1
|
Vivekanandan KE, Kasimani R, Kumar PV, Meenatchisundaram S, Sundar WA. Overview of cloning in lactic acid bacteria: Expression and its application of probiotic potential in inflammatory bowel diseases. Biotechnol Appl Biochem 2024; 71:881-895. [PMID: 38576028 DOI: 10.1002/bab.2584] [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: 10/18/2023] [Accepted: 03/22/2024] [Indexed: 04/06/2024]
Abstract
Inflammatory bowel disease (IBD) imposes a significant impact on the quality of life for affected individuals. However, there was a current lack of a systematic summary regarding the latest epidemic trends and the underlying pathogenesis of IBD. This highlights the need for a thorough examination of both the epidemiological aspects of IBD and the specific mechanisms by which lactic acid bacteria (LAB) contribute to mitigating this condition. In developed countries, higher incidences and death rates of IBD have been observed, influenced by a combination of environmental and genetic factors. LAB offer significant advantages and substantial potential for enhancing IBD treatment. LAB's capabilities include the production of bioactive metabolites, regulation of gut immunity, protection of intestinal mechanical barriers, inhibition of oxidative damage, and restoration of imbalanced gut microbiota. The review suggests that screening effective LAB using cell models and metabolites, optimizing LAB intake through dose-effect studies, enhancing utilization through nanoencapsulation and microencapsulation, investigating mechanisms to deepen the understanding of LAB, and refining clinical study designs. These efforts aim to contribute to comprehending the epidemic trend, pathogenesis, and treatment of IBD, ultimately fostering the development of targeted therapeutic products, such as LAB-based interventions.
Collapse
Affiliation(s)
- K E Vivekanandan
- Department of Microbiology, Nehru Arts and Science College, Coimbatore, Tamil Nadu, India
| | - R Kasimani
- Department of Microbiology, Nehru Arts and Science College, Coimbatore, Tamil Nadu, India
| | - P Vinoth Kumar
- Department of Microbiology, Nehru Arts and Science College, Coimbatore, Tamil Nadu, India
| | - S Meenatchisundaram
- Department of Microbiology, Shree Nehru Maha Vidyalaya College of Arts and Science, Coimbatore, Tamil Nadu, India
| | - William Arputha Sundar
- Department of Pharmaceuticals, Swamy Vivekananda College of Pharmacy, Namakkal, Tamil Nadu, India
| |
Collapse
|
2
|
Wang J, Zhang L, Su Y, Qu Y, Cao Y, Qin W, Liu Y. A Novel Fluorescent Probe Strategy Activated by β-Glucuronidase for Assisting Surgical Resection of Liver Cancer. Anal Chem 2022; 94:7012-7020. [PMID: 35506678 DOI: 10.1021/acs.analchem.1c05635] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Liver cancer is a primary malignant tumor with a very high fatality rate, which has seriously threatened human health and life. In normal hepatocellular lesions, β-glucuronidase (GLU) activity in liver cancer tissues is significantly increased. Therefore, GLU has become one of the important biomarkers of primary liver cancer. Here, a series of fluorescent probes (DCDH, DCDCH3, DCDOCH3, and DCDNO2) for early diagnosis of liver cancer and auxiliary surgical resection were successfully synthesized. Since the electron-withdrawing group -NO2 connected to the probe DCDNO2 accelerates the rapid cleavage of the glycosidic bond, DCDNO2 exhibits superior fluorescence properties that are more sensitive and rapid than the other three probes DCDH, DCDCH3, and DCDOCH3 when detecting GLU. DCDNO2 has been well-applied in real-time fluorescent visualization imaging for the detection of GLU activity in liver cancer cells and tumor tissues. In addition, DCDNO2 has also been successfully used in the early diagnosis of liver cancer and real-time imaging to guide the surgical resection of liver cancer tumors. Therefore, DCDNO2 has great potential for development in bioclinical medicine for the early detection and treatment of liver cancer.
Collapse
Affiliation(s)
- Jiemin Wang
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, State Key Laboratory of Applied Organic Chemistry and Key Laboratory of Special Function Materials and Structure Design (MOE), College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Liang Zhang
- Department of Radiology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, People's Republic of China
| | - Yaling Su
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, State Key Laboratory of Applied Organic Chemistry and Key Laboratory of Special Function Materials and Structure Design (MOE), College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Yi Qu
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, State Key Laboratory of Applied Organic Chemistry and Key Laboratory of Special Function Materials and Structure Design (MOE), College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Yuping Cao
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, State Key Laboratory of Applied Organic Chemistry and Key Laboratory of Special Function Materials and Structure Design (MOE), College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Wenwu Qin
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, State Key Laboratory of Applied Organic Chemistry and Key Laboratory of Special Function Materials and Structure Design (MOE), College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Yun Liu
- Department of Radiology, Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, People's Republic of China
| |
Collapse
|
3
|
Khandelwal R, Jain D, Jaishankar J, Barman A, Srivastava P, Bisaria VS. Characterization of Zymomonas mobilis promoters that are functional in Escherichia coli. J Biosci Bioeng 2022; 133:301-308. [DOI: 10.1016/j.jbiosc.2021.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/19/2021] [Accepted: 12/26/2021] [Indexed: 02/08/2023]
|
4
|
Dineen RL, Penno C, Kelleher P, Bourin MJB, O'Connell‐Motherway M, van Sinderen D. Molecular analysis of the replication functions of the bifidobacterial conjugative megaplasmid pMP7017. Microb Biotechnol 2021; 14:1494-1511. [PMID: 33939264 PMCID: PMC8313286 DOI: 10.1111/1751-7915.13810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 03/22/2021] [Indexed: 11/29/2022] Open
Abstract
pMP7017 is a conjugative megaplasmid isolated from the gut commensal Bifidobacterium breve JCM7017 and was shown to encode two putative replicases, designated here as RepA and RepB. In the current work, RepB was identified as the pMP7017 replicative initiator, as the repB gene, and its surrounding region was shown to be sufficient to allow autonomous replication in two bifidobacterial species, B. breve and Bifidobacterium longum subsp. longum. RepB was shown to bind to repeat sequence downstream of its coding sequence and this region was determined to be essential for efficient replication. Based on our results, we hypothesize that pMP7017 is an iteron-regulated plasmid (IRP) under strict auto-regulatory control. Recombinantly produced and purified RepB was determined to exist as a dimer in solution, differing from replicases of other IRPs, which exist as a mix of dimers and monomers. Furthermore, a stable low-copy Bifidobacterium-E. coli shuttle vector, pRD1.3, was created which can be employed for cloning and expression of large genes, as was demonstrated by the cloning and heterologous expression of the 5.1 kb apuB gene encoding the extracellular amylopullulanase from B. breve UCC2003 into B. longum subsp. longum NCIMB8809.
Collapse
Affiliation(s)
- Rebecca L. Dineen
- APC Microbiome IrelandUniversity College CorkWestern RoadCorkIreland
- School of MicrobiologyUniversity College CorkWestern RoadCorkIreland
| | - Christophe Penno
- CNRS UMR 6553 EcoBioUniversite de Rennes 1Campus de Beaulieu, Bat. 14ARennes cedex35042France
| | - Philip Kelleher
- APC Microbiome IrelandUniversity College CorkWestern RoadCorkIreland
- School of MicrobiologyUniversity College CorkWestern RoadCorkIreland
| | - Maxence J. B. Bourin
- APC Microbiome IrelandUniversity College CorkWestern RoadCorkIreland
- School of MicrobiologyUniversity College CorkWestern RoadCorkIreland
| | | | - Douwe van Sinderen
- APC Microbiome IrelandUniversity College CorkWestern RoadCorkIreland
- School of MicrobiologyUniversity College CorkWestern RoadCorkIreland
| |
Collapse
|
5
|
Yadav SK, Magotra A, Ghosh S, Krishnan A, Pradhan A, Kumar R, Das J, Sharma M, Jha G. Immunity proteins of dual nuclease T6SS effectors function as transcriptional repressors. EMBO Rep 2021; 22:e51857. [PMID: 33786997 PMCID: PMC8183406 DOI: 10.15252/embr.202051857] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 02/26/2021] [Accepted: 03/08/2021] [Indexed: 12/31/2022] Open
Abstract
Bacteria utilize type VI secretion system (T6SS) to deliver antibacterial toxins to target co-habiting bacteria. Here, we report that Burkholderia gladioli strain NGJ1 deploys certain T6SS effectors (TseTBg), having both DNase and RNase activities to kill target bacteria. RNase activity is prominent on NGJ1 as well as other bacterial RNA while DNase activity is pertinent to only other bacteria. The associated immunity (TsiTBg) proteins harbor non-canonical helix-turn-helix motifs and demonstrate transcriptional repression activity, similar to the antitoxins of type II toxin-antitoxin (TA) systems. Genome analysis reveals that homologs of TseTBg are either encoded as TA or T6SS effectors in diverse bacteria. Our results indicate that a new ORF (encoding a hypothetical protein) has evolved as a result of operonic fusion of TA type TseTBg homolog with certain T6SS-related genes by the action of IS3 transposable elements. This has potentially led to the conversion of a TA into T6SS effector in Burkholderia. Our study exemplifies that bacteria can recruit toxins of TA systems as T6SS weapons to diversify its arsenal to dominate during inter-bacterial competitions.
Collapse
Affiliation(s)
- Sunil Kumar Yadav
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| | - Ankita Magotra
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| | - Srayan Ghosh
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| | - Aiswarya Krishnan
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| | - Amrita Pradhan
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| | - Rahul Kumar
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| | - Joyati Das
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| | - Mamta Sharma
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| | - Gopaljee Jha
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| |
Collapse
|
6
|
Fuhren J, Schwalbe M, Rösch C, Nijland R, Wels M, Schols HA, Kleerebezem M. Dietary Inulin Increases Lactiplantibacillus plantarum Strain Lp900 Persistence in Rats Depending on the Dietary-Calcium Level. Appl Environ Microbiol 2021; 87:e00122-21. [PMID: 33608291 PMCID: PMC8091021 DOI: 10.1128/aem.00122-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 02/12/2021] [Indexed: 12/20/2022] Open
Abstract
Synbiotics are food supplements that combine probiotics and prebiotics to synergistically elicit health benefits in the consumer. Lactiplantibacillus plantarum strains display high survival during transit through the mammalian gastrointestinal tract and were shown to have health-promoting properties. Growth on the fructose polysaccharide inulin is relatively uncommon in L. plantarum, and in this study we describe FosE, a plasmid-encoded β-fructosidase of L. plantarum strain Lp900 which has inulin-hydrolyzing properties. FosE contains an LPxTG-like motif involved in sortase-dependent cell wall anchoring but is also (partially) released in the culture supernatant. In addition, we examined the effect of diet supplementation with inulin on the intestinal persistence of Lp900 in adult male Wistar rats in diets with distinct calcium levels. Inulin supplementation in high-dietary-calcium diets significantly increased the intestinal persistence of L. plantarum Lp900, whereas this effect was not observed upon inulin supplementation of the low-calcium diet. Moreover, intestinal persistence of L. plantarum Lp900 was determined when provided as a probiotic (by itself) or as a synbiotic (i.e., in an inulin suspension) in rats that were fed unsupplemented diets containing the different calcium levels, revealing that the synbiotic administration increased bacterial survival and led to higher abundance of L. plantarum Lp900 in rats, particularly in a low-calcium-diet context. Our findings demonstrate that inulin supplementation can significantly enhance the intestinal delivery of L. plantarum Lp900 but that this effect strongly depends on calcium levels in the diet.IMPORTANCE Synbiotics combine probiotics with prebiotics to synergistically elicit a health benefit in the consumer. Previous studies have shown that prebiotics can selectively stimulate the growth in the intestine of specific bacterial strains. In synbiotic supplementations the prebiotics constituent could increase the intestinal persistence and survival of accompanying probiotic strain(s) and/or modulate the endogenous host microbiota to contribute to the synergistic enhancement of the health-promoting effects of the synbiotic constituents. Our study establishes a profound effect of dietary-calcium-dependent inulin supplementation on the intestinal persistence of inulin-utilizing L. plantarum Lp900 in rats. We also show that in rats on a low-dietary-calcium regime, the survival and intestinal abundance of L. plantarum Lp900 are significantly increased by administering it as an inulin-containing synbiotic. This study demonstrates that prebiotics can enhance the intestinal delivery of specific probiotics and that the prebiotic effect is profoundly influenced by the calcium content of the diet.
Collapse
Affiliation(s)
- Jori Fuhren
- Host-Microbe Interactomics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Markus Schwalbe
- Host-Microbe Interactomics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Christiane Rösch
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, The Netherlands
| | - Reindert Nijland
- Marine Animal Ecology Group, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Henk A Schols
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, The Netherlands
| | - Michiel Kleerebezem
- Host-Microbe Interactomics Group, Wageningen University & Research, Wageningen, The Netherlands
| |
Collapse
|
7
|
Hoedt EC, Bottacini F, Cash N, Bongers RS, van Limpt K, Ben Amor K, Knol J, MacSharry J, van Sinderen D. Broad Purpose Vector for Site-Directed Insertional Mutagenesis in Bifidobacterium breve. Front Microbiol 2021; 12:636822. [PMID: 33833740 PMCID: PMC8021953 DOI: 10.3389/fmicb.2021.636822] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/02/2021] [Indexed: 11/28/2022] Open
Abstract
Members of the genus Bifidobacterium are notoriously recalcitrant to genetic manipulation due to their extensive and variable repertoire of Restriction-Modification (R-M) systems. Non-replicating plasmids are currently employed to achieve insertional mutagenesis in Bifidobacterium. One of the limitations of using such insertion vectors is the presence within their sequence of various restriction sites, making them sensitive to the activity of endogenous restriction endonucleases encoded by the target strain. For this reason, vectors have been developed with the aim of methylating and protecting the vector using a methylase-positive Escherichia coli strain, in some cases containing a cloned bifidobacterial methylase. Here, we present a mutagenesis approach based on a modified and synthetically produced version of the suicide vector pORI28 (named pFREM28), where all known restriction sites targeted by Bifidobacterium breve R-M systems were removed by base substitution (thus preserving the codon usage). After validating the integrity of the erythromycin marker, the vector was successfully employed to target an α-galactosidase gene responsible for raffinose metabolism, an alcohol dehydrogenase gene responsible for mannitol utilization and a gene encoding a priming glycosyltransferase responsible for exopolysaccharides (EPS) production in B. breve. The advantage of using this modified approach is the reduction of the amount of time, effort and resources required to generate site-directed mutants in B. breve and a similar approach may be employed to target other (bifido)bacterial species.
Collapse
Affiliation(s)
- Emily C Hoedt
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia
| | - Francesca Bottacini
- NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia.,Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | - Nora Cash
- NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia
| | | | | | | | - Jan Knol
- Danone Nutricia Research, Utrecht, Netherlands.,Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - John MacSharry
- NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia.,School of Microbiology, University College Cork, Cork, Ireland.,School of Medicine, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia.,School of Microbiology, University College Cork, Cork, Ireland
| |
Collapse
|
8
|
A Resource for Cloning and Expression Vectors Designed for Bifidobacteria: Overview of Available Tools and Biotechnological Applications. Methods Mol Biol 2021. [PMID: 33649956 DOI: 10.1007/978-1-0716-1274-3_14] [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] [Indexed: 12/14/2023]
Abstract
Bifidobacteria represent an important group of (mostly) commensal microorganisms, which have enjoyed increasing scientific and industrial attention due to their purported health-promoting attributes. For the latter reason, several species have been granted "generally recognized as safe" (GRAS) and "qualified presumption of safety" (QPS) status by the Food and Drugs Administration (FDA) and European Food Safety Authority (EFSA) organizations. Increasing scientific evidence supports their potential as oral delivery vectors to produce bioactive and therapeutic molecules at intestinal level. In order to achieve an efficient utilization of bifidobacterial strains as health-promoting (food) ingredients, it is necessary to provide evidence on the molecular mechanisms behind their purported beneficial and probiotic traits, and precise mechanisms of interaction with their human (or other mammalian) host. In this context, developing appropriate molecular tools to generate and investigate recombinant strains is necessary. While bifidobacteria have long remained recalcitrant to genetic manipulation, a wide array of Bifidobacterium-specific replicating vectors and genetic modification procedures have been described in literature. The current chapter intends to provide an updated overview on the vectors used to genetically modify and manipulate bifidobacteria, including their general characteristics, reviewing examples of their use to successfully generate recombinant bifidobacterial strains for specific purposes, and providing a general workflow and cautions to design and conduct heterologous expression in bifidobacteria. Knowledge gaps and fields of research that may help to widen the molecular toolbox to improve the functional and technological potential of bifidobacteria are also discussed.
Collapse
|
9
|
Riley LA, Guss AM. Approaches to genetic tool development for rapid domestication of non-model microorganisms. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:30. [PMID: 33494801 PMCID: PMC7830746 DOI: 10.1186/s13068-020-01872-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/30/2020] [Indexed: 05/04/2023]
Abstract
Non-model microorganisms often possess complex phenotypes that could be important for the future of biofuel and chemical production. They have received significant interest the last several years, but advancement is still slow due to the lack of a robust genetic toolbox in most organisms. Typically, "domestication" of a new non-model microorganism has been done on an ad hoc basis, and historically, it can take years to develop transformation and basic genetic tools. Here, we review the barriers and solutions to rapid development of genetic transformation tools in new hosts, with a major focus on Restriction-Modification systems, which are a well-known and significant barrier to efficient transformation. We further explore the tools and approaches used for efficient gene deletion, DNA insertion, and heterologous gene expression. Finally, more advanced and high-throughput tools are now being developed in diverse non-model microbes, paving the way for rapid and multiplexed genome engineering for biotechnology.
Collapse
Affiliation(s)
- Lauren A Riley
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Bredesen Center, University of Tennessee, Knoxville, TN, 37996, USA
| | - Adam M Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
- Bredesen Center, University of Tennessee, Knoxville, TN, 37996, USA.
| |
Collapse
|
10
|
|
11
|
A SAM-I riboswitch with the ability to sense and respond to uncharged initiator tRNA. Nat Commun 2020; 11:2794. [PMID: 32493973 PMCID: PMC7270179 DOI: 10.1038/s41467-020-16417-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 04/29/2020] [Indexed: 11/29/2022] Open
Abstract
All known riboswitches use their aptamer to senese one metabolite signal and their expression platform to regulate gene expression. Here, we characterize a SAM-I riboswitch (SAM-IXcc) from the Xanthomonas campestris that regulates methionine synthesis via the met operon. In vitro and in vivo experiments show that SAM-IXcc controls the met operon primarily at the translational level in response to cellular S-adenosylmethionine (SAM) levels. Biochemical and genetic data demonstrate that SAM-IXcc expression platform not only can repress gene expression in response to SAM binding to SAM-IXcc aptamer but also can sense and bind uncharged initiator Met tRNA, resulting in the sequestering of the anti-Shine-Dalgarno (SD) sequence and freeing the SD for translation initiation. These findings identify a SAM-I riboswitch with a dual functioning expression platform that regulates methionine synthesis through a previously unrecognized mechanism and discover a natural tRNA-sensing RNA element. This SAM-I riboswitch appears to be highly conserved in Xanthomonas species. Riboswitches consist of an aptamer domain and expression platform, which senses a signal and regulates gene expression, respectively. Here the authors show that the expression platform of a SAM-I riboswitch from the Gram-negative bacteria can sense and bind uncharged an initiator Met tRNA to control the met operon.
Collapse
|
12
|
Tran TT, Charles TC. Lactic acid containing polymers produced in engineered Sinorhizobium meliloti and Pseudomonas putida. PLoS One 2020; 15:e0218302. [PMID: 32191710 PMCID: PMC7082056 DOI: 10.1371/journal.pone.0218302] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 02/18/2020] [Indexed: 01/17/2023] Open
Abstract
This study demonstrates that novel polymer production can be achieved by introducing pTAM, a broad-host-range plasmid expressing codon-optimized genes encoding Clostridium propionicum propionate CoA transferase (PctCp, Pct532) and a modified Pseudomonas sp. MBEL 6–19 polyhydroxyalkanoate (PHA) synthase 1 (PhaC1Ps6-19, PhaC1400), into phaC mutant strains of the native polymer producers Sinorhizobium meliloti and Pseudomonas putida. Both phenotypic analysis and gas chromatography analysis indicated the synthesis and accumulation of biopolymers in S. meliloti and P. putida strains. Expression in S. meliloti resulted in the production of PLA homopolymer up to 3.2% dried cell weight (DCW). The quaterpolymer P (3HB-co-LA-co-3HHx-co-3HO) was produced by expression in P. putida. The P. putida phaC mutant strain produced this type of polymer the most efficiently with polymer content of 42% DCW when cultured in defined media with the addition of sodium octanoate. This is the first report, to our knowledge, of the production of a range of different biopolymers using the same plasmid-based system in different backgrounds. In addition, it is the first time that the novel polymer (P(3HB-co-LA-co-3HHx-co-3HO)), has been reported being produced in bacteria.
Collapse
Affiliation(s)
- Tam T. Tran
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Trevor C. Charles
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
- * E-mail:
| |
Collapse
|
13
|
Cho SW, Yim J, Seo SW. Engineering Tools for the Development of Recombinant Lactic Acid Bacteria. Biotechnol J 2020; 15:e1900344. [DOI: 10.1002/biot.201900344] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/27/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Sung Won Cho
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National University 1 Gwanak‐ro Gwanak‐gu Seoul 08826 Republic of Korea
| | - Jaewoo Yim
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National University 1 Gwanak‐ro Gwanak‐gu Seoul 08826 Republic of Korea
| | - Sang Woo Seo
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National University 1 Gwanak‐ro Gwanak‐gu Seoul 08826 Republic of Korea
| |
Collapse
|
14
|
Salze M, Muller C, Bernay B, Hartke A, Clamens T, Lesouhaitier O, Rincé A. Study of key RNA metabolism proteins in Enterococcus faecalis. RNA Biol 2020; 17:794-804. [PMID: 32070211 DOI: 10.1080/15476286.2020.1728103] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
The control of mRNA turnover is essential in bacteria to allow rapid adaptation, especially in opportunistic pathogen like Enterococcus faecalis. This mechanism involves RNase and DEAD-box helicases that are key elements in RNA processing and their associations form the degradosome with accessory proteins. In this study, we investigated the function of four RNases (J1, J2, Y and III) and three DEAD-box helicases (CshA, CshB, CshC) present in most Enterococci. The interactions of all these RNA metabolism actors were investigated in vitro, and the results are in accordance with a degradosome structure close to the one of Bacillus subtilis. At the physiological level, we showed that RNase J1 is essential, whereas RNases J2 and III have a role in cold, oxidative and bile salts stress response, and RNase Y in general fitness. Furthermore, RNases J2, Y and III mutants are affected in virulence in the Galleria mellonella infection model. Concerning DEAD-box helicases, all of them are involved in cold shock response. Since the ΔcshA mutant was the most stress impacted strain, we studied this DEAD-box helicase CshA in more detail. This showed that CshA autoregulates its own expression by binding to its mRNA 5'Unstranslated Region. Interestingly, CshC is also involved in the expression control of CshA by a hitherto unprecedented mechanism.
Collapse
Affiliation(s)
- Marine Salze
- Normandie Univ, UNICAEN, Unité De Recherche Risques Microbiens U2RM , Caen, France
| | - Cécile Muller
- Normandie Univ, UNICAEN, Unité De Recherche Risques Microbiens U2RM , Caen, France
| | - Benoit Bernay
- Proteogen Platform, Normandie Univ, UNICAEN, SFR ICORE , Caen, France
| | - Axel Hartke
- Normandie Univ, UNICAEN, Unité De Recherche Risques Microbiens U2RM , Caen, France
| | - Thomas Clamens
- Laboratoire de Microbiologie Signaux et Microenvironnement LMSM, Normandie Univ, University of Rouen , Evreux, France
| | - Olivier Lesouhaitier
- Laboratoire de Microbiologie Signaux et Microenvironnement LMSM, Normandie Univ, University of Rouen , Evreux, France
| | - Alain Rincé
- Normandie Univ, UNICAEN, Unité De Recherche Risques Microbiens U2RM , Caen, France
| |
Collapse
|
15
|
Grand M, Blancato VS, Espariz M, Deutscher J, Pikis A, Hartke A, Magni C, Sauvageot N. Enterococcus faecalisMalR acts as a repressor of the maltose operons and additionally mediates their catabolite repression via direct interaction with seryl‐phosphorylated‐HPr. Mol Microbiol 2019; 113:464-477. [DOI: 10.1111/mmi.14431] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/13/2019] [Accepted: 11/19/2019] [Indexed: 12/26/2022]
Affiliation(s)
| | - Victor Sebastián Blancato
- Instituto de Biología Molecular y Celular de Rosario (IBR‐CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas Universidad Nacional de Rosario Rosario Argentina
| | - Martín Espariz
- Instituto de Biología Molecular y Celular de Rosario (IBR‐CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas Universidad Nacional de Rosario Rosario Argentina
| | - Josef Deutscher
- Micalis Institute, INRA, AgroParisTech, Université Paris‐Saclay Jouy‐en‐Josas France
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico‐Chimique Paris France
| | - Andreas Pikis
- Center for Drug Evaluation and Research, Food and Drug Administration Silver Spring Maryland
- Microbial Biochemistry and Genetics Unit, Laboratory of Cell and Developmental Biology NIDCR, National Institutes of Health Bethesda Maryland
| | | | - Christian Magni
- Instituto de Biología Molecular y Celular de Rosario (IBR‐CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas Universidad Nacional de Rosario Rosario Argentina
| | | |
Collapse
|
16
|
Cho SJ. Primary structure and characterization of a protease from Bacillus amyloliquefaciens isolated from meju, a traditional Korean soybean fermentation starter. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.02.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
17
|
Chae JP, Pajarillo EA, Hwang IC, Kang DK. Construction of a Bile-responsive Expression System in Lactobacillus plantarum. Food Sci Anim Resour 2019; 39:13-22. [PMID: 30882070 PMCID: PMC6413156 DOI: 10.5851/kosfa.2018.e58] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/14/2018] [Accepted: 11/18/2018] [Indexed: 12/16/2022] Open
Abstract
This study aimed to develop a bile-responsive expression system for lactobacilli. The promoters of four genes, encoding phosphoenolpyruvate-dependent sugar phosphotransferase (mannose-specific), L-lactate dehydrogenase (LDH), HPr kinase, and D-alanine-D-alanine ligase, respectively, which were highly expressed by bile addition in Lactobacillus johnsonii PF01, were chosen. Each promoter was amplified by polymerase chain reaction and fused upstream of the β-glucuronidase gene as a reporter, respectively. Then, these constructs were cloned into E. coli-Lactobacillus shuttle vector pULP2, which was generated by the fusion of pUC19 with the L. plantarum plasmid pLP27. Finally, the constructed vectors were introduced into L. plantarum for a promoter activity assay. The LDH promoter showed the highest activity and its activity increased 1.8-fold by bile addition. The constructed vector maintained in L. plantarum until 80 generations without selection pressure. A bile-responsive expression vector, pULP3-PLDH, for Lactobacillus spp. can be an effective tool for the bile-inducible expression of bioactive proteins in intestine after intake in the form of fermented dairy foods.
Collapse
Affiliation(s)
- Jong Pyo Chae
- Department of Animal Resources Science, Dankook University, Cheonan 31116, Korea
| | | | - In-Chan Hwang
- Department of Animal Resources Science, Dankook University, Cheonan 31116, Korea
| | - Dae-Kyung Kang
- Department of Animal Resources Science, Dankook University, Cheonan 31116, Korea
| |
Collapse
|
18
|
van der Els S, James JK, Kleerebezem M, Bron PA. Versatile Cas9-Driven Subpopulation Selection Toolbox for Lactococcus lactis. Appl Environ Microbiol 2018; 84:e02752-17. [PMID: 29453254 PMCID: PMC5881059 DOI: 10.1128/aem.02752-17] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 02/08/2018] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas9 technology has been exploited for the removal or replacement of genetic elements in a wide range of prokaryotes and eukaryotes. Here, we describe the extension of the Cas9 application toolbox to the industrially important dairy species Lactococcus lactis The Cas9 expression vector pLABTarget, encoding the Streptocccus pyogenes Cas9 under the control of a constitutive promoter, was constructed, allowing plug and play introduction of short guide RNA (sgRNA) sequences to target specific genetic loci. Introduction of a pepN-targeting derivative of pLABTarget into L. lactis strain MG1363 led to a strong reduction in the number of transformants obtained, which did not occur in a pepN deletion derivative of the same strain, demonstrating the specificity and lethality of the Cas9-mediated double-strand breaks in the lactococcal chromosome. Moreover, the same pLABTarget derivative allowed the selection of a pepN deletion subpopulation from its corresponding single-crossover plasmid integrant precursor, accelerating the construction and selection of gene-specific deletion derivatives in L. lactis Finally, pLABTarget, which contained sgRNAs designed to target mobile genetic elements, allowed the effective curing of plasmids, prophages, and integrative conjugative elements (ICEs). These results establish that pLABTarget enables the effective exploitation of Cas9 targeting in L. lactis, while the broad-host-range vector used suggests that this toolbox could readily be expanded to other Gram-positive bacteria.IMPORTANCE Mobile genetic elements in Lactococcus lactis and other lactic acid bacteria (LAB) play an important role in dairy fermentation, having both positive and detrimental effects during the production of fermented dairy products. The pLABTarget vector offers an efficient cloning platform for Cas9 application in lactic acid bacteria. Targeting Cas9 toward mobile genetic elements enabled their effective curing, which is of particular interest in the context of potentially problematic prophages present in a strain. Moreover, Cas9 targeting of other mobile genetic elements enables the deciphering of their contribution to dairy fermentation processes and further establishment of their importance for product characteristics.
Collapse
Affiliation(s)
- Simon van der Els
- Host-Microbe Interactomics Group, Animal Sciences, Wageningen University & Research, Wageningen, The Netherlands
- NIZO B.V., Ede, The Netherlands
- BE-Basic Foundation, Delft, The Netherlands
| | | | - Michiel Kleerebezem
- Host-Microbe Interactomics Group, Animal Sciences, Wageningen University & Research, Wageningen, The Netherlands
- BE-Basic Foundation, Delft, The Netherlands
| | - Peter A Bron
- NIZO B.V., Ede, The Netherlands
- BE-Basic Foundation, Delft, The Netherlands
| |
Collapse
|
19
|
Stevens MJ, Venturini A, Lacroix C, Meile L. Enhancing oxidative stress resistance in Bifidobacterium thermophilum using a novel overexpression vector and transformation protocol. Plasmid 2017; 92:43-48. [DOI: 10.1016/j.plasmid.2017.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 06/09/2017] [Accepted: 06/09/2017] [Indexed: 12/30/2022]
|
20
|
Lanigan N, Bottacini F, Casey PG, O'Connell Motherway M, van Sinderen D. Genome-Wide Search for Genes Required for Bifidobacterial Growth under Iron-Limitation. Front Microbiol 2017; 8:964. [PMID: 28620359 PMCID: PMC5449479 DOI: 10.3389/fmicb.2017.00964] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 05/15/2017] [Indexed: 11/13/2022] Open
Abstract
Bacteria evolved over millennia in the presence of the vital micronutrient iron. Iron is involved in numerous processes within the cell and is essential for nearly all living organisms. The importance of iron to the survival of bacteria is obvious from the large variety of mechanisms by which iron may be acquired from the environment. Random mutagenesis and global gene expression profiling led to the identification of a number of genes, which are essential for Bifidobacterium breve UCC2003 survival under iron-restrictive conditions. These genes encode, among others, Fe-S cluster-associated proteins, a possible ferric iron reductase, a number of cell wall-associated proteins, and various DNA replication and repair proteins. In addition, our study identified several presumed iron uptake systems which were shown to be essential for B. breve UCC2003 growth under conditions of either ferric and/or ferrous iron chelation. Of these, two gene clusters encoding putative iron-uptake systems, bfeUO and sifABCDE, were further characterised, indicating that sifABCDE is involved in ferrous iron transport, while the bfeUO-encoded transport system imports both ferrous and ferric iron. Transcription studies showed that bfeUO and sifABCDE constitute two separate transcriptional units that are induced upon dipyridyl-mediated iron limitation. In the anaerobic gastrointestinal environment ferrous iron is presumed to be of most relevance, though a mutation in the sifABCDE cluster does not affect B. breve UCC2003's ability to colonise the gut of a murine model.
Collapse
Affiliation(s)
- Noreen Lanigan
- APC Microbiome Institute and School of Microbiology, University College CorkCork, Ireland
| | - Francesca Bottacini
- APC Microbiome Institute and School of Microbiology, University College CorkCork, Ireland
| | - Pat G Casey
- APC Microbiome Institute and School of Microbiology, University College CorkCork, Ireland
| | | | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, University College CorkCork, Ireland
| |
Collapse
|
21
|
Fernandez L, Marin ML, Langa S, Martin R, Reviriego C, Fernandez A, Olivares M, Xaus J, Rodriguez JM. A Novel Genetic Label for Detection of Specific Probiotic Lactic Acid Bacteria. FOOD SCI TECHNOL INT 2016. [DOI: 10.1177/1082013204043761] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A novel method for genetic labelling of specific lactic acid bacteria strains was developed. The approach implied the transformation of the hosts with a plasmid containing a heterologous DNA fragment. The sequence of a DNA fragment that has been used to label a variety of genetically modified (GM) soya was used to design a forward primer and three reverse primers yielding PCR products recognisable by their sizes. Stability of the recombinant plasmid in the transformed strains was studied by PCR, and the results varied significantly depending on the strain. To test the usefulness of the DNA label to study in vivo properties of probiotic bacteria, such as viability after transit through the digestive tract, mice were orally inoculated with a genetically-labelled Enterococcus faecium strain. Later, their faeces were aseptically collected and the genetically-labelled strain was detected among the colonies that grew on MRS agar.
Collapse
Affiliation(s)
| | | | | | | | | | - A. Fernandez
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | | | - J. Xaus
- Departamento de Immunología, Puleva Biotech, 18004 Granada, Spain
| | - J. M. Rodriguez
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain
| |
Collapse
|
22
|
Characterization of the transcriptional regulation of the tarIJKL locus involved in ribitol-containing wall teichoic acid biosynthesis in Lactobacillus plantarum. Microbiology (Reading) 2016; 162:420-432. [DOI: 10.1099/mic.0.000229] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
23
|
Lin J, Zou Y, Ma C, She Q, Liang Y, Chen Z, Ge X. Heterologous Expression of Mannanase and Developing a New Reporter Gene System in Lactobacillus casei and Escherichia coli. PLoS One 2015; 10:e0142886. [PMID: 26562012 PMCID: PMC4643024 DOI: 10.1371/journal.pone.0142886] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/28/2015] [Indexed: 12/04/2022] Open
Abstract
Reporter gene systems are useful for studying bacterial molecular biology, including the regulation of gene expression and the histochemical analysis of protein products. Here, two genes, β-1,4-mannanase (manB) from Bacillus pumilus and β-glucuronidase (gusA) from Escherichia coli K12, were cloned into the expression vector pELX1. The expression patterns of these reporter genes in Lactobacillus casei were investigated by measuring their enzymatic activities and estimating their recombinant protein yields using western blot analysis. Whereas mannanase activity was positively correlated with the accumulation of ManB during growth, GusA activity was not; western blot analysis indicated that while the amount of GusA protein increased during later growth stages, GusA activity gradually decreased, indicating that the enzyme was inactive during cell growth. A similar trend was observed in E. coli JM109. We chose to use the more stable mannanase gene as the reporter to test secretion expression in L. casei. Two pELX1-based secretion vectors were constructed: one carried the signal peptide of the unknown secretion protein Usp45 from Lactococcus lactis (pELSH), and the other contained the full-length SlpA protein from the S-layer of L. acidophilus (pELWH). The secretion of ManB was detected in the supernatant of the pELSH-ManB transformants and in the S-layer of the cell surface of the pELWH-ManB transformants. This is the first report demonstrating that the B. pumilus manB gene is a useful reporter gene in L. casei and E.coli.
Collapse
Affiliation(s)
- Jinzhong Lin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Dairy Biotechnology, Technology Center of Bright Dairy & Food Co., Ltd., 1518 Jiangchang Road (W), Shanghai, 200436, China
| | - Yexia Zou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Chengjie Ma
- State Key Laboratory of Dairy Biotechnology, Technology Center of Bright Dairy & Food Co., Ltd., 1518 Jiangchang Road (W), Shanghai, 200436, China
| | - Qunxin She
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Department of Biology, University of Copenhagen, Biocenter, Ole Maaloes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Yunxiang Liang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Zhengjun Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- * E-mail: (ZC); (XG)
| | - Xiangyang Ge
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- * E-mail: (ZC); (XG)
| |
Collapse
|
24
|
Chen J, Shen J, Ingvar Hellgren L, Ruhdal Jensen P, Solem C. Adaptation of Lactococcus lactis to high growth temperature leads to a dramatic increase in acidification rate. Sci Rep 2015; 5:14199. [PMID: 26388459 PMCID: PMC4585701 DOI: 10.1038/srep14199] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 08/21/2015] [Indexed: 01/17/2023] Open
Abstract
Lactococcus lactis is essential for most cheese making, and this mesophilic bacterium has its growth optimum around 30 °C. We have, through adaptive evolution, isolated a mutant TM29 that grows well up to 39 °C, and continuous growth at 40 °C is possible if pre-incubated at a slightly lower temperature. At the maximal permissive temperature for the wild-type, 38 °C, TM29 grows 33% faster and has a 12% higher specific lactate production rate than its parent MG1363, which results in fast lactate accumulation. Genome sequencing was used to reveal the mutations accumulated, most of which were shown to affect thermal tolerance. Of the mutations with more pronounced effects, two affected expression of single proteins (chaperone; riboflavin transporter), two had pleiotropic effects (RNA polymerase) which changed the gene expression profile, and one resulted in a change in the coding sequence of CDP-diglyceride synthase. A large deletion containing 10 genes was also found to affect thermal tolerance significantly. With this study we demonstrate a simple approach to obtain non-GMO derivatives of the important L. lactis that possess properties desirable by the industry, e.g. thermal robustness and increased rate of acidification. The mutations we have identified provide a genetic basis for further investigation of thermal tolerance.
Collapse
Affiliation(s)
- Jun Chen
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Jing Shen
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Lars Ingvar Hellgren
- Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Peter Ruhdal Jensen
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Christian Solem
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| |
Collapse
|
25
|
Yang C, Hu S, Zhu S, Wang D, Gao X, Hong J. Characterizing yeast promoters used in Kluyveromyces marxianus. World J Microbiol Biotechnol 2015; 31:1641-6. [PMID: 26164057 DOI: 10.1007/s11274-015-1899-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 07/06/2015] [Indexed: 10/23/2022]
Abstract
Fermentation at higher temperatures can potentially reduce the cooling cost in large-scale fermentation and reduce the contamination risk. Thus, the thermotolerant yeast, Kluyveromyces marxianus, which can grow and ferment at elevated temperatures, is a promising biotechnological tool for future applications. However, the promoters used in K. marxianus are not well characterized, especially at elevated temperatures, which is important in efficient metabolic pathway construction. In this study, six constitutive promoters (P(TDH3), P(PGK), and P(ADH1) from both Saccharomyces cerevisiae and K. marxianus) were evaluated in K. marxianus through the heterologous expression of the KlLAC4, GUSA, and SH BLE genes at various temperatures, with various carbon sources and oxygen conditions. The expression was evaluated at the transcription and protein level using real-time PCR and protein activity determination to eliminate the effect of heterologous protein stability. While the transcription of all the promoters decreased at higher temperatures, the order of their promoting strength at various temperatures with glucose as the carbon source was P(KmPGK) > P(KmTDH3) > P(ScPGK) > P(ScTDH3) > P(KmADH1) > P(ScADH1). When glycerol or xylose was supplied as the carbon source at 42 °C, the order of promoter strength was P(KmPGK) > P(ScPGK) > P(KmADH1) > P(ScADH1) > P(ScTDH3) > P(KmTDH3). The promoter activity of P TDH3 decreased significantly, while the promoter activity of both of the P(ADH1) promoters increased. Oxygen conditions had non-significant effect. The results of this study provide important information for fine-tuned pathway construction for the metabolic engineering of K. marxianus.
Collapse
Affiliation(s)
- Chun Yang
- School of Life Science, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China.,Hefei National Laboratory for Physical Science at the Microscale, University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China
| | - Shenglin Hu
- School of Life Science, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China.,Hefei National Laboratory for Physical Science at the Microscale, University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China
| | - Songli Zhu
- School of Life Science, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China.,Hefei National Laboratory for Physical Science at the Microscale, University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China
| | - Dongmei Wang
- School of Life Science, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China.,Hefei National Laboratory for Physical Science at the Microscale, University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China
| | - Xiaolian Gao
- School of Life Science, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China.,Hefei National Laboratory for Physical Science at the Microscale, University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China.,Department of Biology and Biochemistry, University of Houston, Houston, 77004-5001, USA
| | - Jiong Hong
- School of Life Science, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China. .,Hefei National Laboratory for Physical Science at the Microscale, University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China.
| |
Collapse
|
26
|
Wen Q, Liu X, Wang H, Lin J. A versatile and efficient markerless gene disruption system forAcidithiobacillus thiooxidans: application for characterizing a copper tolerance related multicopper oxidase gene. Environ Microbiol 2014; 16:3499-514. [DOI: 10.1111/1462-2920.12494] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 04/18/2014] [Accepted: 04/24/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Qing Wen
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
| | - Xiangmei Liu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
| | - Huiyan Wang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
| | - Jianqun Lin
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
| |
Collapse
|
27
|
H(2)O(2) production in species of the Lactobacillus acidophilus group: a central role for a novel NADH-dependent flavin reductase. Appl Environ Microbiol 2014; 80:2229-39. [PMID: 24487531 DOI: 10.1128/aem.04272-13] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hydrogen peroxide production is a well-known trait of many bacterial species associated with the human body. In the presence of oxygen, the probiotic lactic acid bacterium Lactobacillus johnsonii NCC 533 excretes up to 1 mM H(2)O(2), inducing growth stagnation and cell death. Disruption of genes commonly assumed to be involved in H(2)O(2) production (e.g., pyruvate oxidase, NADH oxidase, and lactate oxidase) did not affect this. Here we describe the purification of a novel NADH-dependent flavin reductase encoded by two highly similar genes (LJ_0548 and LJ_0549) that are conserved in lactobacilli belonging to the Lactobacillus acidophilus group. The genes are predicted to encode two 20-kDa proteins containing flavin mononucleotide (FMN) reductase conserved domains. Reductase activity requires FMN, flavin adenine dinucleotide (FAD), or riboflavin and is specific for NADH and not NADPH. The Km for FMN is 30 ± 8 μM, in accordance with its proposed in vivo role in H(2)O(2) production. Deletion of the encoding genes in L. johnsonii led to a 40-fold reduction of hydrogen peroxide formation. H(2)O(2) production in this mutant could only be restored by in trans complementation of both genes. Our work identifies a novel, conserved NADH-dependent flavin reductase that is prominently involved in H(2)O(2) production in L. johnsonii.
Collapse
|
28
|
Genetic engineering techniques for lactic acid bacteria: construction of a stable shuttle vector and expression vector for β-glucuronidase. Biotechnol Lett 2013; 36:327-35. [DOI: 10.1007/s10529-013-1363-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 09/18/2013] [Indexed: 11/26/2022]
|
29
|
Naz H, Islam A, Waheed A, Sly WS, Ahmad F, Hassan MI. Humanβ-Glucuronidase: Structure, Function, and Application in Enzyme Replacement Therapy. Rejuvenation Res 2013; 16:352-63. [DOI: 10.1089/rej.2013.1407] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Huma Naz
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Abdul Waheed
- The Edward A. Doisy Department of Biochemistry and Molecular Biology, St. Louis, University School of Medicine, St. Louis, Missouri
| | - William S. Sly
- The Edward A. Doisy Department of Biochemistry and Molecular Biology, St. Louis, University School of Medicine, St. Louis, Missouri
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| |
Collapse
|
30
|
Oxidative stress at high temperatures in Lactococcus lactis due to an insufficient supply of Riboflavin. Appl Environ Microbiol 2013; 79:6140-7. [PMID: 23913422 DOI: 10.1128/aem.01953-13] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lactococcus lactis MG1363 was found to be unable to grow at temperatures above 37°C in a defined medium without riboflavin, and the cause was identified to be dissolved oxygen introduced during preparation of the medium. At 30°C, growth was unaffected by dissolved oxygen and oxygen was consumed quickly. Raising the temperature to 37°C resulted in severe growth inhibition and only slow removal of dissolved oxygen. Under these conditions, an abnormally low intracellular ratio of [ATP] to [ADP] (1.4) was found (normally around 5), which indicates that the cells are energy limited. By adding riboflavin to the medium, it was possible to improve growth and oxygen consumption at 37°C, and this also normalized the [ATP]-to-[ADP] ratio. A codon-optimized redox-sensitive green fluorescent protein (GFP) was introduced into L. lactis and revealed a more oxidized cytoplasm at 37°C than at 30°C. These results indicate that L. lactis suffers from heat-induced oxidative stress at increased temperatures. A decrease in intracellular flavin adenine dinucleotide (FAD), which is derived from riboflavin, was observed with increasing growth temperature, but the presence of riboflavin made the decrease smaller. The drop was accompanied by a decrease in NADH oxidase and pyruvate dehydrogenase activities, both of which depend on FAD as a cofactor. By overexpressing the riboflavin transporter, it was possible to improve FAD biosynthesis, which resulted in increased NADH oxidase and pyruvate dehydrogenase activities and improved fitness at high temperatures in the presence of oxygen.
Collapse
|
31
|
A two-component regulatory system controls autoregulated serpin expression in Bifidobacterium breve UCC2003. Appl Environ Microbiol 2012; 78:7032-41. [PMID: 22843530 DOI: 10.1128/aem.01776-12] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
This work reports on the identification and molecular characterization of a two-component regulatory system (2CRS), encoded by serRK, which is believed to control the expression of the ser(2003) locus in Bifidobacterium breve UCC2003. The ser(2003) locus consists of two genes, Bbr_1319 (sagA) and Bbr_1320 (serU), which are predicted to encode a hypothetical membrane-associated protein and a serpin-like protein, respectively. The response regulator SerR was shown to bind to the promoter region of ser(2003), and the probable recognition sequence of SerR was determined by a combinatorial approach of in vitro site-directed mutagenesis coupled to transcriptional fusion and electrophoretic mobility shift assays (EMSAs). The importance of the serRK 2CRS in the response of B. breve to protease-mediated induction was confirmed by generating a B. breve serR insertion mutant, which was shown to exhibit altered ser(2003) transcriptional induction patterns compared to the parent strain, UCC2003. Interestingly, the analysis of a B. breve serU mutant revealed that the SerRK signaling pathway appears to include a SerU-dependent autoregulatory loop.
Collapse
|
32
|
A conserved two-component signal transduction system controls the response to phosphate starvation in Bifidobacterium breve UCC2003. Appl Environ Microbiol 2012; 78:5258-69. [PMID: 22635988 DOI: 10.1128/aem.00804-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This work reports on the identification and molecular characterization of the two-component regulatory system (2CRS) PhoRP, which controls the response to inorganic phosphate (P(i)) starvation in Bifidobacterium breve UCC2003. The response regulator PhoP was shown to bind to the promoter region of pstSCAB, specifying a predicted P(i) transporter system, as well as that of phoU, which encodes a putative P(i)-responsive regulatory protein. This interaction is assumed to cause transcriptional modulation under conditions of P(i) limitation. Our data suggest that the phoRP genes are subject to positive autoregulation and, together with pstSCAB and presumably phoU, represent the complete regulon controlled by the phoRP-encoded 2CRS in B. breve UCC2003. Determination of the minimal PhoP binding region combined with bioinformatic analysis revealed the probable recognition sequence of PhoP, designated here as the PHO box, which together with phoRP is conserved among many high-GC-content Gram-positive bacteria. The importance of the phoRP 2CRS in the response of B. breve to P(i) starvation conditions was confirmed by analysis of a B. breve phoP insertion mutant which exhibited decreased growth under phosphate-limiting conditions compared to its parent strain UCC2003.
Collapse
|
33
|
Cronin M, Zomer A, Fitzgerald GF, van Sinderen D. Identification of iron-regulated genes of Bifidobacterium breve UCC2003 as a basis for controlled gene expression. Bioeng Bugs 2012; 3:157-67. [PMID: 22179149 DOI: 10.4161/bbug.18985] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Iron is an essential growth factor for virtually all organisms. However, iron is not readily available in most environments and microorganisms have evolved specialized mechanisms, such as the use of siderophores and high-affinity transport systems, to acquire iron when confronted with iron-limiting conditions. In general these systems are tightly regulated to prevent iron-induced toxicity and because they are quite costly to the microbe. Because of this tight regulation we chose to explore the response of Bifidobacterium breve UCC2003 to iron limitation. Through microarray and complementation analyses we identified and characterized a presumed ferrous iron uptake system, encoded by bfeUOB, from B. breve UCC2003 and exploited its regulated transcription to develop an inducible expression system for use in bifidobacteria.
Collapse
Affiliation(s)
- Michelle Cronin
- Alimentary Pharmabiotic Centre and Department of Microbiology, University College Cork, Cork, Ireland
| | | | | | | |
Collapse
|
34
|
Cheng TC, Roffler SR, Tzou SC, Chuang KH, Su YC, Chuang CH, Kao CH, Chen CS, Harn IH, Liu KY, Cheng TL, Leu YL. An Activity-Based Near-Infrared Glucuronide Trapping Probe for Imaging β-Glucuronidase Expression in Deep Tissues. J Am Chem Soc 2012; 134:3103-10. [DOI: 10.1021/ja209335z] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ta-Chun Cheng
- Graduate Institute
of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Steve R. Roffler
- Institute
of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Shey-Cherng Tzou
- Department
of Biomedical Science
and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Kuo-Hsiang Chuang
- Department
of Biomedical Science
and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yu-Cheng Su
- Institute
of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Institute
of Microbiology and
Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Chih-Hung Chuang
- Institutes
of Basic Medical
Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Chien-Han Kao
- Graduate Institute
of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chien-Shu Chen
- School of Pharmacy, China Medical University, Taichung, Taiwan
| | - I-Hong Harn
- Department
of Biomedical Science
and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Kuan-Yi Liu
- Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan,
Taiwan
| | - Tian-Lu Cheng
- Department
of Biomedical Science
and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Yu-Ling Leu
- Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan,
Taiwan
| |
Collapse
|
35
|
Ruiz L, O'Connell-Motherway M, Zomer A, de los Reyes-Gavilán CG, Margolles A, van Sinderen D. A bile-inducible membrane protein mediates bifidobacterial bile resistance. Microb Biotechnol 2012; 5:523-35. [PMID: 22296641 PMCID: PMC3815329 DOI: 10.1111/j.1751-7915.2011.00329.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Bbr_0838 from Bifidobacterium breve UCC2003 is predicted to encode a 683 residue membrane protein, containing both a permease domain that displays similarity to transporters belonging to the major facilitator superfamily, as well as a CBS (cystathionine beta synthase) domain. The high level of similarity to bile efflux pumps from other bifidobacteria suggests a significant and general role for Bbr_0838 in bile tolerance. Bbr_0838 transcription was shown to be monocistronic and strongly induced upon exposure to bile. Further analysis delineated the transcriptional start site and the minimal region required for promoter activity and bile regulation. Insertional inactivation of Bbr_0838 in B. breve UCC2003 resulted in a strain, UCC2003:838800, which exhibited reduced survival upon cholate exposure as compared with the parent strain, a phenotype that was reversed when a functional, plasmid‐encoded Bbr_0838 gene was introduced into UCC2003:838800. Transcriptome analysis of UCC2003:838800 grown in the presence or absence of bile demonstrated that transcription of Bbr_0832, which is predicted to encode a macrolide efflux transporter gene, was significantly increased in the presence of bile, representing a likely compensatory mechanism for bile removal in the absence of Bbr_0838. This study represents the first in‐depth analysis of a bile‐inducible locus in bifidobacteria, identifying a key gene relevant for bifidobacterial bile tolerance.
Collapse
Affiliation(s)
- Lorena Ruiz
- Departamento de Microbiología y Bioquímica de Productos Lácteos, Instituto de Productos Lácteos de Asturias, Villaviciosa, Asturias, Spain
| | | | | | | | | | | |
Collapse
|
36
|
|
37
|
Palomino MM, Allievi MC, Prado-Acosta M, Sanchez-Rivas C, Ruzal SM. New method for electroporation of Lactobacillus species grown in high salt. J Microbiol Methods 2010; 83:164-7. [DOI: 10.1016/j.mimet.2010.08.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 08/16/2010] [Accepted: 08/17/2010] [Indexed: 11/30/2022]
|
38
|
Shareck J, Choi Y, Lee B, Miguez CB. Cloning Vectors Based on Cryptic Plasmids Isolated from Lactic Acid Bacteria:Their Characteristics and Potential Applications in Biotechnology. Crit Rev Biotechnol 2010; 24:155-208. [PMID: 15707158 DOI: 10.1080/07388550490904288] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Lactic acid bacteria (LAB) are Gram positive bacteria, widely distributed in nature, and industrially important as they are used in a variety of industrial food fermentations. The use of genetic engineering techniques is an effective means of enhancing the industrial applicability of LAB. However, when using genetic engineering technology, safety becomes an essential factor for the application of improved LAB to the food industry. Cloning and expression systems should be derived preferably from LAB cryptic plasmids that generally encode genes for which functions can be proposed, but no phenotypes can be observed. However, some plasmid-encoded functions have been discovered in cryptic plasmids originating from Lactobacillus, Streptococcus thermophilus, and Pediococcus spp. and can be used as selective marker systems in vector construction. This article presents information concerning LAB cryptic plasmids, and their structures, functions, and applications. A total of 134 cryptic plasmids collated are discussed.
Collapse
Affiliation(s)
- Julie Shareck
- Department of Food Science and Agricultural Chemistry, McGill University, Ste-Anne-de-Bellevue, Quebec, Canada
| | | | | | | |
Collapse
|
39
|
Heterologous expression of the Bacillus subtilis (natto) alanine dehydrogenase in Escherichia coli and Lactococcus lactis. Microbiol Res 2010; 165:268-75. [DOI: 10.1016/j.micres.2009.05.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2009] [Revised: 05/18/2009] [Accepted: 05/22/2009] [Indexed: 11/18/2022]
|
40
|
Genetic tool development for a new host for biotechnology, the thermotolerant bacterium Bacillus coagulans. Appl Environ Microbiol 2010; 76:4085-8. [PMID: 20400555 DOI: 10.1128/aem.03060-09] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Bacillus coagulans has good potential as an industrial production organism for platform chemicals from renewable resources but has limited genetic tools available. Here, we present a targeted gene disruption system using the Cre-lox system, development of a LacZ reporter assay for monitoring gene transcription, and heterologous d-lactate dehydrogenase expression.
Collapse
|
41
|
Use of green fluorescent protein to monitor cell envelope stress in Lactococcus lactis. Appl Environ Microbiol 2009; 76:978-81. [PMID: 19948854 DOI: 10.1128/aem.02177-09] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A Lactococcus lactis reporter system suitable to detect cell envelope stress in high-throughput settings was developed by fusing the CesR-regulated promoter of llmg0169 to the gfp(uv) gene. A dot blot assay allowed fast detection of green fluorescent protein (GFP) fluorescence even at low production levels. Unexpectedly, this promoter was also induced by mitomycin C via CesR.
Collapse
|
42
|
An interactive regulatory network controls stress response in Bifidobacterium breve UCC2003. J Bacteriol 2009; 191:7039-49. [PMID: 19734308 DOI: 10.1128/jb.00897-09] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Members of the genus Bifidobacterium are gram-positive bacteria that commonly are found in the gastrointestinal tract (GIT) of mammals, including humans. Because of their perceived probiotic properties, they frequently are incorporated as functional ingredients in food products. From probiotic production to storage and GIT delivery, bifidobacteria encounter a plethora of stresses. To cope with these environmental challenges, they need to protect themselves through stress-induced adaptive responses. We have determined the response of B. breve UCC2003 to various stresses (heat, osmotic, and solvent) using transcriptome analysis, DNA-protein interactions, and GusA reporter fusions, and we combined these with results from an in silico analysis. The integration of these results allowed the formulation of a model for an interacting regulatory network for stress response in B. breve UCC2003 where HspR controls the SOS response and the ClgR regulon, which in turn regulates and is regulated by HrcA. This model of an interacting regulatory network is believed to represent the paradigm for stress adaptation in bifidobacteria.
Collapse
|
43
|
Roces C, Campelo AB, Veiga P, Pinto JPC, Rodríguez A, Martínez B. Contribution of the CesR-regulated genes llmg0169 and llmg2164-2163 to Lactococcus lactis fitness. Int J Food Microbiol 2009; 133:279-85. [PMID: 19559493 DOI: 10.1016/j.ijfoodmicro.2009.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2009] [Revised: 05/28/2009] [Accepted: 06/02/2009] [Indexed: 11/30/2022]
Abstract
Lactococcus lactis is one of the main components of the starter cultures used in cheese manufacture. As starter, L. lactis must tolerate harsh conditions encountered either during their production in bulk quantities or during dairy products processing. To face these hostile conditions, bacteria monitor the environment and respond by modifying gene expression appropriately. Previous transcriptomic studies showed that the two component system CesSR is the main pathway that triggers the cell envelope stress response in L. lactis treated with lactococcin 972 (Lcn972), a cell wall synthesis inhibiting bacteriocin. Among the CesR-regulated genes, llmg0169 and the operon llmg2164-2163, encoding proteins of unknown function, are among the highest up-regulated genes after activation of CesSR. In this study, we have assessed the contribution of these genes to the survival of L. lactis to different technologically-relevant stresses. Overexpressing and knock-out mutants of the genes were generated and their viability to low pH, heat, freeze-drying, presence of NaCl, cell wall antimicrobials and lytic phages attack was compared to the wild type strain. The genes llmg0169 and llmg2164-2163 contributed differently to L. lactis fitness. L. lactis Deltallmg0169 was very sensitive to heat treatment while L. lactis Deltallmg2164 was more sensitive to NaCl. Absence of both genes also compromised viability at low pH. On the contrary, higher expression levels of llmg0169 and llmg2164-2163, up to 26- and 14-fold increase determined by qRT-PCR, respectively, did not enhance L. lactis survival in any of the above stressful conditions (heat, pH and NaCl) or after freeze-drying. All the mutants displayed a similar phage susceptibility profile. Overexpression of llmg2164-2163 seemed to specifically protect L. lactis against the bacteriocin Lcn972 but not against other cell wall active antimicrobials. Based on our phenotypic analysis, the investigated genes are required to mount a proper response to guarantee survival of L. lactis under technologically-relevant stresses and their functionality could be a useful marker to select robust dairy starters.
Collapse
Affiliation(s)
- Clara Roces
- Department of Technology and Biotechnology of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Asturias, Spain
| | | | | | | | | | | |
Collapse
|
44
|
Linares DM, Fernández M, Martín MC, Alvarez MA. Tyramine biosynthesis in Enterococcus durans is transcriptionally regulated by the extracellular pH and tyrosine concentration. Microb Biotechnol 2009; 2:625-33. [PMID: 21255297 PMCID: PMC3815318 DOI: 10.1111/j.1751-7915.2009.00117.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The microbial decarboxylation of some amino acids leads to the undesirable presence of biogenic amines in foods. One of the most abundant and frequent biogenic amines found in fermented foods is tyramine, which is produced by the decarboxylation of tyrosine. In the present work, transcriptional analysis of tyramine biosynthesis in Enterococcus durans IPLA655, a strain isolated from cheese, was studied. The gene coding for the tyrosine decarboxylase (tdcA) and that coding for the tyrosine-tyramine antiporter (tyrP) form an operon transcribed from the promoter P(tdcA), the expression of which is regulated by the extracellular pH and tyrosine concentration. Quantification of gene expression during the log phase of growth showed high concentrations of tyrosine and acidic pH conditions to induce tdcA-tyrP polycistronic messenger transcription.
Collapse
Affiliation(s)
- Daniel M Linares
- Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Carretera de Infiesto s/n, 33300 Villaviciosa, Asturias, Spain
| | | | | | | |
Collapse
|
45
|
Sheng JZ, Ling PX, Zhu XQ, Guo XP, Zhang TM, He YL, Wang FS. Use of induction promoters to regulate hyaluronan synthase and UDP-glucose-6-dehydrogenase of Streptococcus zooepidemicus expression in Lactococcus lactis: a case study of the regulation mechanism of hyaluronic acid polymer. J Appl Microbiol 2009; 107:136-44. [PMID: 19302304 DOI: 10.1111/j.1365-2672.2009.04185.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
AIMS To determine the effects of the ratios of hyaluronan synthase expression level to precursor sugar UDP-GlcA biosynthesis ability on the molecular weight (MW) of hyaluronic acid (HA) in recombinant Lactococcus lactis. METHODS AND RESULTS The genes szHasA (hyaluronan synthase gene) and szHasB (UDP-glucose-6-dehydrogenase gene) of Streptococcus zooepidemicus were introduced into L. lactis under the control of nisA promoter and lacA promoter respectively, resulting in a dual-plasmid controlled expression system. The effects of the ratios of hyaluronan synthase expression level to the precursor sugar UDP-GlcA biosynthesis ability under different induction concentration collocations with nisin and lactose on the MW of HA in recombinant L. lactis were determined. The results showed that the final weight-average molecular weight () of HA correlated with the relative ratios of HasA (hyaluronan synthase) expression level to the concentration of UDP-GlcA. CONCLUSIONS Regulating the relative ratios of HasA expression level to the precursor sugar biosynthesis ability was an efficient method to control the size of HA. SIGNIFICANCE AND IMPACT OF THE STUDY This study put forward a guide to establish an efficacious way to control the size of HA in fermentation.
Collapse
Affiliation(s)
- J Z Sheng
- Institute of Biochemical and Biotechnological Drug, School of Pharmaceutical Science, Shandong University, Jinan, Shandong, China
| | | | | | | | | | | | | |
Collapse
|
46
|
Cronin M, Sleator RD, Hill C, Fitzgerald GF, van Sinderen D. Development of a luciferase-based reporter system to monitor Bifidobacterium breve UCC2003 persistence in mice. BMC Microbiol 2008; 8:161. [PMID: 18816375 PMCID: PMC2564955 DOI: 10.1186/1471-2180-8-161] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Accepted: 09/24/2008] [Indexed: 12/12/2022] Open
Abstract
Background Probiotics such as bifidobacteria have been shown to maintain a healthy intestinal microbial balance and help protect against infections. However, despite these benefits, bifidobacteria still remain poorly understood at the biochemical, physiological and especially the genetic level. Herein we describe, for the first time, the development of a non-invasive luciferase-based reporter system for real-time tracking of Bifidobacterium species in vivo. Results The reporter vector pLuxMC1 is based on the recently described theta-type plasmid pBC1 from B. catenatulatum [1] and the luxABCDE operon from pPL2lux [2]. Derivatives of pLuxMC1, harbouring a bifidobacterial promoter (pLuxMC2) as well as a synthetically derived promoter (pLuxMC3) [3] placed upstream of luxABCDE, were constructed and found to stably replicate in B. breve UCC2003. The subsequent analysis of these strains allowed us to assess the functionality of pLuxMC1 both in vitro and in vivo. Conclusion Our results demonstrate the potential of pLuxMC1 as a real-time, non-invasive reporter system for Bifidobacterium. It has also allowed us, for the first time, to track the colonisation potential and persistence of this probiotic species in real time. An interesting and significant outcome of the study is the identification of the caecum as a niche environment for B. breve UCC2003 within the mouse gastrointestinal tract (GI) tract.
Collapse
Affiliation(s)
- Michelle Cronin
- Alimentary Pharmabiotic Centre, University College Cork, Western Road, Cork, Ireland.
| | | | | | | | | |
Collapse
|
47
|
Yeh CM, Huang XH, Sue CW. Functional secretion of a type 1 antifreeze protein analogue by optimization of promoter, signal peptide, prosequence, and terminator in Lactococcus lactis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2008; 56:8442-8450. [PMID: 18759446 DOI: 10.1021/jf801580s] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Lactococcus lactis is a food-grade microorganism of major commercial importance. Antifreeze protein is a potent cryogenic protection agent for the cryopreservation of food and pharmaceutical materials. In this study, extracellular expression of a novel recombinant type I antifreeze protein analogue (rAFP) in L. lactis was optimized. An efficient SlpA promoter (P SlpA) was fused to various signal peptides (SPs) and propeptide sequences to examine the extracellular expression levels of rAFP. An efficient signal peptide, SP sacB, fused to prosequence AE, enabled higher extracellular rAFP production; use of the SlpA terminator (Ter SlpA) was a further improvement. The extracellularly expressed rAFP successfully inhibited ice recrystallization and is thus potentially applicable for cryogenic preservation.
Collapse
Affiliation(s)
- Chuan-Mei Yeh
- Department of Food Science and Biotechnology, National Chung-Hsing University, Taichung, Taiwan, Republic of China.
| | | | | |
Collapse
|
48
|
Development of multiple strain competitive index assays for Listeria monocytogenes using pIMC; a new site-specific integrative vector. BMC Microbiol 2008; 8:96. [PMID: 18554399 PMCID: PMC2440758 DOI: 10.1186/1471-2180-8-96] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Accepted: 06/13/2008] [Indexed: 11/13/2022] Open
Abstract
Background The foodborne, gram-positive pathogen, Listeria monocytogenes, is capable of causing lethal infections in compromised individuals. In the post genomic era of L. monocytogenes research, techniques are required to identify and validate genes involved in the pathogenicity and environmental biology of the organism. The aim here was to develop a widely applicable method to tag L. monocytogenes strains, with a particular emphasis on the development of multiple strain competitive index assays. Results We have constructed a new site-specific integrative vector, pIMC, based on pPL2, for the selection of L. monocytogenes from complex samples. The pIMC vector was further modified through the incorporation of IPTG inducible markers (antibiotic and phenotypic) to produce a suite of four vectors which allowed the discrimination of multiple strains from a single sample. We were able to perform murine infection studies with up to four EGDe isolates within a single mouse and showed that the tags did not impact upon growth rate or virulence. The system also allowed the identification of subtle differences in virulence between strains of L. monocytogenes commonly used in laboratory studies. Conclusion This study has developed a competitive index assay that can be broadly applied to all L. monocytogenes strains. Improved statistical robustness of the data was observed, resulting in fewer mice being required for virulence assays. The competitive index assays provide a powerful method to analyse the virulence or fitness of L. monocytogenes in complex biological samples.
Collapse
|
49
|
High-throughput identification and validation of in situ-expressed genes of Lactococcus lactis. Appl Environ Microbiol 2008; 74:4727-36. [PMID: 18539793 DOI: 10.1128/aem.00297-08] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Understanding the functional response of bacteria to their natural environment is one of the current challenges in microbiology. Over the past decades several techniques have been developed to study gene expression in complex natural habitats. Most of these methods, however, are laborious, and validation of results under in situ conditions is cumbersome. Here we report the improvement of the recombinase-based in vivo expression technology (R-IVET) by the implementation of two additional reporter genes. The first one is an alpha-galactosidase gene (melA), which facilitates the rapid identification of in vivo-induced genes. Second, the bacterial luciferase genes (luxAB) are transcriptionally coupled to the resolvase gene, which allows rapid validation and characterization of in vivo-induced genes. The system is implemented and validated in the industrially important lactic acid bacterium Lactococcus lactis. We demonstrate the applicability of the advanced R-IVET system by the identification and validation of lactococcal promoter elements that are induced in minimal medium compared to the commonly used rich laboratory medium M17. R-IVET screening led to the identification of 19 promoters that predominantly control expression of genes involved in amino acid and nucleotide metabolism and in transport functions. Furthermore, the luciferase allows high-resolution transcription analysis and enabled the identification of complex medium constituents and specific molecules involved in promoter control. Rapid target validation exemplifies the high-throughput potential of the extended R-IVET system. The system can be applied to other bacterial species, provided that the reporter genes used are functional in the organism of interest.
Collapse
|
50
|
Casitone-dependent transcriptional regulation of the prtP and prtM genes in the natural isolate Lactobacillus paracasei subsp. paracasei. Folia Microbiol (Praha) 2008; 52:577-84. [PMID: 18450219 DOI: 10.1007/bf02932186] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The prtP-prtM intergenic region of Lactobacillus paracasei subsp. paracasei BGHN 14 was cloned and sequenced. The nucleotide sequence of the prtP-prtM intergenic region in BGHN 14, containing divergently orientated P(prtP) and P(prtP) promoters, was shorter by 35 bp in comparison with that in lactococci. The nucleotide sequence involved in casitone-dependent transcriptional regulation of the lactococcal prt genes was not found in the BGHN14. The activity of P(prtM) in L. lactis NZ9000 was very low and insignificantly changed in the presence of casitone, whereas P(prtP) was completely inactive. When L. casei ATCC393(T) was used as host, both P(prtP) and P(prtM) were active and strongly regulated by casitone. The results strongly indicate that the mechanisms of the casitone-dependent regulation of the prt genes in BGHN14 and lactococci are different.
Collapse
|