1
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Wang X, Tang Y, Yue X, Wang S, Yang K, Xu Y, Shen Q, Friman VP, Wei Z. The role of rhizosphere phages in soil health. FEMS Microbiol Ecol 2024; 100:fiae052. [PMID: 38678007 PMCID: PMC11065364 DOI: 10.1093/femsec/fiae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 03/22/2024] [Accepted: 04/25/2024] [Indexed: 04/29/2024] Open
Abstract
While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups-bacterial viruses, i.e. phages-has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation, and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness, and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.
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Affiliation(s)
- Xiaofang Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Yike Tang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiufeng Yue
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuo Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Keming Yang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Yangchun Xu
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Qirong Shen
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Ville-Petri Friman
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Department of Microbiology, University of Helsinki, 00014 Helsinki, Finland
| | - Zhong Wei
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
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2
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Pacheco-Moreno A, Bollmann-Giolai A, Chandra G, Brett P, Davies J, Thornton O, Poole P, Ramachandran V, Brown JKM, Nicholson P, Ridout C, DeVos S, Malone JG. The genotype of barley cultivars influences multiple aspects of their associated microbiota via differential root exudate secretion. PLoS Biol 2024; 22:e3002232. [PMID: 38662644 PMCID: PMC11045101 DOI: 10.1371/journal.pbio.3002232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
Plant-associated microbes play vital roles in promoting plant growth and health, with plants secreting root exudates into the rhizosphere to attract beneficial microbes. Exudate composition defines the nature of microbial recruitment, with different plant species attracting distinct microbiota to enable optimal adaptation to the soil environment. To more closely examine the relationship between plant genotype and microbial recruitment, we analysed the rhizosphere microbiomes of landrace (Chevallier) and modern (NFC Tipple) barley (Hordeum vulgare) cultivars. Distinct differences were observed between the plant-associated microbiomes of the 2 cultivars, with the plant-growth promoting rhizobacterial genus Pseudomonas substantially more abundant in the Tipple rhizosphere. Striking differences were also observed between the phenotypes of recruited Pseudomonas populations, alongside distinct genotypic clustering by cultivar. Cultivar-driven Pseudomonas selection was driven by root exudate composition, with the greater abundance of hexose sugars secreted from Tipple roots attracting microbes better adapted to growth on these metabolites and vice versa. Cultivar-driven selection also operates at the molecular level, with both gene expression and the abundance of ecologically relevant loci differing between Tipple and Chevallier Pseudomonas isolates. Finally, cultivar-driven selection is important for plant health, with both cultivars showing a distinct preference for microbes selected by their genetic siblings in rhizosphere transplantation assays.
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Affiliation(s)
- Alba Pacheco-Moreno
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | | | - Govind Chandra
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Paul Brett
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Jack Davies
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Owen Thornton
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Philip Poole
- Department of Biology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Vinoy Ramachandran
- Department of Biology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - James K. M. Brown
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Paul Nicholson
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Chris Ridout
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- New Heritage Barley, Norwich Research Park, Norwich, United Kingdom
| | - Sarah DeVos
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- New Heritage Barley, Norwich Research Park, Norwich, United Kingdom
| | - Jacob G. Malone
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
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3
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Arce M, Venegas G, Paez K, Latz S, Navarrete P, Caruffo M, Feijoo C, García K, Bastías R. Valp1, a Newly Identified Temperate Phage Facilitating Coexistence of Lysogenic and Non-Lysogenic Populations of Vibrio anguillarum. Pathogens 2024; 13:285. [PMID: 38668240 PMCID: PMC11054321 DOI: 10.3390/pathogens13040285] [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: 02/14/2024] [Revised: 03/23/2024] [Accepted: 03/24/2024] [Indexed: 04/29/2024] Open
Abstract
Vibrio anguillarum is a pathogen for several fish and shellfish species. Its ecology is influenced by diverse factors, including bacteriophages. Here, we identify and characterize a new temperate bacteriophage (Valp1) of V. anguillarum. Valp1 is a myovirus with a 60 nm head and a 90 nm contractile tail. Its double-stranded DNA genome of 42,988 bp contains 68 genes, including a protelomerase gene, typical of telomeric phages. Valp1 inhibits the growth of the virulent strain of V. anguillarum PF4, while the derived lysogenic strain P1.1 presents a slight reduction in its growth but is not affected by the presence of Valp1. Both strains present similar virulence in a larval zebrafish (Danio rerio) model, and only slight differences have been observed in their biochemical profile. Co-culture assays reveal that PF4 and P1.1 can coexist for 10 h in the presence of naturally induced Valp1, with the proportion of PF4 ranging between 28% and 1.6%. By the end of the assay, the phage reached a concentration of ~108 PFU/mL, and all the non-lysogenic PF4 strains were resistant to Valp1. This equilibrium was maintained even after five successive subcultures, suggesting the existence of a coexistence mechanism between the lysogenic and non-lysogenic populations of V. anguillarum in conjunction with the phage Valp1.
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Affiliation(s)
- Manuel Arce
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340000, Chile; (M.A.)
| | - Guillermo Venegas
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340000, Chile; (M.A.)
| | - Karla Paez
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340000, Chile; (M.A.)
| | - Simone Latz
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340000, Chile; (M.A.)
| | - Paola Navarrete
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago 7830490, Chile
| | - Mario Caruffo
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago 7830490, Chile
- Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago 8820000, Chile
| | - Carmen Feijoo
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370146, Chile
| | - Katherine García
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago 8910060, Chile
| | - Roberto Bastías
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340000, Chile; (M.A.)
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Huang D, Xia R, Chen C, Liao J, Chen L, Wang D, Alvarez PJJ, Yu P. Adaptive strategies and ecological roles of phages in habitats under physicochemical stress. Trends Microbiol 2024:S0966-842X(24)00042-8. [PMID: 38433027 DOI: 10.1016/j.tim.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 03/05/2024]
Abstract
Bacteriophages (phages) play a vital role in ecosystem functions by influencing the composition, genetic exchange, metabolism, and environmental adaptation of microbial communities. With recent advances in sequencing technologies and bioinformatics, our understanding of the ecology and evolution of phages in stressful environments has substantially expanded. Here, we review the impact of physicochemical environmental stress on the physiological state and community dynamics of phages, the adaptive strategies that phages employ to cope with environmental stress, and the ecological effects of phage-host interactions in stressful environments. Specifically, we highlight the contributions of phages to the adaptive evolution and functioning of microbiomes and suggest that phages and their hosts can maintain a mutualistic relationship in response to environmental stress. In addition, we discuss the ecological consequences caused by phages in stressful environments, encompassing biogeochemical cycling. Overall, this review advances an understanding of phage ecology in stressful environments, which could inform phage-based strategies to improve microbiome performance and ecosystem resilience and resistance in natural and engineering systems.
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Affiliation(s)
- Dan Huang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Rong Xia
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chengyi Chen
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jingqiu Liao
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Linxing Chen
- Department of Earth and Planetary Sciences, University of California Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94720, USA
| | - Dongsheng Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, USA
| | - Pingfeng Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, 314100, China.
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5
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Bisen M, Kharga K, Mehta S, Jabi N, Kumar L. Bacteriophages in nature: recent advances in research tools and diverse environmental and biotechnological applications. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:22199-22242. [PMID: 38411907 DOI: 10.1007/s11356-024-32535-3] [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: 11/16/2023] [Accepted: 02/15/2024] [Indexed: 02/28/2024]
Abstract
Bacteriophages infect and replicate within bacteria and play a key role in the environment, particularly in microbial ecosystems and bacterial population dynamics. The increasing recognition of their significance stems from their wide array of environmental and biotechnological uses, which encompass the mounting issue of antimicrobial resistance (AMR). Beyond their therapeutic potential in combating antibiotic-resistant infections, bacteriophages also find vast applications such as water quality monitoring, bioremediation, and nutrient cycling within environmental sciences. Researchers are actively involved in isolating and characterizing bacteriophages from different natural sources to explore their applications. Gaining insights into key aspects such as the life cycle of bacteriophages, their host range, immune interactions, and physical stability is vital to enhance their application potential. The establishment of diverse phage libraries has become indispensable to facilitate their wide-ranging uses. Consequently, numerous protocols, ranging from traditional to cutting-edge techniques, have been developed for the isolation, detection, purification, and characterization of bacteriophages from diverse environmental sources. This review offers an exploration of tools, delves into the methods of isolation, characterization, and the extensive environmental applications of bacteriophages, particularly in areas like water quality assessment, the food sector, therapeutic interventions, and the phage therapy in various infections and diseases.
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Affiliation(s)
- Monish Bisen
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Kusum Kharga
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Sakshi Mehta
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Nashra Jabi
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Lokender Kumar
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India.
- Cancer Biology Laboratory, Raj Khosla Centre for Cancer Research, Shoolini University, Himachal Pradesh, Solan, 173229, India.
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6
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Forni D, Pozzoli U, Cagliani R, Sironi M. Dinucleotide biases in the genomes of prokaryotic and eukaryotic dsDNA viruses and their hosts. Mol Ecol 2024; 33:e17287. [PMID: 38263702 DOI: 10.1111/mec.17287] [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: 09/18/2023] [Revised: 12/21/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024]
Abstract
The genomes of cellular organisms display CpG and TpA dinucleotide composition biases. Such biases have been poorly investigated in dsDNA viruses. Here, we show that in dsDNA virus, bacterial, and eukaryotic genomes, the representation of TpA and CpG dinucleotides is strongly dependent on genomic G + C content. Thus, the classical observed/expected ratios do not fully capture dinucleotide biases across genomes. Because a larger portion of the variance in TpA frequency was explained by G + C content, we explored which additional factors drive the distribution of CpG dinucleotides. Using the residuals of the linear regressions as a measure of dinucleotide abundance and ancestral state reconstruction across eukaryotic and prokaryotic virus trees, we identified an important role for phylogeny in driving CpG representation. Nonetheless, phylogenetic ANOVA analyses showed that few host associations also account for significant variations. Among eukaryotic viruses, most significant differences were observed between arthropod-infecting viruses and viruses that infect vertebrates or unicellular organisms. However, an effect of viral DNA methylation status (either driven by the host or by viral-encoded methyltransferases) is also likely. Among prokaryotic viruses, cyanobacteria-infecting phages resulted to be significantly CpG-depleted, whereas phages that infect bacteria in the genera Burkolderia and Staphylococcus were CpG-rich. Comparison with bacterial genomes indicated that this effect is largely driven by the general tendency for phages to resemble the host's genomic CpG content. Notably, such tendency is stronger for temperate than for lytic phages. Our data shed light into the processes that shape virus genome composition and inform manipulation strategies for biotechnological applications.
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Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Uberto Pozzoli
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
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7
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Ye Y, Zhang L, Hong X, Chen M, Liu X, Zhou S. Interspecies ecological competition rejuvenates decayed Geobacter electroactive biofilm. THE ISME JOURNAL 2024; 18:wrae118. [PMID: 38916438 PMCID: PMC11227281 DOI: 10.1093/ismejo/wrae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/05/2024] [Accepted: 06/23/2024] [Indexed: 06/26/2024]
Abstract
Bioelectrochemical systems (BESs) exploit electroactive biofilms (EABs) for promising applications in biosensing, wastewater treatment, energy production, and chemical biosynthesis. However, during the operation of BESs, EABs inevitably decay. Seeking approaches to rejuvenate decayed EABs is critical for the sustainability and practical application of BESs. Prophage induction has been recognized as the primary reason for EAB decay. Herein, we report that introducing a competitive species of Geobacter uraniireducens suspended prophage induction in Geobacter sulfurreducens and thereby rejuvenated the decayed G. sulfurreducens EAB. The transcriptomic profile of G. sulfurreducens demonstrated that the addition of G. uraniireducens significantly affected the expression of metabolism- and stress response system-related genes and in particular suppressed the induction of phage-related genes. Mechanistic analyses revealed that interspecies ecological competition exerted by G. uraniireducens suppressed prophage induction. Our findings not only reveal a novel strategy to rejuvenate decayed EABs, which is significant for the sustainability of BESs, but also provide new knowledge for understanding phage-host interactions from an ecological perspective, with implications for developing therapies to defend against phage attack.
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Affiliation(s)
- Yin Ye
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lu Zhang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaohui Hong
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Man Chen
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xing Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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8
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Contente D, Díaz-Formoso L, Feito J, Hernández PE, Muñoz-Atienza E, Borrero J, Poeta P, Cintas LM. Genomic and Functional Evaluation of Two Lacticaseibacillus paracasei and Two Lactiplantibacillus plantarum Strains, Isolated from a Rearing Tank of Rotifers ( Brachionus plicatilis), as Probiotics for Aquaculture. Genes (Basel) 2024; 15:64. [PMID: 38254954 PMCID: PMC10815930 DOI: 10.3390/genes15010064] [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: 11/06/2023] [Revised: 12/21/2023] [Accepted: 12/30/2023] [Indexed: 01/24/2024] Open
Abstract
Aquaculture plays a crucial role in meeting the increasing global demand for food and protein sources. However, its expansion is followed by increasing challenges, such as infectious disease outbreaks and antibiotic misuse. The present study focuses on the genetic and functional analyses of two Lacticaseibacillus paracasei (BF3 and RT4) and two Lactiplantibacillus plantarum (BF12 and WT12) strains isolated from a rotifer cultivation tank used for turbot larviculture. Whole-genome sequencing (WGS) and bioinformatics analyses confirmed their probiotic potential, the absence of transferable antibiotic resistance genes, and the absence of virulence and pathogenicity factors. Bacteriocin mining identified a gene cluster encoding six plantaricins, suggesting their role in the antimicrobial activity exerted by these strains. In vitro cell-free protein synthesis (IV-CFPS) analyses was used to evaluate the expression of the plantaricin genes. The in vitro-synthesized class IIb (two-peptide bacteriocins) plantaricin E/F (PlnE/F) exerted antimicrobial activity against three indicator microorganisms, including the well-known ichthyopathogen Lactococcus garvieae. Furthermore, MALDI-TOF MS on colonies detected the presence of a major peptide that matches the dimeric form of plantaricins E (PlnE) and F (PlnF). This study emphasizes the importance of genome sequencing and bioinformatic analysis for evaluating aquaculture probiotic candidates. Moreover, it provides valuable insights into their genetic features and antimicrobial mechanisms, paving the way for their application as probiotics in larviculture, which is a major bottleneck in aquaculture.
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Affiliation(s)
- Diogo Contente
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.C.); (L.D.-F.); (P.E.H.); (E.M.-A.); (J.B.); (L.M.C.)
| | - Lara Díaz-Formoso
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.C.); (L.D.-F.); (P.E.H.); (E.M.-A.); (J.B.); (L.M.C.)
| | - Javier Feito
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.C.); (L.D.-F.); (P.E.H.); (E.M.-A.); (J.B.); (L.M.C.)
| | - Pablo E. Hernández
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.C.); (L.D.-F.); (P.E.H.); (E.M.-A.); (J.B.); (L.M.C.)
| | - Estefanía Muñoz-Atienza
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.C.); (L.D.-F.); (P.E.H.); (E.M.-A.); (J.B.); (L.M.C.)
| | - Juan Borrero
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.C.); (L.D.-F.); (P.E.H.); (E.M.-A.); (J.B.); (L.M.C.)
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal;
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
| | - Luis M. Cintas
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.C.); (L.D.-F.); (P.E.H.); (E.M.-A.); (J.B.); (L.M.C.)
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9
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Sevillano E, Lafuente I, Peña N, Cintas LM, Muñoz-Atienza E, Hernández PE, Borrero J. Evaluation of Safety and Probiotic Traits from a Comprehensive Genome-Based In Silico Analysis of Ligilactobacillus salivarius P1CEA3, Isolated from Pigs and Producer of Nisin S. Foods 2023; 13:107. [PMID: 38201135 PMCID: PMC10778751 DOI: 10.3390/foods13010107] [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: 11/17/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Ligilactobacillus salivarius is an important member of the porcine gastrointestinal tract (GIT). Some L. salivarius strains are considered to have a beneficial effect on the host by exerting different probiotic properties, including the production of antimicrobial peptides which help maintain a healthy gut microbiota. L. salivarius P1CEA3, a porcine isolated strain, was first selected and identified by its antimicrobial activity against a broad range of pathogenic bacteria due to the production of the novel bacteriocin nisin S. The assembled L. salivarius P1CEA3 genome includes a circular chromosome, a megaplasmid (pMP1CEA3) encoding the nisin S gene cluster, and two small plasmids. A comprehensive genome-based in silico analysis of the L. salivarius P1CEA3 genome reveals the presence of genes related to probiotic features such as bacteriocin synthesis, regulation and production, adhesion and aggregation, the production of lactic acid, amino acids metabolism, vitamin biosynthesis, and tolerance to temperature, acid, bile salts and osmotic and oxidative stress. Furthermore, the strain is absent of risk-related genes for acquired antibiotic resistance traits, virulence factors, toxic metabolites and detrimental metabolic or enzymatic activities. Resistance to common antibiotics and gelatinase and hemolytic activities have been discarded by in vitro experiments. This study identifies several probiotic and safety traits of L. salivarius P1CEA3 and suggests its potential as a promising probiotic in swine production.
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Affiliation(s)
| | | | | | | | | | | | - Juan Borrero
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Spain; (E.S.); (I.L.); (N.P.); (L.M.C.); (E.M.-A.); (P.E.H.)
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10
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Zhang M, Hao Y, Yi Y, Liu S, Sun Q, Tan X, Tang S, Xiao X, Jian H. Unexplored diversity and ecological functions of transposable phages. THE ISME JOURNAL 2023; 17:1015-1028. [PMID: 37069234 PMCID: PMC10284936 DOI: 10.1038/s41396-023-01414-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 04/02/2023] [Accepted: 04/05/2023] [Indexed: 04/19/2023]
Abstract
Phages are prevalent in diverse environments and play major ecological roles attributed to their tremendous diversity and abundance. Among these viruses, transposable phages (TBPs) are exceptional in terms of their unique lifestyle, especially their replicative transposition. Although several TBPs have been isolated and the life cycle of the representative phage Mu has been extensively studied, the diversity distribution and ecological functions of TBPs on the global scale remain unknown. Here, by mining TBPs from enormous microbial genomes and viromes, we established a TBP genome dataset (TBPGD), that expands the number of accessible TBP genomes 384-fold. TBPs are prevalent in diverse biomes and show great genetic diversity. Based on taxonomic evaluations, we propose the categorization of TBPs into four viral groups, including 11 candidate subfamilies. TBPs infect multiple bacterial phyla, and seem to infect a wider range of hosts than non-TBPs. Diverse auxiliary metabolic genes (AMGs) are identified in the TBP genomes, and genes related to glycoside hydrolases and pyrimidine deoxyribonucleotide biosynthesis are highly enriched. Finally, the influences of TBPs on their hosts are experimentally examined by using the marine bacterium Shewanella psychrophila WP2 and its infecting transposable phage SP2. Collectively, our findings greatly expand the genetic diversity of TBPs, and comprehensively reveal their potential influences in various ecosystems.
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Affiliation(s)
- Mujie Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yali Hao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Yi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shunzhang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qingyang Sun
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoli Tan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shan Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China.
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11
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The Role of Temperate Phages in Bacterial Pathogenicity. Microorganisms 2023; 11:microorganisms11030541. [PMID: 36985115 PMCID: PMC10052878 DOI: 10.3390/microorganisms11030541] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 02/05/2023] [Accepted: 02/16/2023] [Indexed: 02/23/2023] Open
Abstract
Bacteriophages are viruses that infect bacteria and archaea and are classified as virulent or temperate phages based on their life cycles. A temperate phage, also known as a lysogenic phage, integrates its genomes into host bacterial chromosomes as a prophage. Previous studies have indicated that temperate phages are beneficial to their susceptible bacterial hosts by introducing additional genes to bacterial chromosomes, creating a mutually beneficial relationship. This article reviewed three primary ways temperate phages contribute to the bacterial pathogenicity of foodborne pathogens, including phage-mediated virulence gene transfer, antibiotic resistance gene mobilization, and biofilm formation. This study provides insights into mechanisms of phage–bacterium interactions in the context of foodborne pathogens and provokes new considerations for further research to avoid the potential of phage-mediated harmful gene transfer in agricultural environments.
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12
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Evseev P, Lukianova A, Tarakanov R, Tokmakova A, Popova A, Kulikov E, Shneider M, Ignatov A, Miroshnikov K. Prophage-Derived Regions in Curtobacterium Genomes: Good Things, Small Packages. Int J Mol Sci 2023; 24:ijms24021586. [PMID: 36675099 PMCID: PMC9862828 DOI: 10.3390/ijms24021586] [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: 11/30/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
Curtobacterium is a genus of Gram-positive bacteria within the order Actinomycetales. Some Curtobacterium species (C. flaccumfaciens, C. plantarum) are harmful pathogens of agricultural crops such as soybean, dry beans, peas, sugar beet and beetroot, which occur throughout the world. Bacteriophages (bacterial viruses) are considered to be potential curative agents to control the spread of harmful bacteria. Temperate bacteriophages integrate their genomes into bacterial chromosomes (prophages), sometimes substantially influencing bacterial lifestyle and pathogenicity. About 200 publicly available genomes of Curtobacterium species, including environmental metagenomic sequences, were inspected for the presence of sequences of possible prophage origin using bioinformatic methods. The comparison of the search results with several ubiquitous bacterial groups showed the relatively low level of the presence of prophage traces in Curtobacterium genomes. Genomic and phylogenetic analyses were undertaken for the evaluation of the evolutionary and taxonomic positioning of predicted prophages. The analyses indicated the relatedness of Curtobacterium prophage-derived sequences with temperate actinophages of siphoviral morphology. In most cases, the predicted prophages can represent novel phage taxa not described previously. One of the predicted temperate phages was induced from the Curtobacterium genome. Bioinformatic analysis of the modelled proteins encoded in prophage-derived regions led to the discovery of some 100 putative glycopolymer-degrading enzymes that contained enzymatic domains with predicted cell-wall- and cell-envelope-degrading activity; these included glycosidases and peptidases. These proteins can be considered for the experimental design of new antibacterials against Curtobacterium phytopathogens.
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Affiliation(s)
- Peter Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
- Correspondence: (P.E.); (K.M.)
| | - Anna Lukianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
| | - Rashit Tarakanov
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia
| | - Anna Tokmakova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology National Research University, Institutskiy Per, 9, 141701 Dolgoprudny, Russia
| | - Anastasia Popova
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
| | - Eugene Kulikov
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology National Research University, Institutskiy Per, 9, 141701 Dolgoprudny, Russia
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prosp. 60-letia Oktyabrya, 7-2, 117312 Moscow, Russia
| | - Mikhail Shneider
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
| | - Alexander Ignatov
- Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str. 6, 117198 Moscow, Russia
| | - Konstantin Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
- Correspondence: (P.E.); (K.M.)
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13
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Dantas R, Brocchi M, Pacheco Fill T. Chemical-Biology and Metabolomics Studies in Phage-Host Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1439:71-100. [PMID: 37843806 DOI: 10.1007/978-3-031-41741-2_4] [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: 10/17/2023]
Abstract
For many years, several studies have explored the molecular mechanisms involved in the infection of bacteria by their specific phages to understand the main infection strategies and the host defense strategies. The modulation of the mechanisms involved in the infection, as well as the expression of key substances in the development of the different life cycles of phages, function as a natural source of strategies capable of promoting the control of different pathogens that are harmful to human and animal health. Therefore, this chapter aims to provide an overview of the mechanisms involved in virus-bacteria interaction to explore the main compounds produced or altered as a chemical survival strategy and the metabolism modulation when occurring a host-phage interaction. In this context, emphasis will be given to the chemistry of peptides/proteins and enzymes encoded by bacteriophages in the control of pathogenic bacteria and the use of secondary metabolites recently reported as active participants in the mechanisms of phage-bacteria interaction. Finally, metabolomics strategies developed to gain new insights into the metabolism involved in the phage-host interaction and the metabolomics workflow in host-phage interaction will be presented.
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Affiliation(s)
- Rodolfo Dantas
- Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil
| | - Marcelo Brocchi
- Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Taícia Pacheco Fill
- Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil.
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14
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Bruneaux M, Ashrafi R, Kronholm I, Laanto E, Örmälä‐Tiznado A, Galarza JA, Zihan C, Kubendran Sumathi M, Ketola T. The effect of a temperature-sensitive prophage on the evolution of virulence in an opportunistic bacterial pathogen. Mol Ecol 2022; 31:5402-5418. [PMID: 35917247 PMCID: PMC9826266 DOI: 10.1111/mec.16638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/14/2022] [Accepted: 07/21/2022] [Indexed: 01/11/2023]
Abstract
Viruses are key actors of ecosystems and have major impacts on global biogeochemical cycles. Prophages deserve particular attention as they are ubiquitous in bacterial genomes and can enter a lytic cycle when triggered by environmental conditions. We explored how temperature affects the interactions between prophages and other biological levels using an opportunistic pathogen, the bacterium Serratia marcescens, which harbours several prophages and that had undergone an evolution experiment under several temperature regimes. We found that the release of one of the prophages was temperature-sensitive and malleable to evolutionary changes. We further discovered that the virulence of the bacterium in an insect model also evolved and was positively correlated with phage release rates. We determined through analysis of genetic and epigenetic data that changes in the bacterial outer cell wall structure possibly explain this phenomenon. We hypothezise that the temperature-dependent phage release rate acted as a selection pressure on S. marcescens and that it resulted in modified bacterial virulence in the insect host. Our study system illustrates how viruses can mediate the influence of abiotic environmental changes to other biological levels and thus be involved in ecosystem feedback loops.
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Affiliation(s)
- Matthieu Bruneaux
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Roghaieh Ashrafi
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Ilkka Kronholm
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Elina Laanto
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland,Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
| | | | - Juan A. Galarza
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Chen Zihan
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland,Shenzhen Research InstituteThe Chinese University of Hong KongShenzhenChina
| | - Mruthyunjay Kubendran Sumathi
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland,Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizonaUSA
| | - Tarmo Ketola
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
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15
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Phage Diving: An Exploration of the Carcharhinid Shark Epidermal Virome. Viruses 2022; 14:v14091969. [PMID: 36146775 PMCID: PMC9500685 DOI: 10.3390/v14091969] [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: 08/05/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 11/18/2022] Open
Abstract
The epidermal microbiome is a critical element of marine organismal immunity, but the epidermal virome of marine organisms remains largely unexplored. The epidermis of sharks represents a unique viromic ecosystem. Sharks secrete a thin layer of mucus which harbors a diverse microbiome, while their hydrodynamic dermal denticles simultaneously repel environmental microbes. Here, we sampled the virome from the epidermis of three shark species in the family Carcharhinidae: the genetically and morphologically similar Carcharhinus obscurus (n = 6) and Carcharhinus galapagensis (n = 10) and the outgroup Galeocerdo cuvier (n = 15). Virome taxonomy was characterized using shotgun metagenomics and compared with a suite of multivariate analyses. All three sharks retain species-specific but highly similar epidermal viromes dominated by uncharacterized bacteriophages which vary slightly in proportional abundance within and among shark species. Intraspecific variation was lower among C. galapagensis than among C. obscurus and G. cuvier. Using both the annotated and unannotated reads, we were able to determine that the Carcharhinus galapagensis viromes were more similar to that of G. cuvier than they were to that of C. obscurus, suggesting that behavioral niche may be a more prominent driver of virome than host phylogeny.
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16
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Li J, Yang F, Xiao M, Li A. Advances and challenges in cataloging the human gut virome. Cell Host Microbe 2022; 30:908-916. [PMID: 35834962 DOI: 10.1016/j.chom.2022.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 06/02/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022]
Abstract
The human gut virome, which is often referred to as the "dark matter" of the gut microbiome, remains understudied. A better understanding of the composition and variations of the gut virome across populations is critical for exploring its impact on diseases and health. A series of advances in the characterization of human gut virome have unveiled high genetic diversity and various functional potentials of gut viruses. Here, we summarize the recently available human gut virome databases and discuss their features, procedures, and challenges with the intention to provide a reference to researchers to use while choosing a profiling database. We also propose a "best practice" for cataloging the viral population.
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Affiliation(s)
- Junhua Li
- BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China.
| | | | - Minfeng Xiao
- BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China.
| | - Aixin Li
- BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
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17
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Zhang X, Wang R, Xie X, Hu Y, Wang J, Sun Q, Feng X, Lin W, Tong S, Yan W, Wen H, Wang M, Zhai S, Sun C, Wang F, Niu Q, Kropinski A, Cui Y, Jiang X, Peng S, Li S, Tong Y. Mining bacterial NGS data vastly expands the complete genomes of temperate phages. NAR Genom Bioinform 2022; 4:lqac057. [PMID: 35937545 PMCID: PMC9346568 DOI: 10.1093/nargab/lqac057] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 06/13/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Temperate phages (active prophages induced from bacteria) help control pathogenicity, modulate community structure, and maintain gut homeostasis. Complete phage genome sequences are indispensable for understanding phage biology. Traditional plaque techniques are inapplicable to temperate phages due to their lysogenicity, curbing their identification and characterization. Existing bioinformatics tools for prophage prediction usually fail to detect accurate and complete temperate phage genomes. This study proposes a novel computational temperate phage detection method (TemPhD) mining both the integrated active prophages and their spontaneously induced forms (temperate phages) from next-generation sequencing raw data. Applying the method to the available dataset resulted in 192 326 complete temperate phage genomes with different host species, expanding the existing number of complete temperate phage genomes by more than 100-fold. The wet-lab experiments demonstrated that TemPhD can accurately determine the complete genome sequences of the temperate phages, with exact flanking sites, outperforming other state-of-the-art prophage prediction methods. Our analysis indicates that temperate phages are likely to function in the microbial evolution by (i) cross-infecting different bacterial host species; (ii) transferring antibiotic resistance and virulence genes and (iii) interacting with hosts through restriction-modification and CRISPR/anti-CRISPR systems. This work provides a comprehensively complete temperate phage genome database and relevant information, which can serve as a valuable resource for phage research.
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Affiliation(s)
- Xianglilan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing 100071, People's Republic of China
| | - Ruohan Wang
- Department of Computer Science, City University of Hong Kong , Hong Kong 999077, People's Republic of China
| | - Xiangcheng Xie
- College of Computer, National University of Defense Technology , Changsha 410073, People's Republic of China
| | - Yunjia Hu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, People's Republic of China
- School of Medicine, Shanghai University , Shanghai 200444, People's Republic of China
| | - Jianping Wang
- Department of Computer Science, City University of Hong Kong , Hong Kong 999077, People's Republic of China
| | - Qiang Sun
- The 964th Hospital , Changchun 130021, People's Republic of China
| | - Xikang Feng
- School of Software, Northwestern Polytechnical University , Xi’an 710072, People's Republic of China
| | - Wei Lin
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, People's Republic of China
| | - Shanwei Tong
- Bioinformatics Graduate Program, University of British Columbia , Vancouver BC V6T 1Z4, Canada
- Faculty of Health Sciences, Simon Fraser University , Burnaby , BC V5A 1S6, Canada
| | - Wei Yan
- National Library of Medicine, National Institutes of Health , Bethesda , MD 20894, USA
| | - Huiqi Wen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing 100071, People's Republic of China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, People's Republic of China
| | - Mengyao Wang
- Department of Computer Science, City University of Hong Kong , Hong Kong 999077, People's Republic of China
| | - Shixiang Zhai
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences , Yantai 264003, People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049, People's Republic of China
- Center for Ocean Mega-Science, Chinese Academy of Sciences , Qingdao 266071, People's Republic of China
| | - Cheng Sun
- School of Computer Science and Electronic Engineering, Hunan University , Changsha 410082, People's Republic of China
| | - Fangyi Wang
- Department of Statistics, the Ohio State University , Columbus, OH 43210, USA
| | - Qi Niu
- School of Computer Science and Electronic Engineering, Hunan University , Changsha 410082, People's Republic of China
| | - Andrew M Kropinski
- Departments of Food Science, and Pathobiology, University of Guelph , Guelph , ON N1G 2W1 , Canada
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing 100071, People's Republic of China
| | - Xiaofang Jiang
- National Library of Medicine, National Institutes of Health , Bethesda , MD 20894, USA
| | - Shaoliang Peng
- School of Computer Science and Electronic Engineering, Hunan University , Changsha 410082, People's Republic of China
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong , Hong Kong 999077, People's Republic of China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, People's Republic of China
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18
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Shkoporov AN, Turkington CJ, Hill C. Mutualistic interplay between bacteriophages and bacteria in the human gut. Nat Rev Microbiol 2022; 20:737-749. [PMID: 35773472 DOI: 10.1038/s41579-022-00755-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 12/12/2022]
Abstract
Bacteriophages (phages) are often described as obligate predators of their bacterial hosts, and phage predation is one of the leading forces controlling the density and distribution of bacterial populations. Every 48 h half of all bacteria on Earth are killed by phages. Efficient killing also forms the basis of phage therapy in humans and animals and the use of phages as food preservatives. In turn, bacteria have a plethora of resistance systems against phage attack, but very few bacterial species, if any, have entirely escaped phage predation. However, in complex communities and environments such as the human gut, this antagonistic model of attack and counter-defence does not fully describe the scope of phage-bacterium interactions. In this Review, we explore some of the more mutualistic aspects of phage-bacterium interactions in the human gut, and we suggest that the relationship between phages and their bacterial hosts in the gut is best characterized not as a fight to the death between enemies but rather as a mutualistic relationship between partners.
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Affiliation(s)
- Andrey N Shkoporov
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland. .,Department of Medicine, University College Cork, Cork, Ireland.
| | | | - Colin Hill
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland.
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19
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Huang Y, Wang W, Zhang Z, Gu Y, Huang A, Wang J, Hao H. Phage Products for Fighting Antimicrobial Resistance. Microorganisms 2022; 10:microorganisms10071324. [PMID: 35889048 PMCID: PMC9324367 DOI: 10.3390/microorganisms10071324] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 12/19/2022] Open
Abstract
Antimicrobial resistance (AMR) has become a global public health issue and antibiotic agents have lagged behind the rise in bacterial resistance. We are searching for a new method to combat AMR and phages are viruses that can effectively fight bacterial infections, which have renewed interest as antibiotic alternatives with their specificity. Large phage products have been produced in recent years to fight AMR. Using the “one health” approach, this review summarizes the phage products used in plant, food, animal, and human health. In addition, the advantages and disadvantages and future perspectives for the development of phage therapy as an antibiotic alternative to combat AMR are also discussed in this review.
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Affiliation(s)
- Yuanling Huang
- National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China; (Y.H.); (W.W.); (Z.Z.); (Y.G.); (A.H.); (J.W.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenhui Wang
- National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China; (Y.H.); (W.W.); (Z.Z.); (Y.G.); (A.H.); (J.W.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhihao Zhang
- National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China; (Y.H.); (W.W.); (Z.Z.); (Y.G.); (A.H.); (J.W.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Yufeng Gu
- National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China; (Y.H.); (W.W.); (Z.Z.); (Y.G.); (A.H.); (J.W.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Anxiong Huang
- National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China; (Y.H.); (W.W.); (Z.Z.); (Y.G.); (A.H.); (J.W.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Junhao Wang
- National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China; (Y.H.); (W.W.); (Z.Z.); (Y.G.); (A.H.); (J.W.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Haihong Hao
- National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China; (Y.H.); (W.W.); (Z.Z.); (Y.G.); (A.H.); (J.W.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
- Correspondence:
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20
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Elsayed A, Safwat A, Abdelsattar AS, Essam K, Nofal R, Makky S, El-Shibiny A. The antibacterial and biofilm inhibition activity of encapsulated silver nanoparticles in emulsions and its synergistic effect with E. coli bacteriophage. INORG NANO-MET CHEM 2022. [DOI: 10.1080/24701556.2022.2081191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Amera Elsayed
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Anan Safwat
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Abdallah S. Abdelsattar
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
- Center for X-Ray and Determination of Structure of Matter, Zewail City of Science and Technology, Giza, Egypt
| | - Kareem Essam
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Rana Nofal
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Salsabil Makky
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
- Faculty of Environmental Agricultural Sciences, Arish University, Arish, Egypt
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21
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Abril AG, Carrera M, Notario V, Sánchez-Pérez Á, Villa TG. The Use of Bacteriophages in Biotechnology and Recent Insights into Proteomics. Antibiotics (Basel) 2022; 11:653. [PMID: 35625297 PMCID: PMC9137636 DOI: 10.3390/antibiotics11050653] [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: 04/19/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 12/10/2022] Open
Abstract
Phages have certain features, such as their ability to form protein-protein interactions, that make them good candidates for use in a variety of beneficial applications, such as in human or animal health, industry, food science, food safety, and agriculture. It is essential to identify and characterize the proteins produced by particular phages in order to use these viruses in a variety of functional processes, such as bacterial detection, as vehicles for drug delivery, in vaccine development, and to combat multidrug resistant bacterial infections. Furthermore, phages can also play a major role in the design of a variety of cheap and stable sensors as well as in diagnostic assays that can either specifically identify specific compounds or detect bacteria. This article reviews recently developed phage-based techniques, such as the use of recombinant tempered phages, phage display and phage amplification-based detection. It also encompasses the application of phages as capture elements, biosensors and bioreceptors, with a special emphasis on novel bacteriophage-based mass spectrometry (MS) applications.
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Affiliation(s)
- Ana G. Abril
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain;
- Department of Food Technology, Spanish National Research Council (CSIC), Marine Research Institute (IIM), 36208 Vigo, Spain;
| | - Mónica Carrera
- Department of Food Technology, Spanish National Research Council (CSIC), Marine Research Institute (IIM), 36208 Vigo, Spain;
| | - Vicente Notario
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA;
| | - Ángeles Sánchez-Pérez
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW 2006, Australia;
| | - Tomás G. Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain;
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22
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Staes I, Bäcker LE, Simoens K, De Winter K, Marolt G, Cenens W, Wolput S, Vazquez AR, Goos P, Lavigne R, Bernaerts K, Aertsen A. Superinfection exclusion factors drive a history-dependent switch from vertical to horizontal phage transmission. Cell Rep 2022; 39:110804. [PMID: 35545039 DOI: 10.1016/j.celrep.2022.110804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 03/24/2022] [Accepted: 04/19/2022] [Indexed: 11/03/2022] Open
Abstract
Temperate bacterial viruses are commonly thought to favor vertical (lysogenic) transmission over horizontal (lytic) transmission when the virion-to-host-cell ratio is high and available host cells become scarce. In P22-infected Salmonella Typhimurium populations, however, we find that host subpopulations become lytically consumed despite high phage-to-host ratios that would normally favor lysogeny. These subpopulations originate from the proliferation of P22-free siblings that spawn off from P22-carrier cells from which they cytoplasmically inherit P22-borne superinfection exclusion factors (SEFs). In fact, we demonstrate that the gradual dilution of these SEFs in the growing subpopulation of P22-free siblings restricts the number of incoming phages, thereby imposing the perception of a low phage-to-host ratio that favors lytic development. Although their role has so far been neglected, our data indicate that phage-borne SEFs can spur complex infection dynamics and a history-dependent switch from vertical to horizontal transmission in the face of host-cell scarcity.
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Affiliation(s)
- Ines Staes
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 23 - bus 2457, 3001 Leuven, Belgium
| | - Leonard E Bäcker
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 23 - bus 2457, 3001 Leuven, Belgium
| | - Kenneth Simoens
- Department of Chemical Engineering- (Bio)chemical Reactor Engineering and Safety, Faculty of Engineering, KU Leuven, Leuven, Belgium
| | - Kjerstin De Winter
- Department of Chemical Engineering- (Bio)chemical Reactor Engineering and Safety, Faculty of Engineering, KU Leuven, Leuven, Belgium
| | - Gasper Marolt
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 23 - bus 2457, 3001 Leuven, Belgium; Department of Chemical Engineering- (Bio)chemical Reactor Engineering and Safety, Faculty of Engineering, KU Leuven, Leuven, Belgium
| | - William Cenens
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 23 - bus 2457, 3001 Leuven, Belgium
| | - Sanne Wolput
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 23 - bus 2457, 3001 Leuven, Belgium
| | - Alan R Vazquez
- Department of Biosystems, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Peter Goos
- Department of Biosystems, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium; Department of Engineering Management, University of Antwerp, Antwerp, Belgium
| | - Rob Lavigne
- Department of Biosystems, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Kristel Bernaerts
- Department of Chemical Engineering- (Bio)chemical Reactor Engineering and Safety, Faculty of Engineering, KU Leuven, Leuven, Belgium
| | - Abram Aertsen
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 23 - bus 2457, 3001 Leuven, Belgium.
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23
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Azulay G, Pasechnek A, Stadnyuk O, Ran-Sapir S, Fleisacher AM, Borovok I, Sigal N, Herskovits AA. A dual-function phage regulator controls the response of cohabiting phage elements via regulation of the bacterial SOS response. Cell Rep 2022; 39:110723. [PMID: 35443160 PMCID: PMC9043618 DOI: 10.1016/j.celrep.2022.110723] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 02/09/2022] [Accepted: 03/30/2022] [Indexed: 12/02/2022] Open
Abstract
Listeria monocytogenes strain 10403S harbors two phage elements in its chromosome; one produces infective virions and the other tailocins. It was previously demonstrated that induction of the two elements is coordinated, as they are regulated by the same anti-repressor. In this study, we identified AriS as another phage regulator that controls the two elements, bearing the capacity to inhibit their lytic induction under SOS conditions. AriS is a two-domain protein that possesses two distinct activities, one regulating the genes of its encoding phage and the other downregulating the bacterial SOS response. While the first activity associates with the AriS N-terminal AntA/AntB domain, the second associates with its C-terminal ANT/KilAC domain. The ANT/KilAC domain is conserved in many AriS-like proteins of listerial and non-listerial prophages, suggesting that temperate phages acquired such dual-function regulators to align their response with the other phage elements that cohabit the genome. Listeria monocytogenes strain 10403S harbors two phage elements in its chromosome The lytic response of the phage elements is synchronized under SOS conditions AriS, a dual-function phage regulator, fine-tunes the elements’ response under SOS Aris regulates both its encoding phage and the bacterial SOS response
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Affiliation(s)
- Gil Azulay
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Anna Pasechnek
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Olga Stadnyuk
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Shai Ran-Sapir
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Ana Mejia Fleisacher
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Ilya Borovok
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Nadejda Sigal
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Anat A Herskovits
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel.
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24
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Feito J, Contente D, Ponce-Alonso M, Díaz-Formoso L, Araújo C, Peña N, Borrero J, Gómez-Sala B, del Campo R, Muñoz-Atienza E, Hernández PE, Cintas LM. Draft Genome Sequence of Lactococcus lactis Subsp. cremoris WA2-67: A Promising Nisin-Producing Probiotic Strain Isolated from the Rearing Environment of a Spanish Rainbow Trout ( Oncorhynchus mykiss, Walbaum) Farm. Microorganisms 2022; 10:microorganisms10030521. [PMID: 35336097 PMCID: PMC8954438 DOI: 10.3390/microorganisms10030521] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/20/2022] [Accepted: 02/25/2022] [Indexed: 12/30/2022] Open
Abstract
Probiotics are a viable alternative to traditional chemotherapy agents to control infectious diseases in aquaculture. In this regard, Lactococcus lactis subsp. cremoris WA2-67 has previously demonstrated several probiotic features, such as a strong antimicrobial activity against ichthyopathogens, survival in freshwater, resistance to fish bile and low pH, and hydrophobicity. The aim of this manuscript is an in silico analysis of the whole-genome sequence (WGS) of this strain to gain deeper insights into its probiotic properties and their genetic basis. Genomic DNA was purified, and libraries prepared for Illumina sequencing. After trimming and assembly, resulting contigs were subjected to bioinformatic analyses. The draft genome of L. cremoris WA2-67 consists of 30 contigs (2,573,139 bp), and a total number of 2493 coding DNA sequences (CDSs). Via in silico analysis, the bacteriocinogenic genetic clusters encoding the lantibiotic nisin Z (NisZ) and two new bacteriocins were identified, in addition to several probiotic traits, such as the production of vitamins, amino acids, adhesion/aggregation, and stress resistance factors, as well as the absence of transferable antibiotic resistance determinants and genes encoding detrimental enzymatic activities and virulence factors. These results unveil diverse beneficial properties that support the use of L. cremoris WA2-67 as a probiotic for aquaculture.
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Affiliation(s)
- Javier Feito
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda, Puerta de Hierro, s/n., 28040 Madrid, Spain; (J.F.); (D.C.); (L.D.-F.); (C.A.); (N.P.); (J.B.); (P.E.H.); (L.M.C.)
| | - Diogo Contente
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda, Puerta de Hierro, s/n., 28040 Madrid, Spain; (J.F.); (D.C.); (L.D.-F.); (C.A.); (N.P.); (J.B.); (P.E.H.); (L.M.C.)
| | - Manuel Ponce-Alonso
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal & Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ctra. Colmenar Viejo, km. 9, 100., 28034 Madrid, Spain; (M.P.-A.); (R.d.C.)
| | - Lara Díaz-Formoso
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda, Puerta de Hierro, s/n., 28040 Madrid, Spain; (J.F.); (D.C.); (L.D.-F.); (C.A.); (N.P.); (J.B.); (P.E.H.); (L.M.C.)
| | - Carlos Araújo
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda, Puerta de Hierro, s/n., 28040 Madrid, Spain; (J.F.); (D.C.); (L.D.-F.); (C.A.); (N.P.); (J.B.); (P.E.H.); (L.M.C.)
| | - Nuria Peña
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda, Puerta de Hierro, s/n., 28040 Madrid, Spain; (J.F.); (D.C.); (L.D.-F.); (C.A.); (N.P.); (J.B.); (P.E.H.); (L.M.C.)
| | - Juan Borrero
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda, Puerta de Hierro, s/n., 28040 Madrid, Spain; (J.F.); (D.C.); (L.D.-F.); (C.A.); (N.P.); (J.B.); (P.E.H.); (L.M.C.)
| | - Beatriz Gómez-Sala
- APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland;
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Cork, Ireland
| | - Rosa del Campo
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal & Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ctra. Colmenar Viejo, km. 9, 100., 28034 Madrid, Spain; (M.P.-A.); (R.d.C.)
| | - Estefanía Muñoz-Atienza
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda, Puerta de Hierro, s/n., 28040 Madrid, Spain; (J.F.); (D.C.); (L.D.-F.); (C.A.); (N.P.); (J.B.); (P.E.H.); (L.M.C.)
- Correspondence:
| | - Pablo E. Hernández
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda, Puerta de Hierro, s/n., 28040 Madrid, Spain; (J.F.); (D.C.); (L.D.-F.); (C.A.); (N.P.); (J.B.); (P.E.H.); (L.M.C.)
| | - Luis M. Cintas
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda, Puerta de Hierro, s/n., 28040 Madrid, Spain; (J.F.); (D.C.); (L.D.-F.); (C.A.); (N.P.); (J.B.); (P.E.H.); (L.M.C.)
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25
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Fan X, Liu Z, Wan Z, Zou H, Ji M, Sun K, Gao R, Li Z, Li W. Prophage Gene Rv2650c Enhances Intracellular Survival of Mycobacterium smegmatis. Front Microbiol 2022; 12:819837. [PMID: 35111145 PMCID: PMC8801708 DOI: 10.3389/fmicb.2021.819837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 12/29/2021] [Indexed: 11/30/2022] Open
Abstract
Background Induced by the pathogen Mycobacterium tuberculosis, tuberculosis remains one of the most dangerous infectious diseases in the world. As a special virus, prophage is domesticated by its host and are major contributors to virulence factors for bacterial pathogenicity. The function of prophages and their genes in M. tuberculosis is still unknown. Methods Rv2650c is a prophage gene in M. tuberculosis genome. We constructed recombinant Mycobacterium smegmatis (M. smegmatis) to observe bacteria morphology and analyze the resistance to various adverse environments. Recombinant and control strains were used to infect macrophages, respectively. Furthermore, we performed ELISA experiments of infected macrophages. Results Rv2650c affected the spread of colonies of M. smegmatis and enhanced the resistance of M. smegmatis to macrophages and various stress agents such as acid, oxidative stress, and surfactant. ELISA experiments revealed that the Rv2650c can inhibit the expression of inflammatory factors TNF-α, IL-10, IL-1β, and IL-6. Conclusion This study demonstrates that the prophage gene Rv2650c can inhibit the spread of colonies and the expression of inflammatory factors and promote intracellular survival of M. smegmatis. These results build the foundation for the discovery of virulence factors of M. tuberculosis, and provide novel insights into the function of the prophage in Mycobacterium.
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Affiliation(s)
- Xiangyu Fan
- Country College of Biological Science and Technology, University of Jinan, Jinan, China
- *Correspondence: Xiangyu Fan,
| | - Zichen Liu
- Country College of Biological Science and Technology, University of Jinan, Jinan, China
| | - Zhibin Wan
- School of Life Sciences, Neijiang Normal University, Neijiang, China
| | - Hanlu Zou
- School of Life Sciences, Neijiang Normal University, Neijiang, China
| | - Mengzhi Ji
- Country College of Biological Science and Technology, University of Jinan, Jinan, China
| | - Kaili Sun
- Country College of Biological Science and Technology, University of Jinan, Jinan, China
| | - Rongfeng Gao
- Country College of Biological Science and Technology, University of Jinan, Jinan, China
| | - Zhongfang Li
- College of Food and Bioengineering, Hezhou University, Hezhou, China
- Guangxi Key Laboratory of Health Care Food Science and Technology, Hezhou University, Hezhou, China
- Zhongfang Li,
| | - Wu Li
- School of Life Sciences, Neijiang Normal University, Neijiang, China
- Wu Li,
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26
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Peng W, Zeng F, Wu Z, Jin Z, Li W, Zhu M, Wang Q, Tong Y, Chen L, Bai Q. Isolation and genomic analysis of temperate phage 5W targeting multidrug-resistant Acinetobacter baumannii. Arch Microbiol 2021; 204:58. [DOI: 10.1007/s00203-021-02618-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 10/19/2022]
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27
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Fitzgerald SF, Lupolova N, Shaaban S, Dallman TJ, Greig D, Allison L, Tongue SC, Evans J, Henry MK, McNeilly TN, Bono JL, Gally DL. Genome structural variation in Escherichia coli O157:H7. Microb Genom 2021; 7. [PMID: 34751643 PMCID: PMC8743559 DOI: 10.1099/mgen.0.000682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human zoonotic pathogen Escherichia coli O157:H7 is defined by its extensive prophage repertoire including those that encode Shiga toxin, the factor responsible for inducing life-threatening pathology in humans. As well as introducing genes that can contribute to the virulence of a strain, prophage can enable the generation of large-chromosomal rearrangements (LCRs) by homologous recombination. This work examines the types and frequencies of LCRs across the major lineages of the O157:H7 serotype. We demonstrate that LCRs are a major source of genomic variation across all lineages of E. coli O157:H7 and by using both optical mapping and Oxford Nanopore long-read sequencing prove that LCRs are generated in laboratory cultures started from a single colony and that these variants can be recovered from colonized cattle. LCRs are biased towards the terminus region of the genome and are bounded by specific prophages that share large regions of sequence homology associated with the recombinational activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that important virulence phenotypes such as Shiga-toxin production, type-3 secretion and motility can be affected by LCRs. In summary, E. coli O157:H7 has acquired multiple prophage regions over time that act to continually produce structural variants of the genome. These findings raise important questions about the significance of this prophage-mediated genome contingency to enhance adaptability between environments.
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Affiliation(s)
- Stephen F Fitzgerald
- Division of Infection and Immunity, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Nadejda Lupolova
- Division of Infection and Immunity, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Sharif Shaaban
- Division of Infection and Immunity, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Timothy J Dallman
- Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, NW9 5EQ London, UK
| | - David Greig
- Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, NW9 5EQ London, UK
| | - Lesley Allison
- Scottish E. coli O157/VTEC Reference Laboratory, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh EH16 4SA, UK
| | - Sue C Tongue
- Epidemiology Research Unit (Inverness), Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Scotland, IV2 5NA, UK
| | - Judith Evans
- Epidemiology Research Unit (Inverness), Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Scotland, IV2 5NA, UK
| | - Madeleine K Henry
- Epidemiology Research Unit (Inverness), Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Scotland, IV2 5NA, UK
| | - Tom N McNeilly
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, EH26 OPZ, UK
| | - James L Bono
- United States Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, Nebraska, USA
| | - David L Gally
- Division of Infection and Immunity, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
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28
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Liang X, Wang Y, Zhang Y, Li B, Radosevich M. Bacteriophage-host depth distribution patterns in soil are maintained after nutrient stimulation in vitro. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 787:147589. [PMID: 33991924 DOI: 10.1016/j.scitotenv.2021.147589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/16/2021] [Accepted: 05/01/2021] [Indexed: 06/12/2023]
Abstract
Previous research has revealed the ecological importance of viruses in different ecosystems. However, bacteriophage-host distribution patterns in soil depth profiles have not been investigated. Environmental factors such as nutrient availability and physiological stress can impact the mode (either lytic or lysogenic) of viral reproduction and subsequent influence of virus infection on ecological processes. Soil depth profiles with distinct geochemical properties are ideal models to investigate the virus-host relationships as a function of environmental trophic status and cell abundance. Batch enrichment experiments using soil collected at varying depths (0-140 cm) as inoculum were performed to explore the interactions between viruses and co-occurring microbial hosts under nutrient stimulation. Both viral and bacterial abundance increased in the nutrient media compared with those in the original soils. Bacterial abundance was similar in mixed-cultures of soils regardless of sampling depth, whereas viral abundance was negatively correlated with the depth of soil samples which caused a decreasing virus-to-bacteria ratio. The lysogenetic fraction increased with soil depth in a similar manner as in the original soils assessed directly without nutrient stimulation. The bacterial diversity decreased with soil depth, and was influenced primarily by soil type, viral abundance, and virus-to-bacteria ratio. The bacterial communities were dominated by Bacilli, Beta-, Gamma-Proteobacteria, and Clostridia after nutrient stimulation. Viral and bacterial community structure also varied with soil horizons (i.e., depth). The results showed that the patterns for virus-host interactions shaped by the geochemical properties in the original environment were conserved or similar after in vitro nutrient stimulation. These findings suggest that short-term changes in trophic status alone may not significantly alter the balance of viral reproductive strategies in terrestrial ecosystems as in the antecedent environmental conditions that the host community has long adapted to, and other factors such as stress, host diversity or adaptation may be necessary to trigger community-level shifts in the interactions between viruses and hosts that responded most favorably to nutrient addition.
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Affiliation(s)
- Xiaolong Liang
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Yusong Wang
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, TN 37996, USA
| | - Ying Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning Province 110016, China
| | - Bingxue Li
- College of Land and Environment, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Mark Radosevich
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, TN 37996, USA.
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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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30
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Ismail MH, Michie KA, Goh YF, Noorian P, Kjelleberg S, Duggin IG, McDougald D, Rice SA. The Repressor C Protein, Pf4r, Controls Superinfection of Pseudomonas aeruginosa PAO1 by the Pf4 Filamentous Phage and Regulates Host Gene Expression. Viruses 2021; 13:1614. [PMID: 34452479 PMCID: PMC8402870 DOI: 10.3390/v13081614] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 12/17/2022] Open
Abstract
It has been shown that the filamentous phage, Pf4, plays an important role in biofilm development, stress tolerance, genetic variant formation and virulence in Pseudomonas aeruginosa PAO1. These behaviours are linked to the appearance of superinfective phage variants. Here, we have investigated the molecular mechanism of superinfection as well as how the Pf4 phage can control host gene expression to modulate host behaviours. Pf4 exists as a prophage in PAO1 and encodes a homologue of the P2 phage repressor C and was recently named Pf4r. Through a combination of molecular techniques, ChIPseq and transcriptomic analyses, we show a critical site in repressor C (Pf4r) where a mutation in the site, 788799A>G (Ser4Pro), causes Pf4r to lose its function as the immunity factor against reinfection by Pf4. X-ray crystal structure analysis shows that Pf4r forms symmetric homo-dimers homologous to the E.coli bacteriophage P2 RepC protein. A mutation, Pf4r*, associated with the superinfective Pf4r variant, found at the dimer interface, suggests dimer formation may be disrupted, which derepresses phage replication. This is supported by multi-angle light scattering (MALS) analysis, where the Pf4r* protein only forms monomers. The loss of dimerisation also explains the loss of Pf4r's immunity function. Phenotypic assays showed that Pf4r increased LasB activity and was also associated with a slight increase in the percentage of morphotypic variants. ChIPseq and transcriptomic analyses suggest that Pf4r also likely functions as a transcriptional regulator for other host genes. Collectively, these data suggest the mechanism by which filamentous phages play such an important role in P. aeruginosa biofilm development.
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Affiliation(s)
- Muhammad Hafiz Ismail
- Singapore Centre for Environmental Life Sciences Engineering, Singapore 637551, Singapore; (M.H.I.); (Y.F.G.); (S.K.); (D.M.)
- The School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Katharine A. Michie
- Structural Biology Facility, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, NSW 2052, Australia;
| | - Yu Fen Goh
- Singapore Centre for Environmental Life Sciences Engineering, Singapore 637551, Singapore; (M.H.I.); (Y.F.G.); (S.K.); (D.M.)
| | - Parisa Noorian
- The iThree Institute, The University of Technology Sydney, Sydney, NSW 2007, Australia; (P.N.); (I.G.D.)
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Singapore 637551, Singapore; (M.H.I.); (Y.F.G.); (S.K.); (D.M.)
- The School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Iain G. Duggin
- The iThree Institute, The University of Technology Sydney, Sydney, NSW 2007, Australia; (P.N.); (I.G.D.)
| | - Diane McDougald
- Singapore Centre for Environmental Life Sciences Engineering, Singapore 637551, Singapore; (M.H.I.); (Y.F.G.); (S.K.); (D.M.)
- The iThree Institute, The University of Technology Sydney, Sydney, NSW 2007, Australia; (P.N.); (I.G.D.)
| | - Scott A. Rice
- Singapore Centre for Environmental Life Sciences Engineering, Singapore 637551, Singapore; (M.H.I.); (Y.F.G.); (S.K.); (D.M.)
- The School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
- The iThree Institute, The University of Technology Sydney, Sydney, NSW 2007, Australia; (P.N.); (I.G.D.)
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31
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Brady A, Felipe-Ruiz A, Gallego Del Sol F, Marina A, Quiles-Puchalt N, Penadés JR. Molecular Basis of Lysis-Lysogeny Decisions in Gram-Positive Phages. Annu Rev Microbiol 2021; 75:563-581. [PMID: 34343015 DOI: 10.1146/annurev-micro-033121-020757] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Temperate bacteriophages (phages) are viruses of bacteria. Upon infection of a susceptible host, a temperate phage can establish either a lytic cycle that kills the host or a lysogenic cycle as a stable prophage. The life cycle pursued by an infecting temperate phage can have a significant impact not only on the individual host bacterium at the cellular level but also on bacterial communities and evolution in the ecosystem. Thus, understanding the decision processes of temperate phages is crucial. This review delves into the molecular mechanisms behind lysis-lysogeny decision-making in Gram-positive phages. We discuss a variety of molecular mechanisms and the genetic organization of these well-understood systems. By elucidating the strategies used by phages to make lysis-lysogeny decisions, we can improve our understanding of phage-host interactions, which is crucial for a variety of studies including bacterial evolution, community and ecosystem diversification, and phage therapeutics. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Aisling Brady
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom;
| | - Alonso Felipe-Ruiz
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 46010 Valencia, Spain;
| | - Francisca Gallego Del Sol
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 46010 Valencia, Spain;
| | - Alberto Marina
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 46010 Valencia, Spain;
| | - Nuria Quiles-Puchalt
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom;
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom; .,MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom;
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A Metzincin and TIMP-Like Protein Pair of a Phage Origin Sensitize Listeria monocytogenes to Phage Lysins and Other Cell Wall Targeting Agents. Microorganisms 2021; 9:microorganisms9061323. [PMID: 34207021 PMCID: PMC8235301 DOI: 10.3390/microorganisms9061323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 11/17/2022] Open
Abstract
Infection of mammalian cells by Listeria monocytogenes (Lm) was shown to be facilitated by its phage elements. In a search for additional phage remnants that play a role in Lm’s lifecycle, we identified a conserved locus containing two XRE regulators and a pair of genes encoding a secreted metzincin protease and a lipoprotein structurally similar to a TIMP-family metzincin inhibitor. We found that the XRE regulators act as a classic CI/Cro regulatory switch that regulates the expression of the metzincin and TIMP-like genes under intracellular growth conditions. We established that when these genes are expressed, their products alter Lm morphology and increase its sensitivity to phage mediated lysis, thereby enhancing virion release. Expression of these proteins also sensitized the bacteria to cell wall targeting compounds, implying that they modulate the cell wall structure. Our data indicate that these effects are mediated by the cleavage of the TIMP-like protein by the metzincin, and its subsequent release to the extracellular milieu. While the importance of this locus to Lm pathogenicity remains unclear, the observation that this phage-associated protein pair act upon the bacterial cell wall may hold promise in the field of antibiotic potentiation to combat antibiotic resistant bacterial pathogens.
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33
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12/111phiA Prophage Domestication Is Associated with Autoaggregation and Increased Ability to Produce Biofilm in Streptococcus agalactiae. Microorganisms 2021; 9:microorganisms9061112. [PMID: 34063935 PMCID: PMC8223999 DOI: 10.3390/microorganisms9061112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 01/11/2023] Open
Abstract
CC17 Streptococcus agalactiae carrying group-A prophages is increasingly responsible for neonatal infections. To investigate the impact of the genetic features of a group-A prophage, we first conducted an in silico analysis of the genome of 12/111phiA, a group-A prophage carried by a strain responsible for a bloodstream infection in a parturient. This revealed a Restriction Modification system, suggesting a prophage maintenance strategy and five ORFs of interest for the host and encoding a type II toxin antitoxin system RelB/YafQ, an endonuclease, an S-adenosylmethionine synthetase MetK, and an StrP-like adhesin. Using the WT strain cured from 12/111phiA and constructing deleted mutants for the ORFs of interest, and their complemented mutants, we demonstrated an impact of prophage features on growth characteristics, cell morphology and biofilm formation. Our findings argue in favor of 12/111phiA domestication by the host and a role of prophage features in cell autoaggregation, glycocalyx and biofilm formation. We suggest that lysogeny may promote GBS adaptation to the acid environment of the vagina, consequently colonizing and infecting neonates.
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34
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Pasechnek A, Rabinovich L, Stadnyuk O, Azulay G, Mioduser J, Argov T, Borovok I, Sigal N, Herskovits AA. Active Lysogeny in Listeria Monocytogenes Is a Bacteria-Phage Adaptive Response in the Mammalian Environment. Cell Rep 2021; 32:107956. [PMID: 32726621 PMCID: PMC7397523 DOI: 10.1016/j.celrep.2020.107956] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/05/2020] [Accepted: 07/02/2020] [Indexed: 01/20/2023] Open
Abstract
Some Listeria monocytogenes (Lm) strains harbor a prophage within the comK gene, which renders it inactive. During Lm infection of macrophage cells, the prophage turns into a molecular switch, promoting comK gene expression and therefore Lm intracellular growth. During this process, the prophage does not produce infective phages or cause bacterial lysis, suggesting it has acquired an adaptive behavior suited to the pathogenic lifestyle of its host. In this study, we demonstrate that this non-classical phage behavior, named active lysogeny, relies on a transcriptional response that is specific to the intracellular niche. While the prophage undergoes lytic induction, the process is arrested midway, preventing the transcription of the late genes. Further, we demonstrate key phage factors, such as LlgA transcription regulator and a DNA replicase, that support the phage adaptive behavior. This study provides molecular insights into the adaptation of phages to their pathogenic hosts, uncovering unusual cooperative interactions.
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Affiliation(s)
- Anna Pasechnek
- The School of Molecular Cell Biology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel- Aviv 69978, Israel
| | - Lev Rabinovich
- The School of Molecular Cell Biology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel- Aviv 69978, Israel
| | - Olga Stadnyuk
- The School of Molecular Cell Biology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel- Aviv 69978, Israel
| | - Gil Azulay
- The School of Molecular Cell Biology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel- Aviv 69978, Israel
| | - Jessica Mioduser
- The School of Molecular Cell Biology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel- Aviv 69978, Israel
| | - Tal Argov
- The School of Molecular Cell Biology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel- Aviv 69978, Israel
| | - Ilya Borovok
- The School of Molecular Cell Biology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel- Aviv 69978, Israel
| | - Nadejda Sigal
- The School of Molecular Cell Biology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel- Aviv 69978, Israel
| | - Anat A Herskovits
- The School of Molecular Cell Biology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel- Aviv 69978, Israel.
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35
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Das AK, Chichghare SA, Sharma SK, Kumar JPT, Singh S, Baranwal VK, Kumar A, Nerkar S. Genetic diversity and population structure of 'Candidatus Liberibacter asiaticus' associated with citrus Huanglongbing in India based on the prophage types. World J Microbiol Biotechnol 2021; 37:95. [PMID: 33963452 DOI: 10.1007/s11274-021-03057-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/19/2021] [Indexed: 11/30/2022]
Abstract
Huanglongbing (HLB), also known as 'citrus greening', is an extremely destructive disease of citrus worldwide. HLB is associated with three species of the fastidious proteobacterium, Candidatus Liberibacter asiaticus (CaLas), Ca. L. africanus and Ca. L. americanus with CaLas being the most widely distributed around the world and the only species detected and described so far in India, one of the major global citrus fruit producers. Prophages are highly dynamic components in the bacterial genome and play an important role in intraspecies variations. Three types of prophages, Type 1, Type 2 and Type 3 have been identified and described in CaLas so far. In the present study, 441 CaLas isolates sampled across 18 Indian states were used for prophage typing. Based on detection of three prophage types by PCR, all the eight probable combinations of CaLas prophages were identified, including single Type 1 (26.5%), single Type 2 (18.8%), single Type 3 (1.4%), Type 1 + Type 2 (20.4%), Type 1 + Type 3 (12.5%), Type 2 + Type 3 (4.8%), Type 1 + Type 2 + Type 3 (11.3%) and None type (4.3%). Prophage types were confirmed by PCR amplicon sequencing and subsequent phylogenetic analysis. By discovery of all 3 prophages and based on genetic identity and genetic distance, CaLas populations from eighteen citrus growing states were separated into two major Prophage Typing Groups (PTGs): PTG1 and PTG2. The PTG1 comprised of CaLas from North-West India and PTG2 from rest of the country (North-East, Central and South India), and both major groups were further divided into two (PTG1-A, PTG1-B) and three (PTG2-A, PTG2-B and PTG2-C) subgroups respectively. The findings of CaLas population patterns provide evidence for independent origins of HLB-associated CaLas. CRISPR (clustered regularly interspaced short palindromic repeats) array was also detected in CaLas isolates. This is the first report evaluating the genetic variation of a large population of CaLas bacterium in India using the PCR markers from the prophage regions which would certainly assist the ongoing HLB management efforts in India.
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Affiliation(s)
- Ashis K Das
- Plant Pathology Lab, ICAR-Central Citrus Research Institute, Amravati Road, Nagpur, 440033, India.
| | - Subham A Chichghare
- Plant Pathology Lab, ICAR-Central Citrus Research Institute, Amravati Road, Nagpur, 440033, India
| | - Susheel K Sharma
- ICAR Research Complex for NEH Region, Manipur Centre, Imphal, 795004, India
| | - J Prasanth Tej Kumar
- Plant Pathology Lab, ICAR-Central Citrus Research Institute, Amravati Road, Nagpur, 440033, India
| | - Salvinder Singh
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, 785013, India
| | - Virendra K Baranwal
- Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Ashok Kumar
- Plant Pathology Lab, ICAR-Central Citrus Research Institute, Amravati Road, Nagpur, 440033, India
| | - Sagar Nerkar
- Plant Pathology Lab, ICAR-Central Citrus Research Institute, Amravati Road, Nagpur, 440033, India
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36
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Łobocka M, Dąbrowska K, Górski A. Engineered Bacteriophage Therapeutics: Rationale, Challenges and Future. BioDrugs 2021; 35:255-280. [PMID: 33881767 PMCID: PMC8084836 DOI: 10.1007/s40259-021-00480-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2021] [Indexed: 12/20/2022]
Abstract
The current problems with increasing bacterial resistance to antibacterial therapies, resulting in a growing frequency of incurable bacterial infections, necessitates the acceleration of studies on antibacterials of a new generation that could offer an alternative to antibiotics or support their action. Bacteriophages (phages) can kill antibiotic-sensitive as well as antibiotic-resistant bacteria, and thus are a major subject of such studies. Their efficacy in curing bacterial infections has been demonstrated in in vivo experiments and in the clinic. Unlike antibiotics, phages have a narrow range of specificity, which makes them safe for commensal microbiota. However, targeting even only the most clinically relevant strains of pathogenic bacteria requires large collections of well characterized phages, whose specificity would cover all such strains. The environment is a rich source of diverse phages, but due to their complex relationships with bacteria and safety concerns, only some naturally occurring phages can be considered for therapeutic applications. Still, their number and diversity make a detailed characterization of all potentially promising phages virtually impossible. Moreover, no single phage combines all the features required of an ideal therapeutic agent. Additionally, the rapid acquisition of phage resistance by bacteria may make phages already approved for therapy ineffective and turn the search for environmental phages of better efficacy and new specificity into an endless race. An alternative strategy for acquiring phages with desired properties in a short time with minimal cost regarding their acquisition, characterization, and approval for therapy could be based on targeted genome modifications of phage isolates with known properties. The first example demonstrating the potential of this strategy in curing bacterial diseases resistant to traditional therapy is the recent successful treatment of a progressing disseminated Mycobacterium abscessus infection in a teenage patient with the use of an engineered phage. In this review, we briefly present current methods of phage genetic engineering, highlighting their advantages and disadvantages, and provide examples of genetically engineered phages with a modified host range, improved safety or antibacterial activity, and proven therapeutic efficacy. We also summarize novel uses of engineered phages not only for killing pathogenic bacteria, but also for in situ modification of human microbiota to attenuate symptoms of certain bacterial diseases and metabolic, immune, or mental disorders.
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Affiliation(s)
- Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland
| | - Krystyna Dąbrowska
- Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences, Wrocław, Poland
| | - Andrzej Górski
- Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences, Wrocław, Poland
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37
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Shi L, Qin J, Zheng H, Guo Y, Zhang H, Zhong Y, Yang C, Dong S, Yang F, Wu Y, Zhao G, Song Y, Yang R, Wang P, Cui Y. New Genotype of Yersinia pestis Found in Live Rodents in Yunnan Province, China. Front Microbiol 2021; 12:628335. [PMID: 33935990 PMCID: PMC8084289 DOI: 10.3389/fmicb.2021.628335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/24/2021] [Indexed: 12/11/2022] Open
Abstract
Yunnan Province, China is thought to be the original source of biovar Orientalis of Yersinia pestis, the causative agent of the third plague pandemic that has spread globally since the end of the 19th century. Although encompassing a large area of natural plague foci, Y. pestis strains have rarely been found in live rodents during surveillance in Yunnan, and most isolates are from rodent corpses and their fleas. In 2017, 10 Y. pestis strains were isolated from seven live rodents and three fleas in Heqing County of Yunnan. These strains were supposed to have low virulence to local rodents Eothenomys miletus and Apodemus chevrieri because the rodents were healthy and no dead animals were found in surrounding areas, as had occurred in previous epizootic disease. We performed microscopic and biochemical examinations of the isolates, and compared their whole-genome sequences and transcriptome with those of 10 high virulence Y. pestis strains that were isolated from nine rodents and one parasitic flea in adjacent city (Lijiang). We analyzed the phenotypic, genomic, and transcriptomic characteristics of live rodent isolates. The isolates formed a previously undefined monophyletic branch of Y. pestis that was named 1.IN5. Six SNPs, two indels, and one copy number variation were detected between live rodent isolates and the high virulence neighbors. No obvious functional consequence of these variations was found according to the known annotation information. Among genes which expression differential in the live rodent isolates compared to their high virulent neighbors, we found five iron transfer related ones that were significant up-regulated (| log2 (FC) | > 1, p.adjust < 0.05), indicating these genes may be related to the low-virulence phenotype. The novel genotype of Y. pestis reported here provides further insights into the evolution and spread of plague as well as clues that may help to decipher the virulence mechanism of this notorious pathogen.
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Affiliation(s)
- Liyuan Shi
- Yunnan Institute of Endemic Diseases Control and Prevention, Dali, China
| | - Jingliang Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Hongyuan Zheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ying Guo
- Yunnan Institute of Endemic Diseases Control and Prevention, Dali, China
| | - Haipeng Zhang
- Yunnan Institute of Endemic Diseases Control and Prevention, Dali, China
| | - Youhong Zhong
- Yunnan Institute of Endemic Diseases Control and Prevention, Dali, China
| | - Chao Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shanshan Dong
- Yunnan Institute of Endemic Diseases Control and Prevention, Dali, China
| | - Fengyi Yang
- Yunnan Institute of Endemic Diseases Control and Prevention, Dali, China
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Guangyu Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Peng Wang
- Yunnan Institute of Endemic Diseases Control and Prevention, Dali, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,School of Basic Medical Sciences, Anhui Medical University, Hefei, China
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38
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Abril AG, Carrera M, Böhme K, Barros-Velázquez J, Cañas B, Rama JLR, Villa TG, Calo-Mata P. Proteomic Characterization of Bacteriophage Peptides from the Mastitis Producer Staphylococcus aureus by LC-ESI-MS/MS and the Bacteriophage Phylogenomic Analysis. Foods 2021; 10:799. [PMID: 33917943 PMCID: PMC8068337 DOI: 10.3390/foods10040799] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/28/2021] [Accepted: 04/06/2021] [Indexed: 01/21/2023] Open
Abstract
The present work describes LC-ESI-MS/MS MS (liquid chromatography-electrospray ionization-tandem mass spectrometry) analyses of tryptic digestion peptides from phages that infect mastitis-causing Staphylococcus aureus isolated from dairy products. A total of 1933 nonredundant peptides belonging to 1282 proteins were identified and analyzed. Among them, 79 staphylococcal peptides from phages were confirmed. These peptides belong to proteins such as phage repressors, structural phage proteins, uncharacterized phage proteins and complement inhibitors. Moreover, eighteen of the phage origin peptides found were specific to S. aureus strains. These diagnostic peptides could be useful for the identification and characterization of S. aureus strains that cause mastitis. Furthermore, a study of bacteriophage phylogeny and the relationship among the identified phage peptides and the bacteria they infect was also performed. The results show the specific peptides that are present in closely related phages and the existing links between bacteriophage phylogeny and the respective Staphylococcus spp. infected.
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Affiliation(s)
- Ana G. Abril
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain; (A.G.A.); (J.-L.R.R.); (T.G.V.)
| | - Mónica Carrera
- Department of Food Technology, Spanish National Research Council, Marine Research Institute, 36208 Vigo, Spain
| | - Karola Böhme
- Agroalimentary Technological Center of Lugo, 27002 Lugo, Spain;
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, 27002 Lugo, Spain;
| | - Benito Cañas
- Department of Analytical Chemistry, Complutense University of Madrid, 28040 Madrid, Spain;
| | - José-Luis R. Rama
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain; (A.G.A.); (J.-L.R.R.); (T.G.V.)
| | - Tomás G. Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain; (A.G.A.); (J.-L.R.R.); (T.G.V.)
| | - Pilar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, 27002 Lugo, Spain;
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39
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Yilmaz B, Mooser C, Keller I, Li H, Zimmermann J, Bosshard L, Fuhrer T, Gomez de Agüero M, Trigo NF, Tschanz-Lischer H, Limenitakis JP, Hardt WD, McCoy KD, Stecher B, Excoffier L, Sauer U, Ganal-Vonarburg SC, Macpherson AJ. Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice. Cell Host Microbe 2021; 29:650-663.e9. [PMID: 33662276 DOI: 10.1016/j.chom.2021.02.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/23/2020] [Accepted: 01/28/2021] [Indexed: 12/18/2022]
Abstract
Isobiotic mice, with an identical stable microbiota composition, potentially allow models of host-microbial mutualism to be studied over time and between different laboratories. To understand microbiota evolution in these models, we carried out a 6-year experiment in mice colonized with 12 representative taxa. Increased non-synonymous to synonymous mutation rates indicate positive selection in multiple taxa, particularly for genes annotated for nutrient acquisition or replication. Microbial sub-strains that evolved within a single taxon can stably coexist, consistent with niche partitioning of ecotypes in the complex intestinal environment. Dietary shifts trigger rapid transcriptional adaptation to macronutrient and micronutrient changes in individual taxa and alterations in taxa biomass. The proportions of different sub-strains are also rapidly altered after dietary shift. This indicates that microbial taxa within a mouse colony adapt to changes in the intestinal environment by long-term genomic positive selection and short-term effects of transcriptional reprogramming and adjustments in sub-strain proportions.
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Affiliation(s)
- Bahtiyar Yilmaz
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Catherine Mooser
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Irene Keller
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, 3012, Switzerland
| | - Hai Li
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Jakob Zimmermann
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Lars Bosshard
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, 3012, Switzerland; CMPG, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, 8093 Zürich, Switzerland
| | - Mercedes Gomez de Agüero
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Nerea Fernandez Trigo
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Heidi Tschanz-Lischer
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, 3012, Switzerland
| | - Julien P Limenitakis
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | | | - Kathy D McCoy
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Bärbel Stecher
- Max-von-Pettenkofer Institute, LMU Munich, 80336 Munich, Germany; German Center for Infection Research (DZIF), partner site LMU Munich, 80539 Munich, Germany
| | - Laurent Excoffier
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, 3012, Switzerland; CMPG, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, 8093 Zürich, Switzerland
| | - Stephanie C Ganal-Vonarburg
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Andrew J Macpherson
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland.
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40
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Turkington CJR, Varadan AC, Grenier SF, Grasis JA. The Viral Janus: Viruses as Aetiological Agents and Treatment Options in Colorectal Cancer. Front Cell Infect Microbiol 2021; 10:601573. [PMID: 33489934 PMCID: PMC7817644 DOI: 10.3389/fcimb.2020.601573] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/23/2020] [Indexed: 12/24/2022] Open
Abstract
In recent years, our understanding of the importance of microorganisms on and within our bodies has been revolutionized by the ability to characterize entire microbial communities. No more so is this true than in cases of disease. Community studies have revealed strong associations between microbial populations and disease states where such concomitance was previously absent from aetiology: including in cancers. The study of viruses, in particular, has benefited from the development of new community profiling techniques and we are now realising that their prominence within our physiology is nearly as broad as the diversity of the organisms themselves. Here, we examine the relationship between viruses and colorectal cancer (CRC), the leading cause of gastrointestinal cancer-related death worldwide. In CRC, viruses have been suggested to be involved in oncogenesis both directly, through infection of our cells, and indirectly, through modulating the composition of bacterial communities. Interestingly though, these characteristics have also led to their examination from another perspective—as options for treatment. Advances in our understanding of molecular and viral biology have caused many to look at viruses as potential modular biotherapeutics, where deleterious characteristics can be tamed and desirable characteristics exploited. In this article, we will explore both of these perspectives, covering how viral infections and involvement in microbiome dynamics may contribute to CRC, and examine ways in which viruses themselves could be harnessed to treat the very condition their contemporaries may have had a hand in creating.
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Affiliation(s)
| | - Ambarish C Varadan
- School of Natural Sciences, University of California Merced, Merced, CA, United States
| | - Shea F Grenier
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Juris A Grasis
- School of Natural Sciences, University of California Merced, Merced, CA, United States
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41
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Benler S, Koonin EV. Phage lysis‐lysogeny switches and programmed cell death: Danse macabre. Bioessays 2020; 42:e2000114. [DOI: 10.1002/bies.202000114] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/25/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Sean Benler
- National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bethesda Maryland USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bethesda Maryland USA
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42
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Kreienbaum M, Dörrich AK, Brandt D, Schmid NE, Leonhard T, Hager F, Brenzinger S, Hahn J, Glatter T, Ruwe M, Briegel A, Kalinowski J, Thormann KM. Isolation and Characterization of Shewanella Phage Thanatos Infecting and Lysing Shewanella oneidensis and Promoting Nascent Biofilm Formation. Front Microbiol 2020; 11:573260. [PMID: 33072035 PMCID: PMC7530303 DOI: 10.3389/fmicb.2020.573260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/27/2020] [Indexed: 01/21/2023] Open
Abstract
Species of the genus Shewanella are widespread in nature in various habitats, however, little is known about phages affecting Shewanella sp. Here, we report the isolation of phages from diverse freshwater environments that infect and lyse strains of Shewanella oneidensis and other Shewanella sp. Sequence analysis and microscopic imaging strongly indicate that these phages form a so far unclassified genus, now named Shewanella phage Thanatos, which can be positioned within the subfamily of Tevenvirinae (Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Tevenvirinae). We characterized one member of this group in more detail using S. oneidensis MR-1 as a host. Shewanella phage Thanatos-1 possesses a prolate icosahedral capsule of about 110 nm in height and 70 nm in width and a tail of about 95 nm in length. The dsDNA genome exhibits a GC content of about 34.5%, has a size of 160.6 kbp and encodes about 206 proteins (92 with an annotated putative function) and two tRNAs. Out of those 206, MS analyses identified about 155 phage proteins in PEG-precipitated samples of infected cells. Phage attachment likely requires the outer lipopolysaccharide of S. oneidensis, narrowing the phage's host range. Under the applied conditions, about 20 novel phage particles per cell were produced after a latent period of approximately 40 min, which are stable at a pH range from 4 to 12 and resist temperatures up to 55°C for at least 24 h. Addition of Thanatos to S. oneidensis results in partial dissolution of established biofilms, however, early exposure of planktonic cells to Thanatos significantly enhances biofilm formation. Taken together, we identified a novel genus of Myophages affecting S. oneidensis communities in different ways.
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Affiliation(s)
- Maximilian Kreienbaum
- Department of Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Anja K Dörrich
- Department of Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - David Brandt
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Nicole E Schmid
- Department of Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Tabea Leonhard
- Department of Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Fabian Hager
- Department of Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Susanne Brenzinger
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, Netherlands
| | - Julia Hahn
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Timo Glatter
- Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Matthias Ruwe
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Ariane Briegel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, Netherlands
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Kai M Thormann
- Department of Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
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43
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Horiuk Y, Horiuk V, Kukhtyn M, Tsvihun A, Kernychnyi S. Characterization of lytic activity of Phage SAvB14 on Staphylococcus aureus variant bovis. J Adv Vet Anim Res 2020; 7:509-513. [PMID: 33005677 PMCID: PMC7521818 DOI: 10.5455/javar.2020.g447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/02/2020] [Accepted: 04/08/2020] [Indexed: 12/18/2022] Open
Abstract
Objective The objective of this study was to investigate the intensity of phage infection caused by Phage SAvB14, which was isolated from dairy farms, depending on the initial number of Staphylococcus aureus cells in the medium. Material and methods To evaluate the impact of the viable bacteria S. aureus var. bovis on the intensity of phage infection caused by Phage SAvB14, 1 mg of phagolysate (phage titer 105 CFU/ ml) was introduced in 9 ml of nutrient broth with an appropriate amount of daily culture of S. aureus var. bovis under study. The number of viable staphylococci was determined by total viable count/ml. Results In this experiment, we found that the intensity of phages lytic activity was dependent on the number of sensitive bacterial cells in the volume of the culture medium. Effective phage therapy requires a high concentration of phages in the medium (inflammation foci) for rapid contact of the virus with bacteria. Conclusion When developing a phage drug to treat subclinical mastitis, it is necessary to increase the phage titer in the drug or its dosage compared to the clinical form, as there is a lower probability of phage contact with a susceptible microbial cell. Besides, at a high concentration of bacteria, there is a gradual decrease in nutrients in the medium, resulting in phages going back to the condition of lysogeny.
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Affiliation(s)
- Yulia Horiuk
- Faculty of Veterinary Medicine and Technologies in Livestock, Department of Infectious and Parasitic Diseases, State Agrarian and Engineering University in Podilya, Kamianets-Podilskyi, Ukraine
| | - Victor Horiuk
- Faculty of Veterinary Medicine and Technologies in Livestock, Department of Veterinary Obstetrics, Pathology and Surgery, State Agrarian and Engineering University in Podilya, Kamianets-Podilskyi, Ukraine
| | - Mykola Kukhtyn
- Faculty of Engineering of Machines, Structures and Technologies, Department of Food Biotechnology and Chemistry, Ternopil Ivan Pului National Technical University, Ternopil, Ukraine
| | - Anatoliy Tsvihun
- Faculty of Veterinary Medicine and Technologies in Livestock, Department of Animal Feeding, Breeding and Feed Technology, State Agrarian and Engineering University in Podilya, Kamianets-Podilskyi, Ukraine
| | - Sergiy Kernychnyi
- Faculty of Veterinary Medicine and Technologies in Livestock, Department of Veterinary Obstetrics, Pathology and Surgery, State Agrarian and Engineering University in Podilya, Kamianets-Podilskyi, Ukraine
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44
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Gilcrease E, Williams R, Goel R. Evaluating the effect of silver nanoparticles on bacteriophage lytic infection cycle-a mechanistic understanding. WATER RESEARCH 2020; 181:115900. [PMID: 32504909 DOI: 10.1016/j.watres.2020.115900] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 04/10/2020] [Accepted: 04/29/2020] [Indexed: 06/11/2023]
Abstract
Bacteriophages and engineered nano-material (AgNPS) interactions is a relatively unexplored area of research. To answer the fundamental question whether bacteriophage lytic growth cycle is affected by the presence of AgNPs, laboratory experiments were performed with phages of Klebsiella pneumoniae, Delftia tsuruhatensis, Salmonella typhimurium, and Shigella flexneri using silver nanoparticles (AgNPs) with coating materials. One-step growth curves of bacteriophages indicated that the presence of these nanoparticles, and the associated ions of silver, produced pronounced effects on the lytic infection of certain bacteriophages. Effects included 96% reductions in post-infection phage yield in terms of plaque forming units (PFUs) after phages were incubated with silver nanoparticles and 28%-43% reductions from the presence of Ag+ alone. However, when Klebsiella pneumonia phage KL and Salmonella typhimurium phage Det7 were exposed to silver nanoparticles coated with poly-N-vinyl-2 pyrrolidone (PVP), an increase in final phage yield by as much as 250% was observed compared with the same phage not incubated with nanoparticles. A proposed mechanism, observed by transmission electron microscopy and verified using synthetic biology by which the nanoparticle binding phenotype can be produced, is that the binding of metal nanomaterial to phage virions results in potentially inhibitory effects. This binding was found to be dependent on the presence of exposed positively charged C-terminal amino-acid residues on the phage capsid surface, implied at first by amino-acid sequence comparisons between capsid proteins of the different phages used in this study. This was then proven experimentally using targeted DNA editing methods to fuse positive charged amino-acid residues to the coat protein C-terminus of non-binding phage. This induced the AgNP binding phenotype, as observed by TEM, DLS size measurements, and growth curve data that show the mutant constructs to be functionally inhibited after exposure to AgNPs. This research sets up a first platform for further research in the unexplored area of phage and AgNP interactions and provides useful findings.
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Affiliation(s)
- Eddie Gilcrease
- Department of Civil and Environmental Engineering, University of Utah, UT, USA
| | - Ryan Williams
- Department of Civil and Environmental Engineering, University of Utah, UT, USA
| | - Ramesh Goel
- Department of Civil and Environmental Engineering, University of Utah, UT, USA.
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45
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Osuna BA, Karambelkar S, Mahendra C, Christie KA, Garcia B, Davidson AR, Kleinstiver BP, Kilcher S, Bondy-Denomy J. Listeria Phages Induce Cas9 Degradation to Protect Lysogenic Genomes. Cell Host Microbe 2020; 28:31-40.e9. [DOI: 10.1016/j.chom.2020.04.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 03/05/2020] [Accepted: 03/31/2020] [Indexed: 12/26/2022]
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46
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Abril AG, Carrera M, Böhme K, Barros-Velázquez J, Cañas B, Rama JLR, Villa TG, Calo-Mata P. Characterization of Bacteriophage Peptides of Pathogenic Streptococcus by LC-ESI-MS/MS: Bacteriophage Phylogenomics and Their Relationship to Their Host. Front Microbiol 2020; 11:1241. [PMID: 32582130 PMCID: PMC7296060 DOI: 10.3389/fmicb.2020.01241] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/14/2020] [Indexed: 01/21/2023] Open
Abstract
The present work focuses on LC-ESI-MS/MS (liquid chromatography-electrospray ionization-tandem mass spectrometry) analysis of phage-origin tryptic digestion peptides from mastitis-causing Streptococcus spp. isolated from milk. A total of 2,546 non-redundant peptides belonging to 1,890 proteins were identified and analyzed. Among them, 65 phage-origin peptides were determined as specific Streptococcus spp. peptides. These peptides belong to proteins such as phage repressors, phage endopeptidases, structural phage proteins, and uncharacterized phage proteins. Studies involving bacteriophage phylogeny and the relationship between phages encoding the peptides determined and the bacteria they infect were also performed. The results show how specific peptides are present in closely related phages, and a link exists between bacteriophage phylogeny and the Streptococcus spp. they infect. Moreover, the phage peptide M∗ATNLGQAYVQIM∗PSAK is unique and specific for Streptococcus agalactiae. These results revealed that diagnostic peptides, among others, could be useful for the identification and characterization of mastitis-causing Streptococcus spp., particularly peptides that belong to specific functional proteins, such as phage-origin proteins, because of their specificity to bacterial hosts.
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Affiliation(s)
- Ana G. Abril
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Mónica Carrera
- Department of Food Technology, Spanish National Research Council, Marine Research Institute, Vigo, Spain
| | - Karola Böhme
- Agroalimentary Technological Center of Lugo, Lugo, Spain
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Lugo, Spain
| | - Benito Cañas
- Department of Analytical Chemistry, Complutense University of Madrid, Madrid, Spain
| | - Jose L. R. Rama
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Tomás G. Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Pilar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Lugo, Spain
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47
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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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48
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Song W, Sun HX, Zhang C, Cheng L, Peng Y, Deng Z, Wang D, Wang Y, Hu M, Liu W, Yang H, Shen Y, Li J, You L, Xiao M. Prophage Hunter: an integrative hunting tool for active prophages. Nucleic Acids Res 2020; 47:W74-W80. [PMID: 31114893 PMCID: PMC6602508 DOI: 10.1093/nar/gkz380] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/03/2019] [Accepted: 05/17/2019] [Indexed: 01/21/2023] Open
Abstract
Identifying active prophages is critical for studying coevolution of phage and bacteria, investigating phage physiology and biochemistry, and engineering designer phages for diverse applications. We present Prophage Hunter, a tool aimed at hunting for active prophages from whole genome assembly of bacteria. Combining sequence similarity-based matching and genetic features-based machine learning classification, we developed a novel scoring system that exhibits higher accuracy than current tools in predicting active prophages on the validation datasets. The option of skipping similarity matching is also available so that there's higher chance for novel phages to be discovered. Prophage Hunter provides a one-stop web service to extract prophage genomes from bacterial genomes, evaluate the activity of the prophages, identify phylogenetically related phages, and annotate the function of phage proteins. Prophage Hunter is freely available at https://pro-hunter.bgi.com/.
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Affiliation(s)
- Wenchen Song
- BGI-Shenzhen, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China.,Department of Basic Medical Sciences, Qingdao University, Qingdao 266071, China
| | - Hai-Xi Sun
- BGI-Shenzhen, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China
| | - Carolyn Zhang
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Li Cheng
- BGI-Shenzhen, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China.,South China University of Technology, Guangzhou, Guangdong 510640, China
| | - Ye Peng
- BGI-Shenzhen, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China.,South China University of Technology, Guangzhou, Guangdong 510640, China
| | - Ziqing Deng
- BGI-Shenzhen, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China
| | - Dan Wang
- BGI-Shenzhen, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China
| | - Yun Wang
- BGI-Shenzhen, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China
| | - Ming Hu
- Department of Basic Medical Sciences, Qingdao University, Qingdao 266071, China
| | - Wenen Liu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China
| | - Yue Shen
- BGI-Shenzhen, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China
| | - Junhua Li
- BGI-Shenzhen, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China.,South China University of Technology, Guangzhou, Guangdong 510640, China
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27708, USA
| | - Minfeng Xiao
- BGI-Shenzhen, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China
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49
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Bleriot I, Trastoy R, Blasco L, Fernández-Cuenca F, Ambroa A, Fernández-García L, Pacios O, Perez-Nadales E, Torre-Cisneros J, Oteo-Iglesias J, Navarro F, Miró E, Pascual A, Bou G, Martínez-Martínez L, Tomas M. Genomic analysis of 40 prophages located in the genomes of 16 carbapenemase-producing clinical strains of Klebsiella pneumoniae. Microb Genom 2020; 6:e000369. [PMID: 32375972 PMCID: PMC7371120 DOI: 10.1099/mgen.0.000369] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/31/2020] [Indexed: 12/12/2022] Open
Abstract
Klebsiella pneumoniae is the clinically most important species within the genus Klebsiella and, as a result of the continuous emergence of multi-drug resistant (MDR) strains, the cause of severe nosocomial infections. The decline in the effectiveness of antibiotic treatments for infections caused by MDR bacteria has generated particular interest in the study of bacteriophages. In this study, we characterized a total of 40 temperate bacteriophages (prophages) with a genome range of 11.454-84.199 kb, predicted from 16 carbapenemase-producing clinical strains of K. pneumoniae belonging to different sequence types, previously identified by multilocus sequence typing. These prophages were grouped into the three families in the order Caudovirales (27 prophages belonging to the family Myoviridae, 10 prophages belonging to the family Siphoviridae and 3 prophages belonging to the family Podoviridae). Genomic comparison of the 40 prophage genomes led to the identification of four prophages isolated from different strains and of genome sizes of around 33.3, 36.1, 39.6 and 42.6 kb. These prophages showed sequence similarities (query cover >90 %, identity >99.9 %) with international Microbe Versus Phage (MVP) (http://mvp.medgenius.info/home) clusters 4762, 4901, 3499 and 4280, respectively. Phylogenetic analysis revealed the evolutionary proximity among the members of the four groups of the most frequently identified prophages in the bacterial genomes studied (33.3, 36.1, 39.6 and 42.6 kb), with bootstrap values of 100 %. This allowed the prophages to be classified into three clusters: A, B and C. Interestingly, these temperate bacteriophages did not infect the highest number of strains as indicated by a host-range assay, these results could be explained by the development of superinfection exclusion mechanisms. In addition, bioinformatic analysis of the 40 identified prophages revealed the presence of 2363 proteins. In total, 59.7 % of the proteins identified had a predicted function, mainly involving viral structure, transcription, replication and regulation (lysogenic/lysis). Interestingly, some proteins had putative functions associated with bacterial virulence (toxin expression and efflux pump regulators), phage defence profiles such as toxin-antitoxin modules, an anti-CRISPR/Cas9 protein, TerB protein (from terZABCDE operon) and methyltransferase proteins.
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Affiliation(s)
- Ines Bleriot
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
| | - Rocío Trastoy
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
| | - Lucia Blasco
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
| | - Felipe Fernández-Cuenca
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Clinical Unit for Infectious Diseases, Microbiology and Preventive Medicine, Hospital Universitario Virgen Macarena. Deparment of Microbiology and Medicine, University of Seville, Seville, Spain
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
| | - Antón Ambroa
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
| | - Laura Fernández-García
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
| | - Olga Pacios
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
| | - Elena Perez-Nadales
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
- Microbiology Unit, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), University Hospital Reina Sofía, University of Córdoba, Cordoba, Spain
| | - Julian Torre-Cisneros
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
- Microbiology Unit, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), University Hospital Reina Sofía, University of Córdoba, Cordoba, Spain
| | - Jesús Oteo-Iglesias
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
- Reference and Research Laboratory for Antibiotic Resistance and Health Care Infections, National Centre for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain
| | - Ferran Navarro
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Microbiology Department, Sant Pau Hospital, Autonomous University of Barcelona (Bellaterra), Barcelona, Spain
| | - Elisenda Miró
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Microbiology Department, Sant Pau Hospital, Autonomous University of Barcelona (Bellaterra), Barcelona, Spain
| | - Alvaro Pascual
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Clinical Unit for Infectious Diseases, Microbiology and Preventive Medicine, Hospital Universitario Virgen Macarena. Deparment of Microbiology and Medicine, University of Seville, Seville, Spain
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
| | - German Bou
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
| | - Luis Martínez-Martínez
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
- Microbiology Unit, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), University Hospital Reina Sofía, University of Córdoba, Cordoba, Spain
| | - Maria Tomas
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
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Abril AG, Rama JLR, Sánchez-Pérez A, Villa TG. Prokaryotic sigma factors and their transcriptional counterparts in Archaea and Eukarya. Appl Microbiol Biotechnol 2020; 104:4289-4302. [PMID: 32232532 DOI: 10.1007/s00253-020-10577-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/13/2020] [Accepted: 03/22/2020] [Indexed: 12/18/2022]
Abstract
RNA polymerases (RNAPs) carry out transcription in the three domains of life, Bacteria, Archaea, and Eukarya. Transcription initiation is highly regulated by a variety of transcription factors, whose number and subunit complexity increase during evolution. This process is regulated in Bacteria by the σ factor, while the three eukaryotic RNAPs require a complex set of transcription factors (TFs) and a TATA-binding protein (TBP). The archaeal transcription system appears to be an ancestral version of the eukaryotic RNAPII, requiring transcription factor B (TFB), TBP, and transcription factor E (TFE). The function of the bacterial sigma (σ) factor has been correlated to the roles played by the eukaryotic RNAP II and the archaeal RNAP. In addition, σ factors, TFB, and TFIIB all contain multiple DNA binding helix-turn-helix (HTH) structural motifs; although TFIIB and TFB display two HTH domains, while the bacterial σ factor spans 4 HTH motifs. The sequence similarities and structure alignments of the bacterial σ factor, eukaryotic TFIIB, and archaeal TFB evidence that these three proteins are homologs.Key Points• Transcription initiation is highly regulated by TFs.• Transcription is finely regulated in all domains of life by different sets of TFs.• Specific TFs in Bacteria, Eukarya and Archaea are homologs.
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Affiliation(s)
- Ana G Abril
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Jose Luis R Rama
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - A Sánchez-Pérez
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW, 2006, Australia
| | - Tomás G Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain.
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