Amino Acid Biosynthesis and Proteolysis in Lactobacillus Bulgaricus Revisited: A Genomic Comparison


The amino acid biosynthesis and proteolytic system of Lactobacillus bulgaricus (L.Bulgaricus ) is important for its growth in niche-specific environments, as well as for flavour formation in the food industry. Comparative analyses of 4 completed sequences of the L.Bulgaricus strain genome on a genomic scale revealed that genes involved in amino acids synthesis were undergoing reductive evolution. However, the selected industrial strains, namely, L.Bulgaricus 2038 and L.Bulgaricus ND02, retained more complete genes in the amino acid synthesis and proteolytic system category than the laboratory strains, and have some unique genes and pathways for obtaining amino acids that enable these bacteria to adapt to their various environmental niches.

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E. Liu, P. Hao, T. Konno, Y. Yu, M. Oda, H. Zheng and Z. Ji, "Amino Acid Biosynthesis and Proteolysis in Lactobacillus Bulgaricus Revisited: A Genomic Comparison," Computational Molecular Bioscience, Vol. 2 No. 3, 2012, pp. 61-77. doi: 10.4236/cmb.2012.23006.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] J. E. Christensen, E. G. Dudley, et al., “Peptidases and Amino Acid Catabolism in Lactic Acid Bacteria,” Antonie Van Leeuwenhoek, Vol. 76, No. 1-4, 1999, pp. 217-246. doi:10.1023/A:1002001919720
[2] P. Hao, H. Zheng, et al., “Complete Sequencing and Pan-Genomic Analysis of Lactobacillus delbrueckii subsp. bulgaricus Reveal Its Genetic Basis for Industrial Yogurt Production,” Plos One, Vol. 6, No. 1, 2011, p. e15964. doi:10.1371/journal.pone.0015964
[3] M. van de Guchte, S. Penaud, et al., “The Complete Genome Sequence of Lactobacillus bulgaricus Reveals Extensive and Ongoing Reductive Evolution,” Proceedings of the National Academy of Sciences of the United States of America, Vol. 103, No. 24, 2006, pp. 9274-9279. doi:10.1073/pnas.0603024103
[4] M. Liu, J. R. Bayjanov, et al., “The Proteolytic System of Lactic Acid Bacteria Revisited: A Genomic Comparison,” BMC Genomics, Vol. 11, No.1, 2010, p. 36. doi:10.1186/1471-2164-11-36
[5] M. Liu, A. Nauta, et al., “Comparative Genomics of Enzymes in Flavor-Forming Pathways from Amino Acids in Lactic Acid Bacteria,” Applied and Environmental Microbiology, Vol. 74, No. 15, 2008, pp. 4590-4600. doi:10.1128/AEM.00150-08
[6] M. Zhou, D. Theunissen, et al., “LAB-Secretome: A Genome-Scale Comparative Analysis of the Predicted Extracellular and Surface-Associated Proteins of Lactic Acid Bacteria,” BMC Genomics, Vol. 11, No. 1, 2010, p. 651. doi:10.1186/1471-2164-11-651
[7] J. Boekhorst, R. J. Siezen, et al., “The Complete Genomes of Lactobacillus plantarum and Lactobacillus johnsonii Reveal Extensive Differences in Chromosome Organization and Gene Content,” Microbiology, Vol. 150, No. 11, 2004, pp. 3601-3611. doi:10.1099/mic.0.27392-0
[8] H.-J. Zheng, E-N. Liu, et al., “In Silico Analysis of Amino Acid Biosynthesis and Proteolysis in Lactobacillus delbrueckii subsp. bulgaricus 2038 and the Implications for Bovine Milk Fermentation,” Biotechnology Letters, Vol. 34, No. 8, 2012, pp. 1545-1551. doi:10.1007/s10529-012-1006-4
[9] A. E. Darling, B. Mau, et al., “ProgressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement,” PLOS One, Vol. 5, No. 6, 2010, p. e11147. doi:10.1371/journal.pone.0011147
[10] N.D. Rawlings, A.J. Barrett, et al., “MEROPS: The Database of Proteolytic Enzymes, Their Substrates and Inhibitors,” Nucleic Acids Research, Vol. 40, D. 1, 2012, pp. D343-D350. doi:10.1093/nar/gkr987
[11] M. Kanehisa, S. Goto, et al., “The KEGG Resource for Deciphering the Genome,” Nucleic Acids Research, Vol. 32, Suppl. 1, 2004, D277-D280. doi:10.1093/nar/gkh063
[12] J. D. Bendtsen, H. Nielsen, et al., “Improved Prediction of Signal Peptides: SignalP 3.0,” Journal of Molecular Biology, Vol. 340, No. 4, 2004, pp. 783-795. doi:10.1016/j.jmb.2004.05.028
[13] M. Arai, H. Mitsuke, et al., “ConPred II: A Consensus Prediction Method for Obtaining Transmembrane Topology Models with High Reliability,” Nucleic Acids Research, Vol. 32, Suppl. 2, 2004, pp. W390-W393. doi:10.1093/nar/gkh380
[14] J. L. Gardy, C. Spencer, et al., “PSORT-B: Improving Protein Subcellular Localization Prediction for Gram-Negative Bacteria,” Nucleic Acids Research, Vol. 31, No. 13, 2003, pp. 3613-3617. doi:10.1093/nar/gkg602
[15] A. Marchler-Bauer, S. Lu, J. B. Anderson, et al., “CDD: A Conserved Domain Database for the Functional Annotation of Proteins,” Nucleic Acids Research, Vol. 39, Suppl. 1, 2011, pp. D225-D229. doi:10.1093/nar/gkq1189
[16] I. Uchiyama, T. Higuchi, et al., “MBGD Update 2010: Toward a Comprehensive Resource for exploring Microbial Genome Diversity,” Nucleic Acids Research, Vol. 38, Suppl. 1, 2010, pp. D361-365. doi:10.1093/nar/gkp948
[17] G. Talavera and J. Castresana, “Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments,” Systematic Biology, Vol. 56, No. 4, 2007, pp. 564-577. doi:10.1080/10635150701472164
[18] S. Guindon, J. F. Dufayard, et al., “New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0,” Systematic Biology, Vol. 59, No. 3, 2010, pp. 307-321. doi:10.1093/sysbio/syq010
[19] J. E. Germond, M. Delley, et al., “Determination of the Domain of the Lactobacillus delbrueckii subsp. Bulgari- cus Cell Surface Proteinase PrtB Involved in Attachment to the Cell Wall after Heterologous Expression of the PrtB Gene in Lactococcus lactis,” Applied Environmental Microbiology, Vol. 69, No. 6, 2003, pp. 3377-3384. doi:10.1128/AEM.69.6.3377-3384.2003
[20] M. Jacobs, J. B. Andersen, et al., “Bacillus subtilis PrsA Is Required in vivo as an Extracytoplasmic Chaperone for Secretion of Active Enzymes Synthesized either with or without Pro-Sequences,” Molecular Microbiology, Vol. 8, No. 5, 1993, pp. 957-966. doi:10.1111/j.1365-2958.1993.tb01640.x
[21] N. Vermeulen, M. Pavlovic, et al., “Functional Charac- terization of the Proteolytic System of Lactobacillus san- franciscensis DSM 20451T during Growth in Sour- dough,” Applied Environmental Microbiology, Vol. 71, No. 10, 2005, pp. 6260-6266. doi:10.1128/AEM.71.10.6260-6266.2005
[22] S. Tynkkynen, G. Buist, et al., “Genetic and Biochemical Characterization of the Oligopeptide Transport System of Lactococcus lactis,” Journal of Bacteriology, Vol. 175, No. 23, 1993, pp. 7523-7532.
[23] M. Romero, S. Guzman-Leon, et al., “Pathways for Glu- tamate Biosynthesis in the Yeast Kluyveromyces lactis,” Microbiology, Vol. 146, No. 1, 2000, pp. 239-245.
[24] C. Gilbert, D. Atlan, et al., “A New Cell Surface Pro- teinase: Sequencing and Analysis of the PrtB Gene from Lactobacillus delbruekii subsp. bulgaricus,” Journal of Bacteriology, Vol. 178, No. 11, 1996, pp. 3059-3065.

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