151
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Srivastava A, Gogoi P, Deka B, Goswami S, Kanaujia SP. In silico analysis of 5'-UTRs highlights the prevalence of Shine-Dalgarno and leaderless-dependent mechanisms of translation initiation in bacteria and archaea, respectively. J Theor Biol 2016; 402:54-61. [PMID: 27155047 DOI: 10.1016/j.jtbi.2016.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 04/29/2016] [Accepted: 05/02/2016] [Indexed: 11/26/2022]
Abstract
In prokaryotes, a heterogeneous set of protein translation initiation mechanisms such as Shine-Dalgarno (SD) sequence-dependent, SD sequence-independent or ribosomal protein S1 mediated and leaderless transcript-dependent exists. To estimate the distribution of coding sequences employing a particular translation initiation mechanism, a total of 107 prokaryotic genomes were analysed using in silico approaches. Analysis of 5'-untranslated regions (UTRs) of genes reveals the existence of three types of mRNAs described as transcripts with and without SD motif and leaderless transcripts. Our results indicate that although all the three types of translation initiation mechanisms are widespread among prokaryotes, the number of SD-dependent genes in bacteria is higher than that of archaea. In contrast, archaea contain a significantly higher number of leaderless genes than SD-led genes. The correlation analysis between genome size and SD-led & leaderless genes suggests that the SD-led genes are decreasing (increasing) with genome size in bacteria (archaea). However, the leaderless genes are increasing (decreasing) in bacteria (archaea) with genome size. Moreover, an analysis of the start-codon biasness confirms that among ATG, GTG and TTG codons, ATG is indeed the most preferred codon at the translation initiation site in most of the coding sequences. In leaderless genes, however, the codons GTG and TTG are also observed at the translation initiation site in some species contradicting earlier studies which suggested the usage of only ATG codon. Henceforth, the conventional mechanism of translation initiation cannot be generalized as an exclusive way of initiating the process of protein biosynthesis in prokaryotes.
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Affiliation(s)
- Ambuj Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Prerana Gogoi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Bhagyashree Deka
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Shrayanti Goswami
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur 713205, West Bengal, India
| | - Shankar Prasad Kanaujia
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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152
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Allain T, Mansour NM, Bahr MMA, Martin R, Florent I, Langella P, Bermúdez-Humarán LG. A new lactobacilli in vivo expression system for the production and delivery of heterologous proteins at mucosal surfaces. FEMS Microbiol Lett 2016; 363:fnw117. [PMID: 27190148 DOI: 10.1093/femsle/fnw117] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2016] [Indexed: 12/21/2022] Open
Abstract
Food-grade lactic acid bacteria, such as lactobacilli, represent good candidates for the development of mucosal vectors. Indeed, they are generally recognized as safe microorganisms and some strains display beneficial effects (probiotics). In this study, we described a new lactobacilli in vivo expression (LIVE) system for the production and delivery of therapeutic molecules at mucosal surfaces. The versatility and functionality of this system was successfully validated in several lactobacilli species; furthermore, we assessed in vivo LIVE system in two different mouse models of human pathologies: (i) a model of therapy against intestinal inflammation (inflammatory bowel diseases) and (ii) a model of vaccination against dental caries. We demonstrated that Lactobacillus gasseri expressing the anti-inflammatory cytokine IL-10 under LIVE system efficiently delivered the recombinant protein at mucosal surfaces and display anti-inflammatory effects. In the vaccination model against caries, LIVE system allowed the heterologous expression of Streptococcus mutans antigen GbpB by L. gasseri, leading to a stimulation of the host immune response.
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Affiliation(s)
- Thibault Allain
- Micalis Institute, INRA, AgroParisTech, Paris-Saclay University, Domaine de Vilvert, 78350 Jouy-en-Josas, France Team Adaptation of Protozoa to their Environment, UMR 7245 CNRS, National Museum of Natural History, CP52, 61 rue Buffon, 75231 Paris Cedex 05, France
| | - Nahla M Mansour
- Gut Microbiology and Immunology Group, Chemistry of Natural and Microbial Products Department, Pharmaceutical Industries Research Division, National Research Centre, 33 El Bohouth St. (former El Tahrir St.), Dokki 12622, Cairo, Egypt
| | - May M A Bahr
- Gut Microbiology and Immunology Group, Chemistry of Natural and Microbial Products Department, Pharmaceutical Industries Research Division, National Research Centre, 33 El Bohouth St. (former El Tahrir St.), Dokki 12622, Cairo, Egypt
| | - Rebeca Martin
- Micalis Institute, INRA, AgroParisTech, Paris-Saclay University, Domaine de Vilvert, 78350 Jouy-en-Josas, France
| | - Isabelle Florent
- Team Adaptation of Protozoa to their Environment, UMR 7245 CNRS, National Museum of Natural History, CP52, 61 rue Buffon, 75231 Paris Cedex 05, France
| | - Philippe Langella
- Micalis Institute, INRA, AgroParisTech, Paris-Saclay University, Domaine de Vilvert, 78350 Jouy-en-Josas, France
| | - Luis G Bermúdez-Humarán
- Micalis Institute, INRA, AgroParisTech, Paris-Saclay University, Domaine de Vilvert, 78350 Jouy-en-Josas, France
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153
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Douillard FP, Rasinkangas P, Bhattacharjee A, Palva A, de Vos WM. The N-Terminal GYPSY Motif Is Required for Pilin-Specific Sortase SrtC1 Functionality in Lactobacillus rhamnosus Strain GG. PLoS One 2016; 11:e0153373. [PMID: 27070897 PMCID: PMC4829219 DOI: 10.1371/journal.pone.0153373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 03/29/2016] [Indexed: 12/31/2022] Open
Abstract
Predominantly identified in pathogenic Gram-positive bacteria, sortase-dependent pili are also found in commensal species, such as the probiotic-marketed strain Lactobacillus rhamnosus strain GG. Pili are typically associated with host colonization, immune signalling and biofilm formation. Comparative analysis of the N-terminal domains of pilin-specific sortases from various piliated Gram-positive bacteria identified a conserved motif, called GYPSY, within the signal sequence. We investigated the function and role of the GYPSY residues by directed mutagenesis in homologous (rod-shaped) and heterologous (coccoid-shaped) expression systems for pilus formation. Substitutions of some of the GYPSY residues, and more specifically the proline residue, were found to have a direct impact on the degree of piliation of Lb. rhamnosus GG. The present findings uncover a new signalling element involved in the functionality of pilin-specific sortases controlling the pilus biogenesis of Lb. rhamnosus GG and related piliated Gram-positive species.
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Affiliation(s)
- François P. Douillard
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- * E-mail: (FPD); (WMdV)
| | - Pia Rasinkangas
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Arnab Bhattacharjee
- Research Programs Unit Immunobiology, Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - Airi Palva
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Willem M. de Vos
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Research Programs Unit Immunobiology, Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- * E-mail: (FPD); (WMdV)
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154
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Abdellatef AA, Khalil AA. Ameliorated effects of Lactobacillus delbrueckii subsp. lactis DSM 20076 and Pediococcus acidilactici NNRL B-5627 on Fumonisin B1-induced Hepatotoxicity and Nephrotoxicity in rats. Asian J Pharm Sci 2016. [DOI: 10.1016/j.ajps.2016.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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155
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Thakur K, Tomar SK, Brahma B, De S. Screening of Riboflavin-Producing Lactobacilli by a Polymerase-Chain-Reaction-Based Approach and Microbiological Assay. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:1950-1956. [PMID: 26902872 DOI: 10.1021/acs.jafc.5b06165] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Riboflavin has an important role in various cellular metabolic activities through its participation in oxidation-reduction reactions. In this study, as many as 60 lactobacilli were screened for the presence or absence of riboflavin biosynthesis genes and riboflavin production. Of these, only 14 strains were able to grow in a commercial riboflavin-free medium. We observed that the presence of riboflavin biosynthesis genes is strain-specific across different species of lactobacilli. The microbiological assay was found to be appreciably reproducible, sensitive, rapid, and inexpensive and, hence, can be employed for screening the riboflavin-producing strains. The study thus represents a convenient and efficient method for selection of novel riboflavin producers. These riboflavin(+) strains thus identified and characterized could be explored as potent candidates for the development of a wide range of dairy- and cereal-based foods for the delivery of in situ riboflavin to consumers.
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Affiliation(s)
- Kiran Thakur
- Dairy Microbiology Division, and ‡Animal Biotechnology Centre, National Dairy Research Institute , Karnal, Haryana 132001, India
| | - Sudhir Kumar Tomar
- Dairy Microbiology Division, and ‡Animal Biotechnology Centre, National Dairy Research Institute , Karnal, Haryana 132001, India
| | - Biswajit Brahma
- Dairy Microbiology Division, and ‡Animal Biotechnology Centre, National Dairy Research Institute , Karnal, Haryana 132001, India
| | - Sachinandan De
- Dairy Microbiology Division, and ‡Animal Biotechnology Centre, National Dairy Research Institute , Karnal, Haryana 132001, India
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156
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Larsen N, Moslehi-Jenabian S, Werner BB, Jensen ML, Garrigues C, Vogensen FK, Jespersen L. Transcriptome analysis of Lactococcus lactis subsp. lactis during milk acidification as affected by dissolved oxygen and the redox potential. Int J Food Microbiol 2016; 226:5-12. [PMID: 27015296 DOI: 10.1016/j.ijfoodmicro.2016.03.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 01/13/2016] [Accepted: 03/04/2016] [Indexed: 11/30/2022]
Abstract
Performance of Lactococcus lactis as a starter culture in dairy fermentations depends on the levels of dissolved oxygen and the redox state of milk. In this study the microarray analysis was used to investigate the global gene expression of L. lactis subsp. lactis DSM20481(T) during milk acidification as affected by oxygen depletion and the decrease of redox potential. Fermentations were carried out at different initial levels of dissolved oxygen (dO2) obtained by milk sparging with oxygen (high dO2, 63%) or nitrogen (low dO2, 6%). Bacterial exposure to high initial oxygen resulted in overexpression of genes involved in detoxification of reactive oxygen species (ROS), oxidation-reduction processes, biosynthesis of trehalose and down-regulation of genes involved in purine nucleotide biosynthesis, indicating that several factors, among them trehalose and GTP, were implicated in bacterial adaptation to oxidative stress. Generally, transcriptional changes were more pronounced during fermentation of oxygen sparged milk. Genes up-regulated in response to oxygen depletion were implicated in biosynthesis and transport of pyrimidine nucleotides, branched chain amino acids and in arginine catabolic pathways; whereas genes involved in salvage of nucleotides and cysteine pathways were repressed. Expression pattern of genes involved in pyruvate metabolism indicated shifts towards mixed acid fermentation after oxygen depletion with production of specific end-products, depending on milk treatment. Differential expression of genes, involved in amino acid and pyruvate pathways, suggested that initial oxygen might influence the release of flavor compounds and, thereby, flavor development in dairy fermentations. The knowledge of molecular responses involved in adaptation of L. lactis to the shifts of redox state and pH during milk fermentations is important for the dairy industry to ensure better control of cheese production.
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Affiliation(s)
- Nadja Larsen
- Department of Food Science, Food Microbiology, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark.
| | - Saloomeh Moslehi-Jenabian
- Department of Food Science, Food Microbiology, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark
| | - Birgit Brøsted Werner
- Department of Food Science, Food Microbiology, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark
| | | | | | - Finn Kvist Vogensen
- Department of Food Science, Food Microbiology, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark
| | - Lene Jespersen
- Department of Food Science, Food Microbiology, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark
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157
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Ho CH, Stanton-Cook M, Beatson SA, Bansal N, Turner MS. Stability of active prophages in industrial Lactococcus lactis strains in the presence of heat, acid, osmotic, oxidative and antibiotic stressors. Int J Food Microbiol 2016; 220:26-32. [DOI: 10.1016/j.ijfoodmicro.2015.12.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 12/10/2015] [Accepted: 12/27/2015] [Indexed: 11/25/2022]
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158
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Murphy J, Bottacini F, Mahony J, Kelleher P, Neve H, Zomer A, Nauta A, van Sinderen D. Comparative genomics and functional analysis of the 936 group of lactococcal Siphoviridae phages. Sci Rep 2016; 6:21345. [PMID: 26892066 PMCID: PMC4759559 DOI: 10.1038/srep21345] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 01/21/2016] [Indexed: 01/14/2023] Open
Abstract
Genome sequencing and comparative analysis of bacteriophage collections has greatly enhanced our understanding regarding their prevalence, phage-host interactions as well as the overall biodiversity of their genomes. This knowledge is very relevant to phages infecting Lactococcus lactis, since they constitute a significant risk factor for dairy fermentations. Of the eighty four lactococcal phage genomes currently available, fifty five belong to the so-called 936 group, the most prevalent of the ten currently recognized lactococcal phage groups. Here, we report the genetic characteristics of a new collection of 936 group phages. By combining these genomes to those sequenced previously we determined the core and variable elements of the 936 genome. Genomic variation occurs across the 936 phage genome, such as genetic elements that (i) lead to a +1 translational frameshift resulting in the formation of additional structures on the phage tail, (ii) specify a double neck passage structure, and (iii) encode packaging module-associated methylases. Hierarchical clustering of the gene complement of the 936 group phages and nucleotide alignments allowed grouping of the ninety 936 group phages into distinct clusters, which in general appear to correspond with their geographical origin.
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Affiliation(s)
- James Murphy
- School of Microbiology, University College Cork, Cork, Ireland
| | | | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork, Ireland
| | - Philip Kelleher
- School of Microbiology, University College Cork, Cork, Ireland
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany
| | - Aldert Zomer
- School of Microbiology, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Arjen Nauta
- FrieslandCampina, Amersfoort, The Netherlands
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
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159
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Draft Genome Sequence of Lactococcus lactis subsp. lactis bv. diacetylactis CRL264, a Citrate-Fermenting Strain. GENOME ANNOUNCEMENTS 2016; 4:4/1/e01575-15. [PMID: 26847906 PMCID: PMC4742675 DOI: 10.1128/genomea.01575-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the draft genome sequence of Lactococcus lactis subsp. lactis bv. diacetylactis CRL264, a natural strain isolated from artisanal cheese from northwest Argentina. L. lactis subsp. lactis bv. diacetylactis is one of the most important microorganisms used as starter culture around the world. The CRL264 strain constitutes a model microorganism in the studies on the generation of aroma compounds (diacetyl, acetoin, and 2,3-butanediol) by lactic acid bacteria. Our genome analysis shows similar genetic organization to other available genomes of L. lactis bv. diacetylactis strains.
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160
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Zhu D, Li R, Liu F, Xu H, Li B, Yuan Y, Saris P, Qiao M. Mu insertion in feuD
triggers the increase in nisin immunity in Lactococcus lactis
subsp. lactis
N8. J Appl Microbiol 2016; 120:402-12. [DOI: 10.1111/jam.13015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 10/21/2015] [Accepted: 11/20/2015] [Indexed: 11/29/2022]
Affiliation(s)
- D. Zhu
- Key Laboratory of Molecular Microbiology and Technology; Ministry of Education; Nankai University; Tianjin China
| | - R. Li
- School of Life Sciences and Technology; ShanghaiTech University; Shanghai China
| | - F. Liu
- Key Laboratory of Molecular Microbiology and Technology; Ministry of Education; Nankai University; Tianjin China
| | - H. Xu
- Key Laboratory of Molecular Microbiology and Technology; Ministry of Education; Nankai University; Tianjin China
| | - B. Li
- Key Laboratory of Systems Bioengineering; Ministry of Education; Department of Pharmaceutical Engineering; Tianjin University; Tianjin China
| | - Y. Yuan
- Key Laboratory of Systems Bioengineering; Ministry of Education; Department of Pharmaceutical Engineering; Tianjin University; Tianjin China
| | - P.E.J. Saris
- Department of Food and Environmental Sciences; University of Helsinki; Helsinki Finland
| | - M. Qiao
- Key Laboratory of Molecular Microbiology and Technology; Ministry of Education; Nankai University; Tianjin China
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161
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Najjari A, Amairi H, Chaillou S, Mora D, Boudabous A, Zagorec M, Ouzari H. Phenotypic and genotypic characterization of peptidoglycan hydrolases of Lactobacillus sakei. J Adv Res 2016; 7:155-63. [PMID: 26843981 PMCID: PMC4703478 DOI: 10.1016/j.jare.2015.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 11/26/2022] Open
Abstract
Lactobacillus sakei, a lactic acid bacterium naturally found in fresh meat and sea products, is considered to be one of the most important bacterial species involved in meat fermentation and bio-preservation. Several enzymes of Lb. sakei species contributing to microbial safeguarding and organoleptic properties of fermented-meat were studied. However, the specific autolytic mechanisms and associated enzymes involved in Lb. sakei are not well understood. The autolytic phenotype of 22 Lb. sakei strains isolated from Tunisian meat and seafood products was evaluated under starvation conditions, at pH 6.5 and 8.5, and in the presence of different carbon sources. A higher autolytic rate was observed when cells were grown in the presence of glucose and incubated at pH 6.5. Almost all strains showed high resistance to mutanolysin, indicating a minor role of muramidases in Lb. sakei cell lysis. Using Micrococcus lysodeikticus cells as a substrate in activity gels zymogram, peptidoglycan hydrolase (PGH) patterns for all strains was characterized by two lytic bands of ∼80 (B1) and ∼70 kDa (B2), except for strain BMG.167 which harbored two activity signals at a lower MW. Lytic activity was retained in high salt and in acid/basic conditions and was active toward cells of Lb. sakei, Listeria monocytogenes, Listeria ivanovii and Listeria innocua. Analysis of five putative PGH genes found in the Lb. sakei 23 K model strain genome, indicated that one gene, lsa1437, could encode a PGH (N-acetylmuramoyl-L-alanine amidase) containing B1 and B2 as isoforms. According to this hypothesis, strain BMG.167 showed an allelic version of lsa1437 gene deleted of one of the five LysM domains, leading to a reduction in the MW of lytic bands and the high autolytic rate of this strain. Characterization of autolytic phenotype of Lb. sakei should expand the knowledge of their role in fermentation processes where they represent the dominant species.
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Affiliation(s)
- Afef Najjari
- Université Tunis El Manar, Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Campus Universitaire, 2092 Tunis, Tunisia
| | - Houda Amairi
- Université Tunis El Manar, Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Campus Universitaire, 2092 Tunis, Tunisia
| | - Stéphane Chaillou
- Unité Flore Lactique et Environnement Carné, UR309, INRA, Domaine de Vilvert, F-78350 Jouy en Josas, France
| | - Diego Mora
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Università degli Studi di Milano, Milan, Italy
| | - Abdellatif Boudabous
- Université Tunis El Manar, Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Campus Universitaire, 2092 Tunis, Tunisia
| | - Monique Zagorec
- Unité Flore Lactique et Environnement Carné, UR309, INRA, Domaine de Vilvert, F-78350 Jouy en Josas, France
| | - Hadda Ouzari
- Université Tunis El Manar, Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Campus Universitaire, 2092 Tunis, Tunisia
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162
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Abstract
Twin-arginine protein translocation systems (Tat) translocate fully folded and co-factor-containing proteins across biological membranes. In this review, we focus on the Tat pathway of Gram-positive bacteria. The minimal Tat pathway is composed of two components, namely a TatA and TatC pair, which are often complemented with additional TatA-like proteins. We provide overviews of our current understanding of Tat pathway composition and mechanistic aspects related to Tat-dependent cargo protein translocation. This includes Tat pathway flexibility, requirements for the correct folding and incorporation of co-factors in cargo proteins and the functions of known cargo proteins. Tat pathways of several Gram-positive bacteria are discussed in detail, with emphasis on the Tat pathway of Bacillus subtilis. We discuss both shared and unique features of the different Gram-positive bacterial Tat pathways. Lastly, we highlight topics for future research on Tat, including the development of this protein transport pathway for the biotechnological secretion of high-value proteins and its potential applicability as an antimicrobial drug target in pathogens.
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Affiliation(s)
- Vivianne J Goosens
- MRC Centre for Molecular Bacteriology and Infection, Section of Microbiology, Imperial College London, London, SW7 2AZ, UK
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700, RB, Groningen, The Netherlands.
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163
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Draft Genome Sequence of the Moderately Heat-Tolerant Lactococcus lactis subsp. lactis bv. diacetylactis Strain GL2 from Algerian Dromedary Milk. GENOME ANNOUNCEMENTS 2015; 3:3/6/e01334-15. [PMID: 26586883 PMCID: PMC4653785 DOI: 10.1128/genomea.01334-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Lactococcus lactis subsp. lactis bv. diacetylactis GL2 is a moderately thermotolerant lactic acid bacterium isolated from dromedary raw milk. Here, we present the draft genome sequence of this potential new dairy starter strain, which combines thermotolerance and the capacity to metabolize lactose, casein, and citrate.
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164
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Relative Rates of Amino Acid Import via the ABC Transporter GlnPQ Determine the Growth Performance of Lactococcus lactis. J Bacteriol 2015; 198:477-85. [PMID: 26553850 DOI: 10.1128/jb.00685-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/04/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The GlnPQ transporter from Lactococcus lactis has the remarkable feature of having two substrate-binding domains (SBDs) fused to the N terminus of the transmembrane domain (TMD), and thus four SBDs are present in the homodimeric complex. Although X-ray structures and ligand binding data are available for both SBDs, little is known of how different amino acids compete with each other for transport via GlnPQ. Here we show GlnPQ has a broader substrate specificity than previously thought, with the ability to take up asparagine, glutamine, and glutamic acid, albeit via different routes and with different affinities. Asparagine and glutamine compete with each other at the level of binding to SBD1 and SBD2 (with differences in dissociation constant), but at the same time SBD1 and SBD2 compete with each other at the level of interaction with the translocator domain (with differences in affinity constant and rate of transport). Although glutamine transport via SBD1 is outcompeted by physiological concentrations of asparagine, SBD2 ensures high rates of import of the essential amino acid glutamine. Taken together, this study demonstrates that even in the presence of competing asparagine concentrations, GlnPQ has a high capacity to transport glutamine, which matches the high needs of the cell for glutamine and glutamate. IMPORTANCE GlnPQ is an ATP-binding cassette (ABC) transporter for glutamine, glutamic acid, and asparagine. The system is essential in various Gram-positive bacteria, including L. lactis and several pathogens. Here we show how the amino acids compete with each other for binding to the multiple SBDs of GlnPQ and how these SBDs compete with each other for substrate delivery to the transporter. Overall, our results show that GlnPQ has evolved to transport diverse substrates via different paths and to optimally acquire the abundant and essential amino acid glutamine.
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165
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Expression of bacteriocin LsbB is dependent on a transcription terminator. Microbiol Res 2015; 179:45-53. [DOI: 10.1016/j.micres.2015.06.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Revised: 06/28/2015] [Accepted: 06/28/2015] [Indexed: 11/21/2022]
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166
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Advances and needs for endotoxin-free production strains. Appl Microbiol Biotechnol 2015; 99:9349-60. [PMID: 26362682 DOI: 10.1007/s00253-015-6947-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 08/16/2015] [Accepted: 08/20/2015] [Indexed: 10/23/2022]
Abstract
The choice of an appropriate microbial host cell and suitable production conditions is crucial for the downstream processing of pharmaceutical- and food-grade products. Although Escherichia coli serves as a highly valuable leading platform for the production of value-added products, like most Gram-negative bacteria, this bacterium contains a potent immunostimulatory lipopolysaccharide (LPS), referred to as an endotoxin. In contrast, Gram-positive bacteria, notably Bacillus, lactic acid bacteria (LAB), Corynebacterium, and yeasts have been extensively used as generally recognized as safe (GRAS) endotoxin-free platforms for the production of a variety of products. This review summarizes the currently available knowledge on the utilization of these representative Gram-positive bacteria for the production of eco- and bio-friendly products, particularly natural polyesters, polyhydroxyalkanoates, bacteriocins, and membrane proteins. The successful case studies presented here serve to inspire the use of these microorganisms as a main-player or by-player depending on their individual properties for the industrial production of these desirable targets.
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167
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Araque I, Gil J, Carreté R, Constantí M, Bordons A, Reguant C. Arginine deiminase pathway genes and arginine degradation variability in Oenococcus oeni strains. Folia Microbiol (Praha) 2015; 61:109-18. [PMID: 26873388 DOI: 10.1007/s12223-015-0416-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 07/10/2015] [Indexed: 01/03/2023]
Abstract
Trace amounts of the carcinogenic ethyl carbamate can appear in wine as a result of a reaction between ethanol and citrulline, which is produced from arginine degradation by some bacteria used in winemaking. In this study, arginine deiminase (ADI) pathway genes were evaluated in 44 Oenococcus oeni strains from wines originating from several locations in order to establish the relationship between the ability of a strain to degrade arginine and the presence of related genes. To detect the presence of arc genes of the ADI pathway in O. oeni, pairs of primers were designed to amplify arcA, arcB, arcC and arcD1 sequences. All strains contained these four genes. The same primers were used to confirm the organization of these genes in an arcABCD1 operon. Nevertheless, considerable variability in the ability to degrade arginine among these O. oeni strains was observed. Therefore, despite the presence of the arc genes in all strains, the expression patterns of individual genes must be strain dependent and influenced by the different wine conditions. Additionally, the presence of arc genes was also determined in the 57 sequenced strains of O. oeni available in GenBank, and the complete operon was found in 83% of strains derived from wine. The other strains were found to lack the arcB, arcC and arcD genes, but all contained sequences homologous to arcA, and some of them had also ADI activity.
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Affiliation(s)
- Isabel Araque
- Departament de Bioquímica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, Tarragona, Catalonia, Spain
| | - Joana Gil
- Departament de Bioquímica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, Tarragona, Catalonia, Spain
| | - Ramon Carreté
- Departament de Bioquímica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, Tarragona, Catalonia, Spain
| | - Magda Constantí
- Departament d'Enginyeria Química, ETSEQ, Universitat Rovira i Virgili, Tarragona, Catalonia, Spain
| | - Albert Bordons
- Departament de Bioquímica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, Tarragona, Catalonia, Spain.
| | - Cristina Reguant
- Departament de Bioquímica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, Tarragona, Catalonia, Spain
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168
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2,4-Di-tert-butyl phenol as the antifungal, antioxidant bioactive purified from a newly isolated Lactococcus sp. Int J Food Microbiol 2015; 211:44-50. [PMID: 26164257 DOI: 10.1016/j.ijfoodmicro.2015.06.025] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 06/06/2015] [Accepted: 06/25/2015] [Indexed: 11/24/2022]
Abstract
The volatile organic compound 2,4-di-tert-butyl phenol (2,4 DTBP) was purified from the cell free supernatant of a newly isolated Lactococcus sp. by solvent extraction and chromatographic techniques. Molecular characterization of the compound by ESI-MS, (1)H NMR and FTIR analysis revealed the structure, C14H22O. Fungicidal activity was demonstrated against Aspergillus niger, Fusarium oxysporum and Penicillium chrysogenum by disc diffusion assay. Among the cell lines tested for cytotoxicity of this compound (normal cell line H9c2 and cancer cell lines HeLa and MCF-7), a remarkable cytotoxicity against HeLa cells with an IC50 value of 10 μg/mL was shown. A biocontrol experiment with 2,4 DTBP supplemented fraction prevented growth of the abovementioned fungi on wheat grains. The study further strengthens the case for development of biopreservatives and dietary antioxidants from lactic acid bacteria for food applications.
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169
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Li C, Dong H, Lu H, Gu X, Tian J, Xu W, Tian H. Development of an antibiotic-free plasmid selection system based on thymine auxotrophy in Lactococcus lactis. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-014-0950-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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170
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Shkoporov AN, Khokhlova EV, Savochkin KA, Kafarskaia LI, Efimov BA. Production of biologically active scFv and VHH antibody fragments in Bifidobacterium longum. FEMS Microbiol Lett 2015; 362:fnv083. [PMID: 25994292 DOI: 10.1093/femsle/fnv083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2015] [Indexed: 01/01/2023] Open
Abstract
Bifidobacteria constitute a significant part of healthy intestinal microbiota in adults and infants and present a promising platform for construction of genetically modified probiotic agents for treatment of gastrointestinal disorders. In this study, three strains of Bifidobacterium longum were constructed that express and secrete biologically active single-chain antibodies against human TNF-α and Clostridium difficile exotoxin A. Anti-TNF-α scFv antibody D2E7 was produced at the level of 25 μg L(-1) in broth culture and was mostly retained in the cytoplasm, while VHH-type antibodies A20.1 and A26.8 against C. difficile exotoxin A were produced at the levels of 0.3-1 mg L(-1) and secreted very efficiently. The biological activity of both antibody types was demonstrated in the mammalian cell-based assays. Expression of A20.1 and A26.8 was also observed in vivo after intragastric administration of transformed B. longum strains to (C57/BL6 × DBA/2)F1 mice. The obtained B. longum strains may serve as prototypes for construction of novel probiotic medications against inflammatory bowel disease and C. difficile-associated disease.
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Affiliation(s)
- A N Shkoporov
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Ostrovitjanova str. 1, Moscow 117997, Russia Pharmbacter LLC, Skladochnaya ul., 1 - 1, Moscow 127018, Russia
| | - E V Khokhlova
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Ostrovitjanova str. 1, Moscow 117997, Russia
| | - K A Savochkin
- Pharmbacter LLC, Skladochnaya ul., 1 - 1, Moscow 127018, Russia
| | - L I Kafarskaia
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Ostrovitjanova str. 1, Moscow 117997, Russia
| | - B A Efimov
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Ostrovitjanova str. 1, Moscow 117997, Russia
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171
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Duffy LC, Raiten DJ, Hubbard VS, Starke-Reed P. Progress and challenges in developing metabolic footprints from diet in human gut microbial cometabolism. J Nutr 2015; 145:1123S-1130S. [PMID: 25833886 PMCID: PMC4410496 DOI: 10.3945/jn.114.194936] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 08/07/2014] [Indexed: 12/13/2022] Open
Abstract
Homo sapiens harbor trillions of microbes, whose microbial metagenome (collective genome of a microbial community) using omic validation interrogation tools is estimated to be at least 100-fold that of human cells, which comprise 23,000 genes. This article highlights some of the current progress and open questions in nutrition-related areas of microbiome research. It also underscores the metabolic capabilities of microbial fermentation on nutritional substrates that require further mechanistic understanding and systems biology approaches of studying functional interactions between diet composition, gut microbiota, and host metabolism. Questions surrounding bacterial fermentation and degradation of dietary constituents (particularly by Firmicutes and Bacteroidetes) and deciphering how microbial encoding of enzymes and derived metabolites affect recovery of dietary energy by the host are more complex than previously thought. Moreover, it is essential to understand to what extent the intestinal microbiota is subject to dietary control and to integrate these data with functional metabolic signatures and biomarkers. Many lines of research have demonstrated the significant role of the gut microbiota in human physiology and disease. Probiotic and prebiotic products are proliferating in the market in response to consumer demand, and the science and technology around these products are progressing rapidly. With high-throughput molecular technologies driving the science, studying the bidirectional interactions of host-microbial cometabolism, epithelial cell maturation, shaping of innate immune development, normal vs. dysfunctional nutrient absorption and processing, and the complex signaling pathways involved is now possible. Substantiating the safety and mechanisms of action of probiotic/prebiotic formulations is critical. Beneficial modulation of the human microbiota by using these nutritional and biotherapeutic strategies holds considerable promise as next-generation drugs, vaccinomics, and metabolic agents and in novel food discovery.
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Affiliation(s)
- Linda C Duffy
- National Center for Complementary and Integrative Health,
| | - Daniel J Raiten
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development
| | - Van S Hubbard
- Division of Nutrition Research Coordination, NIH, US Department of Health and Human Services, Bethesda, MD; and
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172
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Kelleher P, Murphy J, Mahony J, van Sinderen D. Next-generation sequencing as an approach to dairy starter selection. DAIRY SCIENCE & TECHNOLOGY 2015; 95:545-568. [PMID: 26798445 PMCID: PMC4712225 DOI: 10.1007/s13594-015-0227-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/25/2015] [Accepted: 04/02/2015] [Indexed: 02/06/2023]
Abstract
Lactococcal and streptococcal starter strains are crucial ingredients to manufacture fermented dairy products. As commercial starter culture suppliers and dairy producers attempt to overcome issues of phage sensitivity and develop new product ranges, there is an ever increasing need to improve technologies for the rational selection of novel starter culture blends. Whole genome sequencing, spurred on by recent advances in next-generation sequencing platforms, is a promising approach to facilitate rapid identification and selection of such strains based on gene-trait matching. This review provides a comprehensive overview of the available methodologies to analyse the technological potential of candidate starter strains and highlights recent advances in the area of dairy starter genomics.
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Affiliation(s)
- Philip Kelleher
- School of Microbiology, University College Cork, Cork, Ireland
| | - James Murphy
- School of Microbiology, University College Cork, Cork, Ireland
| | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork, Cork, Ireland
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173
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Kim SR, Nguyen TV, Seo NR, Jung S, An HJ, Mills DA, Kim JH. Comparative proteomics: assessment of biological variability and dataset comparability. BMC Bioinformatics 2015; 16:121. [PMID: 25888384 PMCID: PMC4704264 DOI: 10.1186/s12859-015-0561-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 03/30/2015] [Indexed: 11/22/2022] Open
Abstract
Background Comparative proteomics in bacteria are often hampered by the differential nature of dataset quality and/or inherent biological deviations. Although common practice compensates by reproducing and normalizing datasets from a single sample, the degree of certainty is limited in comparison of multiple dataset. To surmount these limitations, we introduce a two-step assessment criterion using: (1) the relative number of total spectra (RTS) to determine if two LC-MS/MS datasets are comparable and (2) nine glycolytic enzymes as internal standards for a more accurate calculation of relative amount of proteins. Lactococcus lactis HR279 and JHK24 strains expressing high or low levels (respectively) of green fluorescent protein (GFP) were used for the model system. GFP abundance was determined by spectral counting and direct fluorescence measurements. Statistical analysis determined relative GFP quantity obtained from our approach matched values obtained from fluorescence measurements. Results L. lactis HR279 and JHK24 demonstrates two datasets with an RTS value less than 1.4 accurately reflects relative differences in GFP levels between high and low expression strains. Without prior consideration of RTS and the use of internal standards, the relative increase in GFP calculated by spectral counting method was 3.92 ± 1.14 fold, which is not correlated with the value determined by the direct fluorescence measurement (2.86 ± 0.42 fold) with the p = 0.024. In contrast, 2.88 ± 0.92 fold was obtained by our approach showing a statistically insignificant difference (p = 0.95). Conclusions Our two-step assessment demonstrates a useful approach to: (1) validate the comparability of two mass spectrometric datasets and (2) accurately calculate the relative amount of proteins between proteomic datasets. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0561-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sa Rang Kim
- Department of Food and Nutrition, Chungnam National University, Daejeon, 305-764, South Korea.
| | - Tuong Vi Nguyen
- Department of Food and Nutrition, Chungnam National University, Daejeon, 305-764, South Korea.
| | - Na Ri Seo
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 305-764, South Korea.
| | - Seunghup Jung
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 305-764, South Korea.
| | - Hyun Joo An
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 305-764, South Korea.
| | - David A Mills
- Robert Mondavi Institute for Wine and Food Science, Department of Food Science, University of California, Davis, CA, 95616, USA.
| | - Jae Han Kim
- Department of Food and Nutrition, Chungnam National University, Daejeon, 305-764, South Korea.
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174
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Draft Genome Sequence of Lactococcus lactis subsp. lactis JCM 5805T, a Strain That Induces Plasmacytoid Dendritic Cell Activation. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00113-15. [PMID: 25792049 PMCID: PMC4395072 DOI: 10.1128/genomea.00113-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Lactococcus lactis subsp. lactis JCM 5805(T) is a dairy lactic acid bacterium that induces plasmacytoid dendritic cell (pDC) activation. Here, we report the 2.55-Mb draft genome and annotation of Lactococcus lactis JCM 5805(T). This genome information will provide further insights into the mechanisms underlying the immunomodulatory function of this strain.
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175
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Wyszyńska A, Kobierecka P, Bardowski J, Jagusztyn-Krynicka EK. Lactic acid bacteria--20 years exploring their potential as live vectors for mucosal vaccination. Appl Microbiol Biotechnol 2015; 99:2967-77. [PMID: 25750046 PMCID: PMC4365182 DOI: 10.1007/s00253-015-6498-0] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/18/2015] [Accepted: 02/19/2015] [Indexed: 12/20/2022]
Abstract
Lactic acid bacteria (LAB) are a diverse group of Gram-positive, nonsporulating, low G + C content bacteria. Many of them have been given generally regarded as safe status. Over the past two decades, intensive genetic and molecular research carried out on LAB, mainly Lactococcus lactis and some species of the Lactobacillus genus, has revealed new, potential biomedical LAB applications, including the use of LAB as adjuvants, immunostimulators, or therapeutic drug delivery systems, or as factories to produce therapeutic molecules. LAB enable immunization via the mucosal route, which increases effectiveness against pathogens that use the mucosa as the major route of entry into the human body. In this review, we concentrate on the encouraging application of Lactococcus and Lactobacillus genera for the development of live mucosal vaccines. First, we present the progress that has recently been made in the field of developing tools for LAB genetic manipulations, which has resulted in the successful expression of many bacterial, parasitic, and viral antigens in LAB strains. Next, we discuss the factors influencing the efficacy of the constructed vaccine prototypes that have been tested in various animal models. Apart from the research focused on an application of live LABs as carriers of foreign antigens, a lot of work has been recently done on the potential usage of nonliving, nonrecombinant L. lactis designated as Gram-positive enhancer matrix (GEM), as a delivery system for mucosal vaccination. The advantages and disadvantages of both strategies are also presented.
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Affiliation(s)
- Agnieszka Wyszyńska
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
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176
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Lactococcal 949 group phages recognize a carbohydrate receptor on the host cell surface. Appl Environ Microbiol 2015; 81:3299-305. [PMID: 25746988 DOI: 10.1128/aem.00143-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 02/25/2015] [Indexed: 12/27/2022] Open
Abstract
Lactococcal bacteriophages represent one of the leading causes of dairy fermentation failure and product inconsistencies. A new member of the lactococcal 949 phage group, named WRP3, was isolated from cheese whey from a Sicilian factory in 2011. The genome sequence of this phage was determined, and it constitutes the largest lactococcal phage genome currently known, at 130,008 bp. Detailed bioinformatic analysis of the genomic region encoding the presumed initiator complex and baseplate of WRP3 has aided in the functional assignment of several open reading frames (ORFs), particularly that for the receptor binding protein required for host recognition. Furthermore, we demonstrate that the 949 phages target cell wall phospho-polysaccharides as their receptors, accounting for the specificity of the interactions of these phages with their lactococcal hosts. Such information may ultimately aid in the identification of strains/strain blends that do not present the necessary saccharidic target for infection by these problematic phages.
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177
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Aller K, Adamberg K, Reile I, Timarova V, Peebo K, Vilu R. Excess of threonine compared with serine promotes threonine aldolase activity in Lactococcus lactis IL1403. MICROBIOLOGY-SGM 2015; 161:1073-1080. [PMID: 25743155 DOI: 10.1099/mic.0.000071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 03/03/2015] [Indexed: 11/18/2022]
Abstract
Lactococcus lactis is an important lactic acid starter for food production as well as a cell factory for production of food grade additives, among which natural flavour production is one of the main interests of food producers. Flavour production is associated with the degradation of amino acids and comprehensive studies are required to elucidate mechanisms behind these pathways. In this study using chemically defined medium, labelled substrate and steady-state cultivation, new data for the catabolism of threonine in Lc. lactis have been obtained. The biosynthesis of glycine in this organism is associated with the catabolic pathways of glucose and serine. Nevertheless, if threonine concentration in the growth environment exceeds that of serine, threonine becomes the main source for glycine biosynthesis and the utilization of serine decreases. Also, the conversion of threonine to glycine was initiated by a threonine aldolase and this was the principal pathway used for threonine degradation. As in Streptococcus thermophilus, serine hydroxymethyltransferase in Lc. lactis may possess a secondary activity as threonine aldolase. Other catabolic pathways of threonine (e.g. threonine dehydrogenase and threonine dehydratase) were not detected.
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Affiliation(s)
- Kadri Aller
- Tallinn University of Technology, Department of Chemistry, Akadeemia tee 15, Tallinn 12618, Estonia.,Competence Center of Food and Fermentation Technologies, Akadeemia tee 15A, Tallinn 12618, Estonia
| | - Kaarel Adamberg
- Tallinn University of Technology, Department of Food Processing, Ehitajate tee 5, Tallinn 19086, Estonia.,Tallinn University of Technology, Department of Chemistry, Akadeemia tee 15, Tallinn 12618, Estonia.,Competence Center of Food and Fermentation Technologies, Akadeemia tee 15A, Tallinn 12618, Estonia
| | - Indrek Reile
- National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
| | - Veronica Timarova
- Tallinn University of Technology, Department of Chemistry, Akadeemia tee 15, Tallinn 12618, Estonia.,Competence Center of Food and Fermentation Technologies, Akadeemia tee 15A, Tallinn 12618, Estonia
| | - Karl Peebo
- Tallinn University of Technology, Department of Chemistry, Akadeemia tee 15, Tallinn 12618, Estonia.,Competence Center of Food and Fermentation Technologies, Akadeemia tee 15A, Tallinn 12618, Estonia
| | - Raivo Vilu
- Tallinn University of Technology, Department of Chemistry, Akadeemia tee 15, Tallinn 12618, Estonia.,Competence Center of Food and Fermentation Technologies, Akadeemia tee 15A, Tallinn 12618, Estonia
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178
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Du L, He X, Zhang H, Liu F, Ju X, Yuan J. First two domains at the lp_1643 protein N terminus inhibit pathogen adhesion to porcine mucus in vitro. J Food Prot 2015; 78:370-5. [PMID: 25710153 DOI: 10.4315/0362-028x.jfp-14-294] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Gastrointestinal probiotics are important members of intestinal microflora in both healthy animals and human beings, and these bacteria may reduce the risk of infection caused by certain opportunistic pathogens through exclusive inhibition, competition, and displacement. The lp_1643 protein on the cell surface of Lactobacillus plantarum WCFSI was assumed to possess a mucus-binding capability. This study aimed to determine if purified His-N2 protein exclusively inhibits pathogen adhesion to porcine mucus. The interaction of the His-N2 protein with porcine mucus was determined by indirect enzyme-linked immunosorbent assay (ELISA), and the adhesion was assessed by a traditional plating method to count the bacteria adhered to the porcine mucus. Indirect ELISA showed that His-N2 protein adhered to porcine mucus, and its interacting molecules existed. The His-N2 protein effectively inhibited the adhesion of Escherichia coli DH5α, Listeria monocytogenes CMCC54004, Salmonella Typhimurium ATCC 14028, and Shigella flexneri CMCC(B)51572 to porcine mucus. Results showed that inhibition of pathogen adhesion to porcine mucus depended on dose and strain. The adhesion of L. monocytogenes CMCC54004, Salmonella Typhimurium ATCC 14028, and S. flexneri CMCC(B)51572 was reduced by 95.7, 97.0, and 95.7%, respectively, by pre-adding 100 μl of 3.92 mg/ml of His-N2 protein, whereas that of E. coli DH5α was only 50.4%. The inhibition of adhesion of some pathogens by His-N2 was different at pH 6.6 and 7.5. The inhibition of E. coli DH5α, L. monocytogenes CMCC54004, and Salmonella Typhimurium ATCC 14028 at pH 6.6 was significantly higher than that at pH 7.5, whereas no statistically significant difference was observed in S. flexneri CMCC(B)51572. These results suggest that various types of inhibition mechanisms of His-N2 were involved in different pathogens.
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Affiliation(s)
- Lihui Du
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, People's Republic of China
| | - Xiaoying He
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, People's Republic of China
| | - Hong Zhang
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, People's Republic of China
| | - Fang Liu
- Institute of Agricultural Products Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, People's Republic of China.
| | - Xingrong Ju
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, People's Republic of China
| | - Jian Yuan
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, People's Republic of China
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179
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Alvarez-Sieiro P, Redruello B, Ladero V, Cañedo E, Martin MC, Fernández M, Alvarez MA. Solubilization of gliadins for use as a source of nitrogen in the selection of bacteria with gliadinase activity. Food Chem 2015; 168:439-44. [DOI: 10.1016/j.foodchem.2014.07.085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 06/11/2014] [Accepted: 07/15/2014] [Indexed: 01/08/2023]
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180
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Wu Q, Cheung CK, Shah NP. Towards galactose accumulation in dairy foods fermented by conventional starter cultures: Challenges and strategies. Trends Food Sci Technol 2015. [DOI: 10.1016/j.tifs.2014.08.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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181
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Bera S, Thillai K, Sriraman K, Jayaraman G. Process strategies for enhancing recombinant streptokinase production in Lactococcus lactis cultures using P170 expression system. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2014.07.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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182
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Mancini S, Abicht HK, Gonskikh Y, Solioz M. A copper-induced quinone degradation pathway provides protection against combined copper/quinone stress inLactococcus lactis IL1403. Mol Microbiol 2014; 95:645-59. [DOI: 10.1111/mmi.12889] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2014] [Indexed: 01/26/2023]
Affiliation(s)
- Stefano Mancini
- Department Clinical Research; University of Bern; Murtenstrasse 35 3010 Bern Switzerland
| | - Helge K. Abicht
- Department Clinical Research; University of Bern; Murtenstrasse 35 3010 Bern Switzerland
| | - Yulia Gonskikh
- Department Clinical Research; University of Bern; Murtenstrasse 35 3010 Bern Switzerland
- Department of Plant Physiology and Biotechnology; Tomsk State University; Prospect Lenina 36 634050 Tomsk Russia
| | - Marc Solioz
- Department Clinical Research; University of Bern; Murtenstrasse 35 3010 Bern Switzerland
- Department of Plant Physiology and Biotechnology; Tomsk State University; Prospect Lenina 36 634050 Tomsk Russia
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183
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van de Bunt B, Bron PA, Sijtsma L, de Vos WM, Hugenholtz J. Use of non-growing Lactococcus lactis cell suspensions for production of volatile metabolites with direct relevance for flavour formation during dairy fermentations. Microb Cell Fact 2014; 13:176. [PMID: 25492249 PMCID: PMC4266196 DOI: 10.1186/s12934-014-0176-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 11/28/2014] [Indexed: 11/10/2022] Open
Abstract
Background Lactococcus lactis is a lactic acid bacterium that has been used for centuries in the production of a variety of cheeses, as these bacteria rapidly acidify milk and greatly contribute to the flavour of the fermentation end-products. After a short growth phase during cheese ripening L. lactis enters an extended non-growing state whilst still strongly contributing to amino acid-derived flavour formation. Here, a research approach is presented that allows investigation of strain- and amino acid-specific flavour formation during the non-growing state. Results Non-growing cells of five selected L. lactis strains were demonstrated to degrade amino acids into flavour compounds that are relevant in food fermentations and differs greatly from production of flavour compounds using growing cells. As observed earlier in other research set-ups and with other microorganisms, addition of NADH, α-ketoglutarate and pyridoxal-5-phosphate was demonstrated to be essential for optimal flavour formation, suggesting that intracellular pools of these substrates are too low for the significant production of the flavour compounds. Production of flavours during the non-growing phase strongly depends on the individual amino acids that were supplied, on the presence of other amino acids (mixtures versus single compounds), and on the strain used. Moreover, we observed that the plasmid-free model strains L. lactis MG1363 and IL1403 produce relatively low amounts of flavour components under the various conditions tested. Conclusions By using this simplified and rapid approach to study flavour formation by non-growing lactic acid bacteria, lengthy ripening periods are no longer required to assess the capacity of strains to produce flavours in the long, non-growing state of dairy fermentation. In addition, this method also provides insight into the conversion of single amino acids versus the conversion of a mixture of amino acids as produced during protein degradation. The generated results are complementary to earlier generated datasets using growing cells, allowing assessment of the full flavour forming potential of strains used as starter cultures in industrial food fermentation processes.
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Affiliation(s)
- Bert van de Bunt
- TI Food and Nutrition, Wageningen, The Netherlands. .,NIZO food research, Ede, The Netherlands.
| | - Peter A Bron
- TI Food and Nutrition, Wageningen, The Netherlands. .,NIZO food research, Ede, The Netherlands. .,The Kluyver Centre for Genomics of Industrial Fermentations/NCSB, Delft, The Netherlands.
| | - Lolke Sijtsma
- TI Food and Nutrition, Wageningen, The Netherlands. .,The Kluyver Centre for Genomics of Industrial Fermentations/NCSB, Delft, The Netherlands. .,Wageningen UR Food & Biobased Research, Wageningen, The Netherlands.
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands. .,Department Veterinary Biosciences, University of Helsinki, Helsinki, Finland.
| | - Jeroen Hugenholtz
- University of Amsterdam, Swammerdam Institute of Life Sciences, Science park 904, PO Box 94216, 1090, GE, Amsterdam, The Netherlands.
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184
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Early adaptation to oxygen is key to the industrially important traits of Lactococcus lactis ssp. cremoris during milk fermentation. BMC Genomics 2014; 15:1054. [PMID: 25467604 PMCID: PMC4289295 DOI: 10.1186/1471-2164-15-1054] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 11/18/2014] [Indexed: 11/17/2022] Open
Abstract
Background Lactococcus lactis is the most used species in the dairy industry. Its ability to adapt to technological stresses, such as oxidative stress encountered during stirring in the first stages of the cheese-making process, is a key factor to measure its technological performance. This study aimed to understand the response to oxidative stress of Lactococcus lactis subsp. cremoris MG1363 at the transcriptional and metabolic levels in relation to acidification kinetics and growth conditions, especially at an early stage of growth. For those purposes, conditions of hyper-oxygenation were initially fixed for the fermentation. Results Kinetics of growth and acidification were not affected by the presence of oxygen, indicating a high resistance to oxygen of the L. lactis MG1363 strain. Its resistance was explained by an efficient consumption of oxygen within the first 4 hours of culture, leading to a drop of the redox potential. The efficient consumption of oxygen by the L. lactis MG1363 strain was supported by a coherent and early adaptation to oxygen after 1 hour of culture at both gene expression and metabolic levels. In oxygen metabolism, the over-expression of all the genes of the nrd (ribonucleotide reductases) operon or fhu (ferrichrome ABC transports) genes was particularly significant. In carbon metabolism, the presence of oxygen led to an early shift at the gene level in the pyruvate pathway towards the acetate/2,3-butanediol pathway confirmed by the kinetics of metabolite production. Finally, the MG1363 strain was no longer able to consume oxygen in the stationary growth phase, leading to a drastic loss of culturability as a consequence of cumulative stresses and the absence of gene adaptation at this stage. Conclusions Combining metabolic and transcriptomic profiling, together with oxygen consumption kinetics, yielded new insights into the whole genome adaptation of L. lactis to initial oxidative stress. An early and transitional adaptation to oxidative stress was revealed for L. lactis subsp. cremoris MG1363 in the presence of initially high levels of oxygen. This enables the cells to maintain key traits that are of great importance for industry, such as rapid acidification and reduction of the redox potential of the growth media. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1054) contains supplementary material, which is available to authorized users.
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185
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Novikova O, Smith D, Hahn I, Beauregard A, Belfort M. Interaction between conjugative and retrotransposable elements in horizontal gene transfer. PLoS Genet 2014; 10:e1004853. [PMID: 25474706 PMCID: PMC4256276 DOI: 10.1371/journal.pgen.1004853] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 10/25/2014] [Indexed: 11/26/2022] Open
Abstract
Mobile genetic elements either encode their own mobilization machineries or hijack them from other mobile elements. Multiple classes of mobile elements often coexist within genomes and it is unclear whether they have the capacity to functionally interact and even collaborate. We investigate the possibility that molecular machineries of disparate mobile elements may functionally interact, using the example of a retrotransposon, in the form of a mobile group II intron, found on a conjugative plasmid pRS01 in Lactococcus lactis. This intron resides within the pRS01 ltrB gene encoding relaxase, the enzyme required for nicking the transfer origin (oriT) for conjugal transmission of the plasmid into a recipient cell. Here, we show that relaxase stimulates both the frequency and diversity of retrotransposition events using a retromobility indicator gene (RIG), and by developing a high-throughput genomic retrotransposition detection system called RIG-Seq. We demonstrate that LtrB relaxase not only nicks ssDNA of its cognate oriT in a sequence- and strand-specific manner, but also possesses weak off-target activity. Together, the data support a model in which the two different mobile elements, one using an RNA-based mechanism, the other using DNA-based transfer, do functionally interact. Intron splicing facilitates relaxase expression required for conjugation, whereas relaxase introduces spurious nicks in recipient DNA that stimulate both the frequency of intron mobility and the density of events. We hypothesize that this functional interaction between the mobile elements would promote horizontal conjugal gene transfer while stimulating intron dissemination in the donor and recipient cells.
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Affiliation(s)
- Olga Novikova
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, New York, United States of America
| | - Dorie Smith
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, New York, United States of America
| | - Ingrid Hahn
- Department of Biomedical Sciences, University at Albany, Wadsworth Center, NYS Department of Health, Albany, New York, United States of America
| | - Arthur Beauregard
- Department of Biomedical Sciences, University at Albany, Wadsworth Center, NYS Department of Health, Albany, New York, United States of America
| | - Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, New York, United States of America
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186
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Zhang X, Hu S, Du X, Li T, Han L, Kong J. Heterologous expression of carcinoembryonic antigen in Lactococcus lactis via LcsB-mediated surface displaying system for oral vaccine development. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2014; 49:851-858. [PMID: 25641594 DOI: 10.1016/j.jmii.2014.11.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 08/22/2014] [Accepted: 11/05/2014] [Indexed: 12/01/2022]
Abstract
BACKGROUND/PURPOSE Carcinoembryonic antigen (CEA) is an attractive target for immunotherapy because it is expressed minimally in normal tissue, but is overexpressed in a wide variety of malignant epithelial tissues. Lactic acid bacteria (LABs), widely used in food processes, are attractive candidates for oral vaccination. Thus, we examined whether LABs could be used as a live vaccine vector to deliver CEA antigen. METHODS CEA was cloned into an Escherichia coli/Lactococcus lactis shuttle vector pSEC:LEISS under the control of a nisin promoter. For displaying the CEA on the cell surface of the L. lactis strain, the anchor motif LcsB from the S-layer protein of Lactobacillus crispatus was fused with CEA. Intracellular and cell surface expression of the CEA-LcsB fusion was confirmed by western blot analysis. RESULTS Significantly higher levels of CEA-specific secretory immunoglobulin A in the sera of mice were observed upon oral administration of strain cultures containing the CEA-LcsB fused protein. In addition, the CEA-LcsB antigen group showed a higher spleen index compared to the CEA antigen alone or negative control, demonstrating that surface-displayed CEA antigen could induce a higher immune response. CONCLUSION These results provided the first evidence for displaying CEA antigen on the cell surfaces of LABs as oral vaccines against cancer or infectious diseases.
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Affiliation(s)
- Xiaowei Zhang
- Health Science Exchange and Service Center of Jinan, Jinan 250013, China.
| | - Shumin Hu
- State Key Laboratory of Biological Fermentation Engineering of Beer, Tsingtao Brewery Co. Ltd., Qingdao, China; State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
| | - Xue Du
- Health Science Exchange and Service Center of Jinan, Jinan 250013, China
| | - Tiejun Li
- Health Science Exchange and Service Center of Jinan, Jinan 250013, China
| | - Lanlan Han
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
| | - Jian Kong
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
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187
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Exploring the Genome of Cheese Starter Lactic Acid Bacterium Lactococcus lactis subsp. lactis CECT 4433. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01142-14. [PMID: 25395632 PMCID: PMC4241658 DOI: 10.1128/genomea.01142-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we present the draft genome sequences of Lactococcus lactis subsp. lactis CECT 4433, a cheese fermentation starter strain. The genome provides further insight into the genomic plasticity, biocomplexity (including gene strain specifics), and evolution of these genera.
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188
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Cavanagh D, Fitzgerald GF, McAuliffe O. From field to fermentation: the origins of Lactococcus lactis and its domestication to the dairy environment. Food Microbiol 2014; 47:45-61. [PMID: 25583337 DOI: 10.1016/j.fm.2014.11.001] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/22/2014] [Accepted: 11/01/2014] [Indexed: 11/18/2022]
Abstract
Lactococcus lactis is an organism of substantial economic importance, used extensively in the production of fermented foods and widely held to have evolved from plant strains. The domestication of this organism to the milk environment is associated with genome reduction and gene decay, and the acquisition of specific genes involved in protein and lactose utilisation by horizontal gene transfer. In recent years, numerous studies have focused on uncovering the physiology and molecular biology of lactococcal strains from the wider environment for exploitation in the dairy industry. This in turn has facilitated comparative genome analysis of lactococci from different environments and provided insight into the natural phenotypic and genetic diversity of L. lactis. This diversity may be exploited in dairy fermentations to develop products with improved quality and sensory attributes. In this review, we discuss the classification of L. lactis and the problems that arise with phenotype/genotype designation. We also discuss the adaptation of non-dairy lactococci to milk, the traits associated with this adaptation and the potential application of non-dairy lactococci to dairy fermentations.
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Affiliation(s)
- Daniel Cavanagh
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; Department of Microbiology, University College Cork, Co. Cork, Ireland.
| | | | - Olivia McAuliffe
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.
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189
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Lactococcus lactis metabolism and gene expression during growth on plant tissues. J Bacteriol 2014; 197:371-81. [PMID: 25384484 DOI: 10.1128/jb.02193-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lactic acid bacteria have been isolated from living, harvested, and fermented plant materials; however, the adaptations these bacteria possess for growth on plant tissues are largely unknown. In this study, we investigated plant habitat-specific traits of Lactococcus lactis during growth in an Arabidopsis thaliana leaf tissue lysate (ATL). L. lactis KF147, a strain originally isolated from plants, exhibited a higher growth rate and reached 7.9-fold-greater cell densities during growth in ATL than the dairy-associated strain L. lactis IL1403. Transcriptome profiling (RNA-seq) of KF147 identified 853 induced and 264 repressed genes during growth in ATL compared to that in GM17 laboratory culture medium. Genes induced in ATL included those involved in the arginine deiminase pathway and a total of 140 carbohydrate transport and metabolism genes, many of which are involved in xylose, arabinose, cellobiose, and hemicellulose metabolism. The induction of those genes corresponded with L. lactis KF147 nutrient consumption and production of metabolic end products in ATL as measured by gas chromatography-time of flight mass spectrometry (GC-TOF/MS) untargeted metabolomic profiling. To assess the importance of specific plant-inducible genes for L. lactis growth in ATL, xylose metabolism was targeted for gene knockout mutagenesis. Wild-type L. lactis strain KF147 but not an xylA deletion mutant was able to grow using xylose as the sole carbon source. However, both strains grew to similarly high levels in ATL, indicating redundancy in L. lactis carbohydrate metabolism on plant tissues. These findings show that certain strains of L. lactis are well adapted for growth on plants and possess specific traits relevant for plant-based food, fuel, and feed fermentations.
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190
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Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis subsp. lactis TOMSC161, Isolated from a Nonscalded Curd Pressed Cheese. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01121-14. [PMID: 25377704 PMCID: PMC4223455 DOI: 10.1128/genomea.01121-14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Lactococcus lactis is a lactic acid bacterium used in the production of many fermented foods, such as dairy products. Here, we report the genome sequence of L. lactis subsp. lactis TOMSC161, isolated from nonscalded curd pressed cheese. This genome sequence provides information in relation to dairy environment adaptation.
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191
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Zuljan FA, Repizo GD, Alarcon SH, Magni C. α-Acetolactate synthase of Lactococcus lactis contributes to pH homeostasis in acid stress conditions. Int J Food Microbiol 2014; 188:99-107. [DOI: 10.1016/j.ijfoodmicro.2014.07.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 06/03/2014] [Accepted: 07/16/2014] [Indexed: 10/25/2022]
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192
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Gagic D, Maclean PH, Li D, Attwood GT, Moon CD. Improving the genetic representation of rare taxa within complex microbial communities using
DNA
normalization methods. Mol Ecol Resour 2014; 15:464-76. [DOI: 10.1111/1755-0998.12321] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 07/28/2014] [Accepted: 08/13/2014] [Indexed: 01/29/2023]
Affiliation(s)
- Dragana Gagic
- AgResearch Ltd Grasslands Research Centre Palmerston North New Zealand
| | | | - Dong Li
- AgResearch Ltd Grasslands Research Centre Palmerston North New Zealand
| | - Graeme T. Attwood
- AgResearch Ltd Grasslands Research Centre Palmerston North New Zealand
| | - Christina D. Moon
- AgResearch Ltd Grasslands Research Centre Palmerston North New Zealand
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193
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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.
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194
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Matoba Y, Miyasako M, Matsuo K, Oda K, Noda M, Higashikawa F, Kumagai T, Sugiyama M. An alternative allosteric regulation mechanism of an acidophilic l-lactate dehydrogenase from Enterococcus mundtii 15-1A. FEBS Open Bio 2014; 4:834-47. [PMID: 25379380 PMCID: PMC4219987 DOI: 10.1016/j.fob.2014.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 08/28/2014] [Accepted: 08/28/2014] [Indexed: 10/28/2022] Open
Abstract
A plant-derived Enterococcus mundtii 15-1A, that has been previously isolated from Brassica rapa L. subsp. nipposinica (L.H. Bailey) Hanelt var. linearifolia by our group, possesses two kinds of l-lactate dehydrogenase (l-LDH): LDH-1 and LDH-2. LDH-1 was activated under low concentration of fluctose-1,6-bisphosphate (FBP) at both pH 5.5 and 7.5. Although LDH-2 was also activated under the low concentration of FBP at pH 5.5, a high concentration of FBP is necessary to activate it at pH 7.5. The present study shows the crystal structures of the acidophilic LDH-2 in a complex with and without FBP and NADH. Although the tertiary structure of the ligands-bound LDH-2 is similar to that of the active form of other bacterial l-LDHs, the structure without the ligands is different from that of any other previously determined l-LDHs. Major structural alterations between the two structures of LDH-2 were observed at two regions in one subunit. At the N-terminal parts of the two regions, the ligands-bound form takes an α-helical structure, while the form without ligands displays more disordered and extended structures. A vacuum-ultraviolet circular dichroism analysis showed that the α-helix content of LDH-2 in solution is approximately 30% at pH 7.5, which is close to that in the crystal structure of the form without ligands. A D241N mutant of LDH-2, which was created by us to easily form an α-helix at one of the two parts, exhibited catalytic activity even in the absence of FBP at both pH 5.5 and 7.5.
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Key Words
- Allosteric regulation
- B., Bacillus
- Bf., Bifidobacterium
- CD, circular dichroism
- Circular dichroism
- Crystal structure
- E., Escherichia
- Ec., Enterococcus
- FBP, fluctose-1,6-bisphosphate
- LAB, lactic acid bacteria
- LDH, lactate dehydrogenase
- Lactic acid bacteria
- Lb., Lactobacillus
- Lc., Lactococcus
- VUV, vacuum-ultraviolet
- l-Lactate dehydrogenase
- rms, root mean square
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Affiliation(s)
- Yasuyuki Matoba
- Department of Molecular Microbiology and Biotechnology, Graduate School of Biomedical & Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8551, Japan
| | - Masashi Miyasako
- Department of Molecular Microbiology and Biotechnology, Graduate School of Biomedical & Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8551, Japan
| | - Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Kagamiyama 2-313, Higashi-Hiroshima 739-0046, Japan
| | - Kosuke Oda
- Department of Molecular Microbiology and Biotechnology, Graduate School of Biomedical & Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8551, Japan
| | - Masafumi Noda
- Department of Molecular Microbiology and Biotechnology, Graduate School of Biomedical & Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8551, Japan
| | - Fumiko Higashikawa
- Department of Molecular Microbiology and Biotechnology, Graduate School of Biomedical & Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8551, Japan
| | - Takanori Kumagai
- Department of Molecular Microbiology and Biotechnology, Graduate School of Biomedical & Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8551, Japan
| | - Masanori Sugiyama
- Department of Molecular Microbiology and Biotechnology, Graduate School of Biomedical & Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8551, Japan
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195
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Abstract
Genome analysis using next generation sequencing technologies has revolutionized the characterization of lactic acid bacteria and complete genomes of all major groups are now available. Comparative genomics has provided new insights into the natural and laboratory evolution of lactic acid bacteria and their environmental interactions. Moreover, functional genomics approaches have been used to understand the response of lactic acid bacteria to their environment. The results have been instrumental in understanding the adaptation of lactic acid bacteria in artisanal and industrial food fermentations as well as their interactions with the human host. Collectively, this has led to a detailed analysis of genes involved in colonization, persistence, interaction and signaling towards to the human host and its health. Finally, massive parallel genome re-sequencing has provided new opportunities in applied genomics, specifically in the characterization of novel non-GMO strains that have potential to be used in the food industry. Here, we provide an overview of the state of the art of these functional genomics approaches and their impact in understanding, applying and designing lactic acid bacteria for food and health.
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196
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Desalermos A, Tan X, Rajamuthiah R, Arvanitis M, Wang Y, Li D, Kourkoumpetis TK, Fuchs BB, Mylonakis E. A multi-host approach for the systematic analysis of virulence factors in Cryptococcus neoformans. J Infect Dis 2014; 211:298-305. [PMID: 25114160 DOI: 10.1093/infdis/jiu441] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A multi-host approach was followed to screen a library of 1201 signature-tagged deletion strains of Cryptococcus neoformans mutants to identify previously unknown virulence factors. The primary screen was performed using a Caenorhabditis elegans-C. neoformans infection assay. The hits among these strains were reconfirmed as less virulent than the wild type in the insect Galleria mellonella-C. neoformans infection assay. After this 2-stage screen, and to prioritize hits, we performed serial evaluations of the selected strains, using the C. elegans model. All hit strains identified through these studies were validated in a murine model of systemic cryptococcosis. Twelve strains were identified through a stepwise screening assay. Among them, 4 (CSN1201, SRE1, RDI1, and YLR243W) were previously discovered, providing proof of principle for this approach, while the role of the remaining 8 genes (CKS101, CNC5600, YOL003C, CND1850, MLH3, HAP502, MSL5, and CNA2580) were not previously described in cryptococcal virulence. The multi-host approach is an efficient method of studying the pathogenesis of C. neoformans. We used diverse model hosts, C. elegans, G. mellonella, and mice, with physiological differences and identified 12 genes associated with mammalian infection. Our approach may be suitable for large pathogenesis screens.
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Affiliation(s)
- Athanasios Desalermos
- Division of Infectious diseases, Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Xiaojiang Tan
- Division of Infectious diseases, Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Rajmohan Rajamuthiah
- Division of Infectious diseases, Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Marios Arvanitis
- Division of Infectious diseases, Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Yan Wang
- Division of Infectious diseases, Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Dedong Li
- Division of Infectious diseases, Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | | | - Beth Burgwyn Fuchs
- Division of Infectious diseases, Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Eleftherios Mylonakis
- Division of Infectious diseases, Warren Alpert Medical School of Brown University, Providence, Rhode Island
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197
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Nakashima N, Akita H, Hoshino T. Establishment of a novel gene expression method, BICES (biomass-inducible chromosome-based expression system), and its application to the production of 2,3-butanediol and acetoin. Metab Eng 2014; 25:204-14. [PMID: 25108217 DOI: 10.1016/j.ymben.2014.07.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 06/23/2014] [Accepted: 07/29/2014] [Indexed: 11/17/2022]
Abstract
In this study, we describe a novel method for producing valuable chemicals from glucose and xylose in Escherichia coli. The notable features in our method are avoidance of plasmids and expensive inducers for foreign gene expression to reduce production costs; foreign genes are knocked into the chromosome, and their expression is induced with xylose that is present in most biomass feedstock. As loci for the gene knock-in, lacZYA and some pseudogenes are chosen to minimize unexpected effects of the knock-in on cell physiology. The promoter of xylF is inducible with xylose and is combined with the T7 RNA polymerase-T7 promoter system to ensure strong gene expression. This expression system was named BICES (biomass-inducible chromosome-based expression system). As examples of BICES application, 2,3-butanediol and acetoin were successfully produced from glucose and xylose, and the maximal concentrations reached 54gL(-1) [99.6% in (R,S)-form] and 31gL(-1), respectively. 2,3-Butanediol and acetoin are industrially important chemicals that are, at present, produced primarily through petrochemical processes. To demonstrate usability of BICES in practical situations, we produced these chemicals from a saccharified cedar solution. From these results, we can conclude that BICES is suitable for practical production of valuable chemicals from biomass.
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Affiliation(s)
- Nobutaka Nakashima
- Bioproduction Research Institute, National Institute of Advanced Industrial Sciences and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan; Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1-M6-5 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
| | - Hironaga Akita
- Biomass Refinery Research Center, National Institute of Advanced Industrial Sciences and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Tamotsu Hoshino
- Bioproduction Research Institute, National Institute of Advanced Industrial Sciences and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan; Biomass Refinery Research Center, National Institute of Advanced Industrial Sciences and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan
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198
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Growth phase-dependent proteomes of the Malaysian isolated Lactococcus lactis dairy strain M4 using label-free qualitative shotgun proteomics analysis. ScientificWorldJournal 2014; 2014:642891. [PMID: 24982972 PMCID: PMC3984853 DOI: 10.1155/2014/642891] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Accepted: 02/10/2014] [Indexed: 11/17/2022] Open
Abstract
Lactococcus lactis is the most studied mesophilic fermentative lactic acid bacterium. It is used extensively in the food industry and plays a pivotal role as a cell factory and also as vaccine delivery platforms. The proteome of the Malaysian isolated L. lactis M4 dairy strain, obtained from the milk of locally bred cows, was studied to elucidate the physiological changes occurring between the growth phases of this bacterium. In this study, ultraperformance liquid chromatography nanoflow electrospray ionization tandem mass spectrometry (UPLC- nano-ESI-MSE) approach was used for qualitative proteomic analysis. A total of 100 and 121 proteins were identified from the midexponential and early stationary growth phases, respectively, of the L. lactis strain M4. During the exponential phase, the most important reaction was the generation of sufficient energy, whereas, in the early stationary phase, the metabolic energy pathways decreased and the biosynthesis of proteins became more important. Thus, the metabolism of the cells shifted from energy production in the exponential phase to the synthesis of macromolecules in the stationary phase. The resultant proteomes are essential in providing an improved view of the cellular machinery of L. lactis during the transition of growth phases and hence provide insight into various biotechnological applications.
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199
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Genomic Features ofLactococcus lactisIO-1, a Lactic Acid Bacterium That Utilizes Xylose and Produces High Levels ofL-Lactic Acid. Biosci Biotechnol Biochem 2014; 77:1804-8. [DOI: 10.1271/bbb.130080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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200
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Al-Saleh AA, Ismail EA, Metwalli AA. Autolysis detection and evaluation of some lactic acid bacteria by renaturing sodium dodecyl sulphate-polyacrylamide gel electrophoresis and polymerase chain reaction assays. INT J DAIRY TECHNOL 2014. [DOI: 10.1111/1471-0307.12113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Abdulrahman A Al-Saleh
- Department of Food Science and Nutrition; King Saud University; P. O. Box 2460 Riyadh 1145 Saudi Arabia
| | - Elsayed A Ismail
- Department of Food Science and Nutrition; King Saud University; P. O. Box 2460 Riyadh 1145 Saudi Arabia
- Faculty of Agriculture; Food Science Department; Benha University; Benha 13518 Egypt
| | - Ali Am Metwalli
- Department of Food Science and Nutrition; King Saud University; P. O. Box 2460 Riyadh 1145 Saudi Arabia
- Dairy Science Department; College of Agriculture; Menia University; Menia 61519 Egypt
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