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Sommerfeld F, Weyersberg L, Vatter P, Hessling M. Photoinactivation of the bacteriophage PhiX174 by UVA radiation and visible light in SM buffer and DMEM-F12. BMC Res Notes 2024; 17:3. [PMID: 38167092 PMCID: PMC10759336 DOI: 10.1186/s13104-023-06658-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
OBJECTIVE It has been observed that viruses can be inactivated by UVA radiation and visible light. The aim of this study is to investigate whether a medium that contains a photosensitizer might have an influence on viral reduction under irradiation by UVA, violet or blue light. Test virus is the bacteriophage PhiX174 in the photosensitizer-free SM buffer and DMEM-F12, which contains the known photosensitizer riboflavin. RESULTS The determined PhiX174 D90 doses in SM buffer and DMEM were 36.8 J/cm² and 13.6 J/cm² at 366 nm, 153.6 J/cm² and 129.1 J/cm² at 408 nm and 4988 J/cm² and 2477.1 J/cm² at 455 nm, respectively. It can be concluded that the medium has a large influence on the results. This might be caused by the photosensitizer riboflavin in DMEM-F12. As riboflavin is a key component in many cell culture media, irradiation experiments with viruses in cell culture media should be avoided if the investigation of intrinsical photoinactivation properties of viruses is aimed for.
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Affiliation(s)
- Florian Sommerfeld
- Department of Medical Engineering and Mechatronics, Ulm University of Applied Sciences, Albert-Einstein-Allee 55, D-89081, Ulm, Germany
| | - Laura Weyersberg
- Department of Medical Engineering and Mechatronics, Ulm University of Applied Sciences, Albert-Einstein-Allee 55, D-89081, Ulm, Germany
| | - Petra Vatter
- Department of Medical Engineering and Mechatronics, Ulm University of Applied Sciences, Albert-Einstein-Allee 55, D-89081, Ulm, Germany
| | - Martin Hessling
- Department of Medical Engineering and Mechatronics, Ulm University of Applied Sciences, Albert-Einstein-Allee 55, D-89081, Ulm, Germany.
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Long X, Wang X, Mao D, Wu W, Luo Y. A Novel XRE-Type Regulator Mediates Phage Lytic Development and Multiple Host Metabolic Processes in Pseudomonas aeruginosa. Microbiol Spectr 2022; 10:e0351122. [PMID: 36445133 PMCID: PMC9769523 DOI: 10.1128/spectrum.03511-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/28/2022] [Indexed: 12/02/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen, the leading cause of acute and chronic infections in immunocompromised patients, frequently with high morbidity and mortality rates. The xenobiotic response element (XRE) family proteins are the second most common transcriptional regulators (TRs) in P. aeruginosa. However, only a few XRE-like TRs have been reported to regulate multiple bacterial cellular processes, encompassing virulence, metabolism, antibiotic synthesis or resistance, stress responses, and phage infection, etc. Our understanding of what roles these XRE-like small regulatory proteins play in P. aeruginosa remains limited. Here, we aimed to decipher the role of a putative XRE-type transcriptional regulator (designated LfsT) from a prophage region on the chromosome of a clinical P. aeruginosa isolate, P8W. Southern blot and reverse transcription quantitative PCR (RT-qPCR) assays demonstrated that LfsT controlled host sensitivity to the phage PP9W2 and was essential for efficient phage replication. In addition, electrophoretic mobility shift assays (EMSAs) and transcriptional lacZ fusion analyses indicated that LfsT repressed the lysogenic development and promoted the lytic cycle of phage PP9W2 by binding to the promoter regions of the gp71 gene (encoding a CI-like repressor) and several vital phage genes. Combined with RNA-seq and a series of phenotypic validation tests, our results showed that LfsT bound to the flexible palindromic sites within the promoters upstream of several genes in the bacterial genome, regulating fatty acid (FA) metabolism, spermidine (SPD) transport, as well as the type III secretion system (T3SS). Overall, this study reveals novel regulatory roles of LfsT in P. aeruginosa, improving our understanding of the molecular mechanisms behind bacterium-phage interactions. IMPORTANCE This work elucidates the novel roles of a putative XRE family TR, LfsT, in the intricate regulatory systems of P. aeruginosa. We found that LfsT bound directly to the core promoter regions upstream of the start codons of numerous genes involved in various processes, including phage infection, FA metabolism, SPD transport, and the T3SS, regulating as the repressor or activator. The identified partial palindromic motif NAACN(5,8)GTTN recognized by LfsT suggests extensive effects of LfsT on gene expression by maintaining preferential binding to nucleotide sites under evolutionary pressure. In summary, these findings indicate that LfsT enhances metabolic activity in P. aeruginosa, while it reduces host resistance to the phage. This study helps us better understand the coevolution of bacteria and phages (e.g., survival comes at a cost) and provides clues for designing novel antimicrobials against P. aeruginosa infections.
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Affiliation(s)
- Xiang Long
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, China
| | - Xiaolong Wang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin, China
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, China
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
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Interaction between Phage T4 Protein RIII and Host Ribosomal Protein S1 Inhibits Endoribonuclease RegB Activation. Int J Mol Sci 2022; 23:ijms23169483. [PMID: 36012768 PMCID: PMC9409239 DOI: 10.3390/ijms23169483] [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: 07/15/2022] [Revised: 08/16/2022] [Accepted: 08/20/2022] [Indexed: 11/17/2022] Open
Abstract
Lytic viruses of bacteria (bacteriophages, phages) are intracellular parasites that take over hosts' biosynthetic processes for their propagation. Most of the knowledge on the host hijacking mechanisms has come from the studies of the lytic phage T4, which infects Escherichia coli. The integrity of T4 development is achieved by strict control over the host and phage processes and by adjusting them to the changing infection conditions. In this study, using in vitro and in vivo biochemical methods, we detected the direct interaction between the T4 protein RIII and ribosomal protein S1 of the host. Protein RIII is known as a cytoplasmic antiholin, which plays a role in the lysis inhibition function of T4. However, our results show that RIII also acts as a viral effector protein mainly targeting S1 RNA-binding domains that are central for all the activities of this multifunctional protein. We confirm that the S1-RIII interaction prevents the S1-dependent activation of endoribonuclease RegB. In addition, we propose that by modulating the multiple processes mediated by S1, RIII could act as a regulator of all stages of T4 infection including the lysis inhibition state.
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Pekkle Lam HY, Peng SY, Paramita P, Wu WJ, Chen LK, Chao HJ, Lai MJ, Chang KC. Biological and genomic characterization of two newly isolated Elizabethkingia anophelis bacteriophages. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:634-642. [PMID: 35717525 DOI: 10.1016/j.jmii.2022.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/21/2022] [Accepted: 05/29/2022] [Indexed: 05/26/2023]
Abstract
BACKGROUND Elizabethkingia anophelis is an opportunistic pathogen that infects newborns and immunocompromised patients. Because the infection is associated with high mortality as a result of its intrinsic resistance to antibiotics, alternative treatment methods are needed. Our previous study successfully isolated the world's first E. anophelis phage, TCUEAP1, which showed beneficial protection to E. anophelis-infected mice. More new bacteriophages are needed in order to provide sufficient choices to combat E. anophelis infections. METHODS In the current study, two new phages infecting E. anophelis were isolated from wastewater and were designated as TCUEAP2 and TCUEAP3. Further experiments, namely, transmission electron microscopy (TEM), infection assay, host-range analysis, and sequencing were performed to determine their biological and genomic characteristics. RESULTS TEM analysis revealed that both TCUEAP2 and TCUEAP3 possess an icosahedral head with a non-contractile tail, and belong to the Siphoviridae family. Further experiments revealed that TCUEAP3 has a longer latent period and higher burst size compared to TCUEAP2. Host range analysis showed that both TCUEAP2 and TCUEAP3 have a narrow host range, infecting only their respective hosts. The genomic size of phage TCUEAP2 was 42,403 bps containing 61 predicted open reading frames (ORFs), whereas the genome size of TCUEAP3 was 37,073 bps containing 40 predicted ORFs. CONCLUSION Due to the distinct biological characteristics of TCUEAP2 and TCUEAP3, they may be satisfactory for clinical uses such as preparation of phage cocktails or decontamination in clinical settings.
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Affiliation(s)
- Ho Yin Pekkle Lam
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien, Taiwan; Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan
| | - Shih-Yi Peng
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien, Taiwan; Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan
| | - Prajna Paramita
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan
| | - Wen-Jui Wu
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan
| | - Li-Kuang Chen
- Department of Laboratory Medicine, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
| | - Huei-Jen Chao
- Department of Laboratory Medicine, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
| | - Meng-Jiun Lai
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan.
| | - Kai-Chih Chang
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan; Department of Laboratory Medicine, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan.
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Bacteriophages in the Control of Aeromonas sp. in Aquaculture Systems: An Integrative View. Antibiotics (Basel) 2022; 11:antibiotics11020163. [PMID: 35203766 PMCID: PMC8868336 DOI: 10.3390/antibiotics11020163] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/23/2022] [Accepted: 01/24/2022] [Indexed: 11/17/2022] Open
Abstract
Aeromonas species often cause disease in farmed fish and are responsible for causing significant economic losses worldwide. Although vaccination is the ideal method to prevent infectious diseases, there are still very few vaccines commercially available in the aquaculture field. Currently, aquaculture production relies heavily on antibiotics, contributing to the global issue of the emergence of antimicrobial-resistant bacteria and resistance genes. Therefore, it is essential to develop effective alternatives to antibiotics to reduce their use in aquaculture systems. Bacteriophage (or phage) therapy is a promising approach to control pathogenic bacteria in farmed fish that requires a heavy understanding of certain factors such as the selection of phages, the multiplicity of infection that produces the best bacterial inactivation, bacterial resistance, safety, the host’s immune response, administration route, phage stability and influence. This review focuses on the need to advance phage therapy research in aquaculture, its efficiency as an antimicrobial strategy and the critical aspects to successfully apply this therapy to control Aeromonas infection in fish.
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Borodovich T, Shkoporov AN, Ross RP, Hill C. OUP accepted manuscript. Gastroenterol Rep (Oxf) 2022; 10:goac012. [PMID: 35425613 PMCID: PMC9006064 DOI: 10.1093/gastro/goac012] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 02/08/2022] [Accepted: 03/04/2022] [Indexed: 11/26/2022] Open
Abstract
Horizontal gene transfer (HGT) in the microbiome has profound consequences for human health and disease. The spread of antibiotic resistance genes, virulence, and pathogenicity determinants predominantly occurs by way of HGT. Evidence exists of extensive horizontal transfer in the human gut microbiome. Phage transduction is a type of HGT event in which a bacteriophage transfers non-viral DNA from one bacterial host cell to another. The abundance of tailed bacteriophages in the human gut suggests that transduction could act as a significant mode of HGT in the gut microbiome. Here we review in detail the known mechanisms of phage-mediated HGT, namely specialized and generalized transduction, lateral transduction, gene-transfer agents, and molecular piracy, as well as methods used to detect phage-mediated HGT, and discuss its potential implications for the human gut microbiome.
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Affiliation(s)
- Tatiana Borodovich
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Corresponding author. APC Microbiome Ireland, Biosciences Institute, University College Cork, Room 3.63, College Road, Cork, T12 YT20, Ireland.
| | - Andrey N Shkoporov
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
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Silva J, Dias R, Junior JI, Marcelino M, Silva M, Carmo A, Sousa M, Silva C, de Paula S. A Rapid Method for Performing a Multivariate Optimization of Phage Production Using the RCCD Approach. Pathogens 2021; 10:1100. [PMID: 34578135 PMCID: PMC8468216 DOI: 10.3390/pathogens10091100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 01/15/2023] Open
Abstract
Bacteriophages can be used in various applications, from the classical approach as substitutes for antibiotics (phage therapy) to new biotechnological uses, i.e., as a protein delivery vehicle, a diagnostic tool for specific strains of bacteria (phage typing), or environmental bioremediation. The demand for bacteriophage production increases daily, and studies that improve these production processes are necessary. This study evaluated the production of a T4-like bacteriophage vB_EcoM-UFV09 (an E. coli-infecting phage with high potential for reducing environmental biofilms) in seven types of culture media (Luria-Bertani broth and the M9 minimal medium with six different carbon sources) employing four cultivation variables (temperature, incubation time, agitation, and multiplicity of infection). For this purpose, the rotatable central composite design (RCCD) methodology was used, combining and comparing all parameters to determine the ideal conditions for starting to scale up the production process. We used the RCCD to set up the experimental design by combining the cultivation parameters in a specific and systematic way. Despite the high number of conditions evaluated, the results showed that when specific conditions were utilized, viral production was effective even when using a minimal medium, such as M9/glucose, which is less expensive and can significantly reduce costs during large-scale phage production.
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Affiliation(s)
- Jessica Silva
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa, Minas Gerais 36570-900, Brazil; (J.S.); (R.D.); (M.M.); (M.S.); (A.C.); (M.S.)
| | - Roberto Dias
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa, Minas Gerais 36570-900, Brazil; (J.S.); (R.D.); (M.M.); (M.S.); (A.C.); (M.S.)
| | - José Ivo Junior
- Department of Statistics, Federal University of Viçosa, Viçosa, Minas Gerais 36570-900, Brazil;
| | - Maraísa Marcelino
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa, Minas Gerais 36570-900, Brazil; (J.S.); (R.D.); (M.M.); (M.S.); (A.C.); (M.S.)
| | - Mirelly Silva
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa, Minas Gerais 36570-900, Brazil; (J.S.); (R.D.); (M.M.); (M.S.); (A.C.); (M.S.)
| | - Adriele Carmo
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa, Minas Gerais 36570-900, Brazil; (J.S.); (R.D.); (M.M.); (M.S.); (A.C.); (M.S.)
| | - Maira Sousa
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa, Minas Gerais 36570-900, Brazil; (J.S.); (R.D.); (M.M.); (M.S.); (A.C.); (M.S.)
- Leopoldo Américo Miguez de Mello Research Center (CENPES), Petrobras, Rio de Janeiro 20230-010, Brazil
| | - Cynthia Silva
- Department of Microbiology, Federal University of Viçosa, Viçosa, Minas Gerais 36570-900, Brazil;
| | - Sergio de Paula
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa, Minas Gerais 36570-900, Brazil; (J.S.); (R.D.); (M.M.); (M.S.); (A.C.); (M.S.)
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Bacteriophage Technology and Modern Medicine. Antibiotics (Basel) 2021; 10:antibiotics10080999. [PMID: 34439049 PMCID: PMC8388951 DOI: 10.3390/antibiotics10080999] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/15/2021] [Accepted: 08/16/2021] [Indexed: 12/26/2022] Open
Abstract
The bacteriophage (or phage for short) has been used as an antibacterial agent for over a century but was abandoned in most countries after the discovery and broad use of antibiotics. The worldwide emergence and high prevalence of antimicrobial-resistant (AMR) bacteria have led to a revival of interest in the long-forgotten antibacterial therapy with phages (phage therapy) as an alternative approach to combatting AMR bacteria. The rapid progress recently made in molecular biology and genetic engineering has accelerated the generation of phage-related products with superior therapeutic potentials against bacterial infection. Nowadays, phage-based technology has been developed for many purposes, including those beyond the framework of antibacterial treatment, such as to suppress viruses by phages, gene therapy, vaccine development, etc. Here, we highlighted the current progress in phage engineering technology and its application in modern medicine.
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Naknaen A, Suttinun O, Surachat K, Khan E, Pomwised R. A Novel Jumbo Phage PhiMa05 Inhibits Harmful Microcystis sp. Front Microbiol 2021; 12:660351. [PMID: 33959116 PMCID: PMC8093824 DOI: 10.3389/fmicb.2021.660351] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/29/2021] [Indexed: 11/27/2022] Open
Abstract
Microcystis poses a concern because of its potential contribution to eutrophication and production of microcystins (MCs). Phage treatment has been proposed as a novel biocontrol method for Microcystis. Here, we isolated a lytic cyanophage named PhiMa05 with high efficiency against MCs-producing Microcystis strains. Its burst size was large, with approximately 127 phage particles/infected cell, a short latent period (1 day), and high stability to broad salinity, pH and temperature ranges. The PhiMa05 structure was composed of an icosahedral capsid (100 nm) and tail (120 nm), suggesting that the PhiMa05 belongs to the Myoviridae family. PhiMa05 inhibited both planktonic and aggregated forms of Microcystis in a concentration-dependent manner. The lysis of Microcystis resulted in a significant reduction of total MCs compared to the uninfected cells. A genome analysis revealed that PhiMa05 is a double-stranded DNA virus with a 273,876 bp genome, considered a jumbo phage. Out of 254 predicted open reading frames (ORFs), only 54 ORFs were assigned as putative functional proteins. These putative proteins are associated with DNA metabolisms, structural proteins, host lysis and auxiliary metabolic genes (AMGs), while no lysogenic, toxin and antibiotic resistance genes were observed in the genome. The AMGs harbored in the phage genome are known to be involved in energy metabolism [photosynthesis and tricarboxylic acid cycle (TCA)] and nucleotide biosynthesis genes. Their functions suggested boosting and redirecting host metabolism during viral infection. Comparative genome analysis with other phages in the database indicated that PhiMa05 is unique. Our study highlights the characteristics and genome analysis of a novel jumbo phage, PhiMa05. PhiMa05 is a potential phage for controlling Microcystis bloom and minimizing MC occurrence.
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Affiliation(s)
- Ampapan Naknaen
- Environmental Assessment and Technology for Hazardous Waste Management Research Center, Faculty of Environmental Management, Prince of Songkla University, Hat Yai, Thailand
| | - Oramas Suttinun
- Environmental Assessment and Technology for Hazardous Waste Management Research Center, Faculty of Environmental Management, Prince of Songkla University, Hat Yai, Thailand
- Center of Excellence on Hazardous Substance Management (HSM), Bangkok, Thailand
| | - Komwit Surachat
- Division of Computational Science, Faculty of Science, Prince of Songkla University, Hat Yai, Thailand
- Molecular Evolution and Computational Biology Research Unit, Prince of Songkla University, Hat Yai, Thailand
| | - Eakalak Khan
- Department of Civil and Environmental Engineering and Construction, University of Nevada, Las Vegas, United States
| | - Rattanaruji Pomwised
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Thailand
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Zhang X, Xiong D, Yu J, Yang H, He P, Wei H. Genetic Polymorphism Drives Susceptibility Between Bacteria and Bacteriophages. Front Microbiol 2021; 12:627897. [PMID: 33841354 PMCID: PMC8024471 DOI: 10.3389/fmicb.2021.627897] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 02/28/2021] [Indexed: 12/15/2022] Open
Abstract
Phage therapy has attracted much attention for the treatment of antibiotic-resistant bacteria in recent years. However, it is common for bacteria to obtain resistance capability in short time after interaction with a lytic phage, as observed in phage therapy and co-culture of host and phage in a lab. In order to understand the mechanisms behind resistance, Staphylococcus aureus AB91118 and its lytic phage LQ7 were studied as a model system. A mutant strain named R1-3-1 resistant to the ancestral phage LQ7 was isolated, and then phages experimentally evolved from LQ7 were able to kill R1-3-1. Genomes of the two bacterial strains and the three phages (LQ7, ELQ7P-10, and ELQ7P-20) were analyzed based on deep sequencing data of NGS. Analyses showed that a few mutations could be identified in R1-3-1 and the evolved phages. Instead, in all the genomes of the bacteria and the phages, there exists genetic polymorphism of minor alleles, which distributes in many functional genes. Specifically, in the AB91118-LQ7 system it was found that the unique polymorphism sites in R1-3-1 associated to metabolic pathways could be inhibited by chloramphenicol (CHL). The resistant mutant R1-3-1 could become sensitive to the phage LQ7 in the presence of CHL. Combined use of CHL and the evolved phage from 20 cycles (ELQ7P-20) could produce the least resistance when killing the bacteria AB91118. The genetic polymorphism of minor alleles would be a new mechanism to drive the co-evolution between a phage and its host, which may enable the phage and the host get ready and fast response to the selective pressure from one to the other.
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Affiliation(s)
- Xiaoxu Zhang
- Key Laboratory of Emerging Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Dongyan Xiong
- Key Laboratory of Emerging Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Junping Yu
- Key Laboratory of Emerging Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Hang Yang
- Key Laboratory of Emerging Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ping He
- Key Laboratory of Emerging Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Hongping Wei
- Key Laboratory of Emerging Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
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Transcriptomic determinants of the response of ST-111 Pseudomonas aeruginosa AG1 to ciprofloxacin identified by a top-down systems biology approach. Sci Rep 2020; 10:13717. [PMID: 32792590 PMCID: PMC7427096 DOI: 10.1038/s41598-020-70581-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/25/2020] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that thrives in diverse environments and causes a variety of human infections. Pseudomonas aeruginosa AG1 (PaeAG1) is a high-risk sequence type 111 (ST-111) strain isolated from a Costa Rican hospital in 2010. PaeAG1 has both blaVIM-2 and blaIMP-18 genes encoding for metallo-β-lactamases, and it is resistant to β-lactams (including carbapenems), aminoglycosides, and fluoroquinolones. Ciprofloxacin (CIP) is an antibiotic commonly used to treat P. aeruginosa infections, and it is known to produce DNA damage, triggering a complex molecular response. In order to evaluate the effects of a sub-inhibitory CIP concentration on PaeAG1, growth curves using increasing CIP concentrations were compared. We then measured gene expression using RNA-Seq at three time points (0, 2.5 and 5 h) after CIP exposure to identify the transcriptomic determinants of the response (i.e. hub genes, gene clusters and enriched pathways). Changes in expression were determined using differential expression analysis and network analysis using a top–down systems biology approach. A hybrid model using database-based and co-expression analysis approaches was implemented to predict gene–gene interactions. We observed a reduction of the growth curve rate as the sub-inhibitory CIP concentrations were increased. In the transcriptomic analysis, we detected that over time CIP treatment resulted in the differential expression of 518 genes, showing a complex impact at the molecular level. The transcriptomic determinants were 14 hub genes, multiple gene clusters at different levels (associated to hub genes or as co-expression modules) and 15 enriched pathways. Down-regulation of genes implicated in several metabolism pathways, virulence elements and ribosomal activity was observed. In contrast, amino acid catabolism, RpoS factor, proteases, and phenazines genes were up-regulated. Remarkably, > 80 resident-phage genes were up-regulated after CIP treatment, which was validated at phenomic level using a phage plaque assay. Thus, reduction of the growth curve rate and increasing phage induction was evidenced as the CIP concentrations were increased. In summary, transcriptomic and network analyses, as well as the growth curves and phage plaque assays provide evidence that PaeAG1 presents a complex, concentration-dependent response to sub-inhibitory CIP exposure, showing pleiotropic effects at the systems level. Manipulation of these determinants, such as phage genes, could be used to gain more insights about the regulation of responses in PaeAG1 as well as the identification of possible therapeutic targets. To our knowledge, this is the first report of the transcriptomic analysis of CIP response in a ST-111 high-risk P. aeruginosa strain, in particular using a top-down systems biology approach.
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Hutinet G, Kot W, Cui L, Hillebrand R, Balamkundu S, Gnanakalai S, Neelakandan R, Carstens AB, Fa Lui C, Tremblay D, Jacobs-Sera D, Sassanfar M, Lee YJ, Weigele P, Moineau S, Hatfull GF, Dedon PC, Hansen LH, de Crécy-Lagard V. 7-Deazaguanine modifications protect phage DNA from host restriction systems. Nat Commun 2019; 10:5442. [PMID: 31784519 PMCID: PMC6884629 DOI: 10.1038/s41467-019-13384-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 11/04/2019] [Indexed: 12/14/2022] Open
Abstract
Genome modifications are central components of the continuous arms race between viruses and their hosts. The archaeosine base (G+), which was thought to be found only in archaeal tRNAs, was recently detected in genomic DNA of Enterobacteria phage 9g and was proposed to protect phage DNA from a wide variety of restriction enzymes. In this study, we identify three additional 2'-deoxy-7-deazaguanine modifications, which are all intermediates of the same pathway, in viruses: 2'-deoxy-7-amido-7-deazaguanine (dADG), 2'-deoxy-7-cyano-7-deazaguanine (dPreQ0) and 2'-deoxy-7- aminomethyl-7-deazaguanine (dPreQ1). We identify 180 phages or archaeal viruses that encode at least one of the enzymes of this pathway with an overrepresentation (60%) of viruses potentially infecting pathogenic microbial hosts. Genetic studies with the Escherichia phage CAjan show that DpdA is essential to insert the 7-deazaguanine base in phage genomic DNA and that 2'-deoxy-7-deazaguanine modifications protect phage DNA from host restriction enzymes.
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Affiliation(s)
- Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA.
| | - Witold Kot
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Liang Cui
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
| | - Roman Hillebrand
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Nitto Denko Avecia, 125 Fortune Boulevard, Milford, MA, 01757, USA
| | - Seetharamsingh Balamkundu
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
| | - Shanmugavel Gnanakalai
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
| | - Ramesh Neelakandan
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
| | | | - Chuan Fa Lui
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Denise Tremblay
- Département de Biochimie, Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC, G1V 0A6, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses and Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Deborah Jacobs-Sera
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Mandana Sassanfar
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yan-Jiun Lee
- Research Department, New England Biolabs, Ipswich, MA, 01938, USA
| | - Peter Weigele
- Research Department, New England Biolabs, Ipswich, MA, 01938, USA
| | - Sylvain Moineau
- Département de Biochimie, Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC, G1V 0A6, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses and Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Graham F Hatfull
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Lars H Hansen
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA.
- University of Florida, Genetics Institute, Gainesville, Florida, 32610, USA.
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Azam AH, Hoshiga F, Takeuchi I, Miyanaga K, Tanji Y. Analysis of phage resistance in Staphylococcus aureus SA003 reveals different binding mechanisms for the closely related Twort-like phages ɸSA012 and ɸSA039. Appl Microbiol Biotechnol 2018; 102:8963-8977. [DOI: 10.1007/s00253-018-9269-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/15/2018] [Accepted: 07/22/2018] [Indexed: 02/01/2023]
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Vale FF, Lehours P. Relating Phage Genomes to Helicobacter pylori Population Structure: General Steps Using Whole-Genome Sequencing Data. Int J Mol Sci 2018; 19:ijms19071831. [PMID: 29933614 PMCID: PMC6073503 DOI: 10.3390/ijms19071831] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/30/2018] [Accepted: 06/15/2018] [Indexed: 12/19/2022] Open
Abstract
The review uses the Helicobacter pylori, the gastric bacterium that colonizes the human stomach, to address how to obtain information from bacterial genomes about prophage biology. In a time of continuous growing number of genomes available, this review provides tools to explore genomes for prophage presence, or other mobile genetic elements and virulence factors. The review starts by covering the genetic diversity of H. pylori and then moves to the biologic basis and the bioinformatics approaches used for studding the H. pylori phage biology from their genomes and how this is related with the bacterial population structure. Aspects concerning H. pylori prophage biology, evolution and phylogeography are discussed.
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Affiliation(s)
- Filipa F Vale
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal.
| | - Philippe Lehours
- Laboratoire de Bacteriologie, Centre National de Référence des Campylobacters et Hélicobacters, Place Amélie Raba Léon, 33076 Bordeaux, France.
- INSERM U1053-UMR Bordeaux Research in Translational Oncology, BaRITOn, 33000 Bordeaux, France.
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15
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Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins. Sci Rep 2017; 7:42471. [PMID: 28205536 PMCID: PMC5311958 DOI: 10.1038/srep42471] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 01/10/2017] [Indexed: 12/19/2022] Open
Abstract
Helicobacter pylori genetic diversity is known to be influenced by mobile genomic elements. Here we focused on prophages, the least characterized mobile elements of H. pylori. We present the full genomic sequences, insertion sites and phylogenetic analysis of 28 prophages found in H. pylori isolates from patients of distinct disease types, ranging from gastritis to gastric cancer, and geographic origins, covering most continents. The genome sizes of these prophages range from 22.6–33.0 Kbp, consisting of 27–39 open reading frames. A 36.6% GC was found in prophages in contrast to 39% in H. pylori genome. Remarkably a conserved integration site was found in over 50% of the cases. Nearly 40% of the prophages harbored insertion sequences (IS) previously described in H. pylori. Tandem repeats were frequently found in the intergenic region between the prophage at the 3′ end and the bacterial gene. Furthermore, prophage genomes present a robust phylogeographic pattern, revealing four distinct clusters: one African, one Asian and two European prophage populations. Evidence of recombination was detected within the genome of some prophages, resulting in genome mosaics composed by different populations, which may yield additional H. pylori phenotypes.
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Bodier-Montagutelli E, Morello E, L’Hostis G, Guillon A, Dalloneau E, Respaud R, Pallaoro N, Blois H, Vecellio L, Gabard J, Heuzé-Vourc’h N. Inhaled phage therapy: a promising and challenging approach to treat bacterial respiratory infections. Expert Opin Drug Deliv 2016; 14:959-972. [DOI: 10.1080/17425247.2017.1252329] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Elsa Bodier-Montagutelli
- Université François Rabelais, UMR 1100, Tours, France
- INSERM, Centre d’Etude des Pathologies Respiratoires, UMR 1100, Tours, France
- CHRU de Tours, Service de Pharmacie, Tours, France
| | - Eric Morello
- Université François Rabelais, UMR 1100, Tours, France
- INSERM, Centre d’Etude des Pathologies Respiratoires, UMR 1100, Tours, France
| | | | - Antoine Guillon
- Université François Rabelais, UMR 1100, Tours, France
- INSERM, Centre d’Etude des Pathologies Respiratoires, UMR 1100, Tours, France
- CHRU de Tours, Service de Réanimation Polyvalente, Tours, France
| | - Emilie Dalloneau
- Université François Rabelais, UMR 1100, Tours, France
- INSERM, Centre d’Etude des Pathologies Respiratoires, UMR 1100, Tours, France
| | - Renaud Respaud
- Université François Rabelais, UMR 1100, Tours, France
- INSERM, Centre d’Etude des Pathologies Respiratoires, UMR 1100, Tours, France
- CHRU de Tours, Service de Pharmacie, Tours, France
| | - Nikita Pallaoro
- Université François Rabelais, UMR 1100, Tours, France
- INSERM, Centre d’Etude des Pathologies Respiratoires, UMR 1100, Tours, France
| | - Hélène Blois
- CHRU de Tours, Service de Pharmacie, Tours, France
| | - Laurent Vecellio
- Université François Rabelais, UMR 1100, Tours, France
- INSERM, Centre d’Etude des Pathologies Respiratoires, UMR 1100, Tours, France
- DTF-Aerodrug, St Etienne, France
| | | | - Nathalie Heuzé-Vourc’h
- Université François Rabelais, UMR 1100, Tours, France
- INSERM, Centre d’Etude des Pathologies Respiratoires, UMR 1100, Tours, France
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17
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Ariff A, Wise MJ, Kahler CM, Tay CY, Peters F, Perkins TT, Chang BJ. Novel Moraxella catarrhalis prophages display hyperconserved non-structural genes despite their genomic diversity. BMC Genomics 2015; 16:860. [PMID: 26497500 PMCID: PMC4619438 DOI: 10.1186/s12864-015-2104-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/16/2015] [Indexed: 11/25/2022] Open
Abstract
Background Moraxella catarrhalis is an important pathogen that often causes otitis media in children, a disease that is not currently vaccine preventable. Asymptomatic colonisation of the human upper respiratory tract is common and lack of clearance by the immune system is likely due to the emergence of seroresistant genetic lineages. No active bacteriophages or prophages have been described in this species. This study was undertaken to identify and categorise prophages in M. catarrhalis, their genetic diversity and the relationship of such diversity with the host-species phylogeny. Results This study presents a comparative analysis of 32 putative prophages identified in 95 phylogenetically variable, newly sequenced M. catarrhalis genomes. The prophages were genotypically classified into four diverse clades. The genetic synteny of each clade is similar to the group 1 phage family Siphoviridae, however, they form genotypic clusters that are distinct from other members of this family. No core genetic sequences exist across the 32 prophages despite clades 2, 3, and 4 sharing the most sequence identity. The analysis of non-structural prophage genes (coding the integrase, and terminase), and portal gene showed that the respective genes were identical for clades 2, 3, and 4, but unique for clade 1. Empirical analysis calculated that these genes are unexpectedly hyperconserved, under purifying selection, suggesting a tightly regulated functional role. As such, it is improbable that the prophages are decaying remnants but stable components of a fluctuating, flexible and unpredictable system ultimately maintained by functional constraints on non-structural and packaging genes. Additionally, the plate encoding genes were well conserved across all four prophage clades, and the tail fibre genes, commonly responsible for receptor recognition, were clustered into three major groups distributed across the prophage clades. A pan-genome of 283,622 bp was identified, and the prophages were mapped onto the diverse M. catarrhalis multi-locus sequence type (MLST) backbone. Conclusion This study has provided the first evidence of putatively mobile prophages in M. catarrhalis, identifying a diverse and fluctuating system dependent on the hyperconservation of a few key, non-structural genes. Some prophages harbour virulence-related genes, and potentially influence the physiology and virulence of M. catarrhalis. Importantly our data will provide supporting information on the identification of novel prophages in other species by adding greater weight to the identification of non-structural genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2104-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amir Ariff
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA, Australia.
| | - Michael J Wise
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA, Australia.
| | - Charlene M Kahler
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA, Australia.
| | - Chin Yen Tay
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA, Australia.
| | - Fanny Peters
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA, Australia.
| | - Timothy T Perkins
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA, Australia.
| | - Barbara J Chang
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA, Australia.
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18
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Nakonieczna A, Cooper CJ, Gryko R. Bacteriophages and bacteriophage-derived endolysins as potential therapeutics to combat Gram-positive spore forming bacteria. J Appl Microbiol 2015; 119:620-31. [PMID: 26109320 DOI: 10.1111/jam.12881] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/28/2015] [Accepted: 06/11/2015] [Indexed: 01/21/2023]
Abstract
Since their discovery in 1915, bacteriophages have been routinely used within Eastern Europe to treat a variety of bacterial infections. Although initially ignored by the West due to the success of antibiotics, increasing levels and diversity of antibiotic resistance is driving a renaissance for bacteriophage-derived therapy, which is in part due to the highly specific nature of bacteriophages as well as their relative abundance. This review focuses on the bacteriophages and derived lysins of relevant Gram-positive spore formers within the Bacillus cereus group and Clostridium genus that could have applications within the medical, food and environmental sectors.
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Affiliation(s)
- A Nakonieczna
- Biological Threats Identification and Countermeasure Center of the Military Institute of Hygiene and Epidemiology, Pulawy, Poland
| | - C J Cooper
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - R Gryko
- Biological Threats Identification and Countermeasure Center of the Military Institute of Hygiene and Epidemiology, Pulawy, Poland
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19
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Friedman CS, Wight N, Crosson LM, Vanblaricom GR, Lafferty KD. Reduced disease in black abalone following mass mortality: phage therapy and natural selection. Front Microbiol 2014; 5:78. [PMID: 24672512 PMCID: PMC3957727 DOI: 10.3389/fmicb.2014.00078] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 02/12/2014] [Indexed: 11/13/2022] Open
Abstract
Black abalone, Haliotis cracherodii, populations along the NE Pacific ocean have declined due to the rickettsial disease withering syndrome (WS). Natural recovery on San Nicolas Island (SNI) of Southern California suggested the development of resistance in island populations. Experimental challenges in one treatment demonstrated that progeny of disease-selected black abalone from SNI survived better than did those from naïve black abalone from Carmel Point in mainland coastal central California. Unexpectedly, the presence of a newly observed bacteriophage infecting the WS rickettsia (WS-RLO) had strong effects on the survival of infected abalone. Specifically, presence of phage-infected RLO (RLOv) reduced the host response to infection, RLO infection loads, and associated mortality. These data suggest that the black abalone: WS-RLO relationship is evolving through dual host mechanisms of resistance to RLO infection in the digestive gland via tolerance to infection in the primary target tissue (the post-esophagus) coupled with reduced pathogenicity of the WS-RLO by phage infection, which effectively reduces the infection load in the primary target tissue by half. Sea surface temperature patterns off southern California, associated with a recent hiatus in global-scale ocean warming, do not appear to be a sufficient explanation for survival patterns in SNI black abalone. These data highlight the potential for natural recovery of abalone populations over time and that further understanding of mechanisms governing host–parasite relationships will better enable us to manage declining populations.
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Affiliation(s)
- Carolyn S Friedman
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - Nathan Wight
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - Lisa M Crosson
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - Glenn R Vanblaricom
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA ; Washington Cooperative Fish and Wildlife Research Unit, U.S. Geological Survey, University of Washington Seattle, WA, USA
| | - Kevin D Lafferty
- Western Ecological Research Center, U.S. Geological Survey, c/o Marine Science Institute, University of California at Santa Barbara Santa Barbara, CA, USA
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20
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Yuan Y, Gao M, Peng Q, Wu D, Liu P, Wu Y. Genomic analysis of a phage and prophage from a Bacillus thuringiensis strain. J Gen Virol 2013; 95:751-761. [PMID: 24285088 DOI: 10.1099/vir.0.058735-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteriophages have been found to be the most abundant and also potentially most diverse biological entities on Earth. In the present study, Bacillus phages were isolated rapidly and shown to have a high degree of diversity. The genomes of a newly isolated phage, phiCM3, and a prophage, proCM3, from the Bacillus thuringiensis strain YM-03 were sequenced and characterized. Comparative genome analysis showed that the phiCM3 genome is highly similar to the genomes of eight other Bacillus phages and seven of these phages were classified as the Wβ group of phages. Analysis of the differential evolution of the genes in the Wβ-group phages indicated that the genes encoding the antirepressor and tail fibre protein were more highly conserved than those encoding the major capsid protein, DNA replication protein, and RNA polymerase σ factor, which might have diverged to acquire mechanisms suitable for survival in different microbial hosts. Genome analysis of proCM3 revealed that proCM3 might be a defective phage because of mutations in the minor structural protein, and it was not inducible by mitomycin C treatment. The proCM3 genome was similar to those of two lytic Bacillus phages in sequence, but had a different genomic structure, composed of three regions in a different order. These data suggest that the three phages might have had a common ancestor and that genome rearrangement might have occurred during evolution. The findings of this study enrich our current knowledge of Bacillus phage diversity and evolution, especially for the Wβ-group and TP21-L-like phages, and may help the development of practical applications of Bacillus phages.
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Affiliation(s)
- Yihui Yuan
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Meiying Gao
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Qin Peng
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Dandan Wu
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Pengming Liu
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Yan Wu
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
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Letarov AV, Krisch HM. The episodic evolution of fibritin: traces of ancient global environmental alterations may remain in the genomes of T4-like phages. Ecol Evol 2013; 3:3628-35. [PMID: 24223296 PMCID: PMC3797505 DOI: 10.1002/ece3.730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 07/19/2013] [Accepted: 07/24/2013] [Indexed: 01/09/2023] Open
Abstract
The evolutionary adaptation of bacteriophages to their environment is achieved by alterations of their genomes involving a combination of both point mutations and lateral gene transfer. A phylogenetic analysis of a large set of collar fiber protein (fibritin) loci from diverse T4-like phages indicates that nearly all the modular swapping involving the C-terminal domain of this gene occurred in the distant past and has since ceased. In phage T4, this fibritin domain encodes the sequence that mediates both the attachment of the long tail fibers to the virion and also controls, in an environmentally sensitive way, the phage's ability to infect its host bacteria. Subsequent to its distant period of modular exchange, the evolution of fibritin has proceeded primarily by the slow vertical divergence mechanism. We suggest that ancient and sudden changes in the environment forced the T4-like phages to alter fibritin's mode of action or function. The genome's response to such episodes of rapid environmental change could presumably only be achieved quickly enough by employing the modular evolution mechanism. A phylogenetic analysis of the fibritin locus reveals the possible traces of such events within the T4 superfamily's genomes.
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Affiliation(s)
- A V Letarov
- Winogradsky Institute of Microbiology Russian Academy of Science 117312, pr. 60-letiya Oktyabrya, Moscow, Russia ; Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de la Recherche Scientifique UMR 5100 Université Paul Sabatier-Toulouse III 118 Route de Narbonne Toulouse, 31062, Toulouse, Cedex 09, France ; Moscow Institute of Physics and Technology State University 141700, Institutskiy lane 9, Dolgoprudny, Moscow Region, Russia
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22
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Uchiyama J, Takeuchi H, Kato SI, Gamoh K, Takemura-Uchiyama I, Ujihara T, Daibata M, Matsuzaki S. Characterization of Helicobacter pylori bacteriophage KHP30. Appl Environ Microbiol 2013; 79:3176-84. [PMID: 23475617 PMCID: PMC3685256 DOI: 10.1128/aem.03530-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 02/28/2013] [Indexed: 01/01/2023] Open
Abstract
Helicobacter pylori inhabits the stomach mucosa and is a causative agent of stomach ulcer and cancer. In general, bacteriophages (phages) are strongly associated with bacterial evolution, including the development of pathogenicity. Several tailed phages have so far been reported in H. pylori. We have isolated an H. pylori phage, KHP30, and reported its genomic sequence. In this study, we examined the biological characteristics of phage KHP30. Phage KHP30 was found to be a spherical lipid-containing phage with a diameter of ca. 69 nm. Interestingly, it was stable from pH 2.5 to pH 10, suggesting that it is adapted to the highly acidic environment of the human stomach. Phage KHP30 multiplied on 63.6% of clinical H. pylori isolates. The latent period was ca. 140 min, shorter than the doubling time of H. pylori (ca. 180 min). The burst size was ca. 13, which was smaller than the burst sizes of other known tailed or spherical phages. Phage KHP30 seemed to be maintained as an episome in H. pylori strain NY43 cells, despite a predicted integrase gene in the KHP30 genomic sequence. Seven possible virion proteins of phage KHP30 were analyzed using N-terminal protein sequencing and mass spectrometry, and their genes were found to be located on its genomic DNA. The genomic organization of phage KHP30 differed from the genomic organizations in the known spherical phage families Corticoviridae and Tectiviridae. This evidence suggests that phage KHP30 is a new type of spherical phage that cannot be classified in any existing virus category.
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Affiliation(s)
- Jumpei Uchiyama
- Department of Microbiology and Infection
- Center for Innovative and Translational Medicine
| | | | | | | | - Iyo Takemura-Uchiyama
- Department of Microbiology and Infection
- Department of Clinical Laboratory Medicine, Faculty of Medicine
| | | | - Masanori Daibata
- Department of Microbiology and Infection
- Center for Innovative and Translational Medicine
| | - Shigenobu Matsuzaki
- Department of Microbiology and Infection
- Center for Innovative and Translational Medicine
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