1
|
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.
Collapse
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
| |
Collapse
|
2
|
Laroute V, Aubry N, Audonnet M, Mercier-Bonin M, Daveran-Mingot ML, Cocaign-Bousquet M. Natural diversity of lactococci in γ-aminobutyric acid (GABA) production and genetic and phenotypic determinants. Microb Cell Fact 2023; 22:178. [PMID: 37689693 PMCID: PMC10492284 DOI: 10.1186/s12934-023-02181-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/18/2023] [Indexed: 09/11/2023] Open
Abstract
BACKGROUND γ-aminobutyric acid (GABA) is a bioactive compound produced by lactic acid bacteria (LAB). The diversity of GABA production in the Lactococcus genus is poorly understood. Genotypic and phenotypic approaches were therefore combined in this study to shed light on this diversity. A comparative genomic study was performed on the GAD-system genes (gadR, gadC and gadB) involved in GABA production in 36 lactococci including L. lactis and L. cremoris species. In addition, 132 Lactococcus strains were screened for GABA production in culture medium supplemented with 34 mM L-glutamic acid with or without NaCl (0.3 M). RESULTS Comparative analysis of the nucleotide sequence alignments revealed the same genetic organization of the GAD system in all strains except one, which has an insertion sequence element (IS981) into the PgadCB promoter. This analysis also highlighted several deletions including a 3-bp deletion specific to the cremoris species located in the PgadR promoter, and a second 39-bp deletion specific to L. cremoris strains with a cremoris phenotype. Phenotypic analysis revealed that GABA production varied widely, but it was higher in L. lactis species than in L. cremoris, with an exceptional GABA production of up to 14 and 24 mM in two L. lactis strains. Moreover, adding chloride increased GABA production in some L. cremoris and L. lactis strains by a factor of up to 16 and GAD activity correlated well with GABA production. CONCLUSIONS This genomic analysis unambiguously characterized the cremoris phenotype of L. cremoris species and modified GadB and GadR proteins explain why the corresponding strains do not produce GABA. Finally, we found that glutamate decarboxylase activity revealing GadB protein amount, varied widely between the strains and correlated well with GABA production both with and without chloride. As this protein level is associated to gene expression, the regulation of GAD gene expression was identified as a major contributor to this diversity.
Collapse
Affiliation(s)
- Valérie Laroute
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Nathalie Aubry
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Marjorie Audonnet
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Muriel Mercier-Bonin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Marie-Line Daveran-Mingot
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Muriel Cocaign-Bousquet
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| |
Collapse
|
3
|
Escobedo S, Campelo AB, Umu ÖCO, López-González MJ, Rodríguez A, Diep DB, Martínez B. Resistance to the Bacteriocin Lcn972 Deciphered by Genome Sequencing. Microorganisms 2023; 11:microorganisms11020501. [PMID: 36838466 PMCID: PMC9964109 DOI: 10.3390/microorganisms11020501] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023] Open
Abstract
In view of the current threat of antibiotic resistance, new antimicrobials with low risk of resistance development are demanded. Lcn972 is a lactococcal bacteriocin that inhibits septum formation by binding to the cell wall precursor lipid II in Lactococcus. It has a species-specific spectrum of activity, making Lcn972 an attractive template to develop or improve existing antibiotics. The aim of this work was to identify mutations present in the Lcn972-resistant clone Lactococcus cremoris D1-20, previously evolved from the sensitive strain L. cremoris MG1614. Whole-genome sequencing and comparison over the reference genome L. cremoris MG1363 identified several unexpected mutations in the parental strain MG1614, likely selected during in-house propagation. In the Lcn972R clone, two previously identified mutations were mapped and confirmed. Additionally, another transposition event deregulating cellobiose uptake was identified along with three point mutations of unknown consequences for Lcn972 resistance. Two new independent evolution experiments exposing L. cremoris MG1614 to Lcn972 revealed transposition of IS981 into the LLMG_RS12285 locus as the predominant mutation selected by Lcn972. This event occurs early during evolution and was found in 100% of the evolved clones, while other mutations were not selected. Therefore, activation of LLMG_RS12285 coding for a putative anti-ECF (extra-cytoplasmic function) sigma factor is regarded as the main Lcn972 resistance factor in L. cremoris MG1614.
Collapse
Affiliation(s)
- Susana Escobedo
- Instituto de Productos Lacteos de Asturias (IPLA), CSIC, 33300 Villaviciosa, Spain
| | - Ana B. Campelo
- Instituto de Productos Lacteos de Asturias (IPLA), CSIC, 33300 Villaviciosa, Spain
| | - Özgün C. O. Umu
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 1432 Ås, Norway
| | | | - Ana Rodríguez
- Instituto de Productos Lacteos de Asturias (IPLA), CSIC, 33300 Villaviciosa, Spain
| | - Dzung B. Diep
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Beatriz Martínez
- Instituto de Productos Lacteos de Asturias (IPLA), CSIC, 33300 Villaviciosa, Spain
- Correspondence: ; Tel.: +34-985-89-21-31
| |
Collapse
|
4
|
Andersen JM, Pedersen CM, Bang-Berthelsen CH. Omics-based comparative analysis of putative mobile genetic elements in Lactococcus lactis. FEMS Microbiol Lett 2019; 366:5487889. [PMID: 31074793 DOI: 10.1093/femsle/fnz102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 05/09/2019] [Indexed: 12/29/2022] Open
Abstract
Lactococcus lactis is globally used in food fermentation. Genomics is useful to investigate speciation and differential occurrence of (un)desired gene functions, often related to mobile DNA. This study investigates L. lactis for putative chromosomal mobile genetic elements through comparative genomics, and analyses how they contribute to chromosomal variation at strain level. Our work identified 95 loci that may range over 10% of the chromosome size when including prophages, and the loci display a marked differential occurrence in the analysed strains. Analysis of differential transcriptomics data revealed how mobile genetic elements may impact the host physiology in response to conditional changes. This insight in the genetic variation of mobile genetic elements in L. lactis holds potential to further identify important functions related to food and biotechnology applications within this important species.
Collapse
Affiliation(s)
- Joakim Mark Andersen
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, 2800 Kgs. Lyngby, Denmark
| | - Christine Møller Pedersen
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, 2800 Kgs. Lyngby, Denmark
| | | |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|