1
|
Ma X, Crespo Tapia N, Koomen J, van Mastrigt O, Zwietering MH, Den Besten HMW, Abee T. Activation of a silent lactose utilization pathway in an evolved Listeria monocytogenes F2365 outbreak isolate. Food Res Int 2024; 189:114554. [PMID: 38876592 DOI: 10.1016/j.foodres.2024.114554] [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: 03/11/2024] [Revised: 05/14/2024] [Accepted: 05/26/2024] [Indexed: 06/16/2024]
Abstract
Listeria monocytogenes, a widespread food-borne pathogen, utilizes diverse growth substrates including mono- and di-saccharides via PEP-phosphotransferase (PTS) systems. We evaluated a collection of L. monocytogenes isolates of different origins for their ability to utilize lactose, a disaccharide composed of galactose and glucose and the main carbon source in milk and dairy products. Notably, the dairy-associated outbreak strain F2365 could not utilize lactose efficiently, conceivably due to a frameshift mutation (lacR887del) resulting in a truncated LacR. Transcriptional activator LacR is involved in the expression of two PTS systems, encoded by the lpo operon lmo1718-1720 in combination with lmo2708 and the lmo2683-2685 operon, and linked to lactose and/or cellobiose metabolism in L. monocytogenes. Via experimental evolution of the ancestral strain F2365, an evolved isolate F2365 EV was obtained which showed enhanced growth and metabolism of lactose. Using the lactose-positive model strain L. monocytogenes EGDe as a control, HPLC experiments showed that EGDe and F2365 EV could consume lactose and utilize the glucose moiety, while the galactose moiety was exported from the cells. Genome sequencing of F2365 EV found the original lacR887del mutation was still present but an additional point mutation lmo2766C415T had occurred, resulting in an amino acid substitution in the putative regulator Lmo2766. The lmo2766 gene is located next to operon lmo2761-2765 with putative PTS genes in the genome. Notably, comparative RNAseq analysis confirmed that the lmo2761-2765 operon was strongly upregulated in F2365 EV in the presence of lactose but not in EGDe and F2365. Conversely, the LacR-regulated lpo operon, lmo2708, and lmo2683-2685 operon were only upregulated in EGDe. Additional growth and HPLC experiments, using mutants constructed in lactose-positive L. monocytogenes EGDe, showed reduced growth of the EGDe lacR887del mutant with no utilization of lactose, while the double mutant EGDe lacR887dellmo2766C415T showed enhanced growth and lactose utilization. Hence, these results demonstrate that an amino acid substitution in the Lmo2766 regulator activates a previously silent lactose utilization pathway encoded by PTS operon lmo2761-2765, facilitating the growth and metabolism of L. monocytogenes with lactose as a substrate. This finding enhances our understanding of the metabolic capabilities and adaptability of L. monocytogenes, offering a broader view of the lactose utilization capacity of this pathogen.
Collapse
Affiliation(s)
- Xuchuan Ma
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Natalia Crespo Tapia
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Jeroen Koomen
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Oscar van Mastrigt
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Marcel H Zwietering
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Heidy M W Den Besten
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Tjakko Abee
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands.
| |
Collapse
|
2
|
Zhang L, Xu H, Cheng H, Song F, Zhang J, Peng Q. Transcriptional regulation of cellobiose utilization by PRD-domain containing Sigma54-dependent transcriptional activator (CelR) and catabolite control protein A (CcpA) in Bacillus thuringiensis. Front Microbiol 2024; 15:1160472. [PMID: 38357353 PMCID: PMC10864463 DOI: 10.3389/fmicb.2024.1160472] [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: 02/07/2023] [Accepted: 01/16/2024] [Indexed: 02/16/2024] Open
Abstract
Cellobiose, a β-1,4-linked glucose dimer, is a major cellodextrin resulting from the enzymatic hydrolysis of cellulose. It is a major source of carbon for soil bacteria. In bacteria, the phosphoenolpyruvate (PEP): carbohydrate phosphotransferase system (PTS), encoded by the cel operon, is responsible for the transport and utilization of cellobiose. In this study, we analyzed the transcription and regulation of the cel operon in Bacillus thuringiensis (Bt). The cel operon is composed of five genes forming one transcription unit. β-Galactosidase assays revealed that cel operon transcription is induced by cellobiose, controlled by Sigma54, and positively regulated by CelR. The HTH-AAA+ domain of CelR recognized and specifically bound to three possible binding sites in the celA promoter region. CelR contains two PTS regulation domains (PRD1 and PRD2), which are separated by two PTS-like domains-the mannose transporter enzyme IIA component domain (EIIAMan) and the galactitol transporter enzyme IIB component domain (EIIBGat). Mutations of His-546 on the EIIAMan domain and Cys-682 on the EIIBGat domain resulted in decreased transcription of the cel operon, and mutations of His-839 on PRD2 increased transcription of the cel operon. Glucose repressed the transcription of the cel operon and catabolite control protein A (CcpA) positively regulated this process by binding the cel promoter. In the celABCDE and celR mutants, PTS activities were decreased, and cellobiose utilization was abolished, suggesting that the cel operon is essential for cellobiose utilization. Bt has been widely used as a biological pesticide. The metabolic properties of Bt are critical for fermentation. Nutrient utilization is also essential for the environmental adaptation of Bt. Glucose is the preferred energy source for many bacteria, and the presence of the phosphotransferase system allows bacteria to utilize other sugars in addition to glucose. Cellobiose utilization pathways have been of particular interest owing to their potential for developing alternative energy sources for bacteria. The data presented in this study improve our understanding of the transcription patterns of cel gene clusters. This will further help us to better understand how cellobiose is utilized for bacterial growth.
Collapse
Affiliation(s)
| | | | | | | | | | - Qi Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| |
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
|
Copley SD, Newton MS, Widney KA. How to Recruit a Promiscuous Enzyme to Serve a New Function. Biochemistry 2023; 62:300-308. [PMID: 35729117 PMCID: PMC9881647 DOI: 10.1021/acs.biochem.2c00249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Promiscuous enzymes can be recruited to serve new functions when a genetic or environmental change makes catalysis of a novel reaction important for fitness or even survival. Subsequently, gene duplication and divergence can lead to evolution of an efficient and specialized new enzyme. Every organism likely has thousands of promiscuous enzyme activities that provide a vast reservoir of catalytic potential. However, much of this potential may not be accessible. We compiled kinetic parameters for promiscuous reactions catalyzed by 108 enzymes. The median value of kcat/KM is a very modest 31 M-1 s-1. Based upon the fluxes through metabolic pathways in E. coli, we estimate that many, if not most, promiscuous activities are too inefficient to impact fitness. However, mutations can elevate the level of an insufficient promiscuous activity by increasing enzyme expression, improving kcat/KM, or altering concentrations of the promiscuous and native substrates and allosteric regulators. Particularly in large bacterial populations, stochastic mutations may provide a viable pathway for recruitment of even inefficient promiscuous activities.
Collapse
|
5
|
Petrova P, Ivanov I, Tsigoriyna L, Valcheva N, Vasileva E, Parvanova-Mancheva T, Arsov A, Petrov K. Traditional Bulgarian Dairy Products: Ethnic Foods with Health Benefits. Microorganisms 2021; 9:microorganisms9030480. [PMID: 33668910 PMCID: PMC7996614 DOI: 10.3390/microorganisms9030480] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 02/21/2021] [Accepted: 02/22/2021] [Indexed: 02/07/2023] Open
Abstract
The reported health effects of fermented dairy foods, which are traditionally manufactured in Bulgaria, are connected with their microbial biodiversity. The screening and development of probiotic starters for dairy products with unique properties are based exclusively on the isolation and characterization of lactic acid bacterial (LAB) strains. This study aims to systematically describe the LAB microbial content of artisanal products such as Bulgarian-type yoghurt, white brined cheese, kashkaval, koumiss, kefir, katak, and the Rhodope's brano mliako. The original technologies for their preparation preserve the valuable microbial content and improve their nutritional and probiotic qualities. This review emphasises the features of LAB starters and the autochthonous microflora, the biochemistry of dairy food production, and the approaches for achieving the fortification of the foods with prebiotics, bioactive peptides (ACE2-inhibitors, bacteriocins, cyclic peptides with antimicrobial activity), immunomodulatory exopolysaccharides, and other metabolites (indol-3-propionic acid, free amino acids, antioxidants, prebiotics) with reported beneficial effects on human health. The link between the microbial content of dairy foods and the healthy human microbiome is highlighted.
Collapse
Affiliation(s)
- Penka Petrova
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (I.I.); (A.A.)
- Correspondence: (P.P.); (K.P.)
| | - Ivan Ivanov
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (I.I.); (A.A.)
| | - Lidia Tsigoriyna
- Institute of Chemical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (L.T.); (N.V.); (E.V.); (T.P.-M.)
| | - Nadezhda Valcheva
- Institute of Chemical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (L.T.); (N.V.); (E.V.); (T.P.-M.)
| | - Evgenia Vasileva
- Institute of Chemical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (L.T.); (N.V.); (E.V.); (T.P.-M.)
| | - Tsvetomila Parvanova-Mancheva
- Institute of Chemical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (L.T.); (N.V.); (E.V.); (T.P.-M.)
| | - Alexander Arsov
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (I.I.); (A.A.)
| | - Kaloyan Petrov
- Institute of Chemical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (L.T.); (N.V.); (E.V.); (T.P.-M.)
- Correspondence: (P.P.); (K.P.)
| |
Collapse
|
6
|
Investigation of genomic characteristics and carbohydrates' metabolic activity of Lactococcus lactis subsp. lactis during ripening of a Swiss-type cheese. Food Microbiol 2019; 87:103392. [PMID: 31948633 DOI: 10.1016/j.fm.2019.103392] [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: 05/14/2019] [Revised: 10/04/2019] [Accepted: 11/20/2019] [Indexed: 01/08/2023]
Abstract
Genetic diversity and metabolic properties of Lactococcus lactis subsp. lactis were explored using phylogenetic, pan-genomic and metatranscriptomic analysis. The genomes, used in the current study, were available and downloaded from the GenBank which were primarily related with microorganisms isolated from dairy products and secondarily from other foodstuffs. To study the genetic diversity of the microorganism, various bioinformatics tools were employed such as average nucleotide identity, digital DNA-DNA hybridization, phylogenetic analysis, clusters of orthologous groups analysis, KEGG orthology analysis and pan-genomic analysis. The results showed that Lc. lactis subsp. lactis strains cannot be sufficiently separated into phylogenetic lineages based on the 16S rRNA gene sequences and core genome-based phylogenetic analysis was more appropriate. Pan-genomic analysis of the strains indicated that the core, accessory and unique genome comprised of 1036, 3146 and 1296 genes, respectively. Considering the results of pan-genomic and KEGG orthology analyses, the metabolic network of Lc. lactis subsp. lactis was rebuild regarding its carbohydrates' metabolic capabilities. Based on the metatranscriptomic data during the ripening of the Swiss-type Maasdam cheese at 20 °C and 5 °C, it was shown that the microorganism performed mixed acid fermentation producing lactate, formate, acetate, ethanol and 2,3-butanediol. Mixed acid fermentation was more pronounced at higher ripening temperatures. At lower ripening temperatures, the genes involved in mixed acid fermentation were repressed while lactate production remained unaffected resembling to a homolactic fermentation. Comparative genomics and metatranscriptomic analysis are powerful tools to gain knowledge on the genomic diversity of the lactic acid bacteria used as starter cultures as well as on the metabolic activities occurring in fermented dairy products.
Collapse
|
7
|
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]
|
8
|
Yang Y, Li N, Jiang Y, Liu Z, Liu X, Zhao J, Zhang H, Chen W. Short communication: Enzymatic perspective of galactosidases reveals variations in lactose metabolism among Lactococcus lactis strains. J Dairy Sci 2019; 102:6027-6031. [PMID: 31056324 DOI: 10.3168/jds.2018-15973] [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: 11/11/2018] [Accepted: 03/13/2019] [Indexed: 01/14/2023]
Abstract
To date, most studies of lactose utilization have focused on the genetic diversity of lactic acid bacteria or its influence on product quality, but phenotypic evaluation has rarely been based on metabolic characteristics. In the present study, we investigated the growth, acid production, β-galactosidase, and 6-phospho-β-galactosidase activities of 16 Lactococcus lactis strains obtained from various habitats with lactose as the sole carbon source. The 15 L. lactis strains obtained from various habitats exhibited significant differences in growth and acid production characteristics in the de Man, Rogosa, and Sharpe-lactose broth, and 4 strains consumed more lactose when cultured in skim milk than the type strain ATCC 19435. Among these strains, DQHXNQ38-12 mainly produced acetoin and diacetyl when cultured in skim milk, whereas the strains 15M2 and 5G2 produced high levels of acid and formed curd rapidly. We concluded that the use of lactose is necessary for strain adaptation to the dairy niche. Comprehensive studies of lactose use and the fermentation characteristics of L. lactis are of significant importance.
Collapse
Affiliation(s)
- Yu Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Nan Li
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy and Food Co. Ltd., Shanghai 200436, China
| | - Yang Jiang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhenmin Liu
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy and Food Co. Ltd., Shanghai 200436, China.
| | - Xiaoming Liu
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Centre for Functional Food, Wuxi, Jiangsu 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Centre for Functional Food, Wuxi, Jiangsu 214122, China; Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
McAuliffe O, Kilcawley K, Stefanovic E. Symposium review: Genomic investigations of flavor formation by dairy microbiota. J Dairy Sci 2018; 102:909-922. [PMID: 30343908 DOI: 10.3168/jds.2018-15385] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 08/24/2018] [Indexed: 01/15/2023]
Abstract
Flavor is one of the most important attributes of any fermented dairy product. Dairy consumers are known to be willing to experiment with different flavors; thus, many companies producing fermented dairy products have looked at culture manipulation as a tool for flavor diversification. The development of flavor is a complex process, originating from a combination of microbiological, biochemical, and technological aspects. A key driver of flavor is the enzymatic activities of the deliberately inoculated starter cultures, in addition to the environmental or "nonstarter" microbiota. The contribution of microbial metabolism to flavor development in fermented dairy products has been exploited for thousands of years, but the availability of the whole genome sequences of the bacteria and yeasts involved in the fermentation process and the possibilities now offered by next-generation sequencing and downstream "omics" technologies is stimulating a more knowledge-based approach to the selection of desirable cultures for flavor development. By linking genomic traits to phenotypic outputs, it is now possible to mine the metabolic diversity of starter cultures, analyze the metabolic routes to flavor compound formation, identify those strains with flavor-forming potential, and select them for possible commercial application. This approach also allows for the identification of species and strains not previously considered as potential flavor-formers, the blending of strains with complementary metabolic pathways, and the potential improvement of key technological characteristics in existing strains, strains that are at the core of the dairy industry. An in-depth knowledge of the metabolic pathways of individual strains and their interactions in mixed culture fermentations can allow starter blends to be custom-made to suit industry needs. Applying this knowledge to starter culture research programs is enabling research and development scientists to develop superior starters, expand flavor profiles, and potentially develop new products for future market expansion.
Collapse
Affiliation(s)
- Olivia McAuliffe
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland P61 C996.
| | - Kieran Kilcawley
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland P61 C996
| | - Ewelina Stefanovic
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland P61 C996
| |
Collapse
|
11
|
Padmanabhan A, Tong Y, Wu Q, Zhang J, Shah NP. Transcriptomic Insights Into the Growth Phase- and Sugar-Associated Changes in the Exopolysaccharide Production of a High EPS-Producing Streptococcus thermophilus ASCC 1275. Front Microbiol 2018; 9:1919. [PMID: 30177921 PMCID: PMC6109772 DOI: 10.3389/fmicb.2018.01919] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 07/30/2018] [Indexed: 12/11/2022] Open
Abstract
In a previous study, incorporation of high exopolysaccharide (EPS) producing dairy starter bacterium Streptococcus thermophilus ASCC 1275 was found to improve functionality of low fat mozzarella cheese and yogurt. This bacterium in its eps gene cluster has a unique pair of chain length determining genes, epsC- epsD, when compared to other sequenced S. thermophilus strains. Hence, the aim of this study was to understand the regulatory mechanism of EPS production in this bacterium using transcriptomic analysis to provide opportunities to improve the yield of EPS. As sugars are considered as one of the major determinants of EPS production, after preliminary screening, we selected three sugars, glucose, sucrose and lactose to identify the EPS producing mechanism of this bacterium in M17 medium. Complete RNA-seq analysis was performed using Illumina HiSeq 2000 sequencing system on S. thermophilus 1275 grown in three different sugars at two-time points, 5 h (log phase) and 10 h (stationary phase) to recognize the genes involved in sugar uptake, UDP-sugar formation, EPS assembly and export of EPS outside the bacterial cell. S. thermophilus 1275 was found to produce high amount of EPS (∼430 mg/L) in sucrose (1%) supplemented M17 medium when compared to other two sugars. Differential gene expression analysis revealed the involvement of phosphoenolpyruvate phosphotransferase system (PEP-PTS) for glucose and sucrose uptake, and lacS gene for lactose uptake. The pathways for the formation of UDP-glucose and UDP-galactose were highly upregulated in all the three sugars. In the presence of sucrose, eps1C1D2C2D were found to be highly expressed which refers to high EPS production. Protein homology study suggested the presence of Wzx/Wzy-dependent EPS synthesis and transport pathway in this bacterium. KEGG pathway and COG functional enrichment analysis were also performed to support the result. This is the first report providing the transcriptomic insights into the EPS production mechanism of a common dairy bacterium, S. thermophilus.
Collapse
Affiliation(s)
- Aparna Padmanabhan
- Food and Nutritional Science, School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Ying Tong
- Cancer Genetics, School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Qinglong Wu
- Food and Nutritional Science, School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Jiangwen Zhang
- Cancer Genetics, School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Nagendra P. Shah
- Food and Nutritional Science, School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| |
Collapse
|
12
|
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
|
13
|
Kok J, van Gijtenbeek LA, de Jong A, van der Meulen SB, Solopova A, Kuipers OP. The Evolution of gene regulation research in Lactococcus lactis. FEMS Microbiol Rev 2018; 41:S220-S243. [PMID: 28830093 DOI: 10.1093/femsre/fux028] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/15/2017] [Indexed: 11/12/2022] Open
Abstract
Lactococcus lactis is a major microbe. This lactic acid bacterium (LAB) is used worldwide in the production of safe, healthy, tasteful and nutritious milk fermentation products. Its huge industrial importance has led to an explosion of research on the organism, particularly since the early 1970s. The upsurge in the research on L. lactis coincided not accidentally with the advent of recombinant DNA technology in these years. The development of methods to take out and re-introduce DNA in L. lactis, to clone genes and to mutate the chromosome in a targeted way, to control (over)expression of proteins and, ultimately, the availability of the nucleotide sequence of its genome and the use of that information in transcriptomics and proteomics research have enabled to peek deep into the functioning of the organism. Among many other things, this has provided an unprecedented view of the major gene regulatory pathways involved in nitrogen and carbon metabolism and their overlap, and has led to the blossoming of the field of L. lactis systems biology. All of these advances have made L. lactis the paradigm of the LAB. This review will deal with the exciting path along which the research on the genetics of and gene regulation in L. lactis has trodden.
Collapse
Affiliation(s)
- Jan Kok
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Lieke A van Gijtenbeek
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Anne de Jong
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Sjoerd B van der Meulen
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Ana Solopova
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| |
Collapse
|
14
|
Ho VTT, Lo R, Bansal N, Turner MS. Characterisation of Lactococcus lactis isolates from herbs, fruits and vegetables for use as biopreservatives against Listeria monocytogenes in cheese. Food Control 2018. [DOI: 10.1016/j.foodcont.2017.09.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
15
|
Abstract
Characterization of PTS-IIC, an endogenous constitutive promoter from L. lactis.. Cellobiose enhances activity from PTS-IIC promoter. PTS-IIC promoter mediates protein expression in B. subtilis and E coli Nissle 1917.
Constitutively active promoter elements for heterologous protein production in Lactococcus lactis are scarce. Here, the promoter of the PTS-IIC gene cluster from L. lactis NZ3900 is described. This promoter was cloned upstream of an enhanced green fluorescent protein, GFPmut3a, and transformed into L. lactis. Transformants produced up to 13.5 μg of GFPmut3a per milliliter of log phase cells. Addition of cellobiose further increased the production of GFPmut3a by up to two-fold when compared to glucose. Analysis of mutations at two specific positions in the PTS-IIC promoter showed that a ‘T’ to ‘G’ mutation within the −35 element resulted in constitutive expression in glucose, while a ‘C’ at nucleotide 7 in the putative cre site enhanced promoter activity in cellobiose. Finally, this PTS-IIC promoter is capable of mediating protein expression in Bacillus subtilis and Escherichia coli Nissle 1917, suggesting the potential for future biotechnological applications of this element and its derivatives.
Collapse
Key Words
- ELISA, enzyme-linked immunosorbent assay
- GFP, green fluorescent protein
- Heterologous protein expression
- LAB, lactic acid bacteria
- LB, Luria-Bertani media
- Lactococcus lactis
- OD600, optical density at 600 nm
- PBS, phosphate buffered saline
- Probiotics
- Promoter
- RFU, relative fluorescence unit
- ccpA, catabolite control protein A
- celA, cellobiose-specific phosphor-β-glucosidase
- cre, catabolite-responsive element
- noxE, NADH oxidase promoter
- nt, nucleotide
- ptcC, cellobiose-specific PTS IIC component
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Zeidan AA, Poulsen VK, Janzen T, Buldo P, Derkx PMF, Øregaard G, Neves AR. Polysaccharide production by lactic acid bacteria: from genes to industrial applications. FEMS Microbiol Rev 2017; 41:S168-S200. [DOI: 10.1093/femsre/fux017] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/29/2017] [Indexed: 01/14/2023] Open
|
18
|
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
|
19
|
Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation. BMC Genomics 2017; 18:267. [PMID: 28356072 PMCID: PMC5372332 DOI: 10.1186/s12864-017-3650-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 03/21/2017] [Indexed: 01/07/2023] Open
Abstract
Background Lactococcus lactis is among the most widely studied lactic acid bacterial species due to its long history of safe use and economic importance to the dairy industry, where it is exploited as a starter culture in cheese production. Results In the current study, we report on the complete sequencing of 16 L. lactis subsp. lactis and L. lactis subsp. cremoris genomes. The chromosomal features of these 16 L. lactis strains in conjunction with 14 completely sequenced, publicly available lactococcal chromosomes were assessed with particular emphasis on discerning the L. lactis subspecies division, evolution and niche adaptation. The deduced pan-genome of L. lactis was found to be closed, indicating that the representative data sets employed for this analysis are sufficient to fully describe the genetic diversity of the taxon. Conclusions Niche adaptation appears to play a significant role in governing the genetic content of each L. lactis subspecies, while (differential) genome decay and redundancy in the dairy niche is also highlighted. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3650-5) contains supplementary material, which is available to authorized users.
Collapse
|
20
|
van der Meulen SB, de Jong A, Kok J. Transcriptome landscape of Lactococcus lactis reveals many novel RNAs including a small regulatory RNA involved in carbon uptake and metabolism. RNA Biol 2016; 13:353-66. [PMID: 26950529 PMCID: PMC4829306 DOI: 10.1080/15476286.2016.1146855] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
RNA sequencing has revolutionized genome-wide transcriptome analyses, and the identification of non-coding regulatory RNAs in bacteria has thus increased concurrently. Here we reveal the transcriptome map of the lactic acid bacterial paradigm Lactococcus lactis MG1363 by employing differential RNA sequencing (dRNA-seq) and a combination of manual and automated transcriptome mining. This resulted in a high-resolution genome annotation of L. lactis and the identification of 60 cis-encoded antisense RNAs (asRNAs), 186 trans-encoded putative regulatory RNAs (sRNAs) and 134 novel small ORFs. Based on the putative targets of asRNAs, a novel classification is proposed. Several transcription factor DNA binding motifs were identified in the promoter sequences of (a)sRNAs, providing insight in the interplay between lactococcal regulatory RNAs and transcription factors. The presence and lengths of 14 putative sRNAs were experimentally confirmed by differential Northern hybridization, including the abundant RNA 6S that is differentially expressed depending on the available carbon source. For another sRNA, LLMGnc_147, functional analysis revealed that it is involved in carbon uptake and metabolism. L. lactis contains 13% leaderless mRNAs (lmRNAs) that, from an analysis of overrepresentation in GO classes, seem predominantly involved in nucleotide metabolism and DNA/RNA binding. Moreover, an A-rich sequence motif immediately following the start codon was uncovered, which could provide novel insight in the translation of lmRNAs. Altogether, this first experimental genome-wide assessment of the transcriptome landscape of L. lactis and subsequent sRNA studies provide an extensive basis for the investigation of regulatory RNAs in L. lactis and related lactococcal species.
Collapse
Affiliation(s)
- Sjoerd B van der Meulen
- a Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute , University of Groningen , Groningen , The Netherlands.,b Top Institute Food and Nutrition (TIFN) , Wageningen , The Netherlands
| | - Anne de Jong
- a Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute , University of Groningen , Groningen , The Netherlands.,b Top Institute Food and Nutrition (TIFN) , Wageningen , The Netherlands
| | - Jan Kok
- a Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute , University of Groningen , Groningen , The Netherlands.,b Top Institute Food and Nutrition (TIFN) , Wageningen , The Netherlands
| |
Collapse
|
21
|
Implementation of the agmatine-controlled expression system for inducible gene expression in Lactococcus lactis. Microb Cell Fact 2015; 14:208. [PMID: 26715338 PMCID: PMC4696319 DOI: 10.1186/s12934-015-0399-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/16/2015] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Lactococcus lactis has been safely consumed in fermented foods for millennia. This Gram-positive bacterium has now become of industrial importance as an expression host for the overproduction of lipopolysaccharide-free recombinant proteins used as food ingredients, therapeutic proteins and biotechnological enzymes. RESULTS This paper reports an agmatine-controlled expression (ACE) system for L. lactis, comprising the lactococcal agmatine-sensor/transcriptional activator AguR and its target promoter P(aguB). The usefulness and efficiency of this system was checked via the reporter gene gfp and by producing PEP (Myxococcus xanthus prolyl-endopeptidase), an enzyme of biomedical interest able to degrade the immunotoxic peptides produced during the gastrointestinal breakdown of gluten. CONCLUSION The ACE system developed in this work was suitable for the efficient expression of the functional recombinant proteins GFP and PEP. The expression system was tightly regulated by the agmatine concentration and allowed high protein production without leakiness.
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Bachmann H, Pronk JT, Kleerebezem M, Teusink B. Evolutionary engineering to enhance starter culture performance in food fermentations. Curr Opin Biotechnol 2015; 32:1-7. [DOI: 10.1016/j.copbio.2014.09.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/05/2014] [Accepted: 09/12/2014] [Indexed: 01/08/2023]
|
24
|
ClaR--a novel key regulator of cellobiose and lactose metabolism in Lactococcus lactis IL1403. Appl Microbiol Biotechnol 2014; 99:337-47. [PMID: 25239037 PMCID: PMC4286628 DOI: 10.1007/s00253-014-6067-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/11/2014] [Accepted: 08/31/2014] [Indexed: 11/21/2022]
Abstract
In a number of previous studies, our group has discovered an alternative pathway for lactose utilization in Lactococcus lactis that, in addition to a sugar-hydrolyzing enzyme with both P-β-glucosidase and P-β-galactosidase activity (BglS), engages chromosomally encoded components of cellobiose-specific PTS (PTSCel-Lac), including PtcA, PtcB, and CelB. In this report, we show that this system undergoes regulation via ClaR, a novel activator protein from the RpiR family of transcriptional regulators. Although RpiR proteins are widely distributed among lactic acid bacteria, their roles have yet to be confirmed by functional assays. Here, we show that ClaR activity depends on intracellular cellobiose-6-phosphate availability, while other sugars such as glucose or galactose have no influence on it. We also show that ClaR is crucial for activation of the bglS and celB expression in the presence of cellobiose, with some limited effects on ptcA and ptcB activation. Among 190 of carbon sources tested, the deletion of claR reduces L. lactis growth only in lactose- and/or cellobiose-containing media, suggesting a narrow specificity of this regulator within the context of sugar metabolism.
Collapse
|
25
|
Schwabe A, Bruggeman FJ. Single yeast cells vary in transcription activity not in delay time after a metabolic shift. Nat Commun 2014; 5:4798. [DOI: 10.1038/ncomms5798] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 07/25/2014] [Indexed: 11/09/2022] Open
|
26
|
Assessment of expression of Leloir pathway genes in wild-type galactose-fermenting Streptococcus thermophilus by real-time PCR. Eur Food Res Technol 2014. [DOI: 10.1007/s00217-014-2286-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
27
|
Abstract
When bacteria grow in a medium with two sugars, they first use the preferred sugar and only then start metabolizing the second one. After the first exponential growth phase, a short lag phase of nongrowth is observed, a period called the diauxie lag phase. It is commonly seen as a phase in which the bacteria prepare themselves to use the second sugar. Here we reveal that, in contrast to the established concept of metabolic adaptation in the lag phase, two stable cell types with alternative metabolic strategies emerge and coexist in a culture of the bacterium Lactococcus lactis. Only one of them continues to grow. The fraction of each metabolic phenotype depends on the level of catabolite repression and the metabolic state-dependent induction of stringent response, as well as on epigenetic cues. Furthermore, we show that the production of alternative metabolic phenotypes potentially entails a bet-hedging strategy. This study sheds new light on phenotypic heterogeneity during various lag phases occurring in microbiology and biotechnology and adjusts the generally accepted explanation of enzymatic adaptation proposed by Monod and shared by scientists for more than half a century.
Collapse
|
28
|
Zaprasis A, Hoffmann T, Wünsche G, Flórez LA, Stülke J, Bremer E. Mutational activation of the RocR activator and of a crypticrocDEFpromoter bypass loss of the initial steps of proline biosynthesis inBacillus subtilis. Environ Microbiol 2013; 16:701-17. [DOI: 10.1111/1462-2920.12193] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 06/07/2013] [Accepted: 06/11/2013] [Indexed: 12/11/2022]
Affiliation(s)
- Adrienne Zaprasis
- Department of Biology, Laboratory for Microbiology; Philipps-University Marburg; Karl-von-Frisch Str. 8 Marburg D-35032 Germany
| | - Tamara Hoffmann
- Department of Biology, Laboratory for Microbiology; Philipps-University Marburg; Karl-von-Frisch Str. 8 Marburg D-35032 Germany
| | - Guido Wünsche
- Department of Biology, Laboratory for Microbiology; Philipps-University Marburg; Karl-von-Frisch Str. 8 Marburg D-35032 Germany
| | - Lope A. Flórez
- Department of General Microbiology; Institute of Microbiology and Genetics; Georg-August University Göttingen; Grisebachstr. 8 Göttingen D-37077 Germany
| | - Jörg Stülke
- Department of General Microbiology; Institute of Microbiology and Genetics; Georg-August University Göttingen; Grisebachstr. 8 Göttingen D-37077 Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology; Philipps-University Marburg; Karl-von-Frisch Str. 8 Marburg D-35032 Germany
| |
Collapse
|
29
|
Zirex: a novel zinc-regulated expression system for Lactococcus lactis. Appl Environ Microbiol 2013; 79:4503-8. [PMID: 23666339 DOI: 10.1128/aem.00866-13] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report a new zinc-inducible expression system for Lactococcus lactis, called Zirex, consisting of the pneumococcal repressor SczA and PczcD. PczcD tightly regulates the expression of green fluorescent protein in L. lactis. We show the applicability of Zirex together with the nisin-controlled expression system, enabling simultaneous but independent regulation of different genes.
Collapse
|