Comparative functional genomics of amino acid metabolism of lactic acid bacteria
The amino acid metabolism of lactic acid bacteria used as starters in industrial fermentations has profound effects on the quality of the fermented foods. The work described in this PhD thesis was initiated to use genomics technologies and a comparative approach to link the gene content of some well-known lactic acid bacteria to flavor formation and to increase our general knowledge in the area of amino acid metabolism. The three well-known lactic acid bacteria that were used in these studies were Streptococcus thermophilus, Lactococcus lactis and Lactobacillus plantarum. The complete genomes of all these model bacteria have been sequenced and annotated in detail. Comparative experimental and in silico studies of Streptococcus thermophilus with the other two lactic acid bacteria, revealed the low degree of amino acid auxotrophies of this species; it only needs two amino acids for (minimal) growth and this strain is able to produce a varied amount of flavors. Lactococcus lactis and Lactobacillus plantarum require more amino acids and produce fewer flavors than S. thermophilus. Furthermore, S. thermophilus has a simple primary metabolism; homolactic growth is the only possible route under anaerobic conditions and, remarkably, it does not have a complete pentose phosphate pathway in contrast to the other two studied bacteria. This latter property has important consequences for the redox metabolism of S. thermophilus and particularly its ability to produce NADPH. A genome-scale metabolic model was developed and predicted that amino acid metabolism, and especially glutamate degradation, and citrate metabolism are the most obvious alternatives for NADPH generation. Several of these predictions were confirmed by constructing a glutamate dehydrogenase mutant of S. thermophilus. This mutant revealed theimportance of the citrate pathway (and other amino acid degradation pathways) in NADPH generation. A comparative and functional genomics study of the three lactic acid bacteria showed that amino acid depletion not only affects amino acid metabolism, but also flavor formation and overall growth. The comparative genomics approach presented in this thesis can be used to understand the amino acid metabolism of different lactic acid bacteria and their potential to produce flavors under different conditions. Finally, it can be applied for optimization of industrial fermentations
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| Format: | Doctoral thesis biblioteca |
| Language: | English |
| Subjects: | amino acid metabolism, comparative genomics, functional genomics, lactic acid bacteria, streptococcus thermophilus, aminozuurmetabolisme, functionele genomica, melkzuurbacteriën, vergelijkende genomica, |
| Online Access: | https://research.wur.nl/en/publications/comparative-functional-genomics-of-amino-acid-metabolism-of-lacti |
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| Summary: | The amino acid metabolism of lactic acid bacteria used as starters in industrial fermentations has profound effects on the quality of the fermented foods. The work described in this PhD thesis was initiated to use genomics technologies and a comparative approach to link the gene content of some well-known lactic acid bacteria to flavor formation and to increase our general knowledge in the area of amino acid metabolism. The three well-known lactic acid bacteria that were used in these studies were Streptococcus thermophilus, Lactococcus lactis and Lactobacillus plantarum. The complete genomes of all these model bacteria have been sequenced and annotated in detail. Comparative experimental and in silico studies of Streptococcus thermophilus with the other two lactic acid bacteria, revealed the low degree of amino acid auxotrophies of this species; it only needs two amino acids for (minimal) growth and this strain is able to produce a varied amount of flavors. Lactococcus lactis and Lactobacillus plantarum require more amino acids and produce fewer flavors than S. thermophilus. Furthermore, S. thermophilus has a simple primary metabolism; homolactic growth is the only possible route under anaerobic conditions and, remarkably, it does not have a complete pentose phosphate pathway in contrast to the other two studied bacteria. This latter property has important consequences for the redox metabolism of S. thermophilus and particularly its ability to produce NADPH. A genome-scale metabolic model was developed and predicted that amino acid metabolism, and especially glutamate degradation, and citrate metabolism are the most obvious alternatives for NADPH generation. Several of these predictions were confirmed by constructing a glutamate dehydrogenase mutant of S. thermophilus. This mutant revealed theimportance of the citrate pathway (and other amino acid degradation pathways) in NADPH generation. A comparative and functional genomics study of the three lactic acid bacteria showed that amino acid depletion not only affects amino acid metabolism, but also flavor formation and overall growth. The comparative genomics approach presented in this thesis can be used to understand the amino acid metabolism of different lactic acid bacteria and their potential to produce flavors under different conditions. Finally, it can be applied for optimization of industrial fermentations |
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