Serratia fonticola KKP 3084 bacterial strains, respectively. Transmission electron microscopy (TEM) and whole-genome sequencing (WGS) identified Enterobacter phage KKP 3263 as an Autographiviridae, and Citrobacter phage KKP 3664, Enterobacter phage KKP 3262, and Serratia phage KKP 3264 as members of the Myoviridae family. Genome sequencing revealed that these phages have linear double-stranded DNA (dsDNA) with sizes of 39,418 bp (KKP 3263), 61,608 bp (KKP 3664), 84,075 bp (KKP 3262), and 148,182 bp (KKP 3264). No antibiotic resistance genes, virulence factors, integrase, recombinase, or repressors, which are the main markers of lysogenic viruses, were annotated in phage genomes. Serratia phage KKP 3264 showed the greatest growth inhibition of Serratia fonticola KKP 3084 strain. The use of MOI 1.0 caused an almost 5-fold decrease in the value of the specific growth rate coefficient. The phages retained their lytic activity in a wide range of temperatures (from -20 °C to 50 °C) and active acidity values (pH from 4 to 11). All phages retained at least 70% of lytic activity at 60 °C. At 80 °C, no lytic activity against tested bacterial strains was observed. Serratia phage KKP 3264 was the most resistant to chemical factors, by maintaining high lytic activity across a broader range of pH from 3 to 11. The results indicated that these phages could be a potential biological control agent against saprophytic bacterial microflora of minimally processed plant-based food products.
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Affiliation(s)
- Michał Wójcicki
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
| | - Paulina Średnicka
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
| | - Stanisław Błażejak
- Department of Biotechnology and Food Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences (WULS-SGGW), Nowoursynowska 166 Street, 02-776 Warsaw, Poland; (S.B.); (I.G.)
| | - Iwona Gientka
- Department of Biotechnology and Food Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences (WULS-SGGW), Nowoursynowska 166 Street, 02-776 Warsaw, Poland; (S.B.); (I.G.)
| | - Monika Kowalczyk
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
| | - Paulina Emanowicz
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
| | - Olga Świder
- Department of Food Safety and Chemical Analysis, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland;
| | - Barbara Sokołowska
- Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland;
| | - Edyta Juszczuk-Kubiak
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
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Bdira FB, Erkelens AM, Qin L, Volkov AN, Lippa A, Bowring N, Boyle A, Ubbink M, Dove S, Dame R. Novel anti-repression mechanism of H-NS proteins by a phage protein. Nucleic Acids Res 2021; 49:10770-10784. [PMID: 34520554 PMCID: PMC8501957 DOI: 10.1093/nar/gkab793] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/16/2021] [Accepted: 09/01/2021] [Indexed: 12/17/2022] Open
Abstract
H-NS family proteins, bacterial xenogeneic silencers, play central roles in genome organization and in the regulation of foreign genes. It is thought that gene repression is directly dependent on the DNA binding modes of H-NS family proteins. These proteins form lateral protofilaments along DNA. Under specific environmental conditions they switch to bridging two DNA duplexes. This switching is a direct effect of environmental conditions on electrostatic interactions between the oppositely charged DNA binding and N-terminal domains of H-NS proteins. The Pseudomonas lytic phage LUZ24 encodes the protein gp4, which modulates the DNA binding and function of the H-NS family protein MvaT of Pseudomonas aeruginosa. However, the mechanism by which gp4 affects MvaT activity remains elusive. In this study, we show that gp4 specifically interferes with the formation and stability of the bridged MvaT-DNA complex. Structural investigations suggest that gp4 acts as an 'electrostatic zipper' between the oppositely charged domains of MvaT protomers, and stabilizes a structure resembling their 'half-open' conformation, resulting in relief of gene silencing and adverse effects on P. aeruginosa growth. The ability to control H-NS conformation and thereby its impact on global gene regulation and growth might open new avenues to fight Pseudomonas multidrug resistance.
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Affiliation(s)
- Fredj Ben Bdira
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Amanda M Erkelens
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Liang Qin
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Alexander N Volkov
- VIB-VUB Structural Biology Research Center, Pleinlaan 2, 1050 Brussels, Belgium
- Jean Jeener NMR Centre, VUB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Andrew M Lippa
- Boston Children's Hospital, Division of Infectious Diseases, Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas Bowring
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Aimee L Boyle
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Marcellus Ubbink
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Simon L Dove
- Boston Children's Hospital, Division of Infectious Diseases, Harvard Medical School, Boston, MA 02115, USA
| | - Remus T Dame
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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30
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Kristensen CS, Varming AK, Leinweber HAK, Hammer K, Lo Leggio L, Ingmer H, Kilstrup M. Characterization of the genetic switch from phage ɸ13 important for Staphylococcus aureus colonization in humans. Microbiologyopen 2021; 10:e1245. [PMID: 34713608 PMCID: PMC8516035 DOI: 10.1002/mbo3.1245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/30/2021] [Indexed: 11/09/2022] Open
Abstract
Temperate phages are bacterial viruses that after infection either reside integrated into a bacterial genome as prophages forming lysogens or multiply in a lytic lifecycle. The decision between lifestyles is determined by a switch involving a phage-encoded repressor, CI, and a promoter region from which lytic and lysogenic genes are divergently transcribed. Here, we investigate the switch of phage ɸ13 from the human pathogen Staphylococcus aureus. ɸ13 encodes several virulence factors and is prevalent in S. aureus strains colonizing humans. We show that the ɸ13 switch harbors a cI gene, a predicted mor (modulator of repression) gene, and three high-affinity operator sites binding CI. To quantify the decision between lytic and lysogenic lifestyle, we introduced reporter plasmids that carry the 1.3 kb switch region from ɸ13 with the lytic promoter fused to lacZ into S. aureus and Bacillus subtilis. Analysis of β-galactosidase expression indicated that decision frequency is independent of host factors. The white "lysogenic" phenotype, which relies on the expression of cI, could be switched to a stable blue "lytic" phenotype by DNA damaging agents. We have characterized lifestyle decisions of phage ɸ13, and our approach may be applied to other temperate phages encoding virulence factors in S. aureus.
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Affiliation(s)
- Camilla S. Kristensen
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | | | | | - Karin Hammer
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Leila Lo Leggio
- Department of ChemistryUniversity of CopenhagenKobenhavnDenmark
| | - Hanne Ingmer
- Department of Veterinary and Animal SciencesUniversity of CopenhagenKobenhavnDenmark
| | - Mogens Kilstrup
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
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31
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Schroven K, Aertsen A, Lavigne R. Bacteriophages as drivers of bacterial virulence and their potential for biotechnological exploitation. FEMS Microbiol Rev 2021; 45:5902850. [PMID: 32897318 DOI: 10.1093/femsre/fuaa041] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/03/2020] [Indexed: 12/20/2022] Open
Abstract
Bacteria-infecting viruses (phages) and their hosts maintain an ancient and complex relationship. Bacterial predation by lytic phages drives an ongoing phage-host arms race, whereas temperate phages initiate mutualistic relationships with their hosts upon lysogenization as prophages. In human pathogens, these prophages impact bacterial virulence in distinct ways: by secretion of phage-encoded toxins, modulation of the bacterial envelope, mediation of bacterial infectivity and the control of bacterial cell regulation. This review builds the argument that virulence-influencing prophages hold extensive, unexplored potential for biotechnology. More specifically, it highlights the development potential of novel therapies against infectious diseases, to address the current antibiotic resistance crisis. First, designer bacteriophages may serve to deliver genes encoding cargo proteins which repress bacterial virulence. Secondly, one may develop small molecules mimicking phage-derived proteins targeting central regulators of bacterial virulence. Thirdly, bacteria equipped with phage-derived synthetic circuits which modulate key virulence factors could serve as vaccine candidates to prevent bacterial infections. The development and exploitation of such antibacterial strategies will depend on the discovery of other prophage-derived, virulence control mechanisms and, more generally, on the dissection of the mutualistic relationship between temperate phages and bacteria, as well as on continuing developments in the synthetic biology field.
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Affiliation(s)
- Kaat Schroven
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
| | - Abram Aertsen
- Laboratory of Food Microbiology, KU Leuven, Kasteelpark Arenberg 23, 3001 Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
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32
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Stanton CR, Rice DTF, Beer M, Batinovic S, Petrovski S. Isolation and Characterisation of the Bundooravirus Genus and Phylogenetic Investigation of the Salasmaviridae Bacteriophages. Viruses 2021; 13:1557. [PMID: 34452423 PMCID: PMC8402886 DOI: 10.3390/v13081557] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/28/2021] [Accepted: 08/02/2021] [Indexed: 01/21/2023] Open
Abstract
Bacillus is a highly diverse genus containing over 200 species that can be problematic in both industrial and medical settings. This is mainly attributed to Bacillus sp. being intrinsically resistant to an array of antimicrobial compounds, hence alternative treatment options are needed. In this study, two bacteriophages, PumA1 and PumA2 were isolated and characterized. Genome nucleotide analysis identified the two phages as novel at the DNA sequence level but contained proteins similar to phi29 and other related phages. Whole genome phylogenetic investigation of 34 phi29-like phages resulted in the formation of seven clusters that aligned with recent ICTV classifications. PumA1 and PumA2 share high genetic mosaicism and form a genus with another phage named WhyPhy, more recently isolated from the United States of America. The three phages within this cluster are the only candidates to infect B. pumilus. Sequence analysis of B. pumilus phage resistant mutants revealed that PumA1 and PumA2 require polymerized and peptidoglycan bound wall teichoic acid (WTA) for their infection. Bacteriophage classification is continuously evolving with the increasing phages' sequences in public databases. Understanding phage evolution by utilizing a combination of phylogenetic approaches provides invaluable information as phages become legitimate alternatives in both human health and industrial processes.
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Affiliation(s)
- Cassandra R. Stanton
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Melbourne, VIC 3086, Australia; (C.R.S.); (D.T.F.R.); (S.B.)
| | - Daniel T. F. Rice
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Melbourne, VIC 3086, Australia; (C.R.S.); (D.T.F.R.); (S.B.)
| | - Michael Beer
- Department of Defence Science and Technology, Port Melbourne, VIC 3207, Australia;
| | - Steven Batinovic
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Melbourne, VIC 3086, Australia; (C.R.S.); (D.T.F.R.); (S.B.)
| | - Steve Petrovski
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Melbourne, VIC 3086, Australia; (C.R.S.); (D.T.F.R.); (S.B.)
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33
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Virus-Host Interaction Gets Curiouser and Curiouser. PART II: Functional Transcriptomics of the E. coli DksA-Deficient Cell upon Phage P1 vir Infection. Int J Mol Sci 2021; 22:ijms22116159. [PMID: 34200430 PMCID: PMC8201110 DOI: 10.3390/ijms22116159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/01/2021] [Indexed: 02/07/2023] Open
Abstract
The virus–host interaction requires a complex interplay between the phage strategy of reprogramming the host machinery to produce and release progeny virions, and the host defense against infection. Using RNA sequencing, we investigated the phage–host interaction to resolve the phenomenon of improved lytic development of P1vir phage in a DksA-deficient E. coli host. Expression of the ant1 and kilA P1vir genes in the wild-type host was the highest among all and most probably leads to phage virulence. Interestingly, in a DksA-deficient host, P1vir genes encoding lysozyme and holin are downregulated, while antiholins are upregulated. Gene expression of RepA, a protein necessary for replication initiating at the phage oriR region, is increased in the dksA mutant; this is also true for phage genes responsible for viral morphogenesis and architecture. Still, it seems that P1vir is taking control of the bacterial protein, sugar, and lipid metabolism in both, the wild type and dksA− hosts. Generally, bacterial hosts are reacting by activating their SOS response or upregulating the heat shock proteins. However, only DksA-deficient cells upregulate their sulfur metabolism and downregulate proteolysis upon P1vir infection. We conclude that P1vir development is enhanced in the dksA mutant due to several improvements, including replication and virion assembly, as well as a less efficient lysis.
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34
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João J, Lampreia J, Prazeres DMF, Azevedo AM. Manufacturing of bacteriophages for therapeutic applications. Biotechnol Adv 2021; 49:107758. [PMID: 33895333 DOI: 10.1016/j.biotechadv.2021.107758] [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] [Received: 11/17/2020] [Revised: 03/14/2021] [Accepted: 04/20/2021] [Indexed: 12/21/2022]
Abstract
Bacteriophages, or simply phages, are the most abundant biological entities on Earth. One of the most interesting characteristics of these viruses, which infect and use bacteria as their host organisms, is their high level of specificity. Since their discovery, phages became a tool for the comprehension of basic molecular biology and originated applications in a variety of areas such as agriculture, biotechnology, food safety, veterinary, pollution remediation and wastewater treatment. In particular, phages offer a solution to one of the major problems in public health nowadays, i.e. the emergence of multidrug-resistant bacteria. In these situations, the use of virulent phages as therapeutic agents offers an alternative to the classic, antibiotic-based strategies. The development of phage therapies should be accompanied by the improvement of phage biomanufacturing processes, both at laboratory and industrial scales. In this review, we first present some historical and general aspects related with the discovery, usage and biology of phages and provide a brief overview of the most relevant phage therapy applications. Then, we showcase current processes used for the production and purification of phages and future alternatives in development. On the production side, key factors such as the bacterial physiological state, the conditions of phage infection and the operation parameters are described alongside with the different operation modes, from batch to semi-continuous and continuous. Traditional purification methods used in the initial phage isolation steps are then described followed by the presentation of current state-of-the-art purification approaches. Continuous purification of phages is finally presented as a future biomanufacturing trend.
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Affiliation(s)
- Jorge João
- iBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal.
| | - João Lampreia
- iBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal.
| | - Duarte Miguel F Prazeres
- iBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal.
| | - Ana M Azevedo
- iBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal.
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Characterization and Full Genome Sequence of Novel KPP-5 Lytic Phage against Klebsiella pneumoniae Responsible for Recalcitrant Infection. Biomedicines 2021; 9:biomedicines9040342. [PMID: 33800632 PMCID: PMC8066614 DOI: 10.3390/biomedicines9040342] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 01/21/2023] Open
Abstract
Klebsiella pneumoniae is a hazardous opportunistic pathogen that is involved in many serious human diseases and is considered to be an important foodborne pathogen found in many food types. Multidrug resistance (MDR) K. pneumoniae strains have recently spread and increased, making bacteriophage therapy an effective alternative to multiple drug-resistant pathogens. As a consequence, this research was conducted to describe the genome and basic biological characteristics of a novel phage capable of lysing MDR K. pneumoniae isolated from food samples in Egypt. The host range revealed that KPP-5 phage had potent lytic activity and was able to infect all selected MDR K. pneumoniae strains from different sources. Electron microscopy images showed that KPP-5 lytic phage was a podovirus morphology. The one-step growth curve exhibited that KPP-5 phage had a relatively short latent period of 25 min, and the burst size was about 236 PFU/infected cells. In addition, KPP-5 phage showed high stability at different temperatures and pH levels. KPP-5 phage has a linear dsDNA genome with a length of 38,245 bp with a GC content of 50.8% and 40 predicted open reading frames (ORFs). Comparative genomics and phylogenetic analyses showed that KPP-5 is most closely associated with the Teetrevirus genus in the Autographviridae family. No tRNA genes have been identified in the KPP-5 phage genome. In addition, phage-borne virulence genes or drug resistance genes were not present, suggesting that KPP-5 could be used safely as a phage biocontrol agent.
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Evseev PV, Lukianova AA, Shneider MM, Korzhenkov AA, Bugaeva EN, Kabanova AP, Miroshnikov KK, Kulikov EE, Toshchakov SV, Ignatov AN, Miroshnikov KA. Origin and Evolution of Studiervirinae Bacteriophages Infecting Pectobacterium: Horizontal Transfer Assists Adaptation to New Niches. Microorganisms 2020; 8:E1707. [PMID: 33142811 PMCID: PMC7693777 DOI: 10.3390/microorganisms8111707] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 10/29/2020] [Accepted: 10/29/2020] [Indexed: 01/25/2023] Open
Abstract
Black leg and soft rot are devastating diseases causing up to 50% loss of potential potato yield. The search for, and characterization of, bacterial viruses (bacteriophages) suitable for the control of these diseases is currently a sought-after task for agricultural microbiology. Isolated lytic Pectobacterium bacteriophages Q19, PP47 and PP81 possess a similar broad host range but differ in their genomic properties. The genomic features of characterized phages have been described and compared to other Studiervirinae bacteriophages. Thorough phylogenetic analysis has clarified the taxonomy of the phages and their positioning relative to other genera of the Autographiviridae family. Pectobacterium phage Q19 seems to represent a new genus not described previously. The genomes of the phages are generally similar to the genome of phage T7 of the Teseptimavirus genus but possess a number of specific features. Examination of the structure of the genes and proteins of the phages, including the tail spike protein, underlines the important role of horizontal gene exchange in the evolution of these phages, assisting their adaptation to Pectobacterium hosts. The results provide the basis for the development of bacteriophage-based biocontrol of potato soft rot as an alternative to the use of antibiotics.
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Affiliation(s)
- Peter V. Evseev
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (A.A.L.); (M.M.S.); (E.N.B.); (A.P.K.)
| | - Anna A. Lukianova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (A.A.L.); (M.M.S.); (E.N.B.); (A.P.K.)
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Mikhail M. Shneider
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (A.A.L.); (M.M.S.); (E.N.B.); (A.P.K.)
| | | | - Eugenia N. Bugaeva
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (A.A.L.); (M.M.S.); (E.N.B.); (A.P.K.)
- Research Center “PhytoEngineering” Ltd., Rogachevo, 141880 Moscow Region, Russia;
| | - Anastasia P. Kabanova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (A.A.L.); (M.M.S.); (E.N.B.); (A.P.K.)
- Research Center “PhytoEngineering” Ltd., Rogachevo, 141880 Moscow Region, Russia;
| | - Kirill K. Miroshnikov
- Winogradsky Institute of Microbiology, Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, 117312 Moscow, Russia; (K.K.M.); (E.E.K.); (S.V.T.)
| | - Eugene E. Kulikov
- Winogradsky Institute of Microbiology, Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, 117312 Moscow, Russia; (K.K.M.); (E.E.K.); (S.V.T.)
| | - Stepan V. Toshchakov
- Winogradsky Institute of Microbiology, Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, 117312 Moscow, Russia; (K.K.M.); (E.E.K.); (S.V.T.)
| | - Alexander N. Ignatov
- Research Center “PhytoEngineering” Ltd., Rogachevo, 141880 Moscow Region, Russia;
| | - Konstantin A. Miroshnikov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (A.A.L.); (M.M.S.); (E.N.B.); (A.P.K.)
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Morimoto D, Šulčius S, Yoshida T. Viruses of freshwater bloom-forming cyanobacteria: genomic features, infection strategies and coexistence with the host. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:486-502. [PMID: 32754956 DOI: 10.1111/1758-2229.12872] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/28/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Freshwater bloom-forming cyanobacteria densely grow in the aquatic environments, leading to an increase in the viral-contact rate. They possess numerous antiviral genes, as well as cell differentiation- and physiological performance-related genes, owing to genome expansion. Their genomic features and unique lifestyles suggest that they coexist with cyanoviruses in ways different from marine cyanobacteria. Furthermore, genome contents of isolated freshwater bloom-forming cyanobacterial viruses have little in common with those of marine cyanoviruses studied to date. They lack the marine cyanoviral hallmark genes that sustain photosynthetic activity and redirect host metabolism to viral reproduction; therefore, they are predicted to share metabolisms and precursor pools with host cyanobacteria to ensure efficient viral reproduction and avoid nutrient deficiencies and antiviral response. Additionally, cyanovirus-cyanobacteria coexistence strategies may change as bloom density increases. Diverse genotypic populations of cyanoviruses and hosts coexist and fluctuate under high viral-contact rate conditions, leading to their rapid coevolution through antiviral responses. The ancestral and newly evolved genotypes coexist, thereby expanding the diversity levels of host and viral populations. Bottleneck events occurring due to season-related decreases in bloom-forming species abundance provide each genotype within cyanobacterial population an equal chance to increase in prevalence during the next bloom and enhance further diversification.
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Affiliation(s)
- Daichi Morimoto
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Sigitas Šulčius
- Laboratory of Algology and Microbial Ecology, Nature Research Centre, Akademijos 2, Vilnius, 08412, Lithuania
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, 606-8502, Japan
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Mutalik VK, Adler BA, Rishi HS, Piya D, Zhong C, Koskella B, Kutter EM, Calendar R, Novichkov PS, Price MN, Deutschbauer AM, Arkin AP. High-throughput mapping of the phage resistance landscape in E. coli. PLoS Biol 2020; 18:e3000877. [PMID: 33048924 PMCID: PMC7553319 DOI: 10.1371/journal.pbio.3000877] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 09/08/2020] [Indexed: 12/18/2022] Open
Abstract
Bacteriophages (phages) are critical players in the dynamics and function of microbial communities and drive processes as diverse as global biogeochemical cycles and human health. Phages tend to be predators finely tuned to attack specific hosts, even down to the strain level, which in turn defend themselves using an array of mechanisms. However, to date, efforts to rapidly and comprehensively identify bacterial host factors important in phage infection and resistance have yet to be fully realized. Here, we globally map the host genetic determinants involved in resistance to 14 phylogenetically diverse double-stranded DNA phages using two model Escherichia coli strains (K-12 and BL21) with known sequence divergence to demonstrate strain-specific differences. Using genome-wide loss-of-function and gain-of-function genetic technologies, we are able to confirm previously described phage receptors as well as uncover a number of previously unknown host factors that confer resistance to one or more of these phages. We uncover differences in resistance factors that strongly align with the susceptibility of K-12 and BL21 to specific phage. We also identify both phage-specific mechanisms, such as the unexpected role of cyclic-di-GMP in host sensitivity to phage N4, and more generic defenses, such as the overproduction of colanic acid capsular polysaccharide that defends against a wide array of phages. Our results indicate that host responses to phages can occur via diverse cellular mechanisms. Our systematic and high-throughput genetic workflow to characterize phage-host interaction determinants can be extended to diverse bacteria to generate datasets that allow predictive models of how phage-mediated selection will shape bacterial phenotype and evolution. The results of this study and future efforts to map the phage resistance landscape will lead to new insights into the coevolution of hosts and their phage, which can ultimately be used to design better phage therapeutic treatments and tools for precision microbiome engineering.
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Affiliation(s)
- Vivek K. Mutalik
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Innovative Genomics Institute, Berkeley, California, United States of America
| | - Benjamin A. Adler
- Innovative Genomics Institute, Berkeley, California, United States of America
- Department of Bioengineering, University of California – Berkeley, Berkeley, California, United States of America
| | - Harneet S. Rishi
- Biophysics Graduate Group, University of California – Berkeley, Berkeley, California, United States of America
- Designated Emphasis Program in Computational and Genomic Biology, University of California – Berkeley, Berkeley, California, United States of America
| | - Denish Piya
- Innovative Genomics Institute, Berkeley, California, United States of America
- Department of Bioengineering, University of California – Berkeley, Berkeley, California, United States of America
| | - Crystal Zhong
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Britt Koskella
- Department of Integrative Biology, University of California – Berkeley, Berkeley, California, United States of America
| | | | - Richard Calendar
- Department of Molecular and Cell Biology, University of California – Berkeley, Berkeley, California, United States of America
| | - Pavel S. Novichkov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Morgan N. Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Innovative Genomics Institute, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California – Berkeley, Berkeley, California, United States of America
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Innovative Genomics Institute, Berkeley, California, United States of America
- Department of Bioengineering, University of California – Berkeley, Berkeley, California, United States of America
- Biophysics Graduate Group, University of California – Berkeley, Berkeley, California, United States of America
- Designated Emphasis Program in Computational and Genomic Biology, University of California – Berkeley, Berkeley, California, United States of America
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Phage-based target discovery and its exploitation towards novel antibacterial molecules. Curr Opin Biotechnol 2020; 68:1-7. [PMID: 33007632 DOI: 10.1016/j.copbio.2020.08.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/27/2020] [Accepted: 08/31/2020] [Indexed: 01/05/2023]
Abstract
The deeply intertwined evolutionary history between bacteriophages and bacteria has endowed phages with highly specific mechanisms to hijack bacterial cell metabolism for their propagation. Here, we present a comprehensive, phage-driven strategy to reveal novel antibacterial targets by the exploitation of phage-bacteria interactions. This strategy will enable the design of small molecules, which mimic the inhibitory phage proteins, and allow the subsequent hit-to-lead development of these antimicrobial compounds. This proposed small molecule approach is distinct from phage therapy and phage enzyme-based antimicrobials and may produce a more sustainable generation of new antibiotics that exploit novel bacterial targets and act in a pathogen-specific manner.
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Zhong Q, Yang L, Li L, Shen W, Li Y, Xu H, Zhong Z, Chen M, Le S. Transcriptomic Analysis Reveals the Dependency of Pseudomonas aeruginosa Genes for Double-Stranded RNA Bacteriophage phiYY Infection Cycle. iScience 2020; 23:101437. [PMID: 32827855 PMCID: PMC7452160 DOI: 10.1016/j.isci.2020.101437] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/16/2020] [Accepted: 08/03/2020] [Indexed: 12/11/2022] Open
Abstract
Bacteriophage phiYY is currently the only double-stranded RNA (dsRNA) phage that infects Pseudomonas aeruginosa and is a potential candidate for phage therapy. Here we applied RNA-seq to investigate the lytic cycle of phiYY infecting P. aeruginosa strain PAO1r. About 12.45% (651/5,229) of the host genes were determined to be differentially expressed genes. Moreover, oxidative stress response genes katB and ahpB are upregulated 64- to 128-fold after phage infection, and the single deletion of each gene blocked phiYY infection, indicating that phiYY is extremely sensitive to oxidative stress. On the contrary, another upregulated gene PA0800 might constrain phage infection, because the deletion of PA0800 resulted in a 3.5-fold increase of the efficiency of plating. Our study highlights a complicated dsRNA phage-phage global interaction and raises new questions toward the host defense mechanisms against dsRNA phage and dsRNA phage-encoded hijacking mechanisms.
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Affiliation(s)
- Qiu Zhong
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, Chongqing 400038, China
- Department of Clinical Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing 400038, China
| | - Lan Yang
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Linlin Li
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Wei Shen
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing 400038, China
| | - Yang Li
- Medical Center of Trauma and War Injury, Daping Hospital, Army Medical University, Chongqing 400038, China
- State Key Laboratory of Trauma, Burns and Combined Injuries, Army Medical University, Chongqing 400038, China
| | - Huan Xu
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, Chongqing 400038, China
| | - Zhuojun Zhong
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing 400038, China
| | - Ming Chen
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, Chongqing 400038, China
- State Key Laboratory of Trauma, Burns and Combined Injuries, Army Medical University, Chongqing 400038, China
| | - Shuai Le
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing 400038, China
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Clokie MR, Blasdel BG, Demars BO, Sicheritz-Pontén T. Rethinking Phage Ecology by Rooting it Within an Established Plant Framework. PHAGE (NEW ROCHELLE, N.Y.) 2020; 1:121-136. [PMID: 36147824 PMCID: PMC9041459 DOI: 10.1089/phage.2020.0015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Despite the abundance and significance of bacteriophages to microbial ecosystems, no broad ecological frameworks exist within which to determine "bacteriophage types" that reflect their ecological strategies and ways in which they interact with bacterial cells. To address this, we repurposed the well-established Grime's triangular CSR framework, which classifies plants according to three axes: competitiveness (C), ability to tolerate stress (S), and capacity to cope with disturbance (R). This framework is distinguished from other accepted schemes, as it seeks to identify individual characteristics of plants to understand their biological strategies and roles within an ecosystem. Our repurposing of the CSR triangle is based on phage transcription and the observation that typically phages have three major distinguishable transcription phases: early, middle, and late. We hypothesize that the proportion of genes expressed in these phases reflects key information about the phage "ecological strategy," namely the C, S, and R strategies, allowing us to examine phages in a similar way to how plants are projected onto the triangle. In the "phage version" of this scheme, we suggest: (1) that some phages prioritize the early phase of transcription that shuts off host defense mechanisms, which reflects competitiveness; (2) other phages prioritize tuning resource management mechanisms in the cell such as nucleotide metabolism during their "mid" expression profile to tolerate stress; and (3) a further subset of phages (termed Ruderals) survive disturbance by investing significant resources into regeneration so they express a higher proportion of their genes during late infection. We examined 42 published phage transcriptomes and show that they fall into discrete CSR categories according to their expression profiles. We discuss these positions in the context of their biology, which is largely consistent with our predictions of specific phage characteristics. In this opinion article, we suggest a starting point to ascribe phages into different functional types and thus understand them in an ecological framework. We suggest that this may have far-reaching implications for the application of phages in therapy and their exploitation to manipulate bacterial communities. We invite further use of this framework via our online tool; www.PhageCSR.ml.
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Affiliation(s)
- Martha R.J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Address correspondence to: Martha R.J. Clokie, PhD, Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | | | | | - Thomas Sicheritz-Pontén
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Address correspondence to: Thomas Sicheritz Pontén, PhD, Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, Bygning 7, Copenhagen 1353, Denmark
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Yu X, Xu J, Gu Y, Zhang R, Zhu Y, Liu X. Molecular Characterization and Comparative Genomic Analysis of vB_PaeP_YA3, a Novel Temperate Bacteriophage of Pseudomonas aeruginosa. Front Microbiol 2020; 11:947. [PMID: 32655502 PMCID: PMC7326022 DOI: 10.3389/fmicb.2020.00947] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/20/2020] [Indexed: 01/21/2023] Open
Abstract
It is well known that bacteriophages play crucial roles in many aspects, such as controlling the number and the diversity of bacteria and participating in horizontal gene transfer, which is a key process in the evolution of bacteria. However, so far, the number of temperate bacteriophages is still limited, and their life processes are severely unknown, except for members of the lambdoid family of coliphages. In this study, a novel temperate phage of Pseudomonas aeruginosa, YA3 (vB_PaeP_YA3), was isolated from waste water. The morphology of YA3 suggested that it is a Podoviridae. The YA3 genome is a circular double-stranded DNA of 45,253 bp, with an average G + C content of 57.2%. A total of 65 open reading frames (ORFs) were predicted according to the sequence of YA3’s genome, of which only 32 (49.2%) ORFs were assigned with putative functions and 13 ORFs were confirmed by the structural proteome. Genome and proteome analyses confirmed the lysogenic nature of this phage, which encodes the typical lysogen-related proteins integrase, CI, Cro, and Q protein. The genome of YA3 is most closely related with that of temperate phage vB_PaeP_Tr60_Ab31, whereas the homology coverage is just 48%. There are many critical differences between their genomes, involving promoters, lysis pathways, and regulation patterns. YA3 is capable of stably lysogenizing its host P. aeruginosa PA14, targeting the integration site within the serine tRNA gene (PA14_RS20820), which is similar with phage vB_PaeP_Tr60_Ab31. The phylogenetic analysis is more complicated than we thought. Based on phage terminase large subunit (TerL) and CI proteins, phage YA3 is related with phage lambda, while their genome coverage is extremely low (<1%). Therefore, phage YA3 is a considerably novel lambda-like temperate phage, and a further study of its genome may deepen our understanding of the interaction between lysogenic phages and their bacterial hosts.
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Affiliation(s)
- Xinyan Yu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Microbiology, Nanjing Medical University, Nanjing, China
| | - Jing Xu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Microbiology, Nanjing Medical University, Nanjing, China
| | - Yu Gu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Microbiology, Nanjing Medical University, Nanjing, China
| | - Ruiyang Zhang
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Microbiology, Nanjing Medical University, Nanjing, China
| | - Yefei Zhu
- Laboratory Medicine Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaoqiu Liu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Microbiology, Nanjing Medical University, Nanjing, China
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Spruit CM, Wicklund A, Wan X, Skurnik M, Pajunen MI. Discovery of Three Toxic Proteins of Klebsiella Phage fHe-Kpn01. Viruses 2020; 12:E544. [PMID: 32429141 PMCID: PMC7291057 DOI: 10.3390/v12050544] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 01/09/2023] Open
Abstract
The lytic phage, fHe-Kpn01 was isolated from sewage water using an extended-spectrum beta-lactamase-producing strain of Klebsiella pneumoniae as a host. The genome is 43,329 bp in size and contains direct terminal repeats of 222 bp. The genome contains 56 predicted genes, of which proteomics analysis detected 29 different proteins in purified phage particles. Comparison of fHe-Kpn01 to other phages, both morphologically and genetically, indicated that the phage belongs to the family Podoviridae and genus Drulisvirus. Because fHe-Kpn01 is strictly lytic and does not carry any known resistance or virulence genes, it is suitable for phage therapy. It has, however, a narrow host range since it infected only three of the 72 tested K. pneumoniae strains, two of which were of capsule type KL62. After annotation of the predicted genes based on the similarity to genes of known function and proteomics results on the virion-associated proteins, 22 gene products remained annotated as hypothetical proteins of unknown function (HPUF). These fHe-Kpn01 HPUFs were screened for their toxicity in Escherichia coli. Three of the HPUFs, encoded by the genes g10, g22, and g38, were confirmed to be toxic.
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Affiliation(s)
- Cindy M. Spruit
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (C.M.S.); (A.W.); (X.W.); (M.S.)
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands
| | - Anu Wicklund
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (C.M.S.); (A.W.); (X.W.); (M.S.)
- Division of Clinical Microbiology, HUSLAB, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Xing Wan
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (C.M.S.); (A.W.); (X.W.); (M.S.)
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00790 Helsinki, Finland
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (C.M.S.); (A.W.); (X.W.); (M.S.)
- Division of Clinical Microbiology, HUSLAB, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Maria I. Pajunen
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (C.M.S.); (A.W.); (X.W.); (M.S.)
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Isolation and Characterization of the Novel Phage JD032 and Global Transcriptomic Response during JD032 Infection of Clostridioides difficile Ribotype 078. mSystems 2020; 5:5/3/e00017-20. [PMID: 32371470 PMCID: PMC7205517 DOI: 10.1128/msystems.00017-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
C. difficile is one of the most clinically significant intestinal pathogens. Although phages have been shown to effectively control C. difficile infection, the host responses to phage predation have not been fully studied. In this study, we reported the isolation and characterization of a new phage, JD032, and analyzed the global transcriptomic changes in the hypervirulent RT078 C. difficile strain, TW11, during phage JD032 infection. We found that bacterial host mRNA was progressively replaced with phage transcripts, three temporal categories of JD032 gene expression, the extensive interplay between phage-bacterium, antiphage-like responses of the host and phage evasion, and decreased expression of sporulation- and virulence-related genes of the host after phage infection. These findings confirmed the complexity of interactions between C. difficile and phages and suggest that phages undergoing a lytic cycle may also cause different phenotypes in hosts, similar to prophages, which may inspire phage therapy for the control of C. difficile. Insights into the interaction between phages and their bacterial hosts are crucial for the development of phage therapy. However, only one study has investigated global gene expression of Clostridioides (formerly Clostridium) difficile carrying prophage, and transcriptional reprogramming during lytic infection has not been studied. Here, we presented the isolation, propagation, and characterization of a newly discovered 35,109-bp phage, JD032, and investigated the global transcriptomes of both JD032 and C. difficile ribotype 078 (RT078) strain TW11 during JD032 infection. Transcriptome sequencing (RNA-seq) revealed the progressive replacement of bacterial host mRNA with phage transcripts. The expressed genes of JD032 were clustered into early, middle, and late temporal categories that were functionally similar. Specifically, a gene (JD032_orf016) involved in the lysis-lysogeny decision was identified as an early expression gene. Only 17.7% (668/3,781) of the host genes were differentially expressed, and more genes were downregulated than upregulated. The expression of genes involved in host macromolecular synthesis (DNA/RNA/proteins) was altered by JD032 at the level of transcription. In particular, the expression of the ropA operon was downregulated. Most noteworthy is that the gene expression of some antiphage systems, including CRISPR-Cas, restriction-modification, and toxin-antitoxin systems, was suppressed by JD032 during infection. In addition, bacterial sporulation, adhesion, and virulence factor genes were significantly downregulated. This study provides the first description of the interaction between anaerobic spore-forming bacteria and phages during lytic infection and highlights new aspects of C. difficile phage-host interactions. IMPORTANCEC. difficile is one of the most clinically significant intestinal pathogens. Although phages have been shown to effectively control C. difficile infection, the host responses to phage predation have not been fully studied. In this study, we reported the isolation and characterization of a new phage, JD032, and analyzed the global transcriptomic changes in the hypervirulent RT078 C. difficile strain, TW11, during phage JD032 infection. We found that bacterial host mRNA was progressively replaced with phage transcripts, three temporal categories of JD032 gene expression, the extensive interplay between phage-bacterium, antiphage-like responses of the host and phage evasion, and decreased expression of sporulation- and virulence-related genes of the host after phage infection. These findings confirmed the complexity of interactions between C. difficile and phages and suggest that phages undergoing a lytic cycle may also cause different phenotypes in hosts, similar to prophages, which may inspire phage therapy for the control of C. difficile.
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Boon M, De Zitter E, De Smet J, Wagemans J, Voet M, Pennemann FL, Schalck T, Kuznedelov K, Severinov K, Van Meervelt L, De Maeyer M, Lavigne R. 'Drc', a structurally novel ssDNA-binding transcription regulator of N4-related bacterial viruses. Nucleic Acids Res 2020; 48:445-459. [PMID: 31724707 PMCID: PMC7145618 DOI: 10.1093/nar/gkz1048] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/16/2019] [Accepted: 10/23/2019] [Indexed: 12/22/2022] Open
Abstract
Bacterial viruses encode a vast number of ORFan genes that lack similarity to any other known proteins. Here, we present a 2.20 Å crystal structure of N4-related Pseudomonas virus LUZ7 ORFan gp14, and elucidate its function. We demonstrate that gp14, termed here as Drc (ssDNA-binding RNA Polymerase Cofactor), preferentially binds single-stranded DNA, yet contains a structural fold distinct from other ssDNA-binding proteins (SSBs). By comparison with other SSB folds and creation of truncation and amino acid substitution mutants, we provide the first evidence for the binding mechanism of this unique fold. From a biological perspective, Drc interacts with the phage-encoded RNA Polymerase complex (RNAPII), implying a functional role as an SSB required for the transition from early to middle gene transcription during phage infection. Similar to the coliphage N4 gp2 protein, Drc likely binds locally unwound middle promoters and recruits the phage RNA polymerase. However, unlike gp2, Drc does not seem to need an additional cofactor for promoter melting. A comparison among N4-related phage genera highlights the evolutionary diversity of SSB proteins in an otherwise conserved transcription regulation mechanism.
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Affiliation(s)
- Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Elke De Zitter
- Department of Chemistry, Biomolecular Architecture, KU Leuven, Leuven 3001, Belgium
| | - Jeroen De Smet
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Jeroen Wagemans
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Marleen Voet
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Friederike L Pennemann
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Thomas Schalck
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | | | | | - Luc Van Meervelt
- Department of Chemistry, Biomolecular Architecture, KU Leuven, Leuven 3001, Belgium
| | - Marc De Maeyer
- Department of Chemistry, Laboratory of Biomolecular Modelling and Design, KU Leuven, Leuven 3001, Belgium
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
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Thammatinna K, Egan ME, Htoo HH, Khanna K, Sugie J, Nideffer JF, Villa E, Tassanakajon A, Pogliano J, Nonejuie P, Chaikeeratisak V. A novel vibriophage exhibits inhibitory activity against host protein synthesis machinery. Sci Rep 2020; 10:2347. [PMID: 32047244 PMCID: PMC7012835 DOI: 10.1038/s41598-020-59396-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/27/2020] [Indexed: 12/27/2022] Open
Abstract
Since the emergence of deadly pathogens and multidrug-resistant bacteria at an alarmingly increased rate, bacteriophages have been developed as a controlling bioagent to prevent the spread of pathogenic bacteria. One of these pathogens, disease-causing Vibrio parahaemolyticus (VPAHPND) which induces acute hepatopancreatic necrosis, is considered one of the deadliest shrimp pathogens, and has recently become resistant to various classes of antibiotics. Here, we discovered a novel vibriophage that specifically targets the vibrio host, VPAHPND. The vibriophage, designated Seahorse, was classified in the family Siphoviridae because of its icosahedral capsid surrounded by head fibers and a non-contractile long tail. Phage Seahorse was able to infect the host in a broad range of pH and temperatures, and it had a relatively short latent period (nearly 30 minutes) in which it produced progeny at 72 particles per cell at the end of its lytic cycle. Upon phage infection, the host nucleoid condensed and became toroidal, similar to the bacterial DNA morphology seen during tetracycline treatment, suggesting that phage Seahorse hijacked host biosynthesis pathways through protein translation. As phage Seahorse genome encodes 48 open reading frames with many hypothetical proteins, this genome could be a potential untapped resource for the discovery of phage-derived therapeutic proteins.
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Affiliation(s)
- Khrongkhwan Thammatinna
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - MacKennon E Egan
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Htut Htut Htoo
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Kanika Khanna
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Joseph Sugie
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Jason F Nideffer
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Elizabeth Villa
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Anchalee Tassanakajon
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Joe Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Poochit Nonejuie
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Vorrapon Chaikeeratisak
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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Dendooven T, Lavigne R. Dip-a-Dee-Doo-Dah: Bacteriophage-Mediated Rescoring of a Harmoniously Orchestrated RNA Metabolism. Annu Rev Virol 2019; 6:199-213. [DOI: 10.1146/annurev-virology-092818-015644] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA turnover and processing in bacteria are governed by the structurally divergent but functionally convergent RNA degradosome, and the mechanisms have been researched extensively in Gram-positive and Gram-negative bacteria. An emerging research field focuses on how bacterial viruses hijack all aspects of the bacterial metabolism, including the host machinery of RNA metabolism. This review addresses research on phage-based influence on RNA turnover, which can act either indirectly or via dedicated effector molecules that target degradosome assemblies. The structural divergence of host RNA turnover mechanisms likely explains the limited number of phage proteins directly targeting these specialized, host-specific complexes. The unique and nonconserved structure of DIP, a phage-encoded inhibitor of the Pseudomonas degradosome, illustrates this hypothesis. However, the natural occurrence of phage-encoded mechanisms regulating RNA turnover indicates a clear evolutionary benefit for this mode of host manipulation. Further exploration of the viral dark matter of unknown phage proteins may reveal more structurally novel interference strategies that, in turn, could be exploited for biotechnological applications.
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Affiliation(s)
- T. Dendooven
- Department of Biochemistry, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - R. Lavigne
- Laboratory of Gene Technology, KU Leuven, 3001 Leuven, Belgium
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Tabib-Salazar A, Mulvenna N, Severinov K, Matthews SJ, Wigneshweraraj S. Xenogeneic Regulation of the Bacterial Transcription Machinery. J Mol Biol 2019; 431:4078-4092. [DOI: 10.1016/j.jmb.2019.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/30/2019] [Accepted: 02/06/2019] [Indexed: 10/27/2022]
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Cooccurrence of Broad- and Narrow-Host-Range Viruses Infecting the Bloom-Forming Toxic Cyanobacterium Microcystis aeruginosa. Appl Environ Microbiol 2019; 85:AEM.01170-19. [PMID: 31324627 DOI: 10.1128/aem.01170-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/11/2019] [Indexed: 12/20/2022] Open
Abstract
Viruses play important roles in regulating the abundance and composition of bacterial populations in aquatic ecosystems. The bloom-forming toxic cyanobacterium Microcystis aeruginosa is predicted to interact with diverse cyanoviruses, resulting in Microcystis population diversification. However, current knowledge of the genomes from these viruses and their infection programs is limited to those of Microcystis virus Ma-LMM01. Here, we performed a time series sampling at a small pond in Japan during a Microcystis bloom and then investigated the genomic information and transcriptional dynamics of Microcystis-interacting viruses using metagenomic and metatranscriptomic approaches. We identified 15 viral genomic fragments classified into three groups, groups I (including Ma-LMM01), II (high abundance and transcriptional activity), and III (new lineages). According to the phylogenetic distribution of Microcystis strains possessing spacers against each viral group, the group II-original viruses interacted with all three phylogenetically distinct Microcystis population types (phylotypes), whereas the groups I and III-original viruses interacted with only one or two phylotypes, indicating the cooccurrence of broad- (group II) and narrow (groups I and III)-host-range viruses in the bloom. These viral fragments showed the highest transcriptional levels during daytime regardless of their genomic differences. Interestingly, M. aeruginosa expressed antiviral defense genes in the environment, unlike what was seen with an Ma-LMM01 infection in a previous culture experiment. Given that broad-host-range viruses often induce antiviral responses within alternative hosts, our findings suggest that such antiviral responses might inhibit viral multiplication, mainly that of broad-host-range viruses like those in group II.IMPORTANCE The bloom-forming toxic cyanobacterium Microcystis aeruginosa is thought to have diversified its population through the interactions between host and viruses in antiviral defense systems. However, current knowledge of viral genomes and infection programs is limited to those of Microcystis virus Ma-LMM01, which was a narrow host range in which it can escape from the highly abundant host defense systems. Our metagenomic approaches unveiled the cooccurrence of narrow- and broad-host-range Microcystis viruses, which included fifteen viral genomic fragments from Microcystis blooms that were classified into three groups. Interestingly, Microcystis antiviral defense genes were expressed against viral infection in the environment, unlike what was seen in a culture experiment with Ma-LMM01. Given that viruses with a broad host range often induce antiviral responses within alternative hosts, our findings suggest that antiviral responses inhibit viral reproduction, especially that of broad-range viruses like those in group II. This paper augments our understanding of the interactions between M. aeruginosa and its viruses and fills an important knowledge gap.
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Voronina MV, Bugaeva EN, Vasiliev DM, Kabanova AP, Barannik AP, Shneider MM, Kulikov EE, Korzhenkov AA, Toschakov SV, Ignatov AN, Miroshnikov KA. Characterization of Pectobacterium carotovorum subsp. carotovorum Bacteriophage PP16 Prospective for Biocontrol of Potato Soft Rot. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719040118] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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