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Kobakhidze S, Koulouris S, Kakabadze N, Kotetishvili M. Genetic recombination-mediated evolutionary interactions between phages of potential industrial importance and prophages of their hosts within or across the domains of Escherichia, Listeria, Salmonella, Campylobacter, and Staphylococcus. BMC Microbiol 2024; 24:155. [PMID: 38704526 PMCID: PMC11069274 DOI: 10.1186/s12866-024-03312-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 04/23/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND The in-depth understanding of the role of lateral genetic transfer (LGT) in phage-prophage interactions is essential to rationalizing phage applications for human and animal therapy, as well as for food and environmental safety. This in silico study aimed to detect LGT between phages of potential industrial importance and their hosts. METHODS A large array of genetic recombination detection algorithms, implemented in SplitsTree and RDP4, was applied to detect LGT between various Escherichia, Listeria, Salmonella, Campylobacter, Staphylococcus, Pseudomonas, and Vibrio phages and their hosts. PHASTER and RAST were employed respectively to identify prophages across the host genome and to annotate LGT-affected genes with unknown functions. PhageAI was used to gain deeper insights into the life cycle history of recombined phages. RESULTS The split decomposition inferences (bootstrap values: 91.3-100; fit: 91.433-100), coupled with the Phi (0.0-2.836E-12) and RDP4 (P being well below 0.05) statistics, provided strong evidence for LGT between certain Escherichia, Listeria, Salmonella, and Campylobacter virulent phages and prophages of their hosts. The LGT events entailed mainly the phage genes encoding for hypothetical proteins, while some of these genetic loci appeared to have been affected even by intergeneric recombination in specific E. coli and S. enterica virulent phages when interacting with their host prophages. Moreover, it is shown that certain L. monocytogenes virulent phages could serve at least as the donors of the gene loci, involved in encoding for the basal promoter specificity factor, for L. monocytogenes. In contrast, the large genetic clusters were determined to have been simultaneously exchanged by many S. aureus prophages and some Staphylococcus temperate phages proposed earlier as potential therapeutic candidates (in their native or modified state). The above genetic clusters were found to encompass multiple genes encoding for various proteins, such as e.g., phage tail proteins, the capsid and scaffold proteins, holins, and transcriptional terminator proteins. CONCLUSIONS It is suggested that phage-prophage interactions, mediated by LGT (including intergeneric recombination), can have a far-reaching impact on the co-evolutionary trajectories of industrial phages and their hosts especially when excessively present across microbially rich environments.
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Affiliation(s)
- Saba Kobakhidze
- Hygiene and Medical Ecology, G. Natadze Scientific-Research Institute of Sanitary, 78 D. Uznadze St. 0102, Tbilisi, Georgia
- Faculty of Medicine, Iv. Javakhishvili Tbilisi State University, 1 Ilia Chavchavadze Ave. 0179, Tbilisi, Georgia
| | - Stylianos Koulouris
- Directorate General for Health and Food Safety (DG-SANTE), European Commission, 1049, Bruxelles/Brussel, Belgium
| | - Nata Kakabadze
- Hygiene and Medical Ecology, G. Natadze Scientific-Research Institute of Sanitary, 78 D. Uznadze St. 0102, Tbilisi, Georgia
| | - Mamuka Kotetishvili
- Hygiene and Medical Ecology, G. Natadze Scientific-Research Institute of Sanitary, 78 D. Uznadze St. 0102, Tbilisi, Georgia.
- Scientific Research Institute, School of Science and Technology, the University of Georgia, 77a M. Kostava St., 0171, Tbilisi, Georgia.
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Zhong Q, Liao B, Liu J, Shen W, Wang J, Wei L, Ma Y, Dong PT, Bor B, McLean JS, Chang Y, Shi W, Cen L, Wu M, Liu J, Li Y, He X, Le S. Episymbiotic Saccharibacteria TM7x modulates the susceptibility of its host bacteria to phage infection and promotes their coexistence. Proc Natl Acad Sci U S A 2024; 121:e2319790121. [PMID: 38593079 PMCID: PMC11032452 DOI: 10.1073/pnas.2319790121] [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: 11/10/2023] [Accepted: 02/21/2024] [Indexed: 04/11/2024] Open
Abstract
Bacteriophages (phages) play critical roles in modulating microbial ecology. Within the human microbiome, the factors influencing the long-term coexistence of phages and bacteria remain poorly investigated. Saccharibacteria (formerly TM7) are ubiquitous members of the human oral microbiome. These ultrasmall bacteria form episymbiotic relationships with their host bacteria and impact their physiology. Here, we showed that during surface-associated growth, a human oral Saccharibacteria isolate (named TM7x) protects its host bacterium, a Schaalia odontolytica strain (named XH001) against lytic phage LC001 predation. RNA-Sequencing analysis identified in XH001 a gene cluster with predicted functions involved in the biogenesis of cell wall polysaccharides (CWP), whose expression is significantly down-regulated when forming a symbiosis with TM7x. Through genetic work, we experimentally demonstrated the impact of the expression of this CWP gene cluster on bacterial-phage interaction by affecting phage binding. In vitro coevolution experiments further showed that the heterogeneous populations of TM7x-associated and TM7x-free XH001, which display differential susceptibility to LC001 predation, promote bacteria and phage coexistence. Our study highlights the tripartite interaction between the bacterium, episymbiont, and phage. More importantly, we present a mechanism, i.e., episymbiont-mediated modulation of gene expression in host bacteria, which impacts their susceptibility to phage predation and contributes to the formation of "source-sink" dynamics between phage and bacteria in biofilm, promoting their long-term coexistence within the human microbiome.
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Affiliation(s)
- Qiu Zhong
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing400038, China
| | - Binyou Liao
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan610041, China
| | - Jiazhen Liu
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing400038, China
| | - Wei Shen
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, the Second Affiliated Hospital of Chongqing Medical University, Chongqing401336, China
| | - Jing Wang
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing400038, China
| | - Leilei Wei
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing400038, China
| | - Yansong Ma
- Department of Orthodontics, Capital Medical University, Beijing100050, China
| | - Pu-Ting Dong
- Department of Microbiology, The American Dental Association Forsyth Institute, Cambridge, MA02142
| | - Batbileg Bor
- Department of Microbiology, The American Dental Association Forsyth Institute, Cambridge, MA02142
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA02115
| | - Jeffrey S. McLean
- Department of Periodontics, University of Washington, Seattle, WA98119
- Department of Microbiology, University of Washington, Seattle, WA98195
| | - Yunjie Chang
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang310058, China
- Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang310058, China
| | - Wenyuan Shi
- Department of Microbiology, The American Dental Association Forsyth Institute, Cambridge, MA02142
| | - Lujia Cen
- Department of Microbiology, The American Dental Association Forsyth Institute, Cambridge, MA02142
| | - Miaomiao Wu
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan610041, China
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT06536
| | - Yan Li
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan610041, China
| | - Xuesong He
- Department of Microbiology, The American Dental Association Forsyth Institute, Cambridge, MA02142
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA02115
| | - Shuai Le
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing400038, China
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3
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Guérin H, Courtin P, Guillot A, Péchoux C, Mahony J, van Sinderen D, Kulakauskas S, Cambillau C, Touzé T, Chapot-Chartier MP. Molecular mechanisms underlying the structural diversity of rhamnose-rich cell wall polysaccharides in lactococci. J Biol Chem 2024; 300:105578. [PMID: 38110036 PMCID: PMC10821137 DOI: 10.1016/j.jbc.2023.105578] [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: 10/18/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023] Open
Abstract
In Gram-positive bacteria, cell wall polysaccharides (CWPS) play critical roles in bacterial cell wall homeostasis and bacterial interactions with their immediate surroundings. In lactococci, CWPS consist of two components: a conserved rhamnan embedded in the peptidoglycan layer and a surface-exposed polysaccharide pellicle (PSP), which are linked together to form a large rhamnose-rich CWPS (Rha-CWPS). PSP, whose structure varies from strain to strain, is a receptor for many bacteriophages infecting lactococci. Here, we examined the first two steps of PSP biosynthesis, using in vitro enzymatic tests with lipid acceptor substrates combined with LC-MS analysis, AlfaFold2 modeling of protein 3D-structure, complementation experiments, and phage assays. We show that the PSP repeat unit is assembled on an undecaprenyl-monophosphate (C55P) lipid intermediate. Synthesis is initiated by the WpsA/WpsB complex with GlcNAc-P-C55 synthase activity and the PSP precursor GlcNAc-P-C55 is then elongated by specific glycosyltransferases that vary among lactococcal strains, resulting in PSPs with diverse structures. Also, we engineered the PSP biosynthesis pathway in lactococci to obtain a chimeric PSP structure, confirming the predicted glycosyltransferase specificities. This enabled us to highlight the importance of a single sugar residue of the PSP repeat unit in phage recognition. In conclusion, our results support a novel pathway for PSP biosynthesis on a lipid-monophosphate intermediate as an extracellular modification of rhamnan, unveiling an assembly machinery for complex Rha-CWPS with structural diversity in lactococci.
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Affiliation(s)
- Hugo Guérin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pascal Courtin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Alain Guillot
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Christine Péchoux
- Université Paris-Saclay INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Jennifer Mahony
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Saulius Kulakauskas
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Christian Cambillau
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland; Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IMM), Aix-Marseille Université - CNRS, UMR 7255, Marseille, France
| | - Thierry Touzé
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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Guérin H, Quénée P, Palussière S, Courtin P, André G, Péchoux C, Costache V, Mahony J, van Sinderen D, Kulakauskas S, Chapot-Chartier MP. PBP2b Mutations Improve the Growth of Phage-Resistant Lactococcus cremoris Lacking Polysaccharide Pellicle. Appl Environ Microbiol 2023; 89:e0210322. [PMID: 37222606 PMCID: PMC10304956 DOI: 10.1128/aem.02103-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/01/2023] [Indexed: 05/25/2023] Open
Abstract
Lactococcus lactis and Lactococcus cremoris are Gram-positive lactic acid bacteria widely used as starter in milk fermentations. Lactococcal cells are covered with a polysaccharide pellicle (PSP) that was previously shown to act as the receptor for numerous bacteriophages of the Caudoviricetes class. Thus, mutant strains lacking PSP are phage resistant. However, because PSP is a key cell wall component, PSP-negative mutants exhibit dramatic alterations of cell shape and severe growth defects, which limit their technological value. In the present study, we isolated spontaneous mutants with improved growth, from L. cremoris PSP-negative mutants. These mutants grow at rates similar to the wild-type strain, and based on transmission electron microscopy analysis, they exhibit improved cell morphology compared to their parental PSP-negative mutants. In addition, the selected mutants maintain their phage resistance. Whole-genome sequencing of several such mutants showed that they carried a mutation in pbp2b, a gene encoding a penicillin-binding protein involved in peptidoglycan biosynthesis. Our results indicate that lowering or turning off PBP2b activity suppresses the requirement for PSP and ameliorates substantially bacterial fitness and morphology. IMPORTANCE Lactococcus lactis and Lactococcus cremoris are widely used in the dairy industry as a starter culture. As such, they are consistently challenged by bacteriophage infections which may result in reduced or failed milk acidification with associated economic losses. Bacteriophage infection starts with the recognition of a receptor at the cell surface, which was shown to be a cell wall polysaccharide (the polysaccharide pellicle [PSP]) for the majority of lactococcal phages. Lactococcal mutants devoid of PSP exhibit phage resistance but also reduced fitness, since their morphology and division are severely impaired. Here, we isolated spontaneous, food-grade non-PSP-producing L. cremoris mutants resistant to bacteriophage infection with a restored fitness. This study provides an approach to isolate non-GMO phage-resistant L. cremoris and L. lactis strains, which can be applied to strains with technological functionalities. Also, our results highlight for the first time the link between peptidoglycan and cell wall polysaccharide biosynthesis.
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Affiliation(s)
- Hugo Guérin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pascal Quénée
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Simon Palussière
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pascal Courtin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Gwenaëlle André
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
| | - Christine Péchoux
- Université Paris-Saclay, INRAE, GABI, Jouy-en-Josas, France
- MIMA2 Imaging Core Facility, Microscopie et Imagerie des Microorganismes, Animaux et Aliments, INRAE, Jouy-en-Josas, France
| | - Vlad Costache
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- MIMA2 Imaging Core Facility, Microscopie et Imagerie des Microorganismes, Animaux et Aliments, INRAE, Jouy-en-Josas, France
| | - Jennifer Mahony
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Saulius Kulakauskas
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
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5
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Yadalam PK, Anegundi RV, Ramadoss R, Saravanan M, Veeramuthu A, Heboyan A. Indigenous Oral and Gut Phages Defeat the Deadly NDM-1 Superbug. Bioinform Biol Insights 2023; 17:11779322231182767. [PMID: 37377794 PMCID: PMC10291530 DOI: 10.1177/11779322231182767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Aim Antibiotics treat various diseases by targeting microorganisms by killing them or reducing their multiplication rate. New Delhi Metallo-beta-lactamase-1 (NDM-1) is produced by bacteria possessing the resistance gene blaNDM-1, the enzyme that makes bacteria resistant to beta-lactams. Bacteriophages, especially Lactococcus, have shown their ability to break down lactams. Hence, the current study computationally evaluated the binding potential of Lactococcus bacteriophages with NDM using Molecular docking and dynamics. Methods Modelling of NDM I-TASSER for Main tail protein gp19 OS=Lactococcus phage LL-H or Lactobacillus delbrueckii subsp. lactis after downloading from UNIPROT ID- Q38344. Cluspro tool helps in Understanding cellular function and organization with protein-protein interactions. MD simulations(19) typically compute atom movements over time. Simulations were used to predict the ligand binding status in the physiological environment. Results The best binding affinity score was found -1040.6 Kcal/mol compared to other docking scores. MD simulations show in RMSD values for target remains within 1.0 Angstrom, which is acceptable. The ligand-protein fit to receptor protein RMSD values of 2.752 fluctuates within 1.5 Angstrom after equilibration. Conclusions Lactococcus bacteriophages showed a strong affinity to the NDM. Hence, this hypothesis, supported by evidence from a computational approach, will solve this life-threatening superbug problem.
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Affiliation(s)
- Pradeep Kumar Yadalam
- Department of Periodontics, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Raghavendra Vamsi Anegundi
- Department of Periodontics, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Ramya Ramadoss
- Department of Oral Pathology & Oral Biology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - M Saravanan
- Department of Pharmacology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - AshokKumar Veeramuthu
- Centre for Transdisciplinary Research, Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Artak Heboyan
- Department of Prosthodontics, Faculty of Stomatology, Mkhitar Heratsi Yerevan State Medical University, Yerevan, Armenia
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Morawska LP, Kuipers OP. Cell-to-cell non-conjugative plasmid transfer between Bacillus subtilis and lactic acid bacteria. Microb Biotechnol 2023; 16:784-798. [PMID: 36547214 PMCID: PMC10034627 DOI: 10.1111/1751-7915.14195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 11/15/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Bacillus subtilis is a soil-dwelling bacterium that can interact with a plethora of other microorganisms in its natural habitat. Due to the versatile interactions and its ability to form nanotubes, i.e., recently described membrane structures that trade cytoplasmic content between neighbouring cells, we investigated the potential of HGT from B. subtilis to industrially-relevant members of lactic acid bacteria (LAB). To explore the interspecies HGT events, we developed a co-culturing protocol and provided proof of transfer of a small high copy non-conjugative plasmid from B. subtilis to LABs. Interestingly, the plasmid transfer did not involve conjugation nor activation of the competent state by B. subtilis. Moreover, our study shows for the first time non-conjugative cell-to-cell intraspecies plasmid transfer for non-competent Lactococcus lactis sp. cremoris strains. Our study indicates that cell-to-cell transformation is a ubiquitous form of HGT and can be potentially utilized as an alternative tool for natural (non-GMO) strain improvement.
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Affiliation(s)
- Luiza P Morawska
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Oscar P Kuipers
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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Walters WA, Granados AC, Ley C, Federman S, Stryke D, Santos Y, Haggerty T, Sotomayor-Gonzalez A, Servellita V, Ley RE, Parsonnet J, Chiu CY. Longitudinal comparison of the developing gut virome in infants and their mothers. Cell Host Microbe 2023; 31:187-198.e3. [PMID: 36758519 PMCID: PMC9950819 DOI: 10.1016/j.chom.2023.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 11/15/2022] [Accepted: 01/05/2023] [Indexed: 02/10/2023]
Abstract
The human gut virome and its early life development are poorly understood. Prior studies have captured single-point assessments with the evolution of the infant virome remaining largely unexplored. We performed viral metagenomic sequencing on stool samples collected longitudinally from a cohort of 53 infants from age 2 weeks to 3 years (80.7 billion reads), and from their mothers (9.8 billion reads) to examine and compare viromes. The asymptomatic infant virome consisted of bacteriophages, nonhuman dietary/environmental viruses, and human-host viruses, predominantly picornaviruses. In contrast, human-host viruses were largely absent from the maternal virome. Previously undescribed, sequence-divergent vertebrate viruses were detected in the maternal but not infant virome. As infants aged, the phage component evolved to resemble the maternal virome, but by age 3, the human-host component remained dissimilar from the maternal virome. Thus, early life virome development is determined predominantly by dietary, infectious, and environmental factors rather than direct maternal acquisition.
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Affiliation(s)
- William A Walters
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Andrea C Granados
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Catherine Ley
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Doug Stryke
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Yale Santos
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Thomas Haggerty
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Julie Parsonnet
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA; Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA.
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8
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Escobedo S, Pérez de Pipaon M, Rendueles C, Rodríguez A, Martínez B. Cell wall modifications that alter the exolytic activity of lactococcal phage endolysins have little impact on phage growth. Front Microbiol 2023; 14:1106049. [PMID: 36744092 PMCID: PMC9894900 DOI: 10.3389/fmicb.2023.1106049] [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: 11/23/2022] [Accepted: 01/04/2023] [Indexed: 01/22/2023] Open
Abstract
Bacteriophages are a nuisance in the production of fermented dairy products driven by starter bacteria and strategies to reduce the risk of phage infection are permanently sought. Bearing in mind that the bacterial cell wall plays a pivotal role in host recognition and lysis, our goal was to elucidate to which extent modifications in the cell wall may alter endolysin activity and influence the outcome of phage infection in Lactococcus. Three lactococcal endolysins with distinct catalytic domains (CHAP, amidase and lysozyme) from phages 1,358, p2 and c2 respectively, were purified and their exolytic activity was tested against lactococcal mutants either overexpressing or lacking genes involved in the cell envelope stress (CES) response or in modifying peptidoglycan (PG) composition. After recombinant production in E. coli, Lys1358 (CHAP) and LysC2 (muramidase) were able to lyse lactococcal cells in turbidity reduction assays, but no activity of LysP2 was detected. The degree of PG acetylation, namely C6-O-acetylation and de-N-acetylation influenced the exolytic activity, being LysC2 more active against cells depleted of the PG deacetylase PgdA and the O-acetyl transferase OatA. On the contrary, both endolysins showed reduced activity on cells with an induced CES response. By measuring several growth parameters of phage c2 on these lactococcal mutants (lytic score, efficiency of plaquing, plaque size and one-step curves), a direct link between the exolytic activity of its endolysin and phage performance could not be stablished.
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Nale JY, Thanki AM, Rashid SJ, Shan J, Vinner GK, Dowah ASA, Cheng JKJ, Sicheritz-Pontén T, Clokie MRJ. Diversity, Dynamics and Therapeutic Application of Clostridioides difficile Bacteriophages. Viruses 2022; 14:v14122772. [PMID: 36560776 PMCID: PMC9784644 DOI: 10.3390/v14122772] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/08/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
Clostridioides difficile causes antibiotic-induced diarrhoea and pseudomembranous colitis in humans and animals. Current conventional treatment relies solely on antibiotics, but C. difficile infection (CDI) cases remain persistently high with concomitant increased recurrence often due to the emergence of antibiotic-resistant strains. Antibiotics used in treatment also induce gut microbial imbalance; therefore, novel therapeutics with improved target specificity are being investigated. Bacteriophages (phages) kill bacteria with precision, hence are alternative therapeutics for the targeted eradication of the pathogen. Here, we review current progress in C. difficile phage research. We discuss tested strategies of isolating C. difficile phages directly, and via enrichment methods from various sample types and through antibiotic induction to mediate prophage release. We also summarise phenotypic phage data that reveal their morphological, genetic diversity, and various ways they impact their host physiology and pathogenicity during infection and lysogeny. Furthermore, we describe the therapeutic development of phages through efficacy testing in different in vitro, ex vivo and in vivo infection models. We also discuss genetic modification of phages to prevent horizontal gene transfer and improve lysis efficacy and formulation to enhance stability and delivery of the phages. The goal of this review is to provide a more in-depth understanding of C. difficile phages and theoretical and practical knowledge on pre-clinical, therapeutic evaluation of the safety and effectiveness of phage therapy for CDI.
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Affiliation(s)
- Janet Y. Nale
- Centre for Epidemiology and Planetary Health, Department of Veterinary and Animal Science, Scotland’s Rural College, Inverness IV2 5NA, UK
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Anisha M. Thanki
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Srwa J. Rashid
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Jinyu Shan
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Gurinder K. Vinner
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Ahmed S. A. Dowah
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- School of Pharmacy, University of Lincoln, Lincoln LN6 7TS, UK
| | | | - Thomas Sicheritz-Pontén
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, 1353 Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Bedong 08100, Kedah, Malaysia
| | - Martha R. J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Correspondence:
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10
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Millen AM, Romero DA, Horvath P, Magill D, Simdon L. Host-encoded, cell surface-associated exopolysaccharide required for adsorption and infection by lactococcal P335 phage subtypes. Front Microbiol 2022; 13:971166. [PMID: 36267184 PMCID: PMC9576995 DOI: 10.3389/fmicb.2022.971166] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
Lactococcus lactis and Lactococcus cremoris compose commercial starter cultures widely used for industrial dairy fermentations. Some lactococcal strains may produce exopolysaccharides (EPS), which have technological applications, including texture production and phage resistance. Two distinct gene clusters associated with EPS production, designated 6073-like and 7127-like, were identified on plasmids in lactococcal strains. Infectivity of two subsets of P335 group phages, distinguished based on their single-component baseplate/receptor-binding protein nucleotide sequences, was correlated to the presence of a host-encoded 6073-like or 7127-like eps gene cluster. Furthermore, phages belonging to these subsets differentially adsorbed to lactococcal strains harboring the respective eps gene cluster. Loss of the respective EPS-encoding plasmid from a fully phage-sensitive strain resulted in loss of phage adsorption and resistance to the phage. Transmission electron microscopy (TEM) showed that the EPS produced by strains encoding the 6073-like or 7127-like eps gene clusters are cell-surface associated, which, coupled with phage plaquing and adsorption data, shows that specific capsular EPS are involved in host recognition by certain P335 phage subgroups. To our knowledge, this is the first description of the involvement of EPS produced via the Wzx/Wzy-dependent pathway in phage sensitivity of L. lactis or L. cremoris. This study also shows strains that do not appear to be phage-related based on plaque formation may still be related by phage adsorption and indicates that optimal formulation of phage-robust cultures should take into account the EPS type of individual strains.
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Affiliation(s)
- Anne M. Millen
- Health and Biosciences, IFF, Madison, WI, United States
- *Correspondence: Anne M. Millen,
| | | | | | - Damian Magill
- Health and Biosciences, IFF, Dangé-Saint-Romain, France
| | - Laura Simdon
- Health and Biosciences, IFF, Madison, WI, United States
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11
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Guérin H, Kulakauskas S, Chapot-Chartier MP. Structural variations and roles of rhamnose-rich cell wall polysaccharides in Gram-positive bacteria. J Biol Chem 2022; 298:102488. [PMID: 36113580 PMCID: PMC9574508 DOI: 10.1016/j.jbc.2022.102488] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 09/08/2022] [Accepted: 09/10/2022] [Indexed: 11/17/2022] Open
Abstract
Rhamnose-rich cell wall polysaccharides (Rha-CWPSs) have emerged as crucial cell wall components of numerous Gram-positive, ovoid-shaped bacteria—including streptococci, enterococci, and lactococci—of which many are of clinical or biotechnological importance. Rha-CWPS are composed of a conserved polyrhamnose backbone with side-chain substituents of variable size and structure. Because these substituents contain phosphate groups, Rha-CWPS can also be classified as polyanionic glycopolymers, similar to wall teichoic acids, of which they appear to be functional homologs. Recent advances have highlighted the critical role of these side-chain substituents in bacterial cell growth and division, as well as in specific interactions between bacteria and infecting bacteriophages or eukaryotic hosts. Here, we review the current state of knowledge on the structure and biosynthesis of Rha-CWPS in several ovoid-shaped bacterial species. We emphasize the role played by multicomponent transmembrane glycosylation systems in the addition of side-chain substituents of various sizes as extracytoplasmic modifications of the polyrhamnose backbone. We provide an overview of the contribution of Rha-CWPS to cell wall architecture and biogenesis and discuss current hypotheses regarding their importance in the cell division process. Finally, we sum up the critical roles that Rha-CWPS can play as bacteriophage receptors or in escaping host defenses, roles that are mediated mainly through their side-chain substituents. From an applied perspective, increased knowledge of Rha-CWPS can lead to advancements in strategies for preventing phage infection of lactococci and streptococci in food fermentation and for combating pathogenic streptococci and enterococci.
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Affiliation(s)
- Hugo Guérin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Saulius Kulakauskas
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
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12
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White K, Yu JH, Eraclio G, Dal Bello F, Nauta A, Mahony J, van Sinderen D. Bacteriophage-host interactions as a platform to establish the role of phages in modulating the microbial composition of fermented foods. MICROBIOME RESEARCH REPORTS 2022; 1:3. [PMID: 38089066 PMCID: PMC10714293 DOI: 10.20517/mrr.2021.04] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/23/2021] [Accepted: 12/31/2021] [Indexed: 02/19/2024]
Abstract
Food fermentation relies on the activity of robust starter cultures, which are commonly comprised of lactic acid bacteria such as Lactococcus and Streptococcus thermophilus. While bacteriophage infection represents a persistent threat that may cause slowed or failed fermentations, their beneficial role in fermentations is also being appreciated. In order to develop robust starter cultures, it is important to understand how phages interact with and modulate the compositional landscape of these complex microbial communities. Both culture-dependent and -independent methods have been instrumental in defining individual phage-host interactions of many lactic acid bacteria (LAB). This knowledge needs to be integrated and expanded to obtain a full understanding of the overall complexity of such interactions pertinent to fermented foods through a combination of culturomics, metagenomics, and phageomics. With such knowledge, it is believed that factory-specific detection and monitoring systems may be developed to ensure robust and reliable fermentation practices. In this review, we explore/discuss phage-host interactions of LAB, the role of both virulent and temperate phages on the microbial composition, and the current knowledge of phageomes of fermented foods.
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Affiliation(s)
- Kelsey White
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
- Authors contributed equally
| | - Jun-Hyeok Yu
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
- Authors contributed equally
| | | | | | - Arjen Nauta
- FrieslandCampina, Amersfoort 3800 BN, The Netherlands
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
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13
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Novel Host Recognition Mechanism of the K1 Capsule-Specific Phage of Escherichia coli: Capsular Polysaccharide as the First Receptor and Lipopolysaccharide as the Secondary Receptor. J Virol 2021; 95:e0092021. [PMID: 34191582 DOI: 10.1128/jvi.00920-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
K1 capsule-specific phages of Escherichia coli have been reported in recent years, but the molecular mechanism involved in host recognition of these phages remains unknown. In this study, the interactions between PNJ1809-36, a new K1-specific phage, and its host bacterium, E. coli DE058, were investigated. A transposon mutation library was used to screen for receptor-related genes. Gene deletion, lysis curve determination, plaque formation test, adsorption assay, and inhibition assay of phage by lipopolysaccharide (LPS) showed that capsular polysaccharide (CPS) was the first receptor for the initial adsorption of PNJ1809-36 to E. coli DE058 and that LPS was a secondary receptor for the irreversible binding of the phage. The penultimate galactose in the outer core was identified as the specific binding region on LPS. Through antibody blocking assay, fluorescence labeling and high-performance gel permeation chromatography, the tail protein ORF261 of phage PNJ1809-36 was identified as the receptor-binding protein on CPS. Given these findings, we propose a model for the recognition process of phage PNJ1809-36 on E. coli DE058: the phage PNJ1809-36 tail protein ORF261 recognizes and adsorbs to the K1 capsule, and then the K1 capsule is partially degraded, exposing the active site of LPS which is recognized by phage PNJ1809-36. This model provides insight into the molecular mechanisms between K1-specific phages and their host bacteria. IMPORTANCE It has been speculated that CPS is the main receptor of K1-specific phages belonging to Siphoviridae. In recent years, a new type of K1-specific phage belonging to Myoviridae has been reported, but its host recognition mechanisms remain unknown. Here, we studied the interactions between PNJ1809-36, a new type of K1 phage, and its host bacterium, E. coli DE058. Our research showed that the phage initially adsorbed to the K1 capsule mediated by ORF261 and then bound to the penultimate galactose of LPS to begin the infection process.
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14
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Martínez B, Rodríguez A, Kulakauskas S, Chapot-Chartier MP. Cell wall homeostasis in lactic acid bacteria: threats and defences. FEMS Microbiol Rev 2021; 44:538-564. [PMID: 32495833 PMCID: PMC7476776 DOI: 10.1093/femsre/fuaa021] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 06/03/2020] [Indexed: 12/16/2022] Open
Abstract
Lactic acid bacteria (LAB) encompasses industrially relevant bacteria involved in food fermentations as well as health-promoting members of our autochthonous microbiota. In the last years, we have witnessed major progresses in the knowledge of the biology of their cell wall, the outermost macrostructure of a Gram-positive cell, which is crucial for survival. Sophisticated biochemical analyses combined with mutation strategies have been applied to unravel biosynthetic routes that sustain the inter- and intra-species cell wall diversity within LAB. Interplay with global cell metabolism has been deciphered that improved our fundamental understanding of the plasticity of the cell wall during growth. The cell wall is also decisive for the antimicrobial activity of many bacteriocins, for bacteriophage infection and for the interactions with the external environment. Therefore, genetic circuits involved in monitoring cell wall damage have been described in LAB, together with a plethora of defence mechanisms that help them to cope with external threats and adapt to harsh conditions. Since the cell wall plays a pivotal role in several technological and health-promoting traits of LAB, we anticipate that this knowledge will pave the way for the future development and extended applications of LAB.
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Affiliation(s)
- Beatriz Martínez
- DairySafe research group. Department of Technology and Biotechnology of Dairy Products. Instituto de Productos Lácteos de Asturias, IPLA-CSIC. Paseo Río Linares s/n. 33300 Villaviciosa, Spain
| | - Ana Rodríguez
- DairySafe research group. Department of Technology and Biotechnology of Dairy Products. Instituto de Productos Lácteos de Asturias, IPLA-CSIC. Paseo Río Linares s/n. 33300 Villaviciosa, Spain
| | - Saulius Kulakauskas
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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15
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Achigar R, Scarrone M, Rousseau GM, Philippe C, Machado F, Duvós V, Campot MP, Dion MB, Shao Y, Pianzzola MJ, Moineau S. Ectopic Spacer Acquisition in Streptococcus thermophilus CRISPR3 Array. Microorganisms 2021; 9:microorganisms9030512. [PMID: 33804420 PMCID: PMC7999890 DOI: 10.3390/microorganisms9030512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 12/17/2022] Open
Abstract
Streptococcus thermophilus relies heavily on two type II-A CRISPR-Cas systems, CRISPR1 and CRISPR3, to resist siphophage infections. One hallmark of these systems is the integration of a new spacer at the 5' end of the CRISPR arrays following phage infection. However, we have previously shown that ectopic acquisition of spacers can occur within the CRISPR1 array. Here, we present evidence of the acquisition of new spacers within the array of CRISPR3 of S. thermophilus. The analysis of randomly selected bacteriophage-insensitive mutants of the strain Uy01 obtained after phage infection, as well as the comparison with other S. thermophilus strains with similar CRISPR3 content, showed that a specific spacer within the array could be responsible for misguiding the adaptation complex. These results also indicate that while the vast majority of new spacers are added at the 5' end of the CRISPR array, ectopic spacer acquisition is a common feature of both CRISPR1 and CRISPR3 systems in S. thermophilus, and it can still provide phage resistance. Ectopic spacer acquisition also appears to have occurred naturally in some strains of Streptococcus pyogenes, suggesting that it is a general phenomenon, at least in type II-A systems.
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Affiliation(s)
- Rodrigo Achigar
- Laboratorio de Biotecnología, Facultad de Ingeniería, Universidad ORT Uruguay, Montevideo 11100, Uruguay; (R.A.); (F.M.); (V.D.); (M.P.C.)
| | - Martina Scarrone
- Département de Biochimie, De Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC G1V 0A6, Canada; (M.S.); (G.M.R.); (C.P.); (M.B.D.); (Y.S.)
| | - Geneviève M. Rousseau
- Département de Biochimie, De Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC G1V 0A6, Canada; (M.S.); (G.M.R.); (C.P.); (M.B.D.); (Y.S.)
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, QC G1V 0A6, Canada
| | - Cécile Philippe
- Département de Biochimie, De Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC G1V 0A6, Canada; (M.S.); (G.M.R.); (C.P.); (M.B.D.); (Y.S.)
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, QC G1V 0A6, Canada
| | - Felipe Machado
- Laboratorio de Biotecnología, Facultad de Ingeniería, Universidad ORT Uruguay, Montevideo 11100, Uruguay; (R.A.); (F.M.); (V.D.); (M.P.C.)
| | - Valentina Duvós
- Laboratorio de Biotecnología, Facultad de Ingeniería, Universidad ORT Uruguay, Montevideo 11100, Uruguay; (R.A.); (F.M.); (V.D.); (M.P.C.)
| | - María Pía Campot
- Laboratorio de Biotecnología, Facultad de Ingeniería, Universidad ORT Uruguay, Montevideo 11100, Uruguay; (R.A.); (F.M.); (V.D.); (M.P.C.)
| | - Moïra B. Dion
- Département de Biochimie, De Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC G1V 0A6, Canada; (M.S.); (G.M.R.); (C.P.); (M.B.D.); (Y.S.)
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, QC G1V 0A6, Canada
| | - Yuyu Shao
- Département de Biochimie, De Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC G1V 0A6, Canada; (M.S.); (G.M.R.); (C.P.); (M.B.D.); (Y.S.)
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, QC G1V 0A6, Canada
| | - María Julia Pianzzola
- Departamento de Biociencias (DEPBIO), Facultad de Química, Universidad de la República, Montevideo 11800, Uruguay;
| | - Sylvain Moineau
- Département de Biochimie, De Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC G1V 0A6, Canada; (M.S.); (G.M.R.); (C.P.); (M.B.D.); (Y.S.)
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, QC G1V 0A6, Canada
- Félix d’Hérelle Reference Center for Bacterial Viruses, Faculté de Médecine Dentaire, Université Laval, Québec, QC G1V 0A6, Canada
- Correspondence: ; Tel.: +1-418-656-3712
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16
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Structure, function and assembly of the long, flexible tail of siphophages. Curr Opin Virol 2020; 45:34-42. [DOI: 10.1016/j.coviro.2020.06.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/15/2020] [Accepted: 06/23/2020] [Indexed: 12/25/2022]
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17
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Philippe C, Chaïb A, Jaomanjaka F, Cluzet S, Lagarde A, Ballestra P, Decendit A, Petrel M, Claisse O, Goulet A, Cambillau C, Le Marrec C. Wine Phenolic Compounds Differently Affect the Host-Killing Activity of Two Lytic Bacteriophages Infecting the Lactic Acid Bacterium Oenococcus oeni. Viruses 2020; 12:E1316. [PMID: 33213034 PMCID: PMC7698478 DOI: 10.3390/v12111316] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 12/15/2022] Open
Abstract
To provide insights into phage-host interactions during winemaking, we assessed whether phenolic compounds modulate the phage predation of Oenococcus oeni. Centrifugal partition chromatography was used to fractionate the phenolic compounds of a model red wine. The ability of lytic oenophage OE33PA to kill its host was reduced in the presence of two collected fractions in which we identified five compounds. Three, namely, quercetin, myricetin and p-coumaric acid, significantly reduced the phage predation of O. oeni when provided as individual pure molecules, as also did other structurally related compounds such as cinnamic acid. Their presence was correlated with a reduced adsorption rate of phage OE33PA on its host. Strikingly, none of the identified compounds affected the killing activity of the distantly related lytic phage Vinitor162. OE33PA and Vinitor162 were shown to exhibit different entry mechanisms to penetrate into bacterial cells. We propose that ligand-receptor interactions that mediate phage adsorption to the cell surface are diverse in O. oeni and are subject to differential interference by phenolic compounds. Their presence did not induce any modifications in the cell surface as visualized by TEM. Interestingly, docking analyses suggest that quercetin and cinnamic acid may interact with the tail of OE33PA and compete with host recognition.
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Affiliation(s)
- Cécile Philippe
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
| | - Amel Chaïb
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
| | - Fety Jaomanjaka
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
| | - Stéphanie Cluzet
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
| | - Aurélie Lagarde
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
| | - Patricia Ballestra
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
| | - Alain Decendit
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
| | - Mélina Petrel
- Bordeaux Imaging Center, UMS3420 CNRS-INSERM, University Bordeaux, F-33000 Bordeaux, France;
| | - Olivier Claisse
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
- INRAE, ISVV, USC 1366 Oenologie, F-33140 Villenave d’Ornon, France
| | - Adeline Goulet
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, F-13020 Marseille, France; (A.G.); (C.C.)
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, F-13020 Marseille, France
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, F-13020 Marseille, France; (A.G.); (C.C.)
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, F-13020 Marseille, France
| | - Claire Le Marrec
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
- Bordeaux INP, ISVV, EA4577 OEnologie, F-33140 Villenave d’Ornon, France
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18
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Lavelle K, Goulet A, McDonnell B, Spinelli S, van Sinderen D, Mahony J, Cambillau C. Revisiting the host adhesion determinants of Streptococcus thermophilus siphophages. Microb Biotechnol 2020; 13:1765-1779. [PMID: 32525270 PMCID: PMC7533335 DOI: 10.1111/1751-7915.13593] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/15/2020] [Accepted: 04/22/2020] [Indexed: 11/29/2022] Open
Abstract
Available 3D structures of bacteriophage modules combined with predictive bioinformatic algorithms enabled the identification of adhesion modules in 57 siphophages infecting Streptococcus thermophilus (St). We identified several carbohydrate-binding modules (CBMs) in so-called evolved distal tail (Dit) and tail-associated lysozyme (Tal) proteins of St phage baseplates. We examined the open reading frame (ORF) downstream of the Tal-encoding ORF and uncovered the presence of a putative p2-like receptor-binding protein (RBP). A 21 Å resolution electron microscopy structure of the baseplate of cos-phage STP1 revealed the presence of six elongated electron densities, surrounding the core of the baseplate, that harbour the p2-like RBPs at their tip. To verify the functionality of these modules, we expressed GFP- or mCherry-coupled Tal and putative RBP CBMs and observed by fluorescence microscopy that both modules bind to their corresponding St host, the putative RBP CBM with higher affinity than the Tal-associated one. The large number of CBM functional domains in St phages suggests that they play a contributory role in the infection process, a feature that we previously described in lactococcal phages and beyond, possibly representing a universal feature of the siphophage host-recognition apparatus.
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Affiliation(s)
| | - Adeline Goulet
- Architecture et Fonction des Macromolécules BiologiquesAix‐Marseille UniversitéCampus de LuminyMarseilleFrance
- Architecture et Fonction des Macromolécules BiologiquesCentre National de la Recherche Scientifique (CNRS)Campus de LuminyMarseilleFrance
| | | | - Silvia Spinelli
- Architecture et Fonction des Macromolécules BiologiquesAix‐Marseille UniversitéCampus de LuminyMarseilleFrance
- Architecture et Fonction des Macromolécules BiologiquesCentre National de la Recherche Scientifique (CNRS)Campus de LuminyMarseilleFrance
| | - Douwe van Sinderen
- School of MicrobiologyUniversity College CorkCorkIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Jennifer Mahony
- School of MicrobiologyUniversity College CorkCorkIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Christian Cambillau
- School of MicrobiologyUniversity College CorkCorkIreland
- Architecture et Fonction des Macromolécules BiologiquesAix‐Marseille UniversitéCampus de LuminyMarseilleFrance
- Architecture et Fonction des Macromolécules BiologiquesCentre National de la Recherche Scientifique (CNRS)Campus de LuminyMarseilleFrance
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Novel Genus of Phages Infecting Streptococcus thermophilus: Genomic and Morphological Characterization. Appl Environ Microbiol 2020; 86:AEM.00227-20. [PMID: 32303549 DOI: 10.1128/aem.00227-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/13/2020] [Indexed: 12/26/2022] Open
Abstract
Streptococcus thermophilus is a lactic acid bacterium commonly used for the manufacture of yogurt and specialty cheeses. Virulent phages represent a major risk for milk fermentation processes worldwide, as they can inactivate the added starter bacterial cells, leading to low-quality fermented dairy products. To date, four genetically distinct groups of phages infecting S. thermophilus have been described. Here, we describe a fifth group. Phages P738 and D4446 are virulent siphophages that infect a few industrial strains of S. thermophilus The genomes of phages P738 and D4446 were sequenced and found to contain 34,037 and 33,656 bp as well as 48 and 46 open reading frames, respectively. Comparative genomic analyses revealed that the two phages are closely related to each other but display very limited similarities to other S. thermophilus phages. In fact, these two novel S. thermophilus phages share similarities with streptococcal phages of nondairy origin, suggesting that they emerged recently in the dairy environment.IMPORTANCE Despite decades of research and adapted antiphage strategies such as CRISPR-Cas systems, virulent phages are still a persistent risk for the milk fermentation industry worldwide, as they can cause manufacturing failures and alter product quality. Phages P738 and D4446 are novel virulent phages that infect the food-grade Gram-positive bacterial species Streptococcus thermophilus These two related viruses represent a fifth group of S. thermophilus phages, as they are significantly distinct from other known S. thermophilus phages. Both phages share similarities with phages infecting nondairy streptococci, suggesting their recent emergence and probable coexistence in dairy environments. These findings highlight the necessity of phage surveillance programs as the phage population evolves in response to the application of antiphage strategies.
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Goulet A, Spinelli S, Mahony J, Cambillau C. Conserved and Diverse Traits of Adhesion Devices from Siphoviridae Recognizing Proteinaceous or Saccharidic Receptors. Viruses 2020; 12:E512. [PMID: 32384698 PMCID: PMC7291167 DOI: 10.3390/v12050512] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/02/2020] [Accepted: 05/03/2020] [Indexed: 01/30/2023] Open
Abstract
Bacteriophages can play beneficial roles in phage therapy and destruction of food pathogens. Conversely, they play negative roles as they infect bacteria involved in fermentation, resulting in serious industrial losses. Siphoviridae phages possess a long non-contractile tail and use a mechanism of infection whose first step is host recognition and binding. They have evolved adhesion devices at their tails' distal end, tuned to recognize specific proteinaceous or saccharidic receptors on the host's surface that span a large spectrum of shapes. In this review, we aimed to identify common patterns beyond this apparent diversity. To this end, we analyzed siphophage tail tips or baseplates, evaluating their known structures, where available, and uncovering patterns with bioinformatics tools when they were not. It was thereby identified that a triad formed by three proteins in complex, i.e., the tape measure protein (TMP), the distal tail protein (Dit), and the tail-associated lysozyme (Tal), is conserved in all phages. This common scaffold may harbor various functional extensions internally while it also serves as a platform for plug-in ancillary or receptor-binding proteins (RBPs). Finally, a group of siphophage baseplates involved in saccharidic receptor recognition exhibits an activation mechanism reminiscent of that observed in Myoviridae.
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Affiliation(s)
- Adeline Goulet
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, 13288 Marseille, France;
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, 13288 Marseille, France
| | - Silvia Spinelli
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, 13288 Marseille, France;
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, 13288 Marseille, France
| | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork T12 YN60, Ireland;
- APC Microbiome Ireland, University College Cork, Cork T12 YN60, Ireland
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, 13288 Marseille, France;
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, 13288 Marseille, France
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21
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Theodorou I, Courtin P, Sadovskaya I, Palussière S, Fenaille F, Mahony J, Chapot-Chartier MP, van Sinderen D. Three distinct glycosylation pathways are involved in the decoration of Lactococcus lactis cell wall glycopolymers. J Biol Chem 2020; 295:5519-5532. [PMID: 32169901 PMCID: PMC7170526 DOI: 10.1074/jbc.ra119.010844] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 03/10/2020] [Indexed: 12/16/2022] Open
Abstract
Extracytoplasmic sugar decoration of glycopolymer components of the bacterial cell wall contributes to their structural diversity. Typically, the molecular mechanism that underpins such a decoration process involves a three-component glycosylation system (TGS) represented by an undecaprenyl-phosphate (Und-P) sugar-activating glycosyltransferase (Und-P GT), a flippase, and a polytopic glycosyltransferase (PolM GT) dedicated to attaching sugar residues to a specific glycopolymer. Here, using bioinformatic analyses, CRISPR-assisted recombineering, structural analysis of cell wall-associated polysaccharides (CWPS) through MALDI-TOF MS and methylation analysis, we report on three such systems in the bacterium Lactococcus lactis On the basis of sequence similarities, we first identified three gene pairs, csdAB, csdCD, and csdEF, each encoding an Und-P GT and a PolM GT, as potential TGS component candidates. Our experimental results show that csdAB and csdCD are involved in Glc side-chain addition on the CWPS components rhamnan and polysaccharide pellicle (PSP), respectively, whereas csdEF plays a role in galactosylation of lipoteichoic acid (LTA). We also identified a potential flippase encoded in the L. lactis genome (llnz_02975, cflA) and confirmed that it participates in the glycosylation of the three cell wall glycopolymers rhamnan, PSP, and LTA, thus indicating that its function is shared by the three TGSs. Finally, we observed that glucosylation of both rhamnan and PSP can increase resistance to bacteriophage predation and that LTA galactosylation alters L. lactis resistance to bacteriocin.
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Affiliation(s)
- Ilias Theodorou
- School of Microbiology, University College Cork, Cork T12 K8AF, Ireland
| | - Pascal Courtin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Irina Sadovskaya
- Équipe BPA, Université du Littoral Côte d'Opale, Institut Régional Charles Violette EA 7394, USC Anses-ULCO, 62202 Boulogne-sur-Mer, France
| | - Simon Palussière
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - François Fenaille
- Université Paris-Saclay, Commissariat à l'Energie Atomique, INRAE, Médicaments et Technologies pour la Santé (MTS), MetaboHUB, 91191 Gif-sur-Yvette, France
| | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork T12 K8AF, Ireland
- APC Microbiome Ireland, University College Cork, Cork T12 K8AF, Ireland
| | | | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork T12 K8AF, Ireland
- APC Microbiome Ireland, University College Cork, Cork T12 K8AF, Ireland
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22
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Johansen E. Use of Natural Selection and Evolution to Develop New Starter Cultures for Fermented Foods. Annu Rev Food Sci Technol 2019; 9:411-428. [PMID: 29580139 DOI: 10.1146/annurev-food-030117-012450] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The fermented foods industry is constantly seeking new starter cultures to deal with changing consumer preferences and new fermentation processes. New cultures can either be composed of strains isolated from nature or improved derivatives of existing isolates. A variety of techniques involving natural selection and evolution are available to enhance the performance of existing strains, including the isolation of mutants with desired properties, adaptive laboratory evolution, genome shuffling, and genome editing. Numerous examples of traits that can be improved are provided. These include resistance to bacteriophages; the secretion of glucose to increase sweetness; the production of vitamins, antifungal compounds, bacteriocins, texture, or aroma; enhancement of acidification rates and acid tolerance; and elimination of biofilm formation. Careful consideration is required to ensure the developed strains are suitable for the desired purpose, as some approaches may lead to regulatory concerns.
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23
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Tkacova A, Orieskova M, Halgasova N, Bocanova L, Bukovska G. Identification of Brevibacterium flavum genes related to receptors involved in bacteriophage BFK20 adsorption. Virus Res 2019; 274:197775. [PMID: 31600527 DOI: 10.1016/j.virusres.2019.197775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/28/2019] [Accepted: 10/04/2019] [Indexed: 12/27/2022]
Abstract
Phage infection of bacterial cells is a process requiring the interaction between phage receptor binding proteins and receptors on the bacterial cell surface. We prepared a Brevibacterium flavum CCM 251 EZ-Tn5 transposon insertional library and isolated phage-resistant mutants. Analysis of the DNA fragments produced by single-primer PCR was used to determine the EZ-Tn5 transposon insertion sites in the genomes of phage-resistant B. flavum mutants. Seven disrupted genes were identified in forty B. flavum mutants. The phage resistance of these mutants was demonstrated by cultivation analysis in the presence of BFK20, and the adsorption rate of BFK20 to these mutants was tested. B. flavum mutants displayed significantly reduced adsorption rates; the lowest rate was observed for mutants containing interrupted major facilitator superfamily (MFS) protein and glycosyltransferase genes. Uninterrupted forms of these genes were cloned into corynebacterial vector pJUP06 and used for in trans complementation of the corresponding B. flavum mutants. The growth of these complemented mutants when infected with BFK20 closely resembled that of wild-type B. flavum. These complemented mutants also exhibited similar BFK20 adsorption as the wild-type control. We infer that the disrupted MFS protein and glycosyltransferase genes are responsible for the phage-resistant phenotype of these B. flavum transposition mutants.
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Affiliation(s)
- Adela Tkacova
- Department of Genomics and Biotechnology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Maria Orieskova
- Department of Genomics and Biotechnology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Nora Halgasova
- Department of Genomics and Biotechnology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Lucia Bocanova
- Department of Genomics and Biotechnology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Gabriela Bukovska
- Department of Genomics and Biotechnology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51, Bratislava, Slovakia.
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24
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Theodorou I, Courtin P, Palussière S, Kulakauskas S, Bidnenko E, Péchoux C, Fenaille F, Penno C, Mahony J, van Sinderen D, Chapot-Chartier MP. A dual-chain assembly pathway generates the high structural diversity of cell-wall polysaccharides in Lactococcus lactis. J Biol Chem 2019; 294:17612-17625. [PMID: 31582566 DOI: 10.1074/jbc.ra119.009957] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/30/2019] [Indexed: 12/12/2022] Open
Abstract
In Lactococcus lactis, cell-wall polysaccharides (CWPSs) act as receptors for many bacteriophages, and their structural diversity among strains explains, at least partially, the narrow host range of these viral predators. Previous studies have reported that lactococcal CWPS consists of two distinct components, a variable chain exposed at the bacterial surface, named polysaccharide pellicle (PSP), and a more conserved rhamnan chain anchored to, and embedded inside, peptidoglycan. These two chains appear to be covalently linked to form a large heteropolysaccharide. The molecular machinery for biosynthesis of both components is encoded by a large gene cluster, named cwps In this study, using a CRISPR/Cas-based method, we performed a mutational analysis of the cwps genes. MALDI-TOF MS-based structural analysis of the mutant CWPS combined with sequence homology, transmission EM, and phage sensitivity analyses enabled us to infer a role for each protein encoded by the cwps cluster. We propose a comprehensive CWPS biosynthesis scheme in which the rhamnan and PSP chains are independently synthesized from two distinct lipid-sugar precursors and are joined at the extracellular side of the cytoplasmic membrane by a mechanism involving a membrane-embedded glycosyltransferase with a GT-C fold. The proposed scheme encompasses a system that allows extracytoplasmic modification of rhamnan by complex substituting oligo-/polysaccharides. It accounts for the extensive diversity of CWPS structures observed among lactococci and may also have relevance to the biosynthesis of complex rhamnose-containing CWPSs in other Gram-positive bacteria.
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Affiliation(s)
- Ilias Theodorou
- School of Microbiology, University College Cork, Western Road, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Pascal Courtin
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Simon Palussière
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Saulius Kulakauskas
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Elena Bidnenko
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Christine Péchoux
- INRA, UMR 1313 Génétique Animale et Biologie Intégrative (GABI), Plate-forme MIMA2, 78350 Jouy-en-Josas, France
| | - François Fenaille
- CEA, Institut Joliot, Service de Pharmacologie et d'Immunoanalyse, UMR 0496, Laboratoire d'Etude du Métabolisme des Médicaments, MetaboHUB-Paris, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Christophe Penno
- School of Microbiology, University College Cork, Western Road, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Jennifer Mahony
- School of Microbiology, University College Cork, Western Road, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Western Road, Cork, Ireland .,APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
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25
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van Tilburg AY, Cao H, van der Meulen SB, Solopova A, Kuipers OP. Metabolic engineering and synthetic biology employing Lactococcus lactis and Bacillus subtilis cell factories. Curr Opin Biotechnol 2019; 59:1-7. [DOI: 10.1016/j.copbio.2019.01.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/05/2018] [Accepted: 01/16/2019] [Indexed: 12/11/2022]
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26
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A Specific Sugar Moiety in the Lactococcus lactis Cell Wall Pellicle Is Required for Infection by CHPC971, a Member of the Rare 1706 Phage Species. Appl Environ Microbiol 2019; 85:AEM.01224-19. [PMID: 31350317 DOI: 10.1128/aem.01224-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 07/17/2019] [Indexed: 12/29/2022] Open
Abstract
Lactococcus lactis is a Gram-positive bacterium widely used as a starter culture for the production of different dairy products, especially a large variety of cheeses. Infection of lactococcal starter cultures by bacteriophages is one of the major causes of fermentation failure and often leads to production halt. Lactococcal bacteriophages belonging to the c2, 936, and P335 species are the most commonly isolated in dairy plants and have been extensively investigated in the past three decades. Information regarding bacteriophages belonging to less commonly isolated species is, on the other hand, less extensive, although these phages can also contribute to starter culture infection. Here, we report the nucleotide sequence of the newly isolated L. lactis phage CHPC971, belonging to the rare 1706 species of lactococcal phages. We investigated the nature of the host receptor recognized by the phage and collected evidence that strongly suggests that it binds to a specific sugar moiety in the cell wall pellicle of its host. An in silico analysis of the genome of phage CHPC971 identified the hypothetical genes involved in receptor binding.IMPORTANCE Gathering information on how lactococcal bacteriophages recognize their host and proliferate in the dairy environment is of vital importance for the establishment of proper starter culture rotation plans and to avoid fermentation failure and consequent great economic losses for dairy industries. We provide strong evidence on the type of receptor recognized by a newly isolated 1706-type lactococcal bacteriophage, increasing knowledge of phage-host interactions relevant to dairying. This information can help to prevent phage infection events that, so far, are hard to predict and avoid.
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27
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Gaudu P, Yamamoto Y, Jensen PR, Hammer K, Lechardeur D, Gruss A. Genetics of Lactococci. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0035-2018. [PMID: 31298208 PMCID: PMC10957224 DOI: 10.1128/microbiolspec.gpp3-0035-2018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Indexed: 11/20/2022] Open
Abstract
Lactococcus lactis is the best characterized species among the lactococci, and among the most consumed food-fermenting bacteria worldwide. Thanks to their importance in industrialized food production, lactococci are among the lead bacteria understood for fundamental metabolic pathways that dictate growth and survival properties. Interestingly, lactococci belong to the Streptococcaceae family, which includes food, commensal and virulent species. As basic metabolic pathways (e.g., respiration, metal homeostasis, nucleotide metabolism) are now understood to underlie virulence, processes elucidated in lactococci could be important for understanding pathogen fitness and synergy between bacteria. This chapter highlights major findings in lactococci and related bacteria, and covers five themes: distinguishing features of lactococci, metabolic capacities including the less known respiration metabolism in Streptococcaceae, factors and pathways modulating stress response and fitness, interbacterial dialogue via metabolites, and novel applications in health and biotechnology.
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Affiliation(s)
| | - Yuji Yamamoto
- Laboratory of Cellular Microbiology, School of Veterinary Medicine, Kitasato University, Towada, 034-8628, Aomori Japan
| | - Peter Ruhdal Jensen
- National Food Institute, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Karin Hammer
- DTU Bioengineering, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
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28
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Renaissance of traditional DNA transfer strategies for improvement of industrial lactic acid bacteria. Curr Opin Biotechnol 2019; 56:61-68. [DOI: 10.1016/j.copbio.2018.09.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/04/2018] [Accepted: 09/09/2018] [Indexed: 01/01/2023]
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29
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Kupczok A, Neve H, Huang KD, Hoeppner MP, Heller KJ, Franz CMAP, Dagan T. Rates of Mutation and Recombination in Siphoviridae Phage Genome Evolution over Three Decades. Mol Biol Evol 2019; 35:1147-1159. [PMID: 29688542 PMCID: PMC5913663 DOI: 10.1093/molbev/msy027] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The evolution of asexual organisms is driven not only by the inheritance of genetic modification but also by the acquisition of foreign DNA. The contribution of vertical and horizontal processes to genome evolution depends on their rates per year and is quantified by the ratio of recombination to mutation. These rates have been estimated for bacteria; however, no estimates have been reported for phages. Here, we delineate the contribution of mutation and recombination to dsDNA phage genome evolution. We analyzed 34 isolates of the 936 group of Siphoviridae phages using a Lactococcus lactis strain from a single dairy over 29 years. We estimate a constant substitution rate of 1.9 × 10−4 substitutions per site per year due to mutation that is within the range of estimates for eukaryotic RNA and DNA viruses. The reconstruction of recombination events reveals a constant rate of five recombination events per year and 4.5 × 10−3 nucleotide alterations due to recombination per site per year. Thus, the recombination rate exceeds the substitution rate, resulting in a relative effect of recombination to mutation (r/m) of ∼24 that is homogenous over time. Especially in the early transcriptional region, we detect frequent gene loss and regain due to recombination with phages of the 936 group, demonstrating the role of the 936 group pangenome as a reservoir of genetic variation. The observed substitution rate homogeneity conforms to the neutral theory of evolution; hence, the neutral theory can be applied to phage genome evolution and also to genetic variation brought about by recombination.
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Affiliation(s)
- Anne Kupczok
- Genomic Microbiology Group, Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food), Kiel, Germany
| | - Kun D Huang
- Genomic Microbiology Group, Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Marc P Hoeppner
- Institute of Clinical Molecular Biology (IKMB), Kiel University, Kiel, Germany
| | - Knut J Heller
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food), Kiel, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food), Kiel, Germany
| | - Tal Dagan
- Genomic Microbiology Group, Institute of General Microbiology, Kiel University, Kiel, Germany
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30
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Chen X, Guo J, Liu Y, Chai S, Ma R, Munguntsetseg B. Characterization and adsorption of a Lactobacillus plantarum virulent phage. J Dairy Sci 2019; 102:3879-3886. [PMID: 30852005 DOI: 10.3168/jds.2018-16019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/19/2019] [Indexed: 12/18/2022]
Abstract
Bacteriophage infection of lactic acid bacteria is considered one of the biggest worldwide problems in the food industry. Bacteriophages may cause negative effects on the fermentation of various dairy-based products. A virulent bacteriophage was isolated from an abnormal fermentation liquid of Lactobacillus plantarum IMAU10120. The characterization and influence of temperature, pH, divalent cations, and chloramphenicol on the adsorption ability of this phage were evaluated. The results showed that this phage belonged to the Siphoviridae family. It exhibited a burst time of 135 min and a burst size of approximately 215 counts expressed per milliliter per infective center. No significant effect was shown to influence its viability and adsorption at 10 to 37°C. More than 90% of phages exhibited infectivity from pH 5 to 9. Divalent ions and chloramphenicol did not have a significant influence on the adsorption of this phage. The information obtained in this study will enrich the database of lactobacilli virulent phages and provide a basis of information for the control of phages in the food fermentation industry.
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Affiliation(s)
- X Chen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - J Guo
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China
| | - Y Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China
| | - S Chai
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China
| | - R Ma
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China
| | - B Munguntsetseg
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China
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31
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Dunne M, Hupfeld M, Klumpp J, Loessner MJ. Molecular Basis of Bacterial Host Interactions by Gram-Positive Targeting Bacteriophages. Viruses 2018; 10:v10080397. [PMID: 30060549 PMCID: PMC6115969 DOI: 10.3390/v10080397] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 12/29/2022] Open
Abstract
The inherent ability of bacteriophages (phages) to infect specific bacterial hosts makes them ideal candidates to develop into antimicrobial agents for pathogen-specific remediation in food processing, biotechnology, and medicine (e.g., phage therapy). Conversely, phage contaminations of fermentation processes are a major concern to dairy and bioprocessing industries. The first stage of any successful phage infection is adsorption to a bacterial host cell, mediated by receptor-binding proteins (RBPs). As the first point of contact, the binding specificity of phage RBPs is the primary determinant of bacterial host range, and thus defines the remediative potential of a phage for a given bacterium. Co-evolution of RBPs and their bacterial receptors has forced endless adaptation cycles of phage-host interactions, which in turn has created a diverse array of phage adsorption mechanisms utilizing an assortment of RBPs. Over the last decade, these intricate mechanisms have been studied intensely using electron microscopy and X-ray crystallography, providing atomic-level details of this fundamental stage in the phage infection cycle. This review summarizes current knowledge surrounding the molecular basis of host interaction for various socioeconomically important Gram-positive targeting phage RBPs to their protein- and saccharide-based receptors. Special attention is paid to the abundant and best-characterized Siphoviridae family of tailed phages. Unravelling these complex phage-host dynamics is essential to harness the full potential of phage-based technologies, or for generating novel strategies to combat industrial phage contaminations.
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Affiliation(s)
- Matthew Dunne
- Institute of Food Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland.
| | - Mario Hupfeld
- Institute of Food Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland.
| | - Jochen Klumpp
- Institute of Food Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland.
| | - Martin J Loessner
- Institute of Food Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland.
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32
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Yan YL, Gänzle MG. Structure and function relationships of the binding of β- and ɑ-galactosylated oligosaccharides to K88 fimbriae of enterotoxigenic Escherichia coli. Int Dairy J 2018. [DOI: 10.1016/j.idairyj.2018.01.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Vinogradov E, Sadovskaya I, Courtin P, Kulakauskas S, Grard T, Mahony J, van Sinderen D, Chapot-Chartier MP. Determination of the cell wall polysaccharide and teichoic acid structures from Lactococcus lactis IL1403. Carbohydr Res 2018; 462:39-44. [DOI: 10.1016/j.carres.2018.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/09/2018] [Accepted: 04/09/2018] [Indexed: 10/17/2022]
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