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Toussaint F, Henry de Frahan M, Poncelet F, Ladrière JM, Horvath P, Fremaux C, Hols P. Unveiling the regulatory network controlling natural transformation in lactococci. PLoS Genet 2024; 20:e1011340. [PMID: 38950059 PMCID: PMC11244767 DOI: 10.1371/journal.pgen.1011340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 07/12/2024] [Accepted: 06/13/2024] [Indexed: 07/03/2024] Open
Abstract
Lactococcus lactis is a lactic acid bacterium of major importance for food fermentation and biotechnological applications. The ability to manipulate its genome quickly and easily through competence for DNA transformation would accelerate its general use as a platform for a variety of applications. Natural transformation in this species requires the activation of the master regulator ComX. However, the growth conditions that lead to spontaneous transformation, as well as the regulators that control ComX production, are unknown. Here, we identified the carbon source, nitrogen supply, and pH as key factors controlling competence development in this species. Notably, we showed that these conditions are sensed by three global regulators (i.e., CcpA, CodY, and CovR), which repress comX transcription directly. Furthermore, our systematic inactivation of known signaling systems suggests that classical pheromone-sensing regulators are not involved. Finally, we revealed that the ComX-degrading MecA-ClpCP machinery plays a predominant role based on the identification of a single amino-acid substitution in the adaptor protein MecA of a highly transformable strain. Contrasting with closely-related streptococci, the master competence regulator in L. lactis is regulated both proximally by general sensors and distantly by the Clp degradation machinery. This study not only highlights the diversity of regulatory networks for competence control in Gram-positive bacteria, but it also paves the way for the use of natural transformation as a tool to manipulate this biotechnologically important bacterium.
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Affiliation(s)
- Frédéric Toussaint
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Marie Henry de Frahan
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Félix Poncelet
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Jean-Marc Ladrière
- IFF Health & Biosciences, Danisco France SAS, Dangé-Saint-Romain, France
| | - Philippe Horvath
- IFF Health & Biosciences, Danisco France SAS, Dangé-Saint-Romain, France
| | - Christophe Fremaux
- IFF Health & Biosciences, Danisco France SAS, Dangé-Saint-Romain, France
| | - Pascal Hols
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
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2
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Morawska LP, Kuipers OP. Cell-to-cell non-conjugative plasmid transfer between Bacillus subtilis and lactic acid bacteria. Microb Biotechnol 2023; 16:784-798. [PMID: 36547214 PMCID: PMC10034627 DOI: 10.1111/1751-7915.14195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 11/15/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Bacillus subtilis is a soil-dwelling bacterium that can interact with a plethora of other microorganisms in its natural habitat. Due to the versatile interactions and its ability to form nanotubes, i.e., recently described membrane structures that trade cytoplasmic content between neighbouring cells, we investigated the potential of HGT from B. subtilis to industrially-relevant members of lactic acid bacteria (LAB). To explore the interspecies HGT events, we developed a co-culturing protocol and provided proof of transfer of a small high copy non-conjugative plasmid from B. subtilis to LABs. Interestingly, the plasmid transfer did not involve conjugation nor activation of the competent state by B. subtilis. Moreover, our study shows for the first time non-conjugative cell-to-cell intraspecies plasmid transfer for non-competent Lactococcus lactis sp. cremoris strains. Our study indicates that cell-to-cell transformation is a ubiquitous form of HGT and can be potentially utilized as an alternative tool for natural (non-GMO) strain improvement.
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Affiliation(s)
- Luiza P Morawska
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Oscar P Kuipers
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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3
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Recent advances in genetic tools for engineering probiotic lactic acid bacteria. Biosci Rep 2023; 43:232386. [PMID: 36597861 PMCID: PMC9842951 DOI: 10.1042/bsr20211299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/19/2022] [Accepted: 01/03/2023] [Indexed: 01/05/2023] Open
Abstract
Synthetic biology has grown exponentially in the last few years, with a variety of biological applications. One of the emerging applications of synthetic biology is to exploit the link between microorganisms, biologics, and human health. To exploit this link, it is critical to select effective synthetic biology tools for use in appropriate microorganisms that would address unmet needs in human health through the development of new game-changing applications and by complementing existing technological capabilities. Lactic acid bacteria (LAB) are considered appropriate chassis organisms that can be genetically engineered for therapeutic and industrial applications. Here, we have reviewed comprehensively various synthetic biology techniques for engineering probiotic LAB strains, such as clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 mediated genome editing, homologous recombination, and recombineering. In addition, we also discussed heterologous protein expression systems used in engineering probiotic LAB. By combining computational biology with genetic engineering, there is a lot of potential to develop next-generation synthetic LAB with capabilities to address bottlenecks in industrial scale-up and complex biologics production. Recently, we started working on Lactochassis project where we aim to develop next generation synthetic LAB for biomedical application.
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Jayasekara S, Dissanayake L, Jayakody LN. Opportunities in the microbial valorization of sugar industrial organic waste to biodegradable smart food packaging materials. Int J Food Microbiol 2022; 377:109785. [PMID: 35752069 DOI: 10.1016/j.ijfoodmicro.2022.109785] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 05/12/2022] [Accepted: 06/07/2022] [Indexed: 12/20/2022]
Abstract
Many petroleum-derived plastics, including food packaging materials are non-biodegradable and designed for single-use applications. Annually, around 175 Mt. of plastic enters the land and ocean ecosystems due to mismanagement and lack of techno economically feasible plastic waste recycling technologies. Renewable sourced, biodegradable polymer-based food packaging materials can reduce this environmental pollution. Sugar production from sugarcane or sugar beet generates organic waste streams that contain fermentable substrates, including sugars, acids, and aromatics. Microbial metabolism can be leveraged to funnel those molecules to platform chemicals or biopolymers to generate biodegradable food packaging materials that have active or sensing molecules embedded in biopolymer matrices. The smart package can real-time monitor food quality, assure health safety, and provide economic and environmental benefits. Active packaging materials display functional properties such as antimicrobial, antioxidant, and light or gas barrier. This article provides an overview of potential biodegradable smart/active polymer packages for food applications by valorizing sugar industry-generated organic waste. We highlight the potential microbial pathways and metabolic engineering strategies to biofunnel the waste carbon efficiently into the targeted platform chemicals such as lactic, succinate, muconate, and biopolymers, including polyhydroxyalkanoates, and bacterial cellulose. The obtained platform chemicals can be used to produce biodegradable polymers such as poly (butylene adipate-co-terephthalate) (PBAT) that could replace incumbent polyethylene and polypropylene food packaging materials. When nanomaterials are added, these polymers can be active/smart. The process can remarkably lower the greenhouse gas emission and energy used to produce food-packaging material via sugar industrial waste carbon relative to the petroleum-based production. The proposed green routes enable the valorization of sugar processing organic waste into biodegradable materials and enable the circular economy.
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Affiliation(s)
- Sandhya Jayasekara
- School of Biological Science, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Lakshika Dissanayake
- School of Biological Science, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Lahiru N Jayakody
- School of Biological Science, Southern Illinois University Carbondale, Carbondale, IL, USA; Fermentation Science Institute, Southern Illinois University Carbondale, Carbondale, IL, USA.
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5
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Di Giacomo S, Toussaint F, Ledesma-García L, Knoops A, Vande Capelle F, Fremaux C, Horvath P, Ladrière JM, Ait-Abderrahim H, Hols P, Mignolet J. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6543703. [PMID: 35254446 PMCID: PMC9300618 DOI: 10.1093/femsre/fuac014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/14/2022] [Accepted: 03/01/2022] [Indexed: 11/14/2022] Open
Abstract
Nowadays, the growing human population exacerbates the need for sustainable resources. Inspiration and achievements in nutrient production or human/animal health might emanate from microorganisms and their adaptive strategies. Here, we exemplify the benefits of lactic acid bacteria (LAB) for numerous biotechnological applications and showcase their natural transformability as a fast and robust method to hereditarily influence their phenotype/traits in fundamental and applied research contexts. We described the biogenesis of the transformation machinery and we analyzed the genome of hundreds of LAB strains exploitable for human needs to predict their transformation capabilities. Finally, we provide a stepwise rational path to stimulate and optimize natural transformation with standard and synthetic biology techniques. A comprehensive understanding of the molecular mechanisms driving natural transformation will facilitate and accelerate the improvement of bacteria with properties that serve broad societal interests.
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Affiliation(s)
- Stefano Di Giacomo
- Biochemistry and Genetics of Microorganisms (BGM), Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud 4-5, (box L7.07.06), B-1348 Louvain-la-Neuve, Belgium
| | - Frédéric Toussaint
- Biochemistry and Genetics of Microorganisms (BGM), Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud 4-5, (box L7.07.06), B-1348 Louvain-la-Neuve, Belgium
| | - Laura Ledesma-García
- Biochemistry and Genetics of Microorganisms (BGM), Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud 4-5, (box L7.07.06), B-1348 Louvain-la-Neuve, Belgium
| | - Adrien Knoops
- Biochemistry and Genetics of Microorganisms (BGM), Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud 4-5, (box L7.07.06), B-1348 Louvain-la-Neuve, Belgium
| | - Florence Vande Capelle
- Biochemistry and Genetics of Microorganisms (BGM), Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud 4-5, (box L7.07.06), B-1348 Louvain-la-Neuve, Belgium
| | - Christophe Fremaux
- Health and Biosciences, IFF Danisco France SAS, CS 10010, F-86220 Dangé-Saint-Romain, France
| | - Philippe Horvath
- Health and Biosciences, IFF Danisco France SAS, CS 10010, F-86220 Dangé-Saint-Romain, France
| | - Jean-Marc Ladrière
- Health and Biosciences, IFF Danisco France SAS, CS 10010, F-86220 Dangé-Saint-Romain, France
| | | | - Pascal Hols
- Corresponding author: Biochemistry and Genetics of Microorganisms, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud 4-5 (box L7.07.06), B-1348 Louvain-La-Neuve, Belgium. Tel: +3210478896; Fax: +3210472825; E-mail:
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6
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Kong LH, Xiong ZQ, Xia YJ, Ai LZ. High-efficiency transformation of Streptococcus thermophilus using electroporation. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:6578-6585. [PMID: 33937994 DOI: 10.1002/jsfa.11292] [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: 02/14/2021] [Revised: 04/20/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Streptococcus thermophilus, one of the most important lactic acid bacteria, is widely used in food fermentation, which is beneficial to improve food quality. However, the current genetic transformation systems are inefficient for S. thermophilus S-3, which hinders its further study. RESULTS We developed three electroporation transformation methods for S. thermophilus S-3, and optimized various parameters to enhance the transformation efficiency up to 1.3 × 106 CFU/μg DNA, which was 32-fold higher than that of unoptimized. Additionally, transcriptional analysis showed that a series of competence genes in S. thermophilus S-3 were remarkedly up-regulated after optimization, indicating that improvement of transformation efficiency was attributed to the expression level of competence genes. Furthermore, to prove their potential, expression of competence genes (comEA, cbpD and comX) were employed to increase transformation efficiency. The maximum transformation efficiency was obtained by overexpression of comEA, which was 14-fold higher than that of control. CONCLUSION This is the first report of competence gene expression for enhancing transformability in S. thermophilus, which exerts a positive effect on the development of desirable characteristics strains. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Ling-Hui Kong
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Zhi-Qiang Xiong
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Yong-Jun Xia
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Lian-Zhong Ai
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
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Three Distinct Proteases Are Responsible for Overall Cell Surface Proteolysis in Streptococcus thermophilus. Appl Environ Microbiol 2021; 87:e0129221. [PMID: 34550764 DOI: 10.1128/aem.01292-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The lactic acid bacterium Streptococcus thermophilus was believed to display only two distinct proteases at the cell surface, namely, the cell envelope protease PrtS and the housekeeping protease HtrA. Using peptidomics, we demonstrate here the existence of an additional active cell surface protease, which shares significant homology with the SepM protease of Streptococcus mutans. Although all three proteases-PrtS, HtrA, and SepM-are involved in the turnover of surface proteins, they demonstrate distinct substrate specificities. In particular, SepM cleaves proteins involved in cell wall metabolism and cell elongation, and its inactivation has consequences for cell morphology. When all three proteases are inactivated, the residual cell-surface proteolysis of S. thermophilus is approximately 5% of that of the wild-type strain. IMPORTANCE Streptococcus thermophilus is a lactic acid bacterium used widely as a starter in the dairy industry. Due to its "generally recognized as safe" status and its weak cell surface proteolytic activity, it is also considered a potential bacterial vector for heterologous protein production. Our identification of a new cell surface protease made it possible to construct a mutant strain with a 95% reduction in surface proteolysis, which could be useful in numerous biotechnological applications.
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Li Q, Zhang J, Yang J, Jiang Y, Yang S. Recent progress on n-butanol production by lactic acid bacteria. World J Microbiol Biotechnol 2021; 37:205. [PMID: 34698975 DOI: 10.1007/s11274-021-03173-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/13/2021] [Indexed: 11/26/2022]
Abstract
n-Butanol is an essential chemical intermediate produced through microbial fermentation. However, its toxicity to microbial cells has limited its production to a great extent. The anaerobe lactic acid bacteria (LAB) are the most resistant to n-butanol, so it should be the first choice for improving n-butanol production. The present article aims to review the following aspects of n-butanol production by LAB: (1) the tolerance of LAB to n-butanol, including its tolerance level and potential tolerance mechanisms; (2) genome editing tools in the n-butanol-resistant LAB; (3) methods of LAB modification for n-butanol production and the production levels after modification. This review will provide a theoretical basis for further research on n-butanol production by LAB.
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Affiliation(s)
- Qi Li
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Jieze Zhang
- Department of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Junjie Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Huzhou, 313000, China
- Shanghai Taoyusheng Biotechnology Company Ltd, Shanghai, 200032, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China.
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Huzhou, 313000, China.
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9
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Tatemichi Y, Nakahara T, Ueda M, Kuroda K. Construction of recombinant Escherichia coli producing nitrogenase-related proteins from Azotobacter vinelandii. Biosci Biotechnol Biochem 2021; 85:2209-2216. [PMID: 34387317 DOI: 10.1093/bbb/zbab144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/05/2021] [Indexed: 11/12/2022]
Abstract
Biological nitrogen fixation by nitrogenase has attracted attention as an alternative method to chemical nitrogen fixation, which requires large amounts of fossil fuels. Azotobacter vinelandii, which produces an oxygen-sensitive nitrogenase, can fix nitrogen even under aerobic conditions; therefore, the heterologous expression of nif-related genes from A. vinelandii is a promising strategy for developing a biological nitrogen fixation method. We assembled 17 nif-related genes, which are scattered throughout the genome of A. vinelandii, into synthetic gene clusters by overlap-extension-PCR and seamless cloning and expressed them in Escherichia coli. The transcription and translation of the 17 nif-related genes were evaluated by RT-qPCR and LC-MS/MS, respectively. The constructed E. coli showed nitrogenase activity under anaerobic and microaerobic conditions. This strain would be a useful model for examining the effect of other genes from A. vinelandii on nitrogen fixation by expressing them in addition to the minimal set of nif-related genes.
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Affiliation(s)
- Yuki Tatemichi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-Ku, Kyoto, Japan
- Research and Development Division, Kikkoman Corporation, Noda-City, Chiba, Japan
| | - Takeharu Nakahara
- Research and Development Division, Kikkoman Corporation, Noda-City, Chiba, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-Ku, Kyoto, Japan
| | - Kouichi Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-Ku, Kyoto, Japan
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10
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Yuan L, Wu H, Wang B, Jia C, Liang D, Caiyin QGL, Qiao J. ComX improves acid tolerance by regulating the expression of late competence proteins in Lactococcus lactis F44. J Dairy Sci 2021; 104:9556-9569. [PMID: 34147226 DOI: 10.3168/jds.2021-20184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/07/2021] [Indexed: 12/22/2022]
Abstract
ComX can improve bacterial competence by modulating global gene expression. Although competence induction may also be a protective mechanism under stress, this has not been investigated in detail. Here, we demonstrated that ComX improved the acid tolerance and nisin yield of Lactococcus lactis, which is an important gram-positive bacterium increasingly used in modern biotechnological applications. We found that overexpression of comX could improve the survival rate up to 36.5% at pH 4.0, compared with only 5.4% and 1.1% with the wild-type and comX knockout strains, respectively. Moreover, quantitative real-time PCR results indicated that comX overexpression stimulated the expression of late competence genes synergistically with exposure to acid stress. Finally, electrophoretic mobility shift assay demonstrated the binding of purified ComX to the cin-box in the promoters of these genes. Taken together, our results reveal a regulation mechanism by which ComX and acid stress can synergistically modulate the expression of late competence genes to enhance cells' acid tolerance and nisin yield.
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Affiliation(s)
- Lin Yuan
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China; Department of Bioengineering, School of Food Science and Bioengineering, Tianjin Agricultural University, Tianjin 300072, P. R. China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, P. R. China
| | - Hao Wu
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, P. R. China; Zhejiang Shaoxing Research Institute of Tianjin University, Shaoxing 312300, P. R. China
| | - Binbin Wang
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, P. R. China; School of Life Science, Shanxi Normal University, Linfen 41000, P. R. China
| | - Cuili Jia
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Dongmei Liang
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China; Zhejiang Shaoxing Research Institute of Tianjin University, Shaoxing 312300, P. R. China
| | - Qing-Ge-Le Caiyin
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Jianjun Qiao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, P. R. China; Zhejiang Shaoxing Research Institute of Tianjin University, Shaoxing 312300, P. R. China.
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Kleerebezem M, Bachmann H, van Pelt-KleinJan E, Douwenga S, Smid EJ, Teusink B, van Mastrigt O. Lifestyle, metabolism and environmental adaptation in Lactococcus lactis. FEMS Microbiol Rev 2021; 44:804-820. [PMID: 32990728 DOI: 10.1093/femsre/fuaa033] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/28/2020] [Indexed: 12/14/2022] Open
Abstract
Lactococcus lactis serves as a paradigm organism for the lactic acid bacteria (LAB). Extensive research into the molecular biology, metabolism and physiology of several model strains of this species has been fundamental for our understanding of the LAB. Genomic studies have provided new insights into the species L. lactis, including the resolution of the genetic basis of its subspecies division, as well as the control mechanisms involved in the fine-tuning of growth rate and energy metabolism. In addition, it has enabled novel approaches to study lactococcal lifestyle adaptations to the dairy application environment, including its adjustment to near-zero growth rates that are particularly relevant in the context of cheese ripening. This review highlights various insights in these areas and exemplifies the strength of combining experimental evolution with functional genomics and bacterial physiology research to expand our fundamental understanding of the L. lactis lifestyle under different environmental conditions.
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Affiliation(s)
- Michiel Kleerebezem
- Host-Microbe Interactomics Group, Animal Sciences Department, Wageningen University, De Elst 1, 6708 WD Wageningen, the Netherlands
| | - Herwig Bachmann
- Systems Bioinformatics, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands.,NIZO food research, Kernhemseweg 2, 6718 ZB Ede, the Netherlands
| | - Eunice van Pelt-KleinJan
- Systems Bioinformatics, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands.,TiFN Food & Nutrition, Nieuwe Kanaal 9A, 6709 PA Wageningen, the Netherlands
| | - Sieze Douwenga
- Systems Bioinformatics, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands.,TiFN Food & Nutrition, Nieuwe Kanaal 9A, 6709 PA Wageningen, the Netherlands
| | - Eddy J Smid
- Laboratory of Food Microbiology, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Bas Teusink
- Systems Bioinformatics, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - Oscar van Mastrigt
- Laboratory of Food Microbiology, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
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Genome-scale exploration of transcriptional regulation in the nisin Z producer Lactococcus lactis subsp. lactis IO-1. Sci Rep 2020; 10:3787. [PMID: 32123183 PMCID: PMC7051946 DOI: 10.1038/s41598-020-59731-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 01/13/2020] [Indexed: 02/06/2023] Open
Abstract
Transcription is of the most crucial steps of gene expression in bacteria, whose regulation guarantees the bacteria's ability to adapt to varying environmental conditions. Discovering the molecular basis and genomic principles of the transcriptional regulation is thus one of the most important tasks in cellular and molecular biology. Here, a comprehensive phylogenetic footprinting framework was implemented to predict maximal regulons of Lactococcus lactis subsp. lactis IO-1, a lactic acid bacterium known for its high potentials in nisin Z production as well as efficient xylose consumption which have made it a promising biotechnological strain. A total set of 321 regulons covering more than 90% of all the bacterium's operons have been elucidated and validated according to available data. Multiple novel biologically-relevant members were introduced amongst which arsC, mtlA and mtl operon for BusR, MtlR and XylR regulons can be named, respectively. Moreover, the effect of riboflavin on nisin biosynthesis was assessed in vitro and a negative correlation was observed. It is believed that understandings from such networks not only can be useful for studying transcriptional regulatory potentials of the target organism but also can be implemented in biotechnology to rationally design favorable production conditions.
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13
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Towards high-throughput genome engineering in lactic acid bacteria. Curr Opin Biotechnol 2020; 61:181-188. [DOI: 10.1016/j.copbio.2019.12.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 12/07/2019] [Accepted: 12/17/2019] [Indexed: 11/22/2022]
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14
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Koko I, Song AAL, Masarudin MJ, Abdul Rahim R. Engineering integrative vectors based on phage site-specific recombination mechanism for Lactococcus lactis. BMC Biotechnol 2019; 19:82. [PMID: 31775775 PMCID: PMC6882331 DOI: 10.1186/s12896-019-0575-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 11/07/2019] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Site-specific integration system allows foreign DNA to be integrated into the specific site of the host genome, enabling stable expression of heterologous protein. In this study, integrative vectors for secretion and surface display of proteins were constructed based on a lactococcal phage TP901-1 integrating system. RESULTS The constructed integration system comprises of a lactococcal promoter (PnisA or P170), phage attachment site (attP) from bacteriophage TP901-1, a signal peptide (USP45 or SPK1) for translocation of the target protein, and a PrtP344 anchor domain in the case of the integrative vectors for surface display. There were eight successfully constructed integrative vectors with each having a different combination of promoter and signal peptide; pS1, pS2, pS3 and pS4 for secretion, and pSD1, pSD2, pSD3 and pSD4 for surface display of desired protein. The integration of the vectors into the host genome was assisted by a helper vector harbouring the integrase gene. A nuclease gene was used as a reporter and was successfully integrated into the L. lactis genome and Nuc was secreted or displayed as expected. The signal peptide SPK1 was observed to be superior to USP45-LEISSTCDA fusion in the secretion of Nuc. As for the surface display integrative vector, all systems developed were comparable with the exception of the combination of P170 promoter with USP45 signal peptide which gave very low signals in whole cell ELISA. CONCLUSION The engineered synthetic integrative vectors have the potential to be used for secretion or surface display of heterologous protein production in lactococcal expression system for research or industrial purposes, especially in live vaccine delivery.
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Affiliation(s)
- Innanurdiani Koko
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM, Serdang, Selangor Malaysia
| | - Adelene Ai-Lian Song
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM, Serdang, Selangor Malaysia
- Institute of Bioscience, University Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
| | - Mas Jaffri Masarudin
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM, Serdang, Selangor Malaysia
- Institute of Bioscience, University Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
| | - Raha Abdul Rahim
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM, Serdang, Selangor Malaysia
- Institute of Bioscience, University Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
- Chancellory, Universiti Teknikal Malaysia, 76100 Durian Tunggal, Melaka, Malaysia
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van Tilburg AY, Cao H, van der Meulen SB, Solopova A, Kuipers OP. Metabolic engineering and synthetic biology employing Lactococcus lactis and Bacillus subtilis cell factories. Curr Opin Biotechnol 2019; 59:1-7. [DOI: 10.1016/j.copbio.2019.01.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/05/2018] [Accepted: 01/16/2019] [Indexed: 12/11/2022]
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16
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Börner RA, Kandasamy V, Axelsen AM, Nielsen AT, Bosma EF. Genome editing of lactic acid bacteria: opportunities for food, feed, pharma and biotech. FEMS Microbiol Lett 2019; 366:5251984. [PMID: 30561594 PMCID: PMC6322438 DOI: 10.1093/femsle/fny291] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/16/2018] [Indexed: 12/16/2022] Open
Abstract
This mini-review provides a perspective of traditional, emerging and future applications of lactic acid bacteria (LAB) and how genome editing tools can be used to overcome current challenges in all these applications. It also describes available tools and how these can be further developed, and takes current legislation into account. Genome editing tools are necessary for the construction of strains for new applications and products, but can also play a crucial role in traditional ones, such as food and probiotics, as a research tool for gaining mechanistic insights and discovering new properties. Traditionally, recombinant DNA techniques for LAB have strongly focused on being food-grade, but they lack speed and the number of genetically tractable strains is still rather limited. Further tool development will enable rapid construction of multiple mutants or mutant libraries on a genomic level in a wide variety of LAB strains. We also propose an iterative Design–Build–Test–Learn workflow cycle for LAB cell factory development based on systems biology, with ‘cell factory’ expanding beyond its traditional meaning of production strains and making use of genome editing tools to advance LAB understanding, applications and strain development.
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Affiliation(s)
- Rosa A Börner
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet B220, 2800 Kongens Lyngby, Denmark
| | - Vijayalakshmi Kandasamy
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet B220, 2800 Kongens Lyngby, Denmark
| | - Amalie M Axelsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet B220, 2800 Kongens Lyngby, Denmark
| | - Alex T Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet B220, 2800 Kongens Lyngby, Denmark
| | - Elleke F Bosma
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet B220, 2800 Kongens Lyngby, Denmark
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17
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Gaudu P, Yamamoto Y, Jensen PR, Hammer K, Lechardeur D, Gruss A. Genetics of Lactococci. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0035-2018. [PMID: 31298208 PMCID: PMC10957224 DOI: 10.1128/microbiolspec.gpp3-0035-2018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Indexed: 11/20/2022] Open
Abstract
Lactococcus lactis is the best characterized species among the lactococci, and among the most consumed food-fermenting bacteria worldwide. Thanks to their importance in industrialized food production, lactococci are among the lead bacteria understood for fundamental metabolic pathways that dictate growth and survival properties. Interestingly, lactococci belong to the Streptococcaceae family, which includes food, commensal and virulent species. As basic metabolic pathways (e.g., respiration, metal homeostasis, nucleotide metabolism) are now understood to underlie virulence, processes elucidated in lactococci could be important for understanding pathogen fitness and synergy between bacteria. This chapter highlights major findings in lactococci and related bacteria, and covers five themes: distinguishing features of lactococci, metabolic capacities including the less known respiration metabolism in Streptococcaceae, factors and pathways modulating stress response and fitness, interbacterial dialogue via metabolites, and novel applications in health and biotechnology.
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Affiliation(s)
| | - Yuji Yamamoto
- Laboratory of Cellular Microbiology, School of Veterinary Medicine, Kitasato University, Towada, 034-8628, Aomori Japan
| | - Peter Ruhdal Jensen
- National Food Institute, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Karin Hammer
- DTU Bioengineering, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
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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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Renaissance of traditional DNA transfer strategies for improvement of industrial lactic acid bacteria. Curr Opin Biotechnol 2019; 56:61-68. [DOI: 10.1016/j.copbio.2018.09.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/04/2018] [Accepted: 09/09/2018] [Indexed: 01/01/2023]
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20
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Mulder J, Wels M, Kuipers OP, Kleerebezem M, Bron PA. Induction of Natural Competence in Genetically-modified Lactococcus lactis. Bio Protoc 2018; 8:e2922. [PMID: 34395748 DOI: 10.21769/bioprotoc.2922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/15/2018] [Accepted: 06/21/2018] [Indexed: 11/02/2022] Open
Abstract
Natural competence can be activated in Lactoccocus lactis subsp lactis and cremoris upon overexpression of ComX, a master regulator of bacterial competence. Herein, we demonstrate a method to activate bacterial competence by regulating the expression of the comX gene by using a nisin-inducible promoter in an L. lactis strain harboring either a chromosomal or plasmid-encoded copy of nisRK. Addition of moderate concentrations of the inducer nisin resulted in concomitant moderate levels of ComX, which led to an optimal transformation rate (1.0 x 10-6 transformants/total cell number/g plasmid DNA). Here, a detailed description of the optimized protocol for competence induction is presented.
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Affiliation(s)
- Joyce Mulder
- NIZO B.V., Ede, The Netherlands.,Molecular Genetics, University of Groningen, Groningen, The Netherlands.,BE-Basic Foundation, Delft, The Netherlands
| | | | - Oscar P Kuipers
- Molecular Genetics, University of Groningen, Groningen, The Netherlands.,BE-Basic Foundation, Delft, The Netherlands
| | - Michiel Kleerebezem
- BE-Basic Foundation, Delft, The Netherlands.,Host-Microbe Interactomics Group, Animal Sciences, Wageningen University, Wageningen, The Netherlands
| | - Peter A Bron
- NIZO B.V., Ede, The Netherlands.,BE-Basic Foundation, Delft, The Netherlands
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