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Schöpping M, Gaspar P, Neves AR, Franzén CJ, Zeidan AA. Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling. NPJ Syst Biol Appl 2021; 7:47. [PMID: 34887435 PMCID: PMC8660834 DOI: 10.1038/s41540-021-00207-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 11/03/2021] [Indexed: 12/14/2022] Open
Abstract
Although bifidobacteria are widely used as probiotics, their metabolism and physiology remain to be explored in depth. In this work, strain-specific genome-scale metabolic models were developed for two industrially and clinically relevant bifidobacteria, Bifidobacterium animalis subsp. lactis BB-12® and B. longum subsp. longum BB-46, and subjected to iterative cycles of manual curation and experimental validation. A constraint-based modeling framework was used to probe the metabolic landscape of the strains and identify their essential nutritional requirements. Both strains showed an absolute requirement for pantethine as a precursor for coenzyme A biosynthesis. Menaquinone-4 was found to be essential only for BB-46 growth, whereas nicotinic acid was only required by BB-12®. The model-generated insights were used to formulate a chemically defined medium that supports the growth of both strains to the same extent as a complex culture medium. Carbohydrate utilization profiles predicted by the models were experimentally validated. Furthermore, model predictions were quantitatively validated in the newly formulated medium in lab-scale batch fermentations. The models and the formulated medium represent valuable tools to further explore the metabolism and physiology of the two species, investigate the mechanisms underlying their health-promoting effects and guide the optimization of their industrial production processes.
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Affiliation(s)
- Marie Schöpping
- Systems Biology, Discovery, Chr. Hansen A/S, 2970, Hørsholm, Denmark
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Paula Gaspar
- Systems Biology, Discovery, Chr. Hansen A/S, 2970, Hørsholm, Denmark
| | - Ana Rute Neves
- Systems Biology, Discovery, Chr. Hansen A/S, 2970, Hørsholm, Denmark
- Arla Foods Ingredients Group P/S, 6920, Videbæk, Denmark
| | - Carl Johan Franzén
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Ahmad A Zeidan
- Systems Biology, Discovery, Chr. Hansen A/S, 2970, Hørsholm, Denmark.
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Ma W, Jia J, Huang X, Xie W, Zhang X, Tang J, Lin C, Zhao L, Fang P. Stable isotope labelling by amino acids in cell culture (SILAC) applied to quantitative proteomics of Edwardsiella tarda ATCC 15947 under prolonged cold stress. Microb Pathog 2018; 125:12-19. [PMID: 30201590 DOI: 10.1016/j.micpath.2018.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 09/01/2018] [Accepted: 09/05/2018] [Indexed: 01/15/2023]
Abstract
Edwardsiella tarda poses a threat to human health and has resulted in enormous economic losses in aquaculture. Low temperatures are usually applied to contain the growth of this microorganism. In this study, stable isotope labelling by amino acids in cell culture (SILAC) was used to conduct comparative proteomic quantitation of E. tarda ATCC 15947 under cold stress for two weeks. We identified 1391 proteins, of which 898 were quantifiable. Of these, 72 proteins were upregulated and 164 were downregulated in response to cold stress. Even though E. tarda ATCC 15947 is not a psychrophile, several key proteins related to DNA synthesis and transcription were significantly upregulated. Additionally, proteins related to haemolytic activities and gluconeogenesis were upregulated, even though E. tarda ATCC 15497 is considered non-virulent in aquaculture. This study therefore delineated the specific proteomic response of this E. tarda ATCC 15947 to prolonged cold stress.
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Affiliation(s)
- Weixing Ma
- Shandong Entry-Exit Inspection and Quarantine Bureau, No. 70, Qutangxia Road, Qingdao, 266002, China; Qingdao University of Science and Technology, No. 53, Zhengzhou Road, Qingdao, 266042, China
| | - Juntao Jia
- Shandong Entry-Exit Inspection and Quarantine Bureau, No. 70, Qutangxia Road, Qingdao, 266002, China.
| | - Xiaohua Huang
- Shandong Entry-Exit Inspection and Quarantine Bureau, No. 70, Qutangxia Road, Qingdao, 266002, China
| | - Wancui Xie
- Qingdao University of Science and Technology, No. 53, Zhengzhou Road, Qingdao, 266042, China
| | - Xiaoliang Zhang
- Shandong Entry-Exit Inspection and Quarantine Bureau, No. 70, Qutangxia Road, Qingdao, 266002, China
| | - Jing Tang
- Shandong Entry-Exit Inspection and Quarantine Bureau, No. 70, Qutangxia Road, Qingdao, 266002, China
| | - Chao Lin
- Shandong Entry-Exit Inspection and Quarantine Bureau, No. 70, Qutangxia Road, Qingdao, 266002, China
| | - Liqing Zhao
- Shandong Entry-Exit Inspection and Quarantine Bureau, No. 70, Qutangxia Road, Qingdao, 266002, China
| | - Peipei Fang
- Shandong Entry-Exit Inspection and Quarantine Bureau, No. 70, Qutangxia Road, Qingdao, 266002, China
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Fredens J, Engholm-Keller K, Møller-Jensen J, Larsen MR, Færgeman NJ. Identification of novel protein functions and signaling mechanisms by genetics and quantitative phosphoproteomics in Caenorhabditis elegans. Methods Mol Biol 2014; 1188:107-124. [PMID: 25059608 DOI: 10.1007/978-1-4939-1142-4_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Stable isotope labeling by amino acids combined with mass spectrometry is a widely used methodology for measuring relative changes in protein and phosphorylation levels at a global level. We have applied this method to the model organism Caenorhabditis elegans in combination with RNAi-mediated gene knockdown by feeding the nematode on pre-labeled lysine auxotroph Escherichia coli. In this chapter, we describe in details the generation of the E. coli strain, incorporation of heavy isotope-labeled lysine in C. elegans, and the procedure for a comprehensive global phosphoproteomic experiment.
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Affiliation(s)
- Julius Fredens
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
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Ruiz L, Gueimonde M, Couté Y, Salminen S, Sanchez JC, de los Reyes-Gavilán CG, Margolles A. Evaluation of the ability of Bifidobacterium longum to metabolize human intestinal mucus. FEMS Microbiol Lett 2010; 314:125-30. [DOI: 10.1111/j.1574-6968.2010.02159.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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Couté Y, Brunner Y, Schvartz D, Hernandez CÃ, Masselot A, Lisacek F, Wollheim CB, Sanchez JC. Early activation of the fatty acid metabolism pathway by chronic high glucose exposure in rat insulin secretory β-cells. Proteomics 2010; 10:59-71. [DOI: 10.1002/pmic.200900080] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Gagnaire V, Jardin J, Jan G, Lortal S. Invited review: Proteomics of milk and bacteria used in fermented dairy products: From qualitative to quantitative advances. J Dairy Sci 2009; 92:811-25. [DOI: 10.3168/jds.2008-1476] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Ruiz L, Couté Y, Sánchez B, de los Reyes-Gavilán CG, Sanchez JC, Margolles A. The cell-envelope proteome of Bifidobacterium longum in an in vitro bile environment. Microbiology (Reading) 2009; 155:957-967. [DOI: 10.1099/mic.0.024273-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Host–bacteria interactions are often mediated via surface-associated proteins. The identification of these proteins is an important goal of bacterial proteomics. To address how bile can influence the cell-envelope proteome of Bifidobacterium longum biotype longum NCIMB 8809, we analysed its membrane protein fraction using stable isotope labelling of amino acids in cell culture (SILAC). We were able to identify 141 proteins in the membrane fraction, including a large percentage of the theoretical transporters of this species. Moreover, the envelope-associated soluble fraction was analysed using different subfractionation techniques and differential in-gel fluorescence electrophoresis (DIGE). This approach identified 128 different proteins. Some of them were well-known cell wall proteins, but others were highly conserved cytoplasmic proteins probably displaying a ‘moonlighting’ function. We were able to identify 11 proteins in the membrane fraction and 6 proteins in the envelope-associated soluble fraction whose concentration varied in the presence of bile. Bile promoted changes in the levels of proteins with important biological functions, such as some ribosomal proteins and enolase. Also, oligopeptide-binding proteins were accumulated on the cell surface, which was reflected in a different tripeptide transport rate in the cells grown with bile. The data reported here will provide the first cell-envelope proteome map for B. longum, and may contribute to understanding the bile tolerance of these bacteria.
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Affiliation(s)
- Lorena Ruiz
- Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (CSIC), Ctra Infiesto s/n, 33300, Villaviciosa, Asturias, Spain
| | - Yohann Couté
- Biomedical Proteomics Research Group, Department of Structural Biology and Bioinformatics, University of Geneva, 1 Rue Michel Servet, 1211 Geneva 14, Switzerland
| | - Borja Sánchez
- UMR 5248 CBMN, CNRS-Université Bordeaux 1-ENITAB, Laboratoire de Microbiologie et Biochimie Appliquée, 1 cours du Général de Gaulle, 33175 Gradignan CEDEX, France
| | - Clara G. de los Reyes-Gavilán
- Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (CSIC), Ctra Infiesto s/n, 33300, Villaviciosa, Asturias, Spain
| | - Jean-Charles Sanchez
- Biomedical Proteomics Research Group, Department of Structural Biology and Bioinformatics, University of Geneva, 1 Rue Michel Servet, 1211 Geneva 14, Switzerland
| | - Abelardo Margolles
- Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (CSIC), Ctra Infiesto s/n, 33300, Villaviciosa, Asturias, Spain
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