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Exploring the diversity of bacteriophage specific to Oenococcus oeni and Lactobacillus spp and their role in wine production. Appl Microbiol Biotechnol 2021; 105:8575-8592. [PMID: 34694447 DOI: 10.1007/s00253-021-11509-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 12/19/2022]
Abstract
The widespread existence of bacteriophage has been of great interest to the biological research community and ongoing investigations continue to explore their diversity and role. They have also attracted attention and in-depth research in connection to fermented food processing, in particular from the dairy and wine industries. Bacteriophage, mostly oenophage, may in fact be a 'double edged sword' for winemakers: whilst they have been implicated as a causal agent of difficulties with malolactic fermentation (although not proven), they are also beginning to be considered as alternatives to using sulphur dioxide to prevent wine spoilage. Investigation and characterisation of oenophage of Oenococcus oeni, the main species used in winemaking, are still limited compared to lactococcal bacteriophage of Lactococcus lactis and Lactiplantibacillus plantarum (formally Lactobacillus plantarum), the drivers of most fermented dairy products. Interestingly, these strains are also being used or considered for use in winemaking. In this review, the genetic diversity and life cycle of phage, together with the debate on the consequent impact of phage predation in wine, and potential control strategies are discussed. KEY POINTS: • Bacteriophage detected in wine are diverse. • Many lysogenic bacteriophage are found in wine bacteria. • Phage impact on winemaking can depend on the stage of the winemaking process. • Bacteriophage as potential antimicrobial agents against spoilage organisms.
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2
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Romero DA, Magill D, Millen A, Horvath P, Fremaux C. Dairy lactococcal and streptococcal phage-host interactions: an industrial perspective in an evolving phage landscape. FEMS Microbiol Rev 2021; 44:909-932. [PMID: 33016324 DOI: 10.1093/femsre/fuaa048] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/18/2020] [Indexed: 12/14/2022] Open
Abstract
Almost a century has elapsed since the discovery of bacteriophages (phages), and 85 years have passed since the emergence of evidence that phages can infect starter cultures, thereby impacting dairy fermentations. Soon afterward, research efforts were undertaken to investigate phage interactions regarding starter strains. Investigations into phage biology and morphology and phage-host relationships have been aimed at mitigating the negative impact phages have on the fermented dairy industry. From the viewpoint of a supplier of dairy starter cultures, this review examines the composition of an industrial phage collection, providing insight into the development of starter strains and cultures and the evolution of phages in the industry. Research advances in the diversity of phages and structural bases for phage-host recognition and an overview of the perpetual arms race between phage virulence and host defense are presented, with a perspective toward the development of improved phage-resistant starter culture systems.
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Affiliation(s)
- Dennis A Romero
- DuPont Nutrition and Biosciences, 3329 Agriculture Dr., Madison, WI 53716, USA
| | - Damian Magill
- DuPont Nutrition and Biosciences, CS 10010, Dangé-Saint-Romain 86220, France
| | - Anne Millen
- DuPont Nutrition and Biosciences, 3329 Agriculture Dr., Madison, WI 53716, USA
| | - Philippe Horvath
- DuPont Nutrition and Biosciences, CS 10010, Dangé-Saint-Romain 86220, France
| | - Christophe Fremaux
- DuPont Nutrition and Biosciences, CS 10010, Dangé-Saint-Romain 86220, France
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3
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De Ste Croix M, Vacca I, Kwun MJ, Ralph JD, Bentley SD, Haigh R, Croucher NJ, Oggioni MR. Phase-variable methylation and epigenetic regulation by type I restriction-modification systems. FEMS Microbiol Rev 2018; 41:S3-S15. [PMID: 28830092 DOI: 10.1093/femsre/fux025] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 05/09/2017] [Indexed: 12/26/2022] Open
Abstract
Epigenetic modifications in bacteria, such as DNA methylation, have been shown to affect gene regulation, thereby generating cells that are isogenic but with distinctly different phenotypes. Restriction-modification (RM) systems contain prototypic methylases that are responsible for much of bacterial DNA methylation. This review focuses on a distinctive group of type I RM loci that , through phase variation, can modify their methylation target specificity and can thereby switch bacteria between alternative patterns of DNA methylation. Phase variation occurs at the level of the target recognition domains of the hsdS (specificity) gene via reversible recombination processes acting upon multiple hsdS alleles. We describe the global distribution of such loci throughout the prokaryotic kingdom and highlight the differences in loci structure across the various bacterial species. Although RM systems are often considered simply as an evolutionary response to bacteriophages, these multi-hsdS type I systems have also shown the capacity to change bacterial phenotypes. The ability of these RM systems to allow bacteria to reversibly switch between different physiological states, combined with the existence of such loci across many species of medical and industrial importance, highlights the potential of phase-variable DNA methylation to act as a global regulatory mechanism in bacteria.
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Affiliation(s)
| | - Irene Vacca
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Min Jung Kwun
- Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK
| | - Joseph D Ralph
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Stephen D Bentley
- Infection Genomics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Richard Haigh
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Nicholas J Croucher
- Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK
| | - Marco R Oggioni
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
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Cui Y, Hu T, Qu X, Zhang L, Ding Z, Dong A. Plasmids from Food Lactic Acid Bacteria: Diversity, Similarity, and New Developments. Int J Mol Sci 2015; 16:13172-202. [PMID: 26068451 PMCID: PMC4490491 DOI: 10.3390/ijms160613172] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 05/09/2015] [Accepted: 05/22/2015] [Indexed: 12/24/2022] Open
Abstract
Plasmids are widely distributed in different sources of lactic acid bacteria (LAB) as self-replicating extrachromosomal genetic materials, and have received considerable attention due to their close relationship with many important functions as well as some industrially relevant characteristics of the LAB species. They are interesting with regard to the development of food-grade cloning vectors. This review summarizes new developments in the area of lactic acid bacteria plasmids and aims to provide up to date information that can be used in related future research.
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Affiliation(s)
- Yanhua Cui
- School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Tong Hu
- School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Xiaojun Qu
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin 150010, China.
| | - Lanwei Zhang
- School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Zhongqing Ding
- School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Aijun Dong
- School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
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5
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Kajala I, Shi Q, Nyyssölä A, Maina NH, Hou Y, Katina K, Tenkanen M, Juvonen R. Cloning and characterization of a Weissella confusa dextransucrase and its application in high fibre baking. PLoS One 2015; 10:e0116418. [PMID: 25603169 PMCID: PMC4300183 DOI: 10.1371/journal.pone.0116418] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 12/08/2014] [Indexed: 01/08/2023] Open
Abstract
Wheat bran offers health benefits as a baking ingredient, but is detrimental to bread textural quality. Dextran production by microbial fermentation improves sourdough bread volume and freshness, but extensive acid production during fermentation may negate this effect. Enzymatic production of dextran in wheat bran was tested to determine if dextran-containing bran could be used in baking without disrupting bread texture. The Weissella confusa VTT E-90392 dextransucrase gene was sequenced and His-tagged dextransucrase Wc392-rDSR was produced in Lactococcus lactis. Purified enzyme was characterized using 14C-sucrose radioisotope and reducing value-based assays, the former yielding Km and Vmax values of 14.7 mM and 8.2 μmol/(mg∙min), respectively, at the pH optimum of 5.4. The structure and size of in vitro dextran product was similar to dextran produced in vivo. Dextran (8.1% dry weight) was produced in wheat bran in 6 h using Wc392-rDSR. Bran with and without dextran was used in wheat baking at 20% supplementation level. Dextran presence improved bread softness and neutralized bran-induced volume loss, clearly demonstrating the potential of using dextransucrases in bran bioprocessing for use in baking.
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Affiliation(s)
- Ilkka Kajala
- VTT Technical Research Centre of Finland, Espoo, Finland
- * E-mail:
| | - Qiao Shi
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Antti Nyyssölä
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Ndegwa Henry Maina
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Yaxi Hou
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Kati Katina
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Maija Tenkanen
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Riikka Juvonen
- VTT Technical Research Centre of Finland, Espoo, Finland
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Mahony J, Bottacini F, van Sinderen D, Fitzgerald GF. Progress in lactic acid bacterial phage research. Microb Cell Fact 2014; 13 Suppl 1:S1. [PMID: 25185514 PMCID: PMC4155818 DOI: 10.1186/1475-2859-13-s1-s1] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Research on lactic acid bacteria (LAB) has advanced significantly over the past number of decades and these developments have been driven by the parallel advances in technologies such as genomics, bioinformatics, protein expression systems and structural biology, combined with the ever increasing commercial relevance of this group of microorganisms. Some of the more significant and impressive outputs have been in the domain of bacteriophage-host interactions which provides a prime example of the cutting-edge model systems represented by LAB research. Here, we present a retrospective overview of the key advances in LAB phage research including phage-host interactions and co-evolution. We describe how in many instances this knowledge can be pivotal in creating real improvements in the application of LAB cultures in commercial practice.
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Ainsworth S, Stockdale S, Bottacini F, Mahony J, van Sinderen D. The Lactococcus lactis plasmidome: much learnt, yet still lots to discover. FEMS Microbiol Rev 2014; 38:1066-88. [PMID: 24861818 DOI: 10.1111/1574-6976.12074] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 04/17/2014] [Accepted: 05/07/2014] [Indexed: 01/20/2023] Open
Abstract
Lactococcus lactis is used extensively worldwide for the production of a variety of fermented dairy products. The ability of L. lactis to successfully grow and acidify milk has long been known to be reliant on a number of plasmid-encoded traits. The recent availability of low-cost, high-quality genome sequencing, and the quest for novel, technologically desirable characteristics, such as novel flavour development and increased stress tolerance, has led to a steady increase in the number of available lactococcal plasmid sequences. We will review both well-known and very recent discoveries regarding plasmid-encoded traits of biotechnological significance. The acquired lactococcal plasmid sequence information has in recent years progressed our understanding of the origin of lactococcal dairy starter cultures. Salient points on the acquisition and evolution of lactococcal plasmids will be discussed in this review, as well as prospects of finding novel plasmid-encoded functions.
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Affiliation(s)
- Stuart Ainsworth
- Department of Microbiology, University College Cork, Cork, Ireland
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The plasmid complement of Lactococcus lactis UC509.9 encodes multiple bacteriophage resistance systems. Appl Environ Microbiol 2014; 80:4341-9. [PMID: 24814781 DOI: 10.1128/aem.01070-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Lactococcus lactis subsp. cremoris strains are used globally for the production of fermented dairy products, particularly hard cheeses. Believed to be of plant origin, L. lactis strains that are used as starter cultures have undergone extensive adaptation to the dairy environment, partially through the acquisition of extrachromosomal DNA in the form of plasmids that specify technologically important phenotypic traits. Here, we present a detailed analysis of the eight plasmids of L. lactis UC509.9, an Irish dairy starter strain. Key industrial phenotypes were mapped, and genes that are typically associated with lactococcal plasmids were identified. Four distinct, plasmid-borne bacteriophage resistance systems were identified, including two abortive infection systems, AbiB and AbiD1, thereby supporting the observed phage resistance of L. lactis UC509.9. AbiB escape mutants were generated for phage sk1, which were found to carry mutations in orf6, which encodes the major capsid protein of this phage.
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9
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Górecki RK, Koryszewska-Bagińska A, Gołębiewski M, Żylińska J, Grynberg M, Bardowski JK. Adaptative potential of the Lactococcus lactis IL594 strain encoded in its 7 plasmids. PLoS One 2011; 6:e22238. [PMID: 21789242 PMCID: PMC3138775 DOI: 10.1371/journal.pone.0022238] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 06/22/2011] [Indexed: 11/19/2022] Open
Abstract
The extrachromosomal gene pool plays a significant role both in evolution and in the environmental adaptation of bacteria. The L. lactis subsp. lactis IL594 strain contains seven plasmids, named pIL1 to pIL7, and is the parental strain of the plasmid-free L. lactis IL1403, which is one of the best characterized lactococcal strains of LAB. Complete nucleotide sequences of pIL1 (6,382 bp), pIL2 (8,277 bp), pIL3 (19,244 bp), pIL4 (48,979), pIL5 (23,395), pIL6 (28,435 bp) and pIL7 (28,546) were established and deposited in the generally accessible database (GeneBank). Nine highly homologous repB-containing replicons, belonging to the lactococcal theta-type replicons, have been identified on the seven plasmids. Moreover, a putative region involved in conjugative plasmid mobilization was found on four plasmids, through identification of the presence of mob genes and/or oriT sequences. Detailed bioinformatic analysis of the plasmid nucleotide sequences provided new insight into the repertoire of plasmid-encoded functions in L. lactis, and indicated that plasmid genes from IL594 strain can be important for L. lactis adaptation to specific environmental conditions (e.g. genes coding for proteins involved in DNA repair or cold shock response) as well as for technological processes (e.g. genes encoding citrate and lactose utilization, oligopeptide transport, restriction-modification system). Moreover, global gene analysis indicated cooperation between plasmid- and chromosome-encoded metabolic pathways.
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Affiliation(s)
- Roman K. Górecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | - Marcin Gołębiewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Department of Biotechnology, Nicolaus Copernicus University, Toruń, Poland
| | - Joanna Żylińska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Marcin Grynberg
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jacek K. Bardowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- * E-mail:
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10
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Shareck J, Choi Y, Lee B, Miguez CB. Cloning Vectors Based on Cryptic Plasmids Isolated from Lactic Acid Bacteria:Their Characteristics and Potential Applications in Biotechnology. Crit Rev Biotechnol 2010; 24:155-208. [PMID: 15707158 DOI: 10.1080/07388550490904288] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Lactic acid bacteria (LAB) are Gram positive bacteria, widely distributed in nature, and industrially important as they are used in a variety of industrial food fermentations. The use of genetic engineering techniques is an effective means of enhancing the industrial applicability of LAB. However, when using genetic engineering technology, safety becomes an essential factor for the application of improved LAB to the food industry. Cloning and expression systems should be derived preferably from LAB cryptic plasmids that generally encode genes for which functions can be proposed, but no phenotypes can be observed. However, some plasmid-encoded functions have been discovered in cryptic plasmids originating from Lactobacillus, Streptococcus thermophilus, and Pediococcus spp. and can be used as selective marker systems in vector construction. This article presents information concerning LAB cryptic plasmids, and their structures, functions, and applications. A total of 134 cryptic plasmids collated are discussed.
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Affiliation(s)
- Julie Shareck
- Department of Food Science and Agricultural Chemistry, McGill University, Ste-Anne-de-Bellevue, Quebec, Canada
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11
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Chang SM, Yan TR. DNA sequence analysis of a cryptic plasmid pL2 from Lactococcus lactis subsp. lactis. Biotechnol Lett 2007; 29:1519-27. [PMID: 17563858 DOI: 10.1007/s10529-007-9418-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2007] [Revised: 05/03/2007] [Accepted: 05/08/2007] [Indexed: 11/28/2022]
Abstract
A cryptic plasmid pL2 was isolated from Lactococcus lactis subsp. lactis and its complete nucleotide sequence was determined (5,299 bp, GenBank accession No. DQ917780). Its replication mode was identified as a theta-type belonging to the pAM beta 1 family. Analysis of the nucleotide sequence revealed that pL2 contained a transfer origin, a replication origin, and five putative open reading frames (ORF1-5). ORF1 (386 amino acids) was homologous to replication protein RepB. The other open reading frames were cryptic. A small counter-transcript RNA (ctRNA) coding region was also observed.
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Affiliation(s)
- Shiao-Ming Chang
- Institute of Bioengineering, Tatung University, Taipei, 104, Taiwan
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12
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Lee JH, Halgerson JS, Kim JH, O'Sullivan DJ. Comparative sequence analysis of plasmids from Lactobacillus delbrueckii and construction of a shuttle cloning vector. Appl Environ Microbiol 2007; 73:4417-24. [PMID: 17526779 PMCID: PMC1932812 DOI: 10.1128/aem.00099-07] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
While plasmids are very commonly associated with the majority of the lactic acid bacteria, they are only very rarely associated with Lactobacillus delbrueckii, with only four characterized to date. In this study, the complete sequence of a native plasmid, pDOJ1, from a strain of Lactobacillus delbrueckii subsp. bulgaricus was determined. It consisted of a circular DNA molecule of 6,220 bp with a G+C content of 44.6% and a characteristic ori and encoded six open reading frames (ORFs), of which functions could be predicted for three-a mobilization (Mob) protein, a transposase, and a fused primase-helicase replication protein. Comparative analysis of pDOJ1 and the other available L. delbrueckii plasmids (pLBB1, pJBL2, pN42, and pLL1212) revealed a very similar organization and amino acid identities between 85 and 98% for the putative proteins of all six predicted ORFs from pDOJ1, reflecting a common origin for L. delbrueckii plasmids. Analysis of the fused primase-helicase replication gene found a similar fused organization only in the theta replicating group B plasmids from Streptococcus thermophilus. This observation and the ability of the replicon to function in S. thermophilus support the idea that the origin of plasmids in L. delbrueckii was likely from S. thermophilus. This may reflect the close association of these two species in dairy fermentations, particularly yogurt production. As no vector based on plasmid replicons from L. delbrueckii has previously been constructed, an Escherichia coli-L. delbrueckii shuttle cloning vector, pDOJ4, was constructed from pDOJ1, the p15A ori, the chloramphenicol resistance gene of pCI372, and the lacZ polylinker from pUC18. This cloning vector was successfully introduced into E. coli, L. delbrueckii subsp. bulgaricus, S. thermophilus, and Lactococcus lactis. This shuttle cloning vector provides a new tool for molecular analysis of Lactobacillus delbrueckii and other lactic acid bacteria.
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Affiliation(s)
- Ju-Hoon Lee
- Department of Food Science and Nutrition and Center for Microbial and Plant Genomics, University of Minnesota, Cargill Building for Microbial and Plant Genomics, St. Paul, MN 55108, USA
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Vegge CS, Vogensen FK, Mc Grath S, Neve H, van Sinderen D, Brøndsted L. Identification of the lower baseplate protein as the antireceptor of the temperate lactococcal bacteriophages TP901-1 and Tuc2009. J Bacteriol 2006; 188:55-63. [PMID: 16352821 PMCID: PMC1317572 DOI: 10.1128/jb.188.1.55-63.2006] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The first step in the infection process of tailed phages is recognition and binding to the host receptor. This interaction is mediated by the phage antireceptor located in the distal tail structure. The temperate Lactococcus lactis phage TP901-1 belongs to the P335 species of the Siphoviridae family, which also includes the related phage Tuc2009. The distal tail structure of TP901-1 is well characterized and contains a double-disk baseplate and a central tail fiber. The structural tail proteins of TP901-1 and Tuc2009 are highly similar, but the phages have different host ranges and must therefore encode different antireceptors. In order to identify the antireceptors of TP901-1 and Tuc2009, a chimeric phage was generated in which the gene encoding the TP901-1 lower baseplate protein (bppL(TP901-1)) was exchanged with the analogous gene (orf53(2009)) of phage Tuc2009. The chimeric phage (TP901-1C) infected the Tuc2009 host strain efficiently and thus displayed an altered host range compared to TP901-1. Genomic analysis and sequencing verified that TP901-1C is a TP901-1 derivative containing the orf53(2009) gene in exchange for bppL(TP901-1); however, a new sequence in the late promoter region was also discovered. Protein analysis confirmed that TP901-1C contains ORF53(2009) and not the lower baseplate protein BppL(TP901-1), and it was concluded that BppL(TP901-1) and ORF53(2009) constitute antireceptor proteins of TP901-1 and Tuc2009, respectively. Electron micrographs revealed altered baseplate morphology of TP901-1C compared to that of the parental phage.
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Affiliation(s)
- Christina S Vegge
- Department of Veterinary Pathobiology, The Royal Veterinary and Agricultural University, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
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Mills S, Coffey A, Hill C, Fitzgerald GF, McAuliffe O, Ross RP. Insertional inactivation of determinants for Mg2+ and Co2+ transport as a tool for screening recombinant Lactococcus species clones. Appl Environ Microbiol 2005; 71:4897-901. [PMID: 16085892 PMCID: PMC1183277 DOI: 10.1128/aem.71.8.4897-4901.2005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Insertional inactivation of the plasmid-encoded determinants for Mg(2+) and Co(2+) transport, orf18/corA, provides a tool for screening recombinant clones in Lactococcus, based on the observation that overexpression of orf18/corA results in cell growth inhibition on certain concentrations of CoCl(2). The lacticin 3147 immunity gene, ltnI, was used to insertionally inactivate orf18/corA. The resulting clones were capable of growth on concentrations of CoCl(2) that were inhibitory to the parent strain. Since only 3 of 17 lactococcal starters naturally harbor corA, the system has potential as a screen for selecting recombinant lactococcal clones.
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Affiliation(s)
- Susan Mills
- Teagasc, Dairy Products Research Centre, Moorepark, Fermoy, County Cork, Ireland
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15
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Sørvig E, Skaugen M, Naterstad K, Eijsink VGH, Axelsson L. Plasmid p256 from Lactobacillus plantarum represents a new type of replicon in lactic acid bacteria, and contains a toxin-antitoxin-like plasmid maintenance system. MICROBIOLOGY-SGM 2005; 151:421-431. [PMID: 15699191 DOI: 10.1099/mic.0.27389-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Lactobacillus plantarum NC7 harbours a single 7.2 kb plasmid called p256. This report describes the complete nucleotide sequence and annotation of p256, as well as the identification of the minimal replicon of the plasmid. Based on sequence features in the unusually small (0.7 kb) minimal replicon, and the absence of a gene for a replication-relevant protein, p256 seems to represent a hitherto unknown type of theta replicon in lactic acid bacteria (LAB), with a relatively low copy-number. In addition, a putative toxin-antitoxin (TA) locus was identified. Experiments with variants of p256 indicated that the TA system was involved in plasmid maintenance. Furthermore, controlled expression of the TA genes stabilized vectors derived from the p256 replicon. To the authors' knowledge, this is the first time a TA locus with a demonstrated plasmid maintenance function has been identified in LAB. Transformation of several LAB with plasmids derived from p256 indicated that it has a narrow host range. Several effective expression vectors based on the p256 replicon have been constructed.
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Affiliation(s)
- Elisabeth Sørvig
- Matforsk, Norwegian Food Research Institute, Osloveien 1, N-1430 Ås, Norway
- Department of Chemistry, Biotechnology and Food Science, Agricultural University of Norway, PO Box 5003, N-1432 Ås, Norway
| | - Morten Skaugen
- Department of Chemistry, Biotechnology and Food Science, Agricultural University of Norway, PO Box 5003, N-1432 Ås, Norway
| | - Kristine Naterstad
- Matforsk, Norwegian Food Research Institute, Osloveien 1, N-1430 Ås, Norway
| | - Vincent G H Eijsink
- Department of Chemistry, Biotechnology and Food Science, Agricultural University of Norway, PO Box 5003, N-1432 Ås, Norway
| | - Lars Axelsson
- Matforsk, Norwegian Food Research Institute, Osloveien 1, N-1430 Ås, Norway
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Sturino JM, Klaenhammer TR. Bacteriophage defense systems and strategies for lactic acid bacteria. ADVANCES IN APPLIED MICROBIOLOGY 2005; 56:331-78. [PMID: 15566985 DOI: 10.1016/s0065-2164(04)56011-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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O'Driscoll J, Glynn F, Cahalane O, O'Connell-Motherway M, Fitzgerald GF, Van Sinderen D. Lactococcal plasmid pNP40 encodes a novel, temperature-sensitive restriction-modification system. Appl Environ Microbiol 2004; 70:5546-56. [PMID: 15345443 PMCID: PMC520859 DOI: 10.1128/aem.70.9.5546-5556.2004] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel restriction-modification system, designated LlaJI, was identified on pNP40, a naturally occurring 65-kb plasmid from Lactococcus lactis. The system comprises four adjacent similarly oriented genes that are predicted to encode two m(5)C methylases and two restriction endonucleases. The LlaJI system, when cloned into a low-copy-number vector, was shown to confer resistance against representatives of the three most common lactococcal phage species. This phage resistance phenotype was found to be strongly temperature dependent, being most effective at 19 degrees C. A functional analysis confirmed that the predicted methylase-encoding genes, llaJIM1 and llaJIM2, were both required to mediate complete methylation, while the assumed restriction enzymes, specified by llaJIR1 and llaJIR2, were both necessary for the complete restriction phenotype. A Northern blot analysis revealed that the four LlaJI genes are part of a 6-kb operon and that the relative abundance of the LlaJI-specific mRNA in the cells does not appear to contribute to the observed temperature-sensitive profile. This was substantiated by use of a LlaJI promoter-lacZ fusion, which further revealed that the LlaJI operon appears to be subject to transcriptional regulation by an as yet unidentified element(s) encoded by pNP40.
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Affiliation(s)
- Jonathan O'Driscoll
- Department of Microbiology, University College Cork, Western Road, Cork, Ireland
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18
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Mruk I, Cichowicz M, Kaczorowski T. Characterization of the LlaCI methyltransferase from Lactococcus lactis subsp. cremoris W15 provides new insights into the biology of type II restriction-modification systems. MICROBIOLOGY-SGM 2004; 149:3331-3341. [PMID: 14600245 DOI: 10.1099/mic.0.26562-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The gene encoding the LlaCI methyltransferase (M.LlaCI) from Lactococcus lactis subsp. cremoris W15 was overexpressed in Escherichia coli. The enzyme was purified to apparent homogeneity using three consecutive steps of chromatography on phosphocellulose, blue-agarose and Superose 12HR, yielding a protein of M(r) 31 300+/-1000 under denaturing conditions. The exact position of the start codon AUG was determined by protein microsequencing. This enzyme recognizes the specific palindromic sequence 5'-AAGCTT-3'. Purified M.LlaCI was characterized. Unlike many other methyltransferases, M.LlaCI exists in solution predominantly as a dimer. It modifies the first adenine residue at the 5' end of the specific sequence to N(6)-methyladenine and thus is functionally identical to the corresponding methyltransferases of the HindIII (Haemophilus influenzae Rd) and EcoVIII (Escherichia coli E1585-68) restriction-modification systems. This is reflected in the identity of M.LlaCI with M.HindIII and M.EcoVIII noted at the amino acid sequence level (50 % and 62 %, respectively) and in the presence of nine sequence motifs conserved among N(6)-adenine beta-class methyltransferases. However, polyclonal antibodies raised against M.EcoVIII cross-reacted with M.LlaCI but not with M.HindIII. Restriction endonucleases require Mg(2+) for phosphodiester bond cleavage. Mg(2+) was shown to be a strong inhibitor of the M.LlaCI enzyme and its isospecific homologues. This observation suggests that sensitivity of the M.LlaCI to Mg(2+) may strengthen the restriction activity of the cognate endonuclease in the bacterial cell. Other biological implications of this finding are also discussed.
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Affiliation(s)
- Iwona Mruk
- Department of Microbiology, University of Gdańsk, Kładki 24, 80-822 Gdańsk, Poland
| | - Magdalena Cichowicz
- Department of Microbiology, University of Gdańsk, Kładki 24, 80-822 Gdańsk, Poland
| | - Tadeusz Kaczorowski
- Department of Microbiology, University of Gdańsk, Kładki 24, 80-822 Gdańsk, Poland
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Turgeon N, Frenette M, Moineau S. Characterization of a theta-replicating plasmid from Streptococcus thermophilus. Plasmid 2004; 51:24-36. [PMID: 14711526 DOI: 10.1016/j.plasmid.2003.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Plasmids of Streptococcus thermophilus were previously classified, based on DNA homology, into at least four groups (A-D). Here, we report the characterization of plasmids of group B and D. The sequence analysis of pSMQ173b (group D) indicates that this plasmid contains 4449 bp, five open reading frames (ORFs) and replicates via the rolling-circle mechanism of the pGI3 family. The plasmid pSMQ308 (group B) contains 8144 bp and six ORFs. Two ORFs likely encode a primase/helicase and an integrase. Northern blot experiments demonstrate that these two orfs are transcribed within the three strains containing plasmids of group B. Two-dimensional agarose gel electrophoresis shows that pSMQ308 replicates via a theta mechanism. To our knowledge, this is the first report of a plasmid replicating via a theta mode in S. thermophilus. Finally, a classification of 20 sequenced S. thermophilus plasmids into six groups based on their mode of replication is proposed.
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Affiliation(s)
- Nathalie Turgeon
- Département de biochimie et de microbiologie, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, Canada G1K 7P4
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20
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Daming R, Yinyu W, Zilai W, Jun C, Hekui L, Jingye Z. Complete DNA sequence and analysis of two cryptic plasmids isolated from Lactobacillus plantarum. Plasmid 2003; 50:70-3. [PMID: 12826059 DOI: 10.1016/s0147-619x(03)00010-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The complete nucleotide sequence of two cryptic plasmids isolated from Lactobacillus plantarum strain AS1.2986 has been determined. The smaller plasmid, designated pLP2000, encodes a 37.0kDa Rep protein and has a 17bp sequence repeated 10 times. Sequence analysis of the larger plasmid, designated pLP9000, revealed nine putative open reading frames (ORFs). Based on sequence similarity, ORF1 codes for a putative magnesium transporter protein that shows similarities to CorA from plasmid pCIS3 (Lactococcus lactis). None of the nine ORFs shows similarity to any known Rep protein. Southern blot analysis indicates these two plasmids both replicate via a rolling circle (RC) mechanism.
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Affiliation(s)
- Ren Daming
- State Key Laboratory of Genetic Engineering, Institute of Genetics, Fudan University, Shanghai 200433, People's Republic of China.
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21
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Kobayashi M, Nomura M, Fujita Y, Okamoto T, Ohmomo S. Influence of lactococcal plasmid on the specific growth rate of host cells. Lett Appl Microbiol 2003; 35:403-8. [PMID: 12390490 DOI: 10.1046/j.1472-765x.2002.01213.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS To investigate a lactococcal plasmid responsible for a reduction in growth rate of its host cell. METHODS AND RESULTS Lactococcus lactis subsp. lactis biovar. diacetylactis DRC1 carries a high number of plasmids. The DRC1 wild-type strain was found to grow more slowly than a plasmid-free derivative of DRC1. The plasmids extracted from DRC1 together with an indicator plasmid were cotransformed into the plasmid-free strain DRC1021. A 7.4-kb cryptic plasmid, designated pDR1-1, was found to significantly affect the maximum specific growth rate ( micro max) of the host cell. Polymerase chain reaction (PCR) analysis was carried out in order to detect the presence of pDR1-1 in the other L. lactis strains. The micro max of the single pDR1-1-positive strain was determined to be the same as that of DRC1. SIGNIFICANCE AND IMPACT OF THE STUDY These results suggest that pDR1-1 (or a pDR1-1-like plasmid) is a critical factor in the reduction of the micro max of DRC1, and that its effect on the micro max is significantly greater than that of any other coexisting plasmid.
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Affiliation(s)
- M Kobayashi
- Department of Animal Products Research, National Institute of Livestock and Grassland Science, Norindanchi, Tsukuba, Japan.
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22
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Bourniquel AA, Casey MG, Mollet B, Pridmore RD. DNA sequence and functional analysis of Lactobacillus delbrueckii subsp. lactis plasmids pN42 and pJBL2. Plasmid 2002; 47:153-7. [PMID: 11982337 DOI: 10.1006/plas.2001.1560] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The plasmids pN42 and pJBL2 were isolated from the Lactobacillus delbrueckii subsp. lactis strains NCC88 and JCL414. DNA sequence determination and bioinformatic analysis revealed a strikingly conserved genetic organization containing five major, highly conserved open reading frames (ORFs). Transformation studies indicated that ORF2 (consisting of a primase fused to a replicative DNA helicase), ori, and ORF3 constitute the minimal requirements for replication of pN42 in the heterologous host Lactococcus lactis. The ORF1's are predicted to encode type I restriction-modification (R-M) system HsdS subunits with different specificities on either plasmid, suggesting that these plasmids may be involved in host defense by expanding their host R-M system repertoire. These plasmids constitute the basis for the construction of novel L. delbrueckii vectors.
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Affiliation(s)
- Aude A Bourniquel
- Department of Molecular Microbiology, Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland
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23
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Boucher I, Emond E, Parrot M, Moineau S. DNA sequence analysis of three Lactococcus lactis plasmids encoding phage resistance mechanisms. J Dairy Sci 2001; 84:1610-20. [PMID: 11467810 DOI: 10.3168/jds.s0022-0302(01)74595-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The three Lactococcus lactis plasmids pSRQ700, pSRQ800, and pSRQ900 encode the previously described anti-phage resistance mechanisms LlaDCHI, AbiK, and AbiQ, respectively. Since these plasmids are likely to be introduced into industrial Lactococcus lactis strains used to manufacture commercial fermented dairy products, their complete DNA sequences were determined and analyzed. The plasmids pSRQ700 (7784 bp), pSRQ800 (7858 bp), and pSRQ900 (10,836 bp) showed a similar genetic organization including a common lactococcal theta-type replicon. A second replication module showing features of the pMV158 family of rolling circle replicons was also found on pSRQ700. The theta replication regions of the three plasmids were associated with two additional coding regions, one of which encodes for HsdS, the specificity subunit of the type I restriction/modification system. When introduced into L. lactis IL1403, the HsdS of pSRQ800 and pSRQ900 conferred a weak resistance against phage P008 (936 species). These results indicated that both HsdS subunits can complement the chromosomally encoded type I restriction/modification system in IL1403. The genes involved in the phage resistance systems LlaDCHI, AbiK, and AbiQ were found in close proximity to and downstream of the replication modules. In pSRQ800 and pSRQ900, transfer origins and putative tyrosine recombinases were found upstream of the theta replicons. Genes encoding recombination proteins were also found on pSRQ700. Finally, open reading frames associated with bacteriocin production were found on pSRQ900, but no anti-lactococcal activity was detected. Based on our current knowledge, these three plasmids are safe and suitable for food-grade applications.
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Affiliation(s)
- I Boucher
- Department of Biochemistry and Microbiology, Faculté des Sciences et de Génie, Faculté de Médecine Dentaire, Université Laval, Quebec, Canada
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24
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Emond E, Lavallée R, Drolet G, Moineau S, LaPointe G. Molecular characterization of a theta replication plasmid and its use for development of a two-component food-grade cloning system for Lactococcus lactis. Appl Environ Microbiol 2001; 67:1700-9. [PMID: 11282624 PMCID: PMC92788 DOI: 10.1128/aem.67.4.1700-1709.2001] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
pCD4, a small, highly stable theta-replicating lactococcal plasmid, was used to develop a food-grade cloning system. Sequence analysis revealed five open reading frames and two putative cis-acting regions. None appears to code for undesirable phenotypes with regard to food applications. Functional analysis of the replication module showed that only the cis-acting ori region and the repB gene coding for the replication initiator protein were needed for the stable replication and maintenance of pCD4 derivatives in Lactococcus lactis. A two-component food-grade cloning system was derived from the pCD4 replicon. The vector pVEC1, which carries the functional pCD4 replicon, is entirely made up of L. lactis DNA and has no selection marker. The companion pCOM1 is a repB-deficient pCD4 derivative that carries an erythromycin resistance gene as a dominant selection marker. The pCOM1 construct can only replicate in L. lactis if trans complemented by the RepB initiator provided by pVEC1. Since only the cotransformants that carry both pVEC1 and pCOM1 can survive on plates containing erythromycin, pCOM1 can be used transiently to select cells that have acquired pVEC1. Due to the intrinsic incompatibility between these plasmids, pCOM1 can be readily cured from the cells grown on an antibiotic-free medium after the selection step. The system was used to introduce a phage resistance mechanism into the laboratory strain MG1363 of L. lactis and two industrial strains. The introduction of the antiphage barrier did not alter the wild-type plasmid profile of the industrial strains. The phenotype was stable after 100 generations and conferred an effective resistance phenotype against phages of the 936 and c2 species.
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Affiliation(s)
- E Emond
- Centre de recherche STELA, Département des sciences des aliments et de nutrition, Université Laval, Québec, Canada G1K 7P4.
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25
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O' Sullivan D, Ross RP, Twomey DP, Fitzgerald GF, Hill C, Coffey A. Naturally occurring lactococcal plasmid pAH90 links bacteriophage resistance and mobility functions to a food-grade selectable marker. Appl Environ Microbiol 2001; 67:929-37. [PMID: 11157264 PMCID: PMC92668 DOI: 10.1128/aem.67.2.929-937.2001] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacteriophage resistance plasmid pAH90 (26,490 bp) is a natural cointegrate plasmid formed via homologous recombination between the type I restriction-modification specificity determinants (hsdS) of two smaller lactococcal plasmids, pAH33 (6,159 bp) and pAH82 (20,331 bp), giving rise to a bacteriophage-insensitive mutant following phage challenge (D. O'Sullivan, D. P. Twomey, A. Coffey, C. Hill, G. F. Fitzgerald, and R. P. Ross, Mol. Microbiol. 36:866-876; 2000). In this communication we provide evidence that the recombination event is favored by phage infection. The entire nucleotide sequence of plasmid pAH90 was determined and found to contain 24 open reading frames (ORFs) responsible for phenotypes which include restriction-modification, phage adsorption inhibition, plasmid replication, cadmium resistance, cobalt transport, and conjugative mobilization. The cadmium resistance property, encoded by the cadA gene, which has an associated regulatory gene (cadC), is of particular interest, as it facilitated the selection of pAH90 in other phage-sensitive lactococci after electroporation. In addition, we report the identification of a group II self-splicing intron bounded by two exons which have the capacity to encode a relaxase implicated in conjugation in gram-positive bacteria. The functionality of this intron was evident by demonstrating splicing in vivo. Given that pAH90 encodes potent phage defense systems which act at different stages in the phage lytic cycle, the linkage of these with a food-grade selectable marker on a replicon that can be mobilized among lactococci has significant potential for natural strain improvement for industrial dairy fermentations which are susceptible to phage inhibition.
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Affiliation(s)
- D O' Sullivan
- Teagasc, Dairy Products Research Centre, Moorepark, Fermoy, Ireland
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26
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O'Sullivan D, Twomey DP, Coffey A, Hill C, Fitzgerald GF, Ross RP. Novel type I restriction specificities through domain shuffling of HsdS subunits in Lactococcus lactis. Mol Microbiol 2000; 36:866-75. [PMID: 10844674 DOI: 10.1046/j.1365-2958.2000.01901.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
This study identifies a natural system in Lactococcus lactis, in which a restriction modification specificity subunit resident on a 6159 bp plasmid (pAH33) alters the specificity of a functional R/M mechanism encoded by a 20.3 kb plasmid, pAH82. The new specificity was identified after phenotypic and molecular analysis of a 26.5 kb co-integrate plasmid (pAH90), which was detected after bacteriophage challenge of the parent strain. Analysis of the regions involved in the co-integration revealed that two novel hybrid hsdS genes had been formed during the co-integration event. The HsdS chimeras had interchanged the C- and N-terminal variable domains of the parent subunits, generating two new restriction specificities. Comparison of the parent hsdS genes with other type I specificity determinants revealed that the region of the hsdS genes responsible for the co-integration event is highly conserved among lactococcal type I hsdS determinants. Thus, as hsdS determinants are widespread in the genus Lactococcus, new restriction specificities may evolve rapidly after homologous recombination between these genes. This study demonstrates that, similar to previous observations in Gram-negative bacteria, a Gram-positive bacterium can acquire novel restriction specificities naturally through domain shuffling of resident HsdS subunits.
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Affiliation(s)
- D O'Sullivan
- Food Quality Department, Teagasc, Dairy Products Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
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