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van der Els S, Sheombarsing R, van Kempen T, Wels M, Boekhorst J, Bron PA, Kleerebezem M. Detection and classification of the integrative conjugative elements of Lactococcus lactis. BMC Genomics 2024; 25:324. [PMID: 38561675 PMCID: PMC10983677 DOI: 10.1186/s12864-024-10255-9] [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: 08/21/2023] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
Lactococcus lactis is widely applied by the dairy industry for the fermentation of milk into products such as cheese. Adaptation of L. lactis to the dairy environment often depends on functions encoded by mobile genetic elements (MGEs) such as plasmids. Other L. lactis MGEs that contribute to industrially relevant traits like antimicrobial production and carbohydrate utilization capacities belong to the integrative conjugative elements (ICE). Here we investigate the prevalence of ICEs in L. lactis using an automated search engine that detects colocalized, ICE-associated core-functions (involved in conjugation or mobilization) in lactococcal genomes. This approach enabled the detection of 36 candidate-ICEs in 69 L. lactis genomes. By phylogenetic analysis of conserved protein functions encoded in all lactococcal ICEs, these 36 ICEs could be classified in three main ICE-families that encompass 7 distinguishable ICE-integrases and are characterized by apparent modular-exchangeability and plasticity. Finally, we demonstrate that phylogenetic analysis of the conjugation-associated VirB4 ATPase function differentiates ICE- and plasmid-derived conjugation systems, indicating that conjugal transfer of lactococcal ICEs and plasmids involves genetically distinct machineries. Our genomic analysis and sequence-based classification of lactococcal ICEs creates a comprehensive overview of the conserved functional repertoires encoded by this family of MGEs in L. lactis, which can facilitate the future exploitation of the functional traits they encode by ICE mobilization to appropriate starter culture strains.
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Affiliation(s)
- Simon van der Els
- Host-Microbe Interactomics Group, Department of Animal Sciences, Wageningen University & Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
- NIZO B.V, Kernhemseweg 2, 6718, ZB, Ede, The Netherlands
- BE-Basic Foundation, Mijnbouwstraat 120, 2628 RX, Delft, The Netherlands
| | - Reshtrie Sheombarsing
- Host-Microbe Interactomics Group, Department of Animal Sciences, Wageningen University & Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
- NIZO B.V, Kernhemseweg 2, 6718, ZB, Ede, The Netherlands
| | | | - Michiel Wels
- NIZO B.V, Kernhemseweg 2, 6718, ZB, Ede, The Netherlands
| | - Jos Boekhorst
- Host-Microbe Interactomics Group, Department of Animal Sciences, Wageningen University & Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - Peter A Bron
- NIZO B.V, Kernhemseweg 2, 6718, ZB, Ede, The Netherlands
- BE-Basic Foundation, Mijnbouwstraat 120, 2628 RX, Delft, The Netherlands
| | - Michiel Kleerebezem
- Host-Microbe Interactomics Group, Department of Animal Sciences, Wageningen University & Research, De Elst 1, 6708 WD, Wageningen, The Netherlands.
- BE-Basic Foundation, Mijnbouwstraat 120, 2628 RX, Delft, The Netherlands.
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2
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Christensen LF, Laforce IN, Wolkers-Rooijackers JCM, Mortensen MS, Smid EJ, Hansen EB. Lactococcus cell envelope proteases enable lactococcal growth in minimal growth media supplemented with high molecular weight proteins of plant and animal origin. FEMS Microbiol Lett 2024; 371:fnae019. [PMID: 38479791 DOI: 10.1093/femsle/fnae019] [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: 11/25/2023] [Revised: 02/19/2024] [Accepted: 03/12/2024] [Indexed: 04/05/2024] Open
Abstract
Lactic acid bacteria (LAB) have evolved into fastidious microorganisms that require amino acids from environmental sources. Some LAB have cell envelope proteases (CEPs) that drive the proteolysis of high molecular weight proteins like casein in milk. CEP activity is typically studied using casein as the predominant substrate, even though CEPs can hydrolyze other protein sources. Plant protein hydrolysis by LAB has rarely been connected to the activity of specific CEPs. This study aims to show the activity of individual CEPs using LAB growth in a minimal growth medium supplemented with high molecular weight casein or potato proteins. Using Lactococcus cremoris MG1363 as isogenic background to express CEPs, we demonstrate that CEP activity is directly related to growth in the protein-supplemented minimal growth media. Proteolysis is analyzed based on the amino acid release, allowing a comparison of CEP activities and analysis of amino acid utilization by L. cremoris MG1363. This approach provides a basis to analyze CEP activity on plant-based protein substrates as casein alternatives and to compare activity of CEP homologs.
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Affiliation(s)
- Lise Friis Christensen
- National Food Institute, Technical University of Denmark, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
| | - Ida Nynne Laforce
- National Food Institute, Technical University of Denmark, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
| | | | - Martin Steen Mortensen
- National Food Institute, Technical University of Denmark, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
| | - Eddy J Smid
- Food Microbiology, Wageningen University & Research, PO Box 17, 6700AA Wageningen, The Netherlands
| | - Egon Bech Hansen
- National Food Institute, Technical University of Denmark, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
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3
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Douwenga S, van Olst B, Boeren S, Luo Y, Lai X, Teusink B, Vervoort J, Kleerebezem M, Bachmann H. The hierarchy of sugar catabolization in Lactococcus cremoris. Microbiol Spectr 2023; 11:e0224823. [PMID: 37888986 PMCID: PMC10715065 DOI: 10.1128/spectrum.02248-23] [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: 05/29/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE The availability of nutrients to microorganisms varies considerably between different environments, and changes can occur rapidly. As a general rule, a fast growth rate-typically growth on glucose-is associated with the repression of other carbohydrate utilization genes, but it is not clear to what extent catabolite repression is exerted by other sugars. We investigated the hierarchy of sugar utilization after substrate transitions in Lactococcus cremoris. For this, we determined the proteome and carbohydrate utilization capacity after growth on different sugars. The results show that the preparedness of cells for the utilization of "slower" sugars is not strictly determined by the growth rate. The data point to individual proteins relevant for various sugar transitions and suggest that the evolutionary history of the organism might be responsible for deviations from a strictly growth rate-related sugar catabolization hierarchy.
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Affiliation(s)
- Sieze Douwenga
- TI Food and Nutrition, Wageningen, the Netherlands
- Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Berdien van Olst
- TI Food and Nutrition, Wageningen, the Netherlands
- Host-Microbe Interactomics, Wageningen University & Research, Wageningen, the Netherlands
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Sjef Boeren
- TI Food and Nutrition, Wageningen, the Netherlands
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Yanzhang Luo
- MAGNEtic resonance research FacilitY (MAGNEFY), Wageningen University & Research, Wageningen, the Netherlands
| | - Xin Lai
- Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Bas Teusink
- TI Food and Nutrition, Wageningen, the Netherlands
- Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Jacques Vervoort
- TI Food and Nutrition, Wageningen, the Netherlands
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Michiel Kleerebezem
- TI Food and Nutrition, Wageningen, the Netherlands
- Host-Microbe Interactomics, Wageningen University & Research, Wageningen, the Netherlands
| | - Herwig Bachmann
- TI Food and Nutrition, Wageningen, the Netherlands
- Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Microbiology Department, NIZO Food Research, Ede, the Netherlands
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4
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Zhao G, Zhao S, Hagner Nielsen L, Zhou F, Gu L, Tilahun Tadesse B, Solem C. Transforming acid whey into a resource by selective removal of lactic acid and galactose using optimized food-grade microorganisms. BIORESOURCE TECHNOLOGY 2023; 387:129594. [PMID: 37532060 DOI: 10.1016/j.biortech.2023.129594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/26/2023] [Accepted: 07/30/2023] [Indexed: 08/04/2023]
Abstract
The presence of lactic acid and galactose makes spray drying of acid whey (AW) a significant challenge for the dairy industry. In this study, a novel approach is explored to remove these compounds, utilizing food-grade microorganisms. For removing lactic acid, Corynebacterium glutamicum was selected, which has an inherent ability to metabolize lactic acid but does so slowly. To accelerate lactic acid metabolism, a mutant strain G6006 was isolated through adaptive laboratory evolution, which metabolized all lactic acid from AW two times faster than its parent strain. To eliminate galactose, a lactose-negative mutant of Lactococcus lactis that cannot produce lactate was generated. This strain was then co-cultured with G6006 to maximize the removal of both lactic acid and galactose. The microbially "filtered" AW could readily be spray dried into a stable lactose powder. This study highlights the potential of utilizing food-grade microorganisms to process AW, which currently constitutes a global challenge.
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Affiliation(s)
- Ge Zhao
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Shuangqing Zhao
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Line Hagner Nielsen
- DTU Health Tech, Department of Health Technology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Fa Zhou
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Liuyan Gu
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Belay Tilahun Tadesse
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Christian Solem
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
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5
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Phenotypic and Safety Assessment of the Cheese Strain Lactiplantibacillus plantarum LL441, and Sequence Analysis of its Complete Genome and Plasmidome. Int J Mol Sci 2022; 24:ijms24010605. [PMID: 36614048 PMCID: PMC9820265 DOI: 10.3390/ijms24010605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
This work describes the phenotypic typing and complete genome analysis of LL441, a dairy Lactiplantibacillus plantarum strain. LL441 utilized a large range of carbohydrates and showed strong activity of some carbohydrate-degrading enzymes. The strain grew slowly in milk and produced acids and ketones along with other volatile compounds. The genome of LL441 included eight circular molecules, the bacterial chromosome, and seven plasmids (pLL441-1 through pLL441-7), ranging in size from 8.7 to 53.3 kbp. Genome analysis revealed vast arrays of genes involved in carbohydrate utilization and flavor formation in milk, as well as genes providing acid and bile resistance. No genes coding for virulence traits or pathogenicity factors were detected. Chromosome and plasmids were packed with insertion sequence (IS) elements. Plasmids were also abundant in genes encoding heavy metal resistance traits and plasmid maintenance functions. Technologically relevant phenotypes linked to plasmids, such as the production of plantaricin C (pLL441-1), lactose utilization (pLL441-2), and bacteriophage resistance (pLL441-4), were also identified. The absence of acquired antibiotic resistance and of phenotypes and genes of concern suggests L. plantarum LL441 be safe. The strain might therefore have a use as a starter or starter component in dairy and other food fermentations or as a probiotic.
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6
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Nagarajan D, Chen CY, Ariyadasa TU, Lee DJ, Chang JS. Macroalgal biomass as a potential resource for lactic acid fermentation. CHEMOSPHERE 2022; 309:136694. [PMID: 36206920 DOI: 10.1016/j.chemosphere.2022.136694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/25/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Lactic acid is an essential platform chemical with various applications in the chemicals, food, pharmaceutical, and cosmetic industries. Currently, the demand for lactic acid is driven by the role of lactic acid as the starting material for the production of bioplastic polylactide. Microbial fermentation for lactic acid production is favored due to the production of enantiomerically pure lactic acid required for polylactide synthesis, as opposed to the racemic mixture obtained via chemical synthesis. The utilization of first-generation feedstock for commercial lactic acid production is challenged by feedstock costs and sustainability issues. Macroalgae are photosynthetic benthic aquatic plants that contribute tremendously towards carbon capture with subsequent carbon-rich biomass production. Macroalgae are commercially cultivated to extract hydrocolloids, and recent studies have focused on applying biomass as a fermentation feedstock. This review provides comprehensive information on the design and development of sustainable and cost-effective, algae-based lactic acid production. The central carbon regulation in lactic acid bacteria and the metabolism of seaweed-derived sugars are described. An exhaustive compilation of lactic acid fermentation of macroalgae hydrolysates revealed that lactic acid bacteria can effectively ferment the mixture of sugars present in the hydrolysate with comparable yields. The environmental impacts and economic prospects of macroalgal lactic acid are analyzed. Valorization of the vast amounts of spent macroalgal biomass residue post hydrocolloid extraction in a biorefinery is a viable strategy for cost-effective lactic acid production.
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Affiliation(s)
- Dillirani Nagarajan
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan.
| | - Chun-Yen Chen
- University Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan; Research Center for Circular Economy, National Cheng Kung University, Tainan, Taiwan
| | - Thilini U Ariyadasa
- Department of Chemical and Process Engineering, Faculty of Engineering, University of Moratuwa, Moratuwa, 10400, Sri Lanka
| | - Duu-Jong Lee
- Department of Mechanical Engineering, City University of Hong Kong, Kowloon Tang, Hong Kong
| | - Jo-Shu Chang
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan; Department of Chemical and Materials Engineering, Tunghai University, Taichung, 407, Taiwan; Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung, 407, Taiwan; Department of Chemical Engineering and Materials Science, Yuan Ze University, Chung-Li, 32003, Taiwan.
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7
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Flórez AB, Vázquez L, Rodríguez J, Mayo B. Directed Recovery and Molecular Characterization of Antibiotic Resistance Plasmids from Cheese Bacteria. Int J Mol Sci 2021; 22:7801. [PMID: 34360567 PMCID: PMC8346141 DOI: 10.3390/ijms22157801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/13/2021] [Accepted: 07/19/2021] [Indexed: 02/07/2023] Open
Abstract
Resistance to antimicrobials is a growing problem of worldwide concern. Plasmids are thought to be major drivers of antibiotic resistance spread. The present work reports a simple way to recover replicative plasmids conferring antibiotic resistance from the bacteria in cheese. Purified plasmid DNA from colonies grown in the presence of tetracycline and erythromycin was introduced into plasmid-free strains of Lactococcus lactis, Lactiplantibacillus plantarum and Lacticaseibacillus casei. Following antibiotic selection, the plasmids from resistant transformants were isolated, analyzed by restriction enzyme digestion, and sequenced. Seven patterns were obtained for the tetracycline-resistant colonies, five from L. lactis, and one each from the lactobacilli strains, as well as a single digestion profile for the erythromycin-resistant transformants obtained in L. lactis. Sequence analysis respectively identified tet(S) and ermB in the tetracycline- and erythromycin-resistance plasmids from L. lactis. No dedicated resistance genes were detected in plasmids conferring tetracycline resistance to L. casei and L. plantarum. The present results highlight the usefulness of the proposed methodology for isolating functional plasmids that confer antibiotic resistance to LAB species, widen our knowledge of antibiotic resistance in the bacteria that inhabit cheese, and emphasize the leading role of plasmids in the spread of resistance genes via the food chain.
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Affiliation(s)
- Ana Belén Flórez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain; (L.V.); (J.R.); (B.M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
| | - Lucía Vázquez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain; (L.V.); (J.R.); (B.M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
| | - Javier Rodríguez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain; (L.V.); (J.R.); (B.M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
| | - Baltasar Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain; (L.V.); (J.R.); (B.M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
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8
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Hansen EB, Marcatili P. Modeled Structure of the Cell Envelope Proteinase of Lactococcus lactis. Front Bioeng Biotechnol 2021; 8:613986. [PMID: 33415101 PMCID: PMC7783315 DOI: 10.3389/fbioe.2020.613986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 12/02/2020] [Indexed: 11/23/2022] Open
Abstract
The cell envelope proteinase (CEP) of Lactococcus lactis is a large extracellular protease covalently linked to the peptidoglycan of the cell wall. Strains of L. lactis are typically auxotrophic for several amino acids and in order to grow to high cell densities in milk they need an extracellular protease. The structure of the entire CEP enzyme is difficult to determine experimentally due to the large size and due to the attachment to the cell surface. We here describe the use of a combination of structure prediction tools to create a structural model for the entire CEP enzyme of Lactococcus lactis. The model has implications for how the bacterium interacts with casein micelles during growth in milk, and it has implications regarding the energetics of the proteolytic system. Our model for the CEP indicates that the catalytic triad is activated through a structural change caused by interaction with the substrate. The CEP of L. lactis might become a useful model for the mode of action for enzymes belonging to the large class of S8 proteinases with a PA (protease associated) domain and a downstream fibronectin like domain.
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Affiliation(s)
- Egon Bech Hansen
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Demark
| | - Paolo Marcatili
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Demark
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9
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Higdon SM, Huang BC, Bennett AB, Weimer BC. Identification of Nitrogen Fixation Genes in Lactococcus Isolated from Maize Using Population Genomics and Machine Learning. Microorganisms 2020; 8:microorganisms8122043. [PMID: 33419343 PMCID: PMC7768417 DOI: 10.3390/microorganisms8122043] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/08/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023] Open
Abstract
Sierra Mixe maize is a landrace variety from Oaxaca, Mexico, that utilizes nitrogen derived from the atmosphere via an undefined nitrogen fixation mechanism. The diazotrophic microbiota associated with the plant’s mucilaginous aerial root exudate composed of complex carbohydrates was previously identified and characterized by our group where we found 23 lactococci capable of biological nitrogen fixation (BNF) without containing any of the proposed essential genes for this trait (nifHDKENB). To determine the genes in Lactococcus associated with this phenotype, we selected 70 lactococci from the dairy industry that are not known to be diazotrophic to conduct a comparative population genomic analysis. This showed that the diazotrophic lactococcal genomes were distinctly different from the dairy isolates. Examining the pangenome followed by genome-wide association study and machine learning identified genes with the functions needed for BNF in the maize isolates that were absent from the dairy isolates. Many of the putative genes received an ‘unknown’ annotation, which led to the domain analysis of the 135 homologs. This revealed genes with molecular functions needed for BNF, including mucilage carbohydrate catabolism, glycan-mediated host adhesion, iron/siderophore utilization, and oxidation/reduction control. This is the first report of this pathway in this organism to underpin BNF. Consequently, we proposed a model needed for BNF in lactococci that plausibly accounts for BNF in the absence of the nif operon in this organism.
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Affiliation(s)
- Shawn M. Higdon
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (S.M.H.); (A.B.B.)
| | - Bihua C. Huang
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA;
- 100 K Pathogen Genome Project, University of California, Davis, CA 95616, USA
| | - Alan B. Bennett
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (S.M.H.); (A.B.B.)
| | - Bart C. Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA;
- 100 K Pathogen Genome Project, University of California, Davis, CA 95616, USA
- Correspondence:
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10
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Ji D, Ma J, Xu M, Agyei D. Cell-envelope proteinases from lactic acid bacteria: Biochemical features and biotechnological applications. Compr Rev Food Sci Food Saf 2020; 20:369-400. [PMID: 33443792 DOI: 10.1111/1541-4337.12676] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/27/2020] [Accepted: 10/30/2020] [Indexed: 01/25/2023]
Abstract
Proteins displayed on the cell surface of lactic acid bacteria (LAB) perform diverse and important biochemical roles. Among these, the cell-envelope proteinases (CEPs) are one of the most widely studied and most exploited for biotechnological applications. CEPs are important players in the proteolytic system of LAB, because they are required by LAB to degrade proteins in the growth media into peptides and/or amino acids required for the nitrogen nutrition of LAB. The most important area of application of CEPs is therefore in protein hydrolysis, especially in dairy products. Also, the physical location of CEPs (i.e., being cell-envelope anchored) allows for relatively easy downstream processing (e.g., extraction) of CEPs. This review describes the biochemical features and organization of CEPs and how this fits them for the purpose of protein hydrolysis. It begins with a focus on the genetic organization and expression of CEPs. The catalytic behavior and cleavage specificities of CEPs from various LAB are also discussed. Following this, the extraction and purification of most CEPs reported to date is described. The industrial applications of CEPs in food technology, health promotion, as well as in the growing area of water purification are discussed. Techniques for improving the production and catalytic efficiency of CEPs are also given an important place in this review.
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Affiliation(s)
- Dawei Ji
- Department of Food Science, University of Otago, Dunedin, New Zealand
| | - Jingying Ma
- Department of Food Science, University of Otago, Dunedin, New Zealand
| | - Min Xu
- Department of Food Science, University of Otago, Dunedin, New Zealand
| | - Dominic Agyei
- Department of Food Science, University of Otago, Dunedin, New Zealand
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11
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The large plasmidome of Lactococcus lactis subsp. lactis bv. diacetylactis S50 confers its biotechnological properties. Int J Food Microbiol 2020; 337:108935. [PMID: 33152568 DOI: 10.1016/j.ijfoodmicro.2020.108935] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 10/09/2020] [Accepted: 10/13/2020] [Indexed: 01/17/2023]
Abstract
Plasmids are autonomous episomally replicating genetic elements, which carry backbone genes important for the replication and maintenance within their host, and accessory genes that might confer an advantage to their host under specific selective pressure in its ecological niche. The genome of dairy isolate L. lactis subsp. lactis bv. diacetylactis S50 was sequenced using the PacBio SMRT Cell Seq-RSII platform and revealed to possess one of the largest plasmidomes among L. lactis strains studied so far, harboring six plasmids: pS6 (5553 bp), pS7a (7308 bp), pS7b (7266 bp), pS19 (19,027 bp), pS74 (74,256 bp) and pS127 (127,002 bp) in total representing 8.9% of genome size (240,412 bp). Based on predicted plasmid replication proteins and origins it appears that all six plasmids replicate via the theta-type mechanism. The two the largest plasmids (pS74 and pS127), carry a number of genes known to be important for growth and survival in the dairy environment. These genes encode technological functions such as bacteriocin production, protein degradation, magnesium and cobalt/nickel transporters, selenium binding, exopolysaccharides (EPS) production, bacteriophage and stress resistance. Beside genes for replication, the small plasmids (pS6, pS7a, pS7a, and pS19) also carry genes important for mobilization and host survival such as type I restriction-modification (R-M) system, metal transporters, enzymes and transcriptional regulators. All plasmids in S50 strain are mobilizable, containing an oriT sequences, while pS127 is self-conjugative and allows for mobilization of the other plasmids. Small plasmids are prone to structural and segregational instability, while pS127 appeared to be segregationally stable thanks to the possession of two partition systems. The main characteristic of plasmid pS74 is EPS production, while plasmid pS127 is characterized by proteinase and multiple bacteriocins, tra locus, phage abortive systems and metal transporters. In addition to LcnA and LcnB, plasmid pS127 encodes several bacteriocin-pheromone molecules and a new bacteriocin named LcnS50, with narrow spectrum of action limited to lactococci, that has been successfully cloned and heterologously expressed.
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12
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Hernandez-Valdes JA, Dalglish MM, Hermans J, Kuipers OP. Development of Lactococcus lactis Biosensors for Detection of Sulfur-Containing Amino Acids. Front Microbiol 2020; 11:1654. [PMID: 32760389 PMCID: PMC7375092 DOI: 10.3389/fmicb.2020.01654] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/25/2020] [Indexed: 11/24/2022] Open
Abstract
The sulfur-containing amino acids methionine and cysteine play an important role in food industry. These amino acids are used to confer a sulfur smell or meat-related aroma to food products. Besides their use as food additives, methionine and cysteine participate in flavor formation in dairy fermentations. For instance, the characteristic aroma of Cheddar cheeses is derived from methionine. Therefore, bacterial strains with the ability to overproduce and secrete these amino acids are relevant for the food industry. In addition, the quantification of these compounds in food matrices is a laborious task that involves sample preparation and specific analytical methods such as high-performance liquid chromatography. The ability of bacteria to naturally sense metabolites has successfully been exploited to develop biosensors. The presence of a specific metabolite is sensed by the biosensors, and it is subsequently translated into the expression of one or more reporter genes. In this study we aim to develop biosensors to detect methionine and cysteine, which are produced and secreted by wild-type Lactococcus lactis strains. We employed two strategies to create L. lactis biosensors, the first one is based on the methionine auxotrophy of this bacterium and the second strategy is based on a cysteine-responsive promoter. The characterization of the biosensors showed their specific response to the presence of these amino acids. Subsequently, we applied the methionine biosensor to quantify the presence of methionine in bacterial supernatants of wild-type L. lactis that naturally secretes methionine to benchmark the performance of our biosensors. The methionine biosensor responded linearly to the amounts of methionine present in the bacterial supernatants, i.e., the increases in the biosensor cell densities were proportional to the amounts of methionine present in the supernatants. The biosensors developed in this study tackle the limitations of amino acid quantification and the selection of strains with secretion of amino acids. These biosensors may eventually be used for screening of engineered strains to increase methionine and cysteine production, and may facilitate the detection of these amino acids in complex food matrices.
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Affiliation(s)
- Jhonatan A. Hernandez-Valdes
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | | | - Jos Hermans
- Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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13
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Ayala-Niño A, Rodríguez-Serrano GM, Jiménez-Alvarado R, Bautista-Avila M, Sánchez-Franco JA, González-Olivares LG, Cepeda-Saez A. Bioactivity of Peptides Released During Lactic Fermentation of Amaranth Proteins with Potential Cardiovascular Protective Effect: An In Vitro Study. J Med Food 2019; 22:976-981. [DOI: 10.1089/jmf.2019.0039] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Alexis Ayala-Niño
- Chemical Research Center, Autonomous University of Hidalgo State, Mineral de la Reforma, Hidalgo, Mexico
| | | | - Ruben Jiménez-Alvarado
- Post Harvest Laboratory, Autonomous University of Hidalgo State, Tulancingo, Hidalgo, Mexico
| | - Mirandeli Bautista-Avila
- Natural Products Pharmacology and Synthesis Laboratory, Autonomous University of Hidalgo State, Pachuca-Actopan, Hidalgo, Mexico
| | - José A. Sánchez-Franco
- Post Harvest Laboratory, Autonomous University of Hidalgo State, Tulancingo, Hidalgo, Mexico
| | - Luis G. González-Olivares
- Chemical Research Center, Autonomous University of Hidalgo State, Mineral de la Reforma, Hidalgo, Mexico
| | - Alberto Cepeda-Saez
- Food Hygiene, Inspection and Control Laboratory, University of Santiago de Compostela, Campus Lugo, University Campus, Lugo, Spain
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14
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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: 6] [Impact Index Per Article: 1.2] [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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15
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Li S, Bu T, Zheng J, Liu L, He G, Wu J. Preparation, Bioavailability, and Mechanism of Emerging Activities of Ile-Pro-Pro and Val-Pro-Pro. Compr Rev Food Sci Food Saf 2019; 18:1097-1110. [PMID: 33337010 DOI: 10.1111/1541-4337.12457] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 03/25/2019] [Accepted: 04/23/2019] [Indexed: 12/31/2022]
Abstract
Ile-Pro-Pro and Val-Pro-Pro are two most well-known food-derived bioactive peptides, initially identified as inhibitors of angiotensin I-converting enzyme (ACE) from a sample of sour milk. These two peptides were identified in fermented and enzymatic hydrolyzed cow and non-cow (that is, goat, sheep, buffalo, yak, camel, mare, and donkey) milk, as well as sourdough prepared from wheat, rye, and malt. Similar to other bioactive peptides, bioavailability of these peptides is low (about 0.1%), reaching picomolar concentration in human plasma; they showed blood pressure lowering activity in animals and in human, via improved endothelial function, activation of ACE2, and anti-inflammatory property. Emerging bioactivities of these two peptides toward against metabolic syndrome and bone-protection received limited attention, but may open up new applications of these peptides as functional food ingredients. Further studies are warranted to determine the best source as well as to identify novel enzymes (particularly from traditional fermented milk products) to improve the efficiency of production, to characterize possible peptide receptors using a combination of omics technology with molecular methods to understand if these two peptides act as signal-like molecules, to improve their bioavailability, and to explore new applications based on emerging bioactivities.
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Affiliation(s)
- Shanshan Li
- Zhejiang Key Laboratory for Agro-Food Processing, Fuli Inst. of Food Science, College of Biosystems Engineering and Food Science, Zhejiang Univ., 866 Yuhangtang Road, Hangzhou, 310058, China.,Ningbo Research Inst., Zhejiang Univ., Ningbo, 315100, China.,ZJU-UA Joint Lab for Molecular Nutrition and Bioactive Peptides, College of Biosystems Engineering and Food Science, Zhejiang Univ., Hangzhou, 310058, China
| | - Tingting Bu
- Zhejiang Key Laboratory for Agro-Food Processing, Fuli Inst. of Food Science, College of Biosystems Engineering and Food Science, Zhejiang Univ., 866 Yuhangtang Road, Hangzhou, 310058, China.,Ningbo Research Inst., Zhejiang Univ., Ningbo, 315100, China.,ZJU-UA Joint Lab for Molecular Nutrition and Bioactive Peptides, College of Biosystems Engineering and Food Science, Zhejiang Univ., Hangzhou, 310058, China
| | - Jiexia Zheng
- Zhejiang Key Laboratory for Agro-Food Processing, Fuli Inst. of Food Science, College of Biosystems Engineering and Food Science, Zhejiang Univ., 866 Yuhangtang Road, Hangzhou, 310058, China.,Ningbo Research Inst., Zhejiang Univ., Ningbo, 315100, China.,ZJU-UA Joint Lab for Molecular Nutrition and Bioactive Peptides, College of Biosystems Engineering and Food Science, Zhejiang Univ., Hangzhou, 310058, China
| | - Ling Liu
- Zhejiang Key Laboratory for Agro-Food Processing, Fuli Inst. of Food Science, College of Biosystems Engineering and Food Science, Zhejiang Univ., 866 Yuhangtang Road, Hangzhou, 310058, China.,Ningbo Research Inst., Zhejiang Univ., Ningbo, 315100, China.,ZJU-UA Joint Lab for Molecular Nutrition and Bioactive Peptides, College of Biosystems Engineering and Food Science, Zhejiang Univ., Hangzhou, 310058, China
| | - Guoqing He
- Zhejiang Key Laboratory for Agro-Food Processing, Fuli Inst. of Food Science, College of Biosystems Engineering and Food Science, Zhejiang Univ., 866 Yuhangtang Road, Hangzhou, 310058, China.,Ningbo Research Inst., Zhejiang Univ., Ningbo, 315100, China.,ZJU-UA Joint Lab for Molecular Nutrition and Bioactive Peptides, College of Biosystems Engineering and Food Science, Zhejiang Univ., Hangzhou, 310058, China
| | - Jianping Wu
- ZJU-UA Joint Lab for Molecular Nutrition and Bioactive Peptides, College of Biosystems Engineering and Food Science, Zhejiang Univ., Hangzhou, 310058, China.,Dept. of Agricultural, Food and Nutritional Science, 4-10 Ag/For Building, Univ. of Alberta, Edmonton, Alberta, T6G 2P5, Canada
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16
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Iskandar CF, Cailliez-Grimal C, Borges F, Revol-Junelles AM. Review of lactose and galactose metabolism in Lactic Acid Bacteria dedicated to expert genomic annotation. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.03.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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17
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Steensels J, Gallone B, Voordeckers K, Verstrepen KJ. Domestication of Industrial Microbes. Curr Biol 2019; 29:R381-R393. [DOI: 10.1016/j.cub.2019.04.025] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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18
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Kelleher P, Mahony J, Bottacini F, Lugli GA, Ventura M, van Sinderen D. The Lactococcus lactis Pan-Plasmidome. Front Microbiol 2019; 10:707. [PMID: 31019500 PMCID: PMC6458302 DOI: 10.3389/fmicb.2019.00707] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/20/2019] [Indexed: 01/01/2023] Open
Abstract
Plasmids are autonomous, self-replicating, extrachromosomal genetic elements that are typically not essential for growth of their host. They may encode metabolic capabilities, which promote the maintenance of these genetic elements, and may allow adaption to specific ecological niches and consequently enhance survival. Genome sequencing of 16 Lactococcus lactis strains revealed the presence of 83 plasmids, including two megaplasmids. The limitations of Pacific Biosciences SMRT sequencing in detecting the total plasmid complement of lactococcal strains is examined, while a combined Illumina/SMRT sequencing approach is proposed to combat these issues. Comparative genome analysis of these plasmid sequences combined with other publicly available plasmid sequence data allowed the definition of the lactococcal plasmidome, and facilitated an investigation into (bio) technologically important plasmid-encoded traits such as conjugation, bacteriocin production, exopolysaccharide (EPS) production, and (bacterio) phage resistance.
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Affiliation(s)
- Philip Kelleher
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Gabriele A. Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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19
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Wels M, Siezen R, van Hijum S, Kelly WJ, Bachmann H. Comparative Genome Analysis of Lactococcus lactis Indicates Niche Adaptation and Resolves Genotype/Phenotype Disparity. Front Microbiol 2019; 10:4. [PMID: 30766512 PMCID: PMC6365430 DOI: 10.3389/fmicb.2019.00004] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/07/2019] [Indexed: 01/21/2023] Open
Abstract
Lactococcus lactis is one of the most important micro-organisms in the dairy industry for the fermentation of cheese and buttermilk. Besides the conversion of lactose to lactate it is responsible for product properties such as flavor and texture, which are determined by volatile metabolites, proteolytic activity and exopolysaccharide production. While the species Lactococcus lactis consists of the two subspecies lactis and cremoris their taxonomic position is confused by a group of strains that, despite of a cremoris genotype, display a lactis phenotype. Here we compared and analyzed the (draft) genomes of 43 L. lactis strains, of which 19 are of dairy and 24 are of non-dairy origin. Machine-learning algorithms facilitated the identification of orthologous groups of protein sequences (OGs) that are predictors for either the taxonomic position or the source of isolation. This allowed the unambiguous categorization of the genotype/phenotype disparity of ssp. lactis and ssp. cremoris strains. A detailed analysis of phenotypic properties including plasmid-encoded genes indicates evolutionary changes during niche adaptations. The results are consistent with the hypothesis that dairy isolates evolved from plant isolates. The analysis further suggests that genomes of cremoris phenotype strains are so eroded that they are restricted to a dairy environment. Overall the genome comparison of a diverse set of strains allowed the identification of niche and subspecies specific genes. This explains evolutionary relationships and will aid the identification and selection of industrial starter cultures.
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Affiliation(s)
- Michiel Wels
- NIZO Food Research B.V., Ede, Netherlands.,TI Food and Nutrition, Wageningen, Netherlands
| | - Roland Siezen
- TI Food and Nutrition, Wageningen, Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands.,Microbial Bioinformatics, Ede, Netherlands
| | - Sacha van Hijum
- NIZO Food Research B.V., Ede, Netherlands.,TI Food and Nutrition, Wageningen, Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Herwig Bachmann
- NIZO Food Research B.V., Ede, Netherlands.,TI Food and Nutrition, Wageningen, Netherlands.,Systems Bioinformatics, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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20
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Flórez AB, Mayo B. Genome Analysis of Lactobacillus plantarum LL441 and Genetic Characterisation of the Locus for the Lantibiotic Plantaricin C. Front Microbiol 2018; 9:1916. [PMID: 30174666 PMCID: PMC6107846 DOI: 10.3389/fmicb.2018.01916] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/30/2018] [Indexed: 11/13/2022] Open
Abstract
Bacteriocins are ribosomally synthesized peptides produced by bacteria with antimicrobial activity. The bacteriocins produced by lactic acid bacteria (LAB) may inhibit food-borne pathogens and spoilage organisms, and therefore have potential as natural preservatives. Lactobacillus plantarum LL441 produces a lantibiotic bacteriocin known as plantaricin C, a pore-forming antimicrobial peptide containing modified amino acids that inhibits cell wall synthesis by forming a complex with the peptidoglycan precursor lipid II. The present work describes the genome sequencing of L. plantarum LL441 and the characterisation of the plantaricin C locus. The draft genome sequence of L. plantarum LL441 consisted of 170 contigs and had a total 3,124,603 bp; the GC content was 44.52%. The plantaricin C locus was found in an 18 kbp-long contig, and consisted of six genes organized in an operon-like arrangement. This locus included the bacteriocin structural gene (plnC), followed by a gene encoding a LanM-like protein thought to be involved in the maturation of plantaricin C, and four downstream genes encoding ABC-type transporter components, probably belonging to its putative immunity and export machinery. plnC encodes a precursor of the bacteriocin, i.e., a 58-amino acid peptide containing a 31-amino acid double-glycine leader peptide and a 27-amino acid core peptide. In silico analysis and hybridisation experiments placed the plantaricin C locus to be located on pLL441-1, a large plasmid of L. plantarum LL441. Joining up the gaps between the contigs by conventional PCR, sequencing of the amplicons, and sequence assemblage, allowed the complete 55.3 kbp pLL441-1 molecule to be established. A portion of pLL441-1 larger than 34 kbp, which included the plantaricin C region, was identified in a plasmid-derived contig from the L. plantarum Nizo 3893 genome. Further, the plantaricin C coding locus (about 8.7 kbp) was shown to share 91% nucleotide identity with a portion of the plasmids pPECL-6 from Pediococcus claussenii ATCC BAA-344 and pL11995-4 from Lactobacillus paracollinoides TMW 1.1995. Knowledge of the sequence of the plantaricin C coding region will help in studying its molecular components and allow their involvement in bacteriocin synthesis to be investigated, facilitating the use of the bacteriocin or its genetic elements in new biotechnological applications.
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Affiliation(s)
- Ana B Flórez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas, Villaviciosa, Spain
| | - Baltasar Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas, Villaviciosa, Spain
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21
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van Mastrigt O, Di Stefano E, Hartono S, Abee T, Smid EJ. Large plasmidome of dairy Lactococcus lactis subsp. lactis biovar diacetylactis FM03P encodes technological functions and appears highly unstable. BMC Genomics 2018; 19:620. [PMID: 30119641 PMCID: PMC6098607 DOI: 10.1186/s12864-018-5005-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 08/09/2018] [Indexed: 11/17/2022] Open
Abstract
Background Important industrial traits have been linked to plasmids in Lactococcus lactis. Results The dairy isolate L. lactis subsp. lactis biovar diacetylactis FM03P was sequenced revealing the biggest plasmidome of all completely sequenced and published L. lactis strains up till now. The 12 plasmids that were identified are: pLd1 (8277 bp), pLd2 (15,218 bp), pLd3 (4242 bp), pLd4 (12,005 bp), pLd5 (7521 bp), pLd6 (3363 bp), pLd7 (30,274 bp), pLd8 (47,015 bp), pLd9 (15,313 bp), pLd10 (39,563 bp), pLd11 (9833 bp) and pLd12 (3321 bp). Structural analysis of the repB promoters and the RepB proteins showed that eleven of the plasmids replicate via the theta-type mechanism, while only plasmid pLd3 replicates via a rolling-circle replication mechanism. Plasmids pLd2, pLd7 and pLd10 contain a highly similar operon involved in mobilisation of the plasmids. Examination of the twelve plasmids of L. lactis FM03P showed that 10 of the plasmids carry putative genes known to be important for growth and survival in the dairy environment. These genes encode technological functions such as lactose utilisation (lacR-lacABCDFEGX), citrate uptake (citQRP), peptide degradation (pepO and pepE) and oligopeptide uptake (oppDFBCA), uptake of magnesium and manganese (2 mntH, corA), exopolysaccharides production (eps operon), bacteriophage resistance (1 hsdM, 1 hsdR and 7 different hsdS genes of a type I restriction-modification system, an operon of three genes encoding a putative type II restriction-modification system and an abortive infection gene) and stress resistance (2 uspA, cspC and cadCA). Acquisition of these plasmids most likely facilitated the adaptation of the recipient strain to the dairy environment. Some plasmids were already lost during a single propagation step signifying their instability in the absence of a selective pressure. Conclusions Lactococcus lactis FM03P carries 12 plasmids important for its adaptation to the dairy environment. Some of the plasmids were easily lost demonstrating that propagation outside the dairy environment should be minimised when studying dairy isolates of L. lactis. Electronic supplementary material The online version of this article (10.1186/s12864-018-5005-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Oscar van Mastrigt
- Food Microbiology, Wageningen University & Research, P.O. Box 17, 6700AA, Wageningen, The Netherlands
| | - Elisa Di Stefano
- Food Microbiology, Wageningen University & Research, P.O. Box 17, 6700AA, Wageningen, The Netherlands
| | - Sylviani Hartono
- Food Microbiology, Wageningen University & Research, P.O. Box 17, 6700AA, Wageningen, The Netherlands
| | - Tjakko Abee
- Food Microbiology, Wageningen University & Research, P.O. Box 17, 6700AA, Wageningen, The Netherlands
| | - Eddy J Smid
- Food Microbiology, Wageningen University & Research, P.O. Box 17, 6700AA, Wageningen, The Netherlands.
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22
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Solopova A, Bachmann H, Teusink B, Kok J, Kuipers OP. Further Elucidation of Galactose Utilization in Lactococcus lactis MG1363. Front Microbiol 2018; 9:1803. [PMID: 30123211 PMCID: PMC6085457 DOI: 10.3389/fmicb.2018.01803] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/17/2018] [Indexed: 11/20/2022] Open
Abstract
Since the 1970s, galactose metabolism in Lactococcus lactis has been in debate. Different studies led to diverse outcomes making it difficult to conclude whether galactose uptake was PEP- or ATP- dependent and decide what the exact connection was between galactose and lactose uptake and metabolism. It was shown that some Lactococcus strains possess two galactose-specific systems – a permease and a PTS, even if they lack the lactose utilization plasmid, proving that a lactose-independent PTSGal exists. However, the PTSGal transporter was never identified. Here, with the help of transcriptome analyses and genetic knock-out mutants, we reveal the identities of two low-affinity galactose PTSs. A novel plant-niche-related PTS component Llmg_0963 forming a hybrid transporter Llmg_0963PtcBA and a glucose/mannose-specific PTS are shown to be involved in galactose transport in L. lactis MG1363.
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Affiliation(s)
- Ana Solopova
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Herwig Bachmann
- Faculty of Earth and Life Sciences, Systems Bioinformatics IBIVU/NISB, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Bas Teusink
- Faculty of Earth and Life Sciences, Systems Bioinformatics IBIVU/NISB, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Jan Kok
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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23
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He Q, Hou Q, Wang Y, Li J, Li W, Kwok LY, Sun Z, Zhang H, Zhong Z. Comparative genomic analysis of Enterococcus faecalis: insights into their environmental adaptations. BMC Genomics 2018; 19:527. [PMID: 29996769 PMCID: PMC6042284 DOI: 10.1186/s12864-018-4887-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 06/19/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Enterococcus faecalis is widely studied as a common gut commensal and a nosocomial pathogen. In fact, Enterococcus faecalis is ubiquitous in nature, and it has been isolated from various niches, including the gastrointestinal tract, faeces, blood, urine, water, and fermented foods (such as dairy products). In order to elucidate the role of habitat in shaping the genome of Enterococcus faecalis, we performed a comparative genomic analysis of 78 strains of various origins. RESULTS Although no correlation was found between the strain isolation habitat and the phylogeny of Enterococcus faecalis from our whole genome-based phylogenetic analysis, our results revealed some environment-associated features in the analysed Enterococcus faecalis genomes. Significant differences were found in the genome size and the number of predicted open reading frames (ORFs) between strains originated from different environments. In general, strains from water sources had the smallest genome size and the least number of predicted ORFs. We also identified 293 environment-specific genes, some of which might link to the adaptive strategies for survival in particular environments. In addition, the number of antibiotic resistance genes was significantly different between strains isolated from dairy products, water, and blood. Strains isolated from blood had the largest number of antibiotic resistance genes. CONCLUSION These findings improve our understanding of the role of habitat in shaping the genomes of Enterococcus faecalis.
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Affiliation(s)
- Qiuwen He
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R. C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture P.R.C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China
| | - Qiangchuan Hou
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R. C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture P.R.C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China
| | - Yanjie Wang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R. C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture P.R.C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China
| | - Jing Li
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R. C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture P.R.C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China
| | - Weicheng Li
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R. C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture P.R.C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R. C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture P.R.C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R. C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture P.R.C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R. C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture P.R.C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China
| | - Zhi Zhong
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R. C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China. .,Key Laboratory of Dairy Products Processing, Ministry of Agriculture P.R.C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China.
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Dynamics in Copy Numbers of Five Plasmids of a Dairy Lactococcus lactis Strain under Dairy-Related Conditions Including Near-Zero Growth Rates. Appl Environ Microbiol 2018; 84:AEM.00314-18. [PMID: 29572209 DOI: 10.1128/aem.00314-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 03/19/2018] [Indexed: 11/20/2022] Open
Abstract
Lactic acid bacteria can carry multiple plasmids affecting their performance in dairy fermentations. The expression of plasmid-borne genes and the activity of the corresponding proteins are severely affected by changes in the numbers of plasmid copies. We studied the impact of growth rate on the dynamics of plasmid copy numbers at high growth rates in chemostat cultures and down to near-zero growth rates in retentostat cultures. Five plasmids of the dairy strain Lactococcus lactis FM03-V1 were selected, and these varied in size (3 to 39 kb), in replication mechanism (theta or rolling circle), and in putative (dairy-associated) functions. The copy numbers ranged from 1.5 to 40.5, and the copy number of theta-type replicating plasmids was negatively correlated to the plasmid size. Despite the extremely wide range of growth rates (0.0003 h-1 to 0.6 h-1), the copy numbers of the five plasmids were stable and only slightly increased at near-zero growth rates, showing that the plasmid replication rate was strictly controlled. One low-copy-number plasmid, carrying a large exopolysaccharide gene cluster, was segregationally unstable during retentostat cultivations, reflected in a complete loss of the plasmid in one of the retentostat cultures. The copy number of the five plasmids was also hardly affected by varying the pH value, nutrient limitation, or the presence of citrate (maximum 2.2-fold), signifying the stability in copy number of the plasmids.IMPORTANCE Lactococcus lactis is extensively used in starter cultures for dairy fermentations. Important traits for the growth and survival of L. lactis in dairy fermentations are encoded by genes located on plasmids, such as genes involved in lactose and citrate metabolism, protein degradation, oligopeptide uptake, and bacteriophage resistance. Because the number of plasmid copies could affect the expression of plasmid-borne genes, it is important to know the factors that influence the plasmid copy numbers. We monitored the plasmid copy numbers of L. lactis at near-zero growth rates, characteristic for cheese ripening. Moreover, we analyzed the effects of pH, nutrient limitation, and the presence of citrate. This showed that the plasmid copy numbers were stable, giving insight into plasmid copy number dynamics in dairy fermentations.
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Genome-Wide Comparison Reveals a Probiotic Strain Lactococcus Lactis WFLU12 Isolated from the Gastrointestinal Tract of Olive Flounder (Paralichthys Olivaceus) Harboring Genes Supporting Probiotic Action. Mar Drugs 2018; 16:md16050140. [PMID: 29695124 PMCID: PMC5983272 DOI: 10.3390/md16050140] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/06/2018] [Accepted: 04/19/2018] [Indexed: 02/06/2023] Open
Abstract
Our previous study has shown that dietary supplementation with Lactococcus lactis WFLU12 can enhance the growth of olive flounder and its resistance against streptococcal infection. The objective of the present study was to use comparative genomics tools to investigate genomic characteristics of strain WFLU12 and the presence of genes supporting its probiotic action using sequenced genomes of L. lactis strains. Dispensable and singleton genes of strain WFLU12 were found to be more enriched in genes associated with metabolism (e.g., energy production and conversion, and carbohydrate transport and metabolism) than pooled dispensable and singleton genes in other L. lactis strains, reflecting WFLU12 strain-specific ecosystem origin and its ability to metabolize different energy sources. Strain WFLU12 produced antimicrobial compounds that could inhibit several bacterial fish pathogens. It possessed the nisin gene cluster (nisZBTCIPRKFEG) and genes encoding lysozyme and colicin V. However, only three other strains (CV56, IO-1, and SO) harbor a complete nisin gene cluster. We also found that L. lactis WFLU12 possessed many other important functional genes involved in stress responses to the gastrointestinal tract environment, dietary energy extraction, and metabolism to support the probiotic action of this strain found in our previous study. This strongly indicates that not all L. lactis strains can be used as probiotics. This study highlights comparative genomics approaches as very useful and powerful tools to select probiotic candidates and predict their probiotic effects.
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Comparative genomic and metabolic analysis of three Lactobacillus paracasei cheese isolates reveals considerable genomic differences in strains from the same niche. BMC Genomics 2018; 19:205. [PMID: 29554864 PMCID: PMC5859408 DOI: 10.1186/s12864-018-4586-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/08/2018] [Indexed: 11/10/2022] Open
Abstract
Background Strains of Lactobacillus paracasei are present in many diverse environments, including dairy and plant materials and the intestinal tracts of humans and animals. Their adaptation to various niches is correlated to intra-species diversity at the genomic and metabolic level. In this study, we compared the genome sequences of three L. paracasei strains isolated from mature Cheddar cheeses, two of which (DPC4206 and DPC4536) shared the same genomic fingerprint by PFGE, but demonstrated varying metabolic capabilities. Results Genome sizes varied from 2.9 Mbp for DPC2071, to 3.09 Mbp for DPC4206 and 3.08 Mpb for DPC4536. The presence of plasmids was a distinguishing feature between the strains with strain DPC2071 possessing an unusually high number of plasmids (up to 11), while DPC4206 had one plasmid and DPC4536 harboured no plasmids. Each of the strains possessed specific genes not present in the other two analysed strains. The three strains differed in their abundance of sugar-converting genes, and in the types of sugars that could be used as energy sources. Genes involved in the metabolism of sugars not usually connected with the dairy niche, such as myo-inositol and pullulan were also detected, but strains did not utilise these sugars. The genetic content of the three strains differed in regard to specific genes for arginine and sulfur-containing amino acid metabolism and genes contributing to resistance to heavy metal ions. In addition, variability in the presence of phage remnants and phage protection systems was evident. Conclusions The findings presented in this study confirm a considerable level of heterogeneity of Lactobacillus paracasei strains, even between strains isolated from the same niche.
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Solopova A, Kok J, Kuipers OP. Disruption of a Transcriptional Repressor by an Insertion Sequence Element Integration Leads to Activation of a Novel Silent Cellobiose Transporter in Lactococcus lactis MG1363. Appl Environ Microbiol 2017; 83:e01279-17. [PMID: 28970222 PMCID: PMC5691405 DOI: 10.1128/aem.01279-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/21/2017] [Indexed: 11/20/2022] Open
Abstract
Lactococcus lactis subsp. cremoris strains typically carry many dairy niche-specific adaptations. During adaptation to the milk environment these former plant strains have acquired various pseudogenes and insertion sequence elements indicative of ongoing genome decay and frequent transposition events in their genomes. Here we describe the reactivation of a silenced plant sugar utilization cluster in an L. lactis MG1363 derivative lacking the two main cellobiose transporters, PtcBA-CelB and PtcBAC, upon applying selection pressure to utilize cellobiose. A disruption of the transcriptional repressor gene llmg_1239 by an insertion sequence (IS) element allows expression of the otherwise silent novel cellobiose transporter Llmg_1244 and leads to growth of mutant strains on cellobiose. Llmg_1239 was labeled CclR, for cellobiose cluster repressor.IMPORTANCE Insertion sequences (ISs) play an important role in the evolution of lactococci and other bacteria. They facilitate DNA rearrangements and are responsible for creation of new genetic variants with selective advantages under certain environmental conditions. L. lactis MG1363 possesses 71 copies in a total of 11 different types of IS elements. This study describes yet another example of an IS-mediated adaptive evolution. An integration of IS981 or IS905 into a gene coding for a transcriptional repressor led to activation of the repressed gene cluster coding for a plant sugar utilization pathway. The expression of the gene cluster allowed assembly of a novel cellobiose-specific transporter and led to cell growth on cellobiose.
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Affiliation(s)
- Ana Solopova
- Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, the Netherlands
| | - Jan Kok
- Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, the Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, the Netherlands
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Gómez de Cadiñanos LP, Peláez C, Martínez-Cuesta MC, García-Cayuela T, Requena T. Identification and characterization of glutamate dehydrogenase activity in wild Lactococcus lactis isolated from raw milk cheeses. Eur Food Res Technol 2017. [DOI: 10.1007/s00217-017-2988-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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29
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Unleashing Natural Competence in Lactococcus lactis by Induction of the Competence Regulator ComX. Appl Environ Microbiol 2017; 83:AEM.01320-17. [PMID: 28778888 DOI: 10.1128/aem.01320-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/01/2017] [Indexed: 11/20/2022] Open
Abstract
In biotechnological workhorses like Streptococcus thermophilus and Bacillus subtilis, natural competence can be induced, which facilitates genetic manipulation of these microbes. However, in strains of the important dairy starter Lactococcus lactis, natural competence has not been established to date. However, in silico analysis of the complete genome sequences of 43 L. lactis strains revealed complete late competence gene sets in 2 L. lactis subsp. cremoris strains (KW2 and KW10) and at least 10 L. lactis subsp. lactis strains, including the model strain IL1403 and the plant-derived strain KF147. The remainder of the strains, including all dairy isolates, displayed genomic decay in one or more of the late competence genes. Nisin-controlled expression of the competence regulator comX in L. lactis subsp. lactis KF147 resulted in the induction of expression of the canonical competence regulon and elicited a state of natural competence in this strain. In contrast, comX expression in L. lactis NZ9000, which was predicted to encode an incomplete competence gene set, failed to induce natural competence. Moreover, mutagenesis of the comEA-EC operon in strain KF147 abolished the comX-driven natural competence, underlining the involvement of the competence machinery. Finally, introduction of nisin-inducible comX expression into nisRK-harboring derivatives of strains IL1403 and KW2 allowed the induction of natural competence in these strains also, expanding this phenotype to other L. lactis strains of both subspecies.IMPORTANCE Specific bacterial species are able to enter a state of natural competence in which DNA is taken up from the environment, allowing the introduction of novel traits. Strains of the species Lactococcus lactis are very important starter cultures for the fermentation of milk in the cheese production process, where these bacteria contribute to the flavor and texture of the end product. The activation of natural competence in this industrially relevant organism can accelerate research aiming to understand industrially relevant traits of these bacteria and can facilitate engineering strategies to harness the natural biodiversity of the species in optimized starter strains.
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Tarazanova M, Huppertz T, Beerthuyzen M, van Schalkwijk S, Janssen P, Wels M, Kok J, Bachmann H. Cell Surface Properties of Lactococcus lactis Reveal Milk Protein Binding Specifically Evolved in Dairy Isolates. Front Microbiol 2017; 8:1691. [PMID: 28936202 PMCID: PMC5594101 DOI: 10.3389/fmicb.2017.01691] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 08/21/2017] [Indexed: 01/18/2023] Open
Abstract
Surface properties of bacteria are determined by the molecular composition of the cell wall and they are important for interactions of cells with their environment. Well-known examples of bacterial interactions with surfaces are biofilm formation and the fermentation of solid materials like food and feed. Lactococcus lactis is broadly used for the fermentation of cheese and buttermilk and it is primarily isolated from either plant material or the dairy environment. In this study, we characterized surface hydrophobicity, charge, emulsification properties, and the attachment to milk proteins of 55 L. lactis strains in stationary and exponential growth phases. The attachment to milk protein was assessed through a newly developed flow cytometry-based protocol. Besides finding a high degree of biodiversity, phenotype-genotype matching allowed the identification of candidate genes involved in the modification of the cell surface. Overexpression and gene deletion analysis allowed to verify the predictions for three identified proteins that altered surface hydrophobicity and attachment of milk proteins. The data also showed that lactococci isolated from a dairy environment bind higher amounts of milk proteins when compared to plant isolates. It remains to be determined whether the alteration of surface properties also has potential to alter starter culture functionalities.
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Affiliation(s)
- Mariya Tarazanova
- NIZOEde, Netherlands
- TI Food and NutritionWageningen, Netherlands
- Molecular Genetics, University of GroningenGroningen, Netherlands
| | - Thom Huppertz
- NIZOEde, Netherlands
- TI Food and NutritionWageningen, Netherlands
| | | | | | - Patrick Janssen
- NIZOEde, Netherlands
- TI Food and NutritionWageningen, Netherlands
| | - Michiel Wels
- NIZOEde, Netherlands
- TI Food and NutritionWageningen, Netherlands
| | - Jan Kok
- TI Food and NutritionWageningen, Netherlands
- Molecular Genetics, University of GroningenGroningen, Netherlands
| | - Herwig Bachmann
- NIZOEde, Netherlands
- TI Food and NutritionWageningen, Netherlands
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Bachmann H, Molenaar D, Branco dos Santos F, Teusink B. Experimental evolution and the adjustment of metabolic strategies in lactic acid bacteria. FEMS Microbiol Rev 2017. [DOI: 10.1093/femsre/fux024] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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32
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Laroute V, Tormo H, Couderc C, Mercier-Bonin M, Le Bourgeois P, Cocaign-Bousquet M, Daveran-Mingot ML. From Genome to Phenotype: An Integrative Approach to Evaluate the Biodiversity of Lactococcus lactis. Microorganisms 2017; 5:microorganisms5020027. [PMID: 28534821 PMCID: PMC5488098 DOI: 10.3390/microorganisms5020027] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/09/2017] [Accepted: 05/12/2017] [Indexed: 01/09/2023] Open
Abstract
Lactococcus lactis is one of the most extensively used lactic acid bacteria for the manufacture of dairy products. Exploring the biodiversity of L. lactis is extremely promising both to acquire new knowledge and for food and health-driven applications. L. lactis is divided into four subspecies: lactis, cremoris, hordniae and tructae, but only subsp. lactis and subsp. cremoris are of industrial interest. Due to its various biotopes, Lactococcus subsp. lactis is considered the most diverse. The diversity of L. lactis subsp. lactis has been assessed at genetic, genomic and phenotypic levels. Multi-Locus Sequence Type (MLST) analysis of strains from different origins revealed that the subsp. lactis can be classified in two groups: “domesticated” strains with low genetic diversity, and “environmental” strains that are the main contributors of the genetic diversity of the subsp. lactis. As expected, the phenotype investigation of L. lactis strains reported here revealed highly diverse carbohydrate metabolism, especially in plant- and gut-derived carbohydrates, diacetyl production and stress survival. The integration of genotypic and phenotypic studies could improve the relevance of screening culture collections for the selection of strains dedicated to specific functions and applications.
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Affiliation(s)
- Valérie Laroute
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
| | - Hélène Tormo
- Département des Sciences Agronomiques et Agroalimentaire, équipe Agroalimentaire et Nutrition, Université de Toulouse, INP-Purpan, Toulouse, France.
| | - Christel Couderc
- Département des Sciences Agronomiques et Agroalimentaire, équipe Agroalimentaire et Nutrition, Université de Toulouse, INP-Purpan, Toulouse, France.
| | - Muriel Mercier-Bonin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France.
| | - Pascal Le Bourgeois
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
- Université de Toulouse III, Université Paul Sabatier, F-31062 Toulouse, France.
| | | | - Marie-Line Daveran-Mingot
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
- Université de Toulouse III, Université Paul Sabatier, F-31062 Toulouse, France.
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Oliveira LC, Saraiva TDL, Silva WM, Pereira UP, Campos BC, Benevides LJ, Rocha FS, Figueiredo HCP, Azevedo V, Soares SC. Analyses of the probiotic property and stress resistance-related genes of Lactococcus lactis subsp. lactis NCDO 2118 through comparative genomics and in vitro assays. PLoS One 2017; 12:e0175116. [PMID: 28384209 PMCID: PMC5383145 DOI: 10.1371/journal.pone.0175116] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 03/21/2017] [Indexed: 11/19/2022] Open
Abstract
Lactococcus lactis subsp. lactis NCDO 2118 was recently reported to alleviate colitis symptoms via its anti-inflammatory and immunomodulatory activities, which are exerted by exported proteins that are not produced by L. lactis subsp. lactis IL1403. Here, we used in vitro and in silico approaches to characterize the genomic structure, the safety aspects, and the immunomodulatory activity of this strain. Through comparative genomics, we identified genomic islands, phage regions, bile salt and acid stress resistance genes, bacteriocins, adhesion-related and antibiotic resistance genes, and genes encoding proteins that are putatively secreted, expressed in vitro and absent from IL1403. The high degree of similarity between all Lactococcus suggests that the Symbiotic Islands commonly shared by both NCDO 2118 and KF147 may be responsible for their close relationship and their adaptation to plants. The predicted bacteriocins may play an important role against the invasion of competing strains. The genes related to the acid and bile salt stresses may play important roles in gastrointestinal tract survival, whereas the adhesion proteins are important for persistence in the gut, culminating in the competitive exclusion of other bacteria. Finally, the five secreted and expressed proteins may be important targets for studies of new anti-inflammatory and immunomodulatory proteins. Altogether, the analyses performed here highlight the potential use of this strain as a target for the future development of probiotic foods.
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Affiliation(s)
- Letícia C. Oliveira
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte—MG, Brazil
| | - Tessália D. L. Saraiva
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte—MG, Brazil
| | - Wanderson M. Silva
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte—MG, Brazil
| | - Ulisses P. Pereira
- Department of Preventive Veterinary Medicine, State University of Londrina, Londrina—PR, Brazil
| | - Bruno C. Campos
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte—MG, Brazil
| | - Leandro J. Benevides
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte—MG, Brazil
| | - Flávia S. Rocha
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte—MG, Brazil
| | - Henrique C. P. Figueiredo
- Official Laboratory of Fisheries Ministry—Veterinary School, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Vasco Azevedo
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte—MG, Brazil
| | - Siomar C. Soares
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte—MG, Brazil
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba—MG, Brazil
- * E-mail:
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Abstract
The lactic acid bacterium Lactococcus lactis is widely used for the production of fermented dairy products. Here, we present the draft genome sequences of 24 L. lactis strains isolated from different environments and geographic locations.
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35
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Draft Genome Sequences of 11 Lactococcus lactis subsp. cremoris Strains. GENOME ANNOUNCEMENTS 2017; 5:5/11/e01739-16. [PMID: 28302789 PMCID: PMC5356066 DOI: 10.1128/genomea.01739-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The lactic acid bacterium Lactococcus lactis is widely used for the fermentation of dairy products. Here, we present the draft genome sequences of 11 L. lactis subsp. cremoris strains isolated from different environments.
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Tarazanova M, Beerthuyzen M, Siezen R, Fernandez-Gutierrez MM, de Jong A, van der Meulen S, Kok J, Bachmann H. Plasmid Complement of Lactococcus lactis NCDO712 Reveals a Novel Pilus Gene Cluster. PLoS One 2016; 11:e0167970. [PMID: 27941999 PMCID: PMC5152845 DOI: 10.1371/journal.pone.0167970] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/24/2016] [Indexed: 12/13/2022] Open
Abstract
Lactococcus lactis MG1363 is an important gram-positive model organism. It is a plasmid-free and phage-cured derivative of strain NCDO712. Plasmid-cured strains facilitate studies on molecular biological aspects, but many properties which make L. lactis an important organism in the dairy industry are plasmid encoded. We sequenced the total DNA of strain NCDO712 and, contrary to earlier reports, revealed that the strain carries 6 rather than 5 plasmids. A new 50-kb plasmid, designated pNZ712, encodes functional nisin immunity (nisCIP) and copper resistance (lcoRSABC). The copper resistance could be used as a marker for the conjugation of pNZ712 to L. lactis MG1614. A genome comparison with the plasmid cured daughter strain MG1363 showed that the number of single nucleotide polymorphisms that accumulated in the laboratory since the strains diverted more than 30 years ago is limited to 11 of which only 5 lead to amino acid changes. The 16-kb plasmid pSH74 was found to contain a novel 8-kb pilus gene cluster spaCB-spaA-srtC1-srtC2, which is predicted to encode a pilin tip protein SpaC, a pilus basal subunit SpaB, and a pilus backbone protein SpaA. The sortases SrtC1/SrtC2 are most likely involved in pilus polymerization while the chromosomally encoded SrtA could act to anchor the pilus to peptidoglycan in the cell wall. Overexpression of the pilus gene cluster from a multi-copy plasmid in L. lactis MG1363 resulted in cell chaining, aggregation, rapid sedimentation and increased conjugation efficiency of the cells. Electron microscopy showed that the over-expression of the pilus gene cluster leads to appendices on the cell surfaces. A deletion of the gene encoding the putative basal protein spaB, by truncating spaCB, led to more pilus-like structures on the cell surface, but cell aggregation and cell chaining were no longer observed. This is consistent with the prediction that spaB is involved in the anchoring of the pili to the cell.
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Affiliation(s)
- Mariya Tarazanova
- NIZO food research B.V., Ede, The Netherlands
- TI Food and Nutrition, Wageningen, The Netherlands
- Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Marke Beerthuyzen
- NIZO food research B.V., Ede, The Netherlands
- TI Food and Nutrition, Wageningen, The Netherlands
| | - Roland Siezen
- TI Food and Nutrition, Wageningen, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud UMC, Nijmegen, The Netherlands
- Microbial Bioinformatics, Ede, The Netherlands
| | - Marcela M. Fernandez-Gutierrez
- TI Food and Nutrition, Wageningen, The Netherlands
- Host-Microbe Interactomics Group, Animal Sciences, Wageningen University, Wageningen, The Netherlands
| | - Anne de Jong
- TI Food and Nutrition, Wageningen, The Netherlands
- Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Sjoerd van der Meulen
- TI Food and Nutrition, Wageningen, The Netherlands
- Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Jan Kok
- TI Food and Nutrition, Wageningen, The Netherlands
- Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Herwig Bachmann
- NIZO food research B.V., Ede, The Netherlands
- TI Food and Nutrition, Wageningen, The Netherlands
- * E-mail:
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Abstract
Lactic acid bacteria (LAB) are important starter, commensal, or pathogenic microorganisms. The stress physiology of LAB has been studied in depth for over 2 decades, fueled mostly by the technological implications of LAB robustness in the food industry. Survival of probiotic LAB in the host and the potential relatedness of LAB virulence to their stress resilience have intensified interest in the field. Thus, a wealth of information concerning stress responses exists today for strains as diverse as starter (e.g., Lactococcus lactis), probiotic (e.g., several Lactobacillus spp.), and pathogenic (e.g., Enterococcus and Streptococcus spp.) LAB. Here we present the state of the art for LAB stress behavior. We describe the multitude of stresses that LAB are confronted with, and we present the experimental context used to study the stress responses of LAB, focusing on adaptation, habituation, and cross-protection as well as on self-induced multistress resistance in stationary phase, biofilms, and dormancy. We also consider stress responses at the population and single-cell levels. Subsequently, we concentrate on the stress defense mechanisms that have been reported to date, grouping them according to their direct participation in preserving cell energy, defending macromolecules, and protecting the cell envelope. Stress-induced responses of probiotic LAB and commensal/pathogenic LAB are highlighted separately due to the complexity of the peculiar multistress conditions to which these bacteria are subjected in their hosts. Induction of prophages under environmental stresses is then discussed. Finally, we present systems-based strategies to characterize the "stressome" of LAB and to engineer new food-related and probiotic LAB with improved stress tolerance.
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Larsen N, Brøsted Werner B, Jespersen L. Transcriptional responses in Lactococcus lactis
subsp. cremoris
to the changes in oxygen and redox potential during milk acidification. Lett Appl Microbiol 2016; 63:117-23. [DOI: 10.1111/lam.12596] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/17/2016] [Accepted: 05/24/2016] [Indexed: 11/29/2022]
Affiliation(s)
- N. Larsen
- Department of Food Science; Food Microbiology; University of Copenhagen; Frederiksberg C Denmark
| | - B. Brøsted Werner
- Department of Food Science; Food Microbiology; University of Copenhagen; Frederiksberg C Denmark
| | - L. Jespersen
- Department of Food Science; Food Microbiology; University of Copenhagen; Frederiksberg C Denmark
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Ho CH, Stanton-Cook M, Beatson SA, Bansal N, Turner MS. Stability of active prophages in industrial Lactococcus lactis strains in the presence of heat, acid, osmotic, oxidative and antibiotic stressors. Int J Food Microbiol 2016; 220:26-32. [DOI: 10.1016/j.ijfoodmicro.2015.12.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 12/10/2015] [Accepted: 12/27/2015] [Indexed: 11/25/2022]
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Son YJ, Ryu AJ, Li L, Han NS, Jeong KJ. Development of a high-copy plasmid for enhanced production of recombinant proteins in Leuconostoc citreum. Microb Cell Fact 2016; 15:12. [PMID: 26767787 PMCID: PMC4714500 DOI: 10.1186/s12934-015-0400-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 12/16/2015] [Indexed: 11/17/2022] Open
Abstract
Background Leuconostoc is a hetero-fermentative lactic acid bacteria, and its importance is widely recognized in the dairy industry. However, due to limited genetic tools including plasmids for Leuconostoc, there has not been much extensive research on the genetics and engineering of Leuconostoc yet. Thus, there is a big demand for high-copy-number plasmids for useful gene manipulation and overproduction of recombinant proteins in Leuconostoc. Results Using an existing low-copy plasmid, the copy number of plasmid was increased by random mutagenesis followed by FACS-based high-throughput screening. First, a random library of plasmids was constructed by randomizing the region responsible for replication in Leuconostoc citreum; additionally, a superfolder green fluorescent protein (sfGFP) was used as a reporter protein. With a high-speed FACS sorter, highly fluorescent cells were enriched, and after two rounds of sorting, single clone exhibiting the highest level of sfGFP was isolated. The copy number of the isolated plasmid (pCB4270) was determined by quantitative PCR (qPCR). It was found that the isolated plasmid has approximately a 30-fold higher copy number (approx. 70 copies per cell) than that of the original plasmid. From the sequence analysis, a single mutation (C→T) at position 4690 was found, and we confirmed that this single mutation was responsible for the increased plasmid copy number. The effectiveness of the isolated high-copy-number plasmid for the overproduction of recombinant proteins was successfully demonstrated with two protein models Glutathione-S-transferase (GST) and α–amylase. Conclusions The high-copy number plasmid was successfully isolated by FACS-based high-throughput screening of a plasmid library in L. citreum. The isolated plasmid could be a useful genetic tool for high-level gene expression in Leuconostoc, and for extending the applications of this useful bacteria to various areas in the dairy and pharmaceutical industries.
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Affiliation(s)
- Yeon Jeong Son
- Department of Chemical and Biomolecular Engineering, BK21 Plus PROGRAM, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Ae Jin Ryu
- Department of Chemical and Biomolecular Engineering, BK21 Plus PROGRAM, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Ling Li
- Division of Animal, Horticultural and Food Sciences, Brain Korea 21 Center for Bio-Resource Development, Chungbuk National University, Cheongju, 28644, Republic of Korea.
| | - Nam Soo Han
- Division of Animal, Horticultural and Food Sciences, Brain Korea 21 Center for Bio-Resource Development, Chungbuk National University, Cheongju, 28644, Republic of Korea.
| | - Ki Jun Jeong
- Department of Chemical and Biomolecular Engineering, BK21 Plus PROGRAM, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea. .,Institute for the BioCentury, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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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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Flórez AB, Mayo B. The Plasmid Complement of the Cheese Isolate Lactococcus garvieae IPLA 31405 Revealed Adaptation to the Dairy Environment. PLoS One 2015; 10:e0126101. [PMID: 25942497 PMCID: PMC4420470 DOI: 10.1371/journal.pone.0126101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 03/29/2015] [Indexed: 01/21/2023] Open
Abstract
Lactococcus garvieae is a lactic acid bacterium found in raw-milk dairy products as well as a range of aquatic and terrestrial environments. The plasmids in L. garvieae have received little attention compared to those of dairy Lactococcus lactis, in which the genes carried by these extrachromosomal elements are considered of adaptive value. The present work reports the sequencing and analysis of the plasmid complement of L. garvieae IPLA 31405, a strain isolated from a traditional, Spanish, starter-free cheese made from raw-milk. It consists of pLG9 and pLG42, of 9,124 and 42,240 nucleotides, respectively. Based on sequence and structural homology in the putative origin of replication (ori) region, pLG9 and pLG42 are predicted to replicate via a theta mechanism. Real-time, quantitative PCR showed the number of copies per chromosome equivalent of pLG9 and pLG42 to be around two and five, respectively. Sequence analysis identified eight complete open reading frames (orfs) in pLG9 and 36 in pLG42; these were organized into functional modules or cassettes containing different numbers of genes. These modules were flanked by complete or interrupted insertion sequence (IS)-like elements. Among the modules of pLG42 was a gene cluster encoding specific components of a phosphoenolpyruvate-phosphotransferase (PEP-PTS) system, including a phospho-β-galacosidase. The cluster showed a complete nucleotide identity respect to that in plasmids of L. lactis. Loss of pLG42 showed this to be involved in lactose assimilation. In the same plasmid, an operon encoding a type I restriction/modification (R/M) system was also identified. The specificity of this R/M system might be broadened by different R/M specificity subunits detected in pLG9 and in the bacterial chromosome. However, challenges of L. garvieae IPLA 31405 against L. lactis phages proved that the R/M system was not involved in phage resistance. Together, these results support the hypothesis that, as in L. lactis, pLG42 contribute towards the adaptation of L. garvieae to the dairy environment.
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Affiliation(s)
- Ana Belén Flórez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Carretera de Infiesto, s/n, 33300-Villaviciosa, Asturias, Spain
| | - Baltasar Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Carretera de Infiesto, s/n, 33300-Villaviciosa, Asturias, Spain
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Kelleher P, Murphy J, Mahony J, van Sinderen D. Next-generation sequencing as an approach to dairy starter selection. DAIRY SCIENCE & TECHNOLOGY 2015; 95:545-568. [PMID: 26798445 PMCID: PMC4712225 DOI: 10.1007/s13594-015-0227-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/25/2015] [Accepted: 04/02/2015] [Indexed: 02/06/2023]
Abstract
Lactococcal and streptococcal starter strains are crucial ingredients to manufacture fermented dairy products. As commercial starter culture suppliers and dairy producers attempt to overcome issues of phage sensitivity and develop new product ranges, there is an ever increasing need to improve technologies for the rational selection of novel starter culture blends. Whole genome sequencing, spurred on by recent advances in next-generation sequencing platforms, is a promising approach to facilitate rapid identification and selection of such strains based on gene-trait matching. This review provides a comprehensive overview of the available methodologies to analyse the technological potential of candidate starter strains and highlights recent advances in the area of dairy starter genomics.
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Affiliation(s)
- Philip Kelleher
- School of Microbiology, University College Cork, Cork, Ireland
| | - James Murphy
- School of Microbiology, University College Cork, Cork, Ireland
| | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork, Cork, Ireland
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Papadimitriou K, Anastasiou R, Maistrou E, Plakas T, Papandreou NC, Hamodrakas SJ, Ferreira S, Supply P, Renault P, Pot B, Tsakalidou E. Acquisition through horizontal gene transfer of plasmid pSMA198 by Streptococcus macedonicus ACA-DC 198 points towards the dairy origin of the species. PLoS One 2015; 10:e0116337. [PMID: 25584532 PMCID: PMC4293149 DOI: 10.1371/journal.pone.0116337] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Accepted: 12/05/2014] [Indexed: 12/22/2022] Open
Abstract
Background Streptococcus macedonicus is an intriguing streptococcal species whose most frequent source of isolation is fermented foods similarly to Streptococcus thermophilus. However, S. macedonicus is closely related to commensal opportunistic pathogens of the Streptococcus bovis/Streptococcus equinus complex. Methodology/Principal Findings We analyzed the pSMA198 plasmid isolated from the dairy strain Streptococcus macedonicus ACA-DC 198 in order to provide novel clues about the main ecological niche of this bacterium. pSMA198 belongs to the narrow host range pCI305/pWV02 family found primarily in lactococci and to the best of our knowledge it is the first such plasmid to be reported in streptococci. Comparative analysis of the pSMA198 sequence revealed a high degree of similarity with plasmids isolated from Lactococcus lactis strains deriving from milk or its products. Phylogenetic analysis of the pSMA198 Rep showed that the vast majority of closely related proteins derive from lactococcal dairy isolates. Additionally, cloning of the pSMA198 ori in L. lactis revealed a 100% stability of replication over 100 generations. Both pSMA198 and the chromosome of S. macedonicus exhibit a high percentage of potential pseudogenes, indicating that they have co-evolved under the same gene decay processes. We identified chromosomal regions in S. macedonicus that may have originated from pSMA198, also supporting a long co-existence of the two replicons. pSMA198 was also found in divergent biotypes of S. macedonicus and in strains isolated from dispersed geographic locations (e.g. Greece and Switzerland) showing that pSMA198’s acquisition is not a recent event. Conclusions/Significance Here we propose that S. macedonicus acquired plasmid pSMA198 from L. lactis via an ancestral genetic exchange event that took place most probably in milk or dairy products. We provide important evidence that point towards the dairy origin of this species.
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Affiliation(s)
- Konstantinos Papadimitriou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
- * E-mail:
| | - Rania Anastasiou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - Eleni Maistrou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - Thomas Plakas
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 157 01, Athens, Greece
| | - Nikos C. Papandreou
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 157 01, Athens, Greece
| | - Stavros J. Hamodrakas
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 157 01, Athens, Greece
| | - Stéphanie Ferreira
- Genoscreen, Service of Research, Development and Innovation in Health and Environment, Campus de l’Institut Pasteur, 1 rue du Professeur Calmette, 59000, Lille, France
| | - Philip Supply
- Genoscreen, Service of Research, Development and Innovation in Health and Environment, Campus de l’Institut Pasteur, 1 rue du Professeur Calmette, 59000, Lille, France
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), F-59019, Lille, France
- Inserm U1019, F-59019, Lille, France
- CNRS UMR8204, F-59019, Lille, France
- Univ Lille de Nord France, F-59019, Lille, France
| | - Pierre Renault
- INRA, UMR1319 Micalis, Jouy-en-Josas, F-78352, France
- AgroParisTech, UMR Micalis, Jouy-en-Josas, F-78352, France
| | - Bruno Pot
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), F-59019, Lille, France
- Inserm U1019, F-59019, Lille, France
- CNRS UMR8204, F-59019, Lille, France
- Univ Lille de Nord France, F-59019, Lille, France
| | - Effie Tsakalidou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
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Cavanagh D, Fitzgerald GF, McAuliffe O. From field to fermentation: the origins of Lactococcus lactis and its domestication to the dairy environment. Food Microbiol 2014; 47:45-61. [PMID: 25583337 DOI: 10.1016/j.fm.2014.11.001] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/22/2014] [Accepted: 11/01/2014] [Indexed: 11/18/2022]
Abstract
Lactococcus lactis is an organism of substantial economic importance, used extensively in the production of fermented foods and widely held to have evolved from plant strains. The domestication of this organism to the milk environment is associated with genome reduction and gene decay, and the acquisition of specific genes involved in protein and lactose utilisation by horizontal gene transfer. In recent years, numerous studies have focused on uncovering the physiology and molecular biology of lactococcal strains from the wider environment for exploitation in the dairy industry. This in turn has facilitated comparative genome analysis of lactococci from different environments and provided insight into the natural phenotypic and genetic diversity of L. lactis. This diversity may be exploited in dairy fermentations to develop products with improved quality and sensory attributes. In this review, we discuss the classification of L. lactis and the problems that arise with phenotype/genotype designation. We also discuss the adaptation of non-dairy lactococci to milk, the traits associated with this adaptation and the potential application of non-dairy lactococci to dairy fermentations.
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Affiliation(s)
- Daniel Cavanagh
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; Department of Microbiology, University College Cork, Co. Cork, Ireland.
| | | | - Olivia McAuliffe
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.
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46
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Zuljan FA, Repizo GD, Alarcon SH, Magni C. α-Acetolactate synthase of Lactococcus lactis contributes to pH homeostasis in acid stress conditions. Int J Food Microbiol 2014; 188:99-107. [DOI: 10.1016/j.ijfoodmicro.2014.07.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 06/03/2014] [Accepted: 07/16/2014] [Indexed: 10/25/2022]
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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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Genomic Features ofLactococcus lactisIO-1, a Lactic Acid Bacterium That Utilizes Xylose and Produces High Levels ofL-Lactic Acid. Biosci Biotechnol Biochem 2014; 77:1804-8. [DOI: 10.1271/bbb.130080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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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: 14] [Impact Index Per Article: 1.4] [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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Papadimitriou K, Anastasiou R, Mavrogonatou E, Blom J, Papandreou NC, Hamodrakas SJ, Ferreira S, Renault P, Supply P, Pot B, Tsakalidou E. Comparative genomics of the dairy isolate Streptococcus macedonicus ACA-DC 198 against related members of the Streptococcus bovis/Streptococcus equinus complex. BMC Genomics 2014; 15:272. [PMID: 24713045 PMCID: PMC4051162 DOI: 10.1186/1471-2164-15-272] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 04/01/2014] [Indexed: 12/21/2022] Open
Abstract
Background Within the genus Streptococcus, only Streptococcus
thermophilus is used as a starter culture in food fermentations.
Streptococcus macedonicus though, which belongs to the
Streptococcus bovis/Streptococcus equinus complex
(SBSEC), is also frequently isolated from fermented foods mainly of dairy
origin. Members of the SBSEC have been implicated in human endocarditis and
colon cancer. Here we compare the genome sequence of the dairy isolate
S. macedonicus ACA-DC 198 to the other SBSEC genomes in order
to assess in silico its potential adaptation to milk and its
pathogenicity status. Results Despite the fact that the SBSEC species were found tightly related based on
whole genome phylogeny of streptococci, two distinct patterns of evolution
were identified among them. Streptococcus macedonicus, Streptococcus
infantarius CJ18 and Streptococcus pasteurianus ATCC 43144
seem to have undergone reductive evolution resulting in significantly
diminished genome sizes and increased percentages of potential pseudogenes
when compared to Streptococcus gallolyticus subsp.
gallolyticus. In addition, the three species seem to have lost
genes for catabolizing complex plant carbohydrates and for detoxifying toxic
substances previously linked to the ability of S. gallolyticus to
survive in the rumen. Analysis of the S. macedonicus genome
revealed features that could support adaptation to milk, including an extra
gene cluster for lactose and galactose metabolism, a proteolytic system for
casein hydrolysis, auxotrophy for several vitamins, an increased ability to
resist bacteriophages and horizontal gene transfer events with the dairy
Lactococcus lactis and S. thermophilus as potential
donors. In addition, S. macedonicus lacks several
pathogenicity-related genes found in S. gallolyticus. For example,
S. macedonicus has retained only one (i.e. the pil3)
of the three pilus gene clusters which may mediate the binding of S.
gallolyticus to the extracellular matrix. Unexpectedly, similar
findings were obtained not only for the dairy S. infantarius CJ18,
but also for the blood isolate S. pasteurianus ATCC 43144. Conclusions Our whole genome analyses suggest traits of adaptation of S.
macedonicus to the nutrient-rich dairy environment. During this
process the bacterium gained genes presumably important for this new
ecological niche. Finally, S. macedonicus carries a reduced number
of putative SBSEC virulence factors, which suggests a diminished pathogenic
potential.
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Affiliation(s)
- Konstantinos Papadimitriou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece.
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