Christensen JE, Dudley EG, Pederson JA, Steele JL: Peptidases and amino acid catabolism in lactic acid bacteria. Antonie Van Leeuwenhoek. 1999, 76: 217-246. 10.1023/A:1002001919720.
Article
CAS
PubMed
Google Scholar
Kim YK, Yaguchi M, Rose D: Isolation and Amino Acid Composition of Para-Kappa-Casein. J Dairy Sci. 1969, 52: 316-320.
Article
CAS
Google Scholar
Stewart AF, Bonsing J, Beattie CW, Shah F, Willis IM, Mackinlay AG: Complete nucleotide sequences of bovine alpha S2- and beta-casein cDNAs: comparisons with related sequences in other species. Mol Biol Evol. 1987, 4: 231-241.
CAS
PubMed
Google Scholar
Liu M, Nauta A, Francke C, Siezen RJ: Comparative genomics of enzymes in flavor-forming pathways from amino acids in lactic acid bacteria. Appl Environ Microbiol. 2008, 74: 4590-4600. 10.1128/AEM.00150-08.
Article
CAS
PubMed Central
PubMed
Google Scholar
Kunji ER, Mierau I, Hagting A, Poolman B, Konings WN: The proteolytic systems of lactic acid bacteria. Antonie Van Leeuwenhoek. 1996, 70: 187-221. 10.1007/BF00395933.
Article
CAS
PubMed
Google Scholar
Savijoki K, Ingmer H, Varmanen P: Proteolytic systems of lactic acid bacteria. Appl Microbiol Biotechnol. 2006, 71: 394-406. 10.1007/s00253-006-0427-1.
Article
CAS
PubMed
Google Scholar
Sousa MJ, Ardö Y, McSweeney PLH: Advances in the study of proteolysis during cheese ripening. International Dairy Journal. 2001, 11: 327-345. 10.1016/S0958-6946(01)00062-0.
Article
CAS
Google Scholar
Doeven MK, Kok J, Poolman B: Specificity and selectivity determinants of peptide transport in Lactococcus lactis and other microorganisms. Mol Microbiol. 2005, 57: 640-649. 10.1111/j.1365-2958.2005.04698.x.
Article
CAS
PubMed
Google Scholar
Liu M, Siezen R: Comparative genomics of flavour-forming pathways in lactic acid bacteria. Australian Journal of Dairy Technology. 2006, 61: 61-68.
CAS
Google Scholar
Makarova K, Slesarev A, Wolf Y, Sorokin A, Mirkin B, Koonin E, Pavlov A, Pavlova N, Karamychev V, Polouchine N: Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci USA. 2006, 103: 15611-15616. 10.1073/pnas.0607117103.
Article
PubMed Central
PubMed
Google Scholar
Wegmann U, O'Connell-Motherway M, Zomer A, Buist G, Shearman C, Canchaya C, Ventura M, Goesmann A, Gasson MJ, Kuipers OP: Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363. J Bacteriol. 2007, 189: 3256-3270. 10.1128/JB.01768-06.
Article
CAS
PubMed Central
PubMed
Google Scholar
Callanan M, Kaleta P, O'Callaghan J, O'Sullivan O, Jordan K, McAuliffe O, Sangrador-Vegas A, Slattery L, Fitzgerald GF, Beresford T: Genome sequence of Lactobacillus helveticus, an organism distinguished by selective gene loss and insertion sequence element expansion. J Bacteriol. 2008, 190: 727-735. 10.1128/JB.01295-07.
Article
CAS
PubMed Central
PubMed
Google Scholar
Kankainen M, Paulin L, Tynkkynen S, von Ossowski I, Reunanen J, Partanen P, Satokari R, Vesterlund S, Hendrickx AP, Lebeer S: Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human-mucus binding protein. Proc Natl Acad Sci USA. 2009, 106: 17193-17198. 10.1073/pnas.0908876106.
Article
CAS
PubMed Central
PubMed
Google Scholar
Bayjanov JR, Wels M, Starrenburg M, van Hylckama Vlieg JE, Siezen RJ, Molenaar D: PanCGH: a genotype-calling algorithm for pangenome CGH data. Bioinformatics. 2009, 25: 309-314. 10.1093/bioinformatics/btn632.
Article
CAS
PubMed Central
PubMed
Google Scholar
Smit G, Smit BA, Engels WJM: Flavour formation by lactic acid bacteria and biochemical flavour profiling of cheese products. FEMS Microbiology Reviews. 2005, 29: 591-610. 10.1016/j.femsre.2005.04.002.
Article
CAS
PubMed
Google Scholar
Siezen RJ, Starrenburg MJ, Boekhorst J, Renckens B, Molenaar D, van Hylckama Vlieg JE: Genome-scale genotype-phenotype matching of two Lactococcus lactis isolates from plants identifies mechanisms of adaptation to the plant niche. Appl Environ Microbiol. 2008, 74: 424-436. 10.1128/AEM.01850-07.
Article
CAS
PubMed Central
PubMed
Google Scholar
UniProt Consortium: The universal protein resource (UniProt). Nucleic Acids Res. 2008, 36: D190-195. 10.1093/nar/gkn141.
Article
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410.
Article
CAS
PubMed
Google Scholar
Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer ELL: The Pfam protein families database. Nucleic Acids Res. 2004, 32: D138-D141. 10.1093/nar/gkh121.
Article
CAS
PubMed Central
PubMed
Google Scholar
Francke C, Kerkhoven R, Wels M, Siezen RJ: A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1. BMC Genomics. 2008, 9: 145-10.1186/1471-2164-9-145.
Article
PubMed Central
PubMed
Google Scholar
Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32: 1792-1797. 10.1093/nar/gkh340.
Article
CAS
PubMed Central
PubMed
Google Scholar
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R: Clustal W and Clustal X version 2.0. Bioinformatics. 2007, 23: 2947-2948. 10.1093/bioinformatics/btm404.
Article
CAS
PubMed
Google Scholar
Heijden van der RT, Snel B, van Noort V, Huynen MA: Orthology prediction at scalable resolution by phylogenetic tree analysis. BMC Bioinformatics. 2007, 8: 83-10.1186/1471-2105-8-83.
Article
PubMed Central
PubMed
Google Scholar
Overbeek R, Larsen N, Walunas T, D'Souza M, Pusch G, Selkov E, Liolios K, Joukov V, Kaznadzey D, Anderson I: The ERGO (TM) genome analysis and discovery system. Nucleic Acids Res. 2003, 31: 164-171. 10.1093/nar/gkg148.
Article
CAS
PubMed Central
PubMed
Google Scholar
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000, 28: 235-242. 10.1093/nar/28.1.235.
Article
CAS
PubMed Central
PubMed
Google Scholar
Folkertsma S, van Noort P, Van Durme J, Joosten HJ, Bettler E, Fleuren W, Oliveira L, Horn F, de Vlieg J, Vriend G: A family-based approach reveals the function of residues in the nuclear receptor ligand-binding domain. J Mol Biol. 2004, 341: 321-335. 10.1016/j.jmb.2004.05.075.
Article
CAS
PubMed
Google Scholar
Siezen RJ, Renckens B, van Swam I, Peters S, van Kranenburg R, Kleerebezem M, de Vos WM: Complete sequences of four plasmids of Lactococcus lactis subsp. cremoris SK11 reveal extensive adaptation to the dairy environment. Appl Environ Microbiol. 2005, 71: 8371-8382. 10.1128/AEM.71.12.8371-8382.2005.
Article
CAS
PubMed Central
PubMed
Google Scholar
Matos J, Nardi M, Kumura H, Monnet V: Genetic characterization of pepP, which encodes an aminopeptidase P whose deficiency does not affect Lactococcus lactis growth in milk, unlike deficiency of the X-prolyl dipeptidyl aminopeptidase. Appl Environ Microbiol. 1998, 64: 4591-4595.
CAS
PubMed Central
PubMed
Google Scholar
Rantanen T, Palva A: Lactobacilli carry cryptic genes encoding peptidase-related proteins: characterization of a prolidase gene (pepQ) and a related cryptic gene (orfZ) from Lactobacillus delbrueckii subsp. bulgaricus. Microbiology. 1997, 143 (Pt 12): 3899-3905. 10.1099/00221287-143-12-3899.
Article
CAS
PubMed
Google Scholar
Morel F, Frot-Coutaz J, Aubel D, Portalier R, Atlan D: Characterization of a prolidase from Lactobacillus delbrueckii subsp. bulgaricus CNRZ 397 with an unusual regulation of biosynthesis. Microbiology. 1999, 145 (Pt 2): 437-446. 10.1099/13500872-145-2-437.
Article
CAS
PubMed
Google Scholar
Vesanto E, Peltoniemi K, Purtsi T, Steele JL, Palva A: Molecular characterization, over-expression and purification of a novel dipeptidase from Lactobacillus helveticus. Appl Microbiol Biotechnol. 1996, 45: 638-645. 10.1007/s002530050741.
Article
CAS
PubMed
Google Scholar
Smeianov VV, Wechter P, Broadbent JR, Hughes JE, Rodriguez BT, Christensen TK, Ardo Y, Steele JL: Comparative high-density microarray analysis of gene expression during growth of Lactobacillus helveticus in milk versus rich culture medium. Appl Environ Microbiol. 2007, 73: 2661-2672. 10.1128/AEM.00005-07.
Article
CAS
PubMed Central
PubMed
Google Scholar
Klein JR, Dick A, Schick J, Matern HT, Henrich B, Plapp R: Molecular cloning and DNA sequence analysis of pepL, a leucyl aminopeptidase gene from Lactobacillus delbrueckii subsp. lactis DSM7290. Eur J Biochem. 1995, 228: 570-578. 10.1111/j.1432-1033.1995.0570m.x.
Article
CAS
PubMed
Google Scholar
Goettig P, Groll M, Kim JS, Huber R, Brandstetter H: Structures of the tricorn-interacting aminopeptidase F1 with different ligands explain its catalytic mechanism. EMBO J. 2002, 21: 5343-5352. 10.1093/emboj/cdf552.
Article
CAS
PubMed Central
PubMed
Google Scholar
Medrano FJ, Alonso J, Garcia JL, Romero A, Bode W, Gomis-Ruth FX: Structure of proline iminopeptidase from Xanthomonas campestris pv. citri: a prototype for the prolyl oligopeptidase family. EMBO J. 1998, 17: 1-9. 10.1093/emboj/17.1.1.
Article
CAS
PubMed Central
PubMed
Google Scholar
Inoue T, Ito K, Tozaka T, Hatakeyama S, Tanaka N, Nakamura KT, Yoshimoto T: Novel inhibitor for prolyl aminopeptidase from Serratia marcescens and studies on the mechanism of substrate recognition of the enzyme using the inhibitor. Arch Biochem Biophys. 2003, 416: 147-154. 10.1016/S0003-9861(03)00293-5.
Article
CAS
PubMed
Google Scholar
Kim MH, Kang BS, Kim S, Kim KJ, Lee CH, Oh BC, Park SC, Oh TK: The crystal structure of the estA protein, a virulence factor from Streptococcus pneumoniae. Proteins. 2008, 70: 578-583. 10.1002/prot.21680.
Article
CAS
PubMed
Google Scholar
Dudley EG, Steele JL: Nucleotide sequence and distribution of the pepPN gene from Lactobacillus helveticus CNRZ32. FEMS Microbiol Lett. 1994, 119: 41-45. 10.1111/j.1574-6968.1994.tb06864.x.
Article
CAS
PubMed
Google Scholar
Shao W, Yuksel GU, Dudley EG, Parkin KL, Steele JL: Biochemical and molecular characterization of PepR, a dipeptidase, from Lactobacillus helveticus CNRZ32. Appl Environ Microbiol. 1997, 63: 3438-3443.
CAS
PubMed Central
PubMed
Google Scholar
Atlan D, Gilbert C, Blanc B, Portalier R: Cloning, sequencing and characterization of the pepIP gene encoding a proline iminopeptidase from Lactobacillus delbrueckii subsp. bulgaricus CNRZ 397. Microbiology. 1994, 140 (Pt 3): 527-535. 10.1099/00221287-140-3-527.
Article
CAS
PubMed
Google Scholar
Morel F, Gilbert C, Geourjon C, Frot-Coutaz J, Portalier R, Atlan D: The prolyl aminopeptidase from Lactobacillus delbrueckii subsp. bulgaricus belongs to the alpha/beta hydrolase fold family. Biochim Biophys Acta. 1999, 1429: 501-505.
Article
CAS
PubMed
Google Scholar
Fernandez L, Beerthuyzen MM, Brown J, Siezen RJ, Coolbear T, Holland R, Kuipers OP: Cloning, characterization, controlled overexpression, and inactivation of the major tributyrin esterase gene of Lactococcus lactis. Appl Environ Microbiol. 2000, 66: 1360-1368. 10.1128/AEM.66.4.1360-1368.2000.
Article
CAS
PubMed Central
PubMed
Google Scholar
Yebra MJ, Viana R, Monedero V, Deutscher J, Perez-Martinez G: An esterase gene from Lactobacillus casei cotranscribed with genes encoding a phosphoenolpyruvate:sugar phosphotransferase system and regulated by a LevR-like activator and sigma54 factor. J Mol Microbiol Biotechnol. 2004, 8: 117-128. 10.1159/000084567.
Article
CAS
PubMed
Google Scholar
Varmanen P, Rantanen T, Palva A: An operon from Lactobacillus helveticus composed of a proline iminopeptidase gene (pepI) and two genes coding for putative members of the ABC transporter family of proteins. Microbiology. 1996, 142 (Pt 12): 3459-3468. 10.1099/13500872-142-12-3459.
Article
CAS
PubMed
Google Scholar
Yuksel GU, Steele JL: DNA sequence analysis, expression, distribution, and physiological role of the Xaa-prolyldipeptidyl aminopeptidase gene from Lactobacillus helveticus CNRZ32. Appl Microbiol Biotechnol. 1996, 44: 766-773. 10.1007/BF00178616.
Article
CAS
PubMed
Google Scholar
Varmanen P, Rantanen T, Palva A, Tynkkynen S: Cloning and characterization of a prolinase gene (pepR) from Lactobacillus rhamnosus. Appl Environ Microbiol. 1998, 64: 1831-1836.
CAS
PubMed Central
PubMed
Google Scholar
Sieuwerts S, de Bok FA, Hugenholtz J, van Hylckama Vlieg JE: Unraveling microbial interactions in food fermentations: from classical to genomics approaches. Appl Environ Microbiol. 2008, 74: 4997-5007. 10.1128/AEM.00113-08.
Article
CAS
PubMed Central
PubMed
Google Scholar
Sridhar VR, Hughes JE, Welker DL, Broadbent JR, Steele JL: Identification of endopeptidase genes from the genomic sequence of Lactobacillus helveticus CNRZ32 and the role of these genes in hydrolysis of model bitter peptides. Appl Environ Microbiol. 2005, 71: 3025-3032. 10.1128/AEM.71.6.3025-3032.2005.
Article
CAS
PubMed Central
PubMed
Google Scholar
Siezen RJ, Renckens B, Boekhorst J: Evolution of prokaryotic subtilases: Genome-wide analysis reveals novel subfamilies with different catalytic residues. Proteins: Structure, Function and Bioinformatics. 2007, 67: 681-694. 10.1002/prot.21290.
Article
CAS
Google Scholar
Polgar L: The catalytic triad of serine peptidases. Cell Mol Life Sci. 2005, 62: 2161-2172. 10.1007/s00018-005-5160-x.
Article
CAS
PubMed
Google Scholar
Dodson G, Wlodawer A: Catalytic triads and their relatives. Trends Biochem Sci. 1998, 23: 347-352. 10.1016/S0968-0004(98)01254-7.
Article
CAS
PubMed
Google Scholar
Seo JM, Ji GE, Cho SH, Park MS, Lee HJ: Characterization of a Bifidobacterium longum BORI dipeptidase belonging to the U34 family. Appl Environ Microbiol. 2007, 73: 5598-5606. 10.1128/AEM.00642-07.
Article
CAS
PubMed Central
PubMed
Google Scholar
Rademaker JL, Herbet H, Starrenburg MJ, Naser SM, Gevers D, Kelly WJ, Hugenholtz J, Swings J, van Hylckama Vlieg JE: Diversity analysis of dairy and nondairy Lactococcus lactis isolates, using a novel multilocus sequence analysis scheme and (GTG)5-PCR fingerprinting. Appl Environ Microbiol. 2007, 73: 7128-7137. 10.1128/AEM.01017-07.
Article
CAS
PubMed Central
PubMed
Google Scholar