Systematic identification of Lactobacillus plantarum auxotrophs for fermented Nham using genome-scale metabolic model

Journal of Biotechnology

Volumn 162, Issue 2-3, 2012, Pages 327-335

  Chiewchankaset, Porntip ^a   Srimarut, Yanee ^b   Klanchui, Amornpan ^a   Kurdi, Peter ^b   Plengvidhya, Vethachai ^b   Meechai, Asawin ^a  

^a KING MONGKUT'S UNIVERSITY OF TECHNOLOGY THONBURI   (Thailand)

^b NATIONAL SCIENCE AND TECHNOLOGY DEVELOPMENT AGENCY   (Thailand)

Author keywords

Auxotroph; Essential gene; Genome scale metabolic model; Lactobacillus plantarum; Phenotypic characteristics

Indexed keywords

BACILLI; BIOMOLECULES; FLAVOR COMPOUNDS; METABOLISM; METABOLITES;

AUXOTROPH; ESSENTIAL GENE; GENOME SCALE METABOLIC MODEL; LACTOBACILLUS PLANTARUM; PHENOTYPIC CHARACTERISTICS;

GENES;

CARBOXYLIC ACID; NUTRITION SUPPLEMENT;

ARTICLE; AUXOTROPHIC MUTANT; AUXOTROPHY; BACTERIAL CELL; BATCH FERMENTATION; BIOMASS; CELL GROWTH; CONCENTRATION AT STEADY-STATE; ESSENTIAL GENE; FERMENTED PRODUCT; FLAVOR; FOOD INDUSTRY; GENE DELETION; LACTOBACILLUS PLANTARUM; MAXIMUM FLUX; METABOLIC ENGINEERING; NHAM; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; BACTERIAL GENOME; BIOENGINEERING; BIOLOGICAL MODEL; COMPUTER SIMULATION; FERMENTATION; GENETICS; MEAT; METABOLISM; METHODOLOGY; MICROBIOLOGY; PHYSIOLOGY; SYSTEMS BIOLOGY;

BIOENGINEERING; COMPUTER SIMULATION; FERMENTATION; GENE DELETION; GENOME, BACTERIAL; LACTOBACILLUS PLANTARUM; MEAT PRODUCTS; MODELS, BIOLOGICAL; PHENOTYPE; SYSTEMS BIOLOGY;

EID: 84868486541     PISSN: 01681656     EISSN: 18734863     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2012.08.019     Document Type: Article

References (33)

1. Becker, S.A., Feist, A.M., Mo, M.L., Hannum, G., Palsson, B.O., Herrgard, M.J., Quantitative prediction of cellular metabolism with constraint-based models: the Cobra Toolbox. Nature Protocols 2 (2007), 727–738.
2. Chang, S.-T., Miles, P.G., Mushrooms: Cultivation, Nutritional Value, Medicinal Effect, and Environmental Impact. second ed., 2004, CRC Press, Boca Raton, FL pp. 121–122.
3. Durot, M., Bourguignon, P.-Y., Schachter, V., Genome-scale models of bacterial metabolism: reconstruction and applications. FEMS Microbiology Review 33:1 (2009), 164–190.
4. Edwards, J.S., Palsson, B.O., Systems properties of the Haemophilus influenzae Rd metabolic genotype. Journal of Biological Chemistry 274:25 (1999), 17410–17416.
5. Edwards, J.S., Palsson, B.O., The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proceedings of the National Academy of Sciences of the United States of America 97:10 (2000), 5528–5533.
6. Feist, A.M., Henry, C.S., Reed, J.L., Krummenacker, M., Joyce, A.R., Karp, P.D., Broadbelt, L.J., Hatzimanikatis, V., Palsson, B.O., A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Molecular Systems Biology 3:121 (2007), 1–18.
7. Feist, A.M., Palsson, B.O., The growing scope of applications of genome-scale metabolic reconstructions: the case of E. coli. Nature Biotechnology 26:6 (2008), 659–667.
8. Genomes OnLine Database, Genomes OnLine Database (GOLD), http://www.genomeonline.org (accessed 30.04.12).
9. Joyce, A.R., Palsson, B.O., Predicting gene essentiality using genome-scale in silico models. Methods in Molecular Biology 416 (2008), 433–457.
10. Khumphati, S., Kiatpathomchai, K., Praphailong, W., Smitinont, T., Organic acids and volatile compounds of Nham. Proceedings of the 4th Asia Pacific Food Analysis Conference. November 16–19 1998, Chiang Mai, Thailand, 1998.
11. Kim, H.U., Kim, T.Y., Lee, S.Y., Metabolic flux analysis and metabolic engineering of microorganisms. Molecular Biosystems 4:2 (2008), 113–120.
12. Kurdi, P., Smitinont, T., Valyasevi, R., Isolation and characterization of acid-sensitive mutants of Pediococcus acidilactici. Food Microbiology 26:1 (2009), 82–87.
13. Lee, J., Yun, H., Feist, A.M., Palsson, B.O., Lee, S.Y., Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network. Applied Microbiology and Biotechnology 80:5 (2008), 849–862.
14. Liu, L., Agren, R., Bordel, S., Nielsen, J., Use of genome-scale metabolic models for understanding microbial physiology. FEBS Letters 584:12 (2010), 2556–2564.
15. Luxananil, P., Promchai, R., Wanasen, S., Kamdee, S., Thepkasikul, P., Plengvidhya, V., Visessanguan, W., Valyasevi, R., Monitoring Lactobacillus plantarum BCC 9546 starter culture during fermentation of Nham, a traditional Thai pork sausage. International Journal of Food Microbiology 129 (2009), 312–315.
16. Madigan, M.T., Martinko, J.M., Parker, J., Biology of Microorganisms. 1997, Prentice Hall, Upper Saddle River, NJ p. 156.
17. Mahadevan, R., Schilling, C.H., The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metabolic Engineering 5 (2003), 264–276.
18. Nogales, J., Palsson, B.O., Thiele, I., A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Systems Biology 2:79 (2008), 1–20.
19. Notebaart, R.A., van Enckevort, F.H., Francke, C., Siezen, R.J., Teusink, B., Accelerating the reconstruction of genome-scale metabolic networks. BMC Bioinformatics 7:296 (2006), 1–10.
20. Oh, Y.-K., Palsson, B.O., Park, S.M., Schilling, C.H., Mahadevan, R., Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data. Journal of Biological Chemistry 282 (2007), 28791–28799.
21. Oliveira, A.P., Nielsen, J., Förster, J., Modeling Lactococcus lactis using a genome-scale flux model. BMC Microbiology 5:39 (2005), 1–15.
22. Palumbo, E., Favier, C.F., Deghorain, M., Cocconcelli, P.S., Grangette, C., Mercenier, A., Vaughan, E.E., Hols, P., Knockout of the alanine racemase gene in Lactobacillus plantarum results in septation defects and cell wall perforation. FEMS Microbiology Letters 233 (2004), 131–138.
23. Reed, J.L., Vo, T.D., Schilling, C.H., Palsson, B.O., An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biology, 4(9), 2003, R54.
24. Rocha, I., Förster, J., Nielsen, J., Design and application of genome-scale reconstructed metabolic models. Methods in Molecular Biology 416 (2008), 409–431.
25. Smitinont, T., Praphailong, W., Khumphati, S., Chaiseri, S., Rojsajakul, P., Kiatpathomchai, K., Profiles of flavor compounds in traditional Thai fermented pork sausage. Proceedings of the 7th ASEAN Food Conference, November 19–22. Philippines, 2000.
26. Srimarut, Y., 2004. Mathematical model for predicting fermentation rates of Nham using Lactobacillus sakei. M. Thesis. Bangkok: King Mongkut's University of Technology Thonburi.
27. Tanasupawat, S., Komagata, K., Lactic acid bacteria in fermented foods in Thailand. World Journal of Microbiology and Biotechnology 11 (1995), 253–256.
28. Teusink, B., van Enckevort, F.H., Francke, C., Wiersma, A., Wegkamp, A., Smid, E.J., Siezen, R.J., In silico reconstruction of the metabolic pathways of Lactobacillus plantarum: comparing predictions of nutrient requirements with those from growth experiments. Applied and Environment Microbiology 71:11 (2005), 7253–7262.
29. Teusink, B., Wiersma, A., Jacobs, L., Notebaart, R.A., Smid, E.J., Understanding the adaptive growth strategy of Lactobacillus plantarum by in silico optimisation. PLoS Computational Biology, 5(6), 2009, e1000410.
30. Teusink, B., Wiersma, A., Molenaar, D., Francke, C., de Vos, W.M., Siezen, R.J., Smid, E.J., Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model. Journal of Biological Chemistry 281 (2006), 40041–40048.
31. Valyasevi, R., Rolle, R.S., An overview of small-scale food fermentation technologies in developing countries with special reference to Thailand: scope for their improvement. International Journal of Food Microbiology 75 (2002), 231–239.
32. Visessanguan, W., Benjakul, S., Riebroy, S., Thepkasikul, P., Changes in composition and functional properties of proteins and their contributions to Nham characteristics. Meat Science 66 (2004), 579–588.
33. Visessanguan, W., Yachai, M., Thepkasikul, P., Kittikun, C., Smitinont, T., Tarnchompoo, B., Valyasevi, R., Influence of starter type on changes in free amino acid content during Nham fermentation. Proceedings of the 9th Asean Food Conference, August 8–10. Indonesia, 2005.