LAB-Secretome: A genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Zhou, Miaomiao ^a,c   Theunissen, Daniel ^b,c   Wels, Michiel ^a,b,c   Siezen, Roland J ^a,b,c  

^a RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^b TOP INSTITUTE FOOD AND NUTRITION   (Netherlands)

^c NIZO FOOD RESEARCH   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; EXOPROTEIN; SURFACE ASSOCIATED PROTEIN; UNCLASSIFIED DRUG; MEMBRANE PROTEIN;

ARTICLE; BACTERIAL GENOME; CELLULAR DISTRIBUTION; CLUSTER ANALYSIS; CONTROLLED STUDY; ECOLOGICAL NICHE; EVOLUTIONARY ADAPTATION; LACTIC ACID BACTERIUM; MOLECULAR EVOLUTION; NONHUMAN; PREDICTION; PROTEIN DATABASE; PSEUDOGENE; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE; STRAIN DIFFERENCE; CHEMISTRY; COMPARATIVE STUDY; ENZYMOLOGY; EXTRACELLULAR SPACE; GENETICS; LACTOBACILLACEAE; METABOLISM; OPEN READING FRAME; PROTEIN TERTIARY STRUCTURE; SECRETION; SEQUENCE HOMOLOGY;

BACTERIA (MICROORGANISMS);

BACTERIAL PROTEINS; CLUSTER ANALYSIS; DATABASES, PROTEIN; EXTRACELLULAR SPACE; GENOME, BACTERIAL; LACTOBACILLACEAE; MEMBRANE PROTEINS; OPEN READING FRAMES; PROTEIN STRUCTURE, TERTIARY; PSEUDOGENES; SEQUENCE HOMOLOGY, AMINO ACID; SPECIES SPECIFICITY;

EID: 78549296762     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-651     Document Type: Article

References (132)

1. Goh YJ, Klaenhammer TR. Genomic features of Lactobacillus species. Front Biosci 2009, 14:1362-1386. 10.2741/3313, 19273135.
2. Johannessen EA, Wang L, Wyse C, Cumming DR, Cooper JM. Biocompatibility of a lab-on-a-pill sensor in artificial gastrointestinal environments. IEEE Trans Biomed Eng 2006, 53(11):2333-2340. 10.1109/TBME.2006.883698, 17073339.
3. Ljungh A, Wadstrom T. Lactic acid bacteria as probiotics. Curr Issues Intest Microbiol 2006, 7(2):73-89.
4. Vaughan EE, de Vries MC, Zoetendal EG, Ben-Amor K, Akkermans AD, de Vos WM. The intestinal LABs. Antonie Van Leeuwenhoek 2002, 82(1-4):341-352. 10.1023/A:1020672724450, 12369201.
5. Klaenhammer TR, Altermann E, Pfeiler E, Buck BL, Goh YJ, O'Flaherty S, Barrangou R, Duong T. Functional genomics of probiotic Lactobacilli. J Clin Gastroenterol 2008, 42(Suppl 3 Pt 2):S160-162. 10.1097/MCG.0b013e31817da140, 18685516.
6. Settanni L, Corsetti A. Application of bacteriocins in vegetable food biopreservation. Int J Food Microbiol 2008, 121(2):123-138. 10.1016/j.ijfoodmicro.2007.09.001, 18022269.
7. Reddy G, Altaf M, Naveena BJ, Venkateshwar M, Kumar EV. Amylolytic bacterial lactic acid fermentation - a review. Biotechnol Adv 2008, 26(1):22-34. 10.1016/j.biotechadv.2007.07.004, 17884326.
8. Lindgren SE, Dobrogosz WJ. Antagonistic activities of lactic acid bacteria in food and feed fermentations. FEMS Microbiol Rev 1990, 7(1-2):149-163.
9. Vandamme P, Pot B, Gillis M, de Vos P, Kersters K, Swings J. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 1996, 60(2):407-438. 239450, 8801440.
10. Stiles ME, Holzapfel WH, Holzapfel WH. Lactic acid bacteria of foods and their current taxonomy. Int J Food Microbiol 1997, 36(1):1-29. 10.1016/S0168-1605(96)01233-0, 9168311.
11. Wood BJB, Holzapfel WH, . (eds) The genera of lactic acid bacteria. 1995, Glasgow, United Kingdom.: Blackie Academic and Professional, 1, (eds).
12. Salminen S, von Wright A, Ouwehand AC, Lahtinen S, . (eds) Lactic Acid Bacteria: Microbiological and Functional Aspects. 2004, New York: Marcel Dekker, Inc, Third, (eds).
13. Callon C, Millet L, Montel MC. Diversity of lactic acid bacteria isolated from AOC Salers cheese. J Dairy Res 2004, 71(2):231-244. 10.1017/S0022029904000159, 15190953.
14. Ennahar S, Cai Y, Fujita Y. Phylogenetic diversity of lactic acid bacteria associated with paddy rice silage as determined by 16 S ribosomal DNA analysis. Appl Environ Microbiol 2003, 69(1):444-451. 10.1128/AEM.69.1.444-451.2003, 152408, 12514026.
15. Michel C, Pelletier C, Boussaha M, Douet DG, Lautraite A, Tailliez P. Diversity of lactic acid bacteria associated with fish and the fish farm environment, established by amplified rRNA gene restriction analysis. Appl Environ Microbiol 2007, 73(9):2947-2955. 10.1128/AEM.01852-06, 1892897, 17337536.
16. Ouoba LI, Nyanga-Koumou CA, Parkouda C, Sawadogo H, Kobawila SC, Keleke S, Diawara B, Louembe D, Sutherland JP. Genotypic diversity of lactic acid bacteria isolated from African traditional alkaline-fermented foods. J Appl Microbiol 2010, 108(6):2019-2029.
17. Lebeer S, Vanderleyden J, De Keersmaecker SC. Genes and molecules of lactobacilli supporting probiotic action. Microbiol Mol Biol Rev 2008, 72(4):728-764. Table of Contents, 10.1128/MMBR.00017-08, 2593565, 19052326.
18. Kleerebezem M, Vaughan EE. Probiotic and gut lactobacilli and bifidobacteria: molecular approaches to study diversity and activity. Annu Rev Microbiol 2009, 63:269-290. 10.1146/annurev.micro.091208.073341, 19575569.
19. van der Flier M, Chhun N, Wizemann TM, Min J, McCarthy JB, Tuomanen EI. Adherence of Streptococcus pneumoniae to immobilized fibronectin. Infect Immun 1995, 63(11):4317-4322. 173614, 7591065.
20. Nitsche-Schmitz DP, Rohde M, Chhatwal GS. Invasion mechanisms of Gram-positive pathogenic cocci. Thromb Haemost 2007, 98(3):488-496.
21. Chaussee MS, Somerville GA, Reitzer L, Musser JM. Rgg coordinates virulence factor synthesis and metabolism in Streptococcus pyogenes. J Bacteriol 2003, 185(20):6016-6024. 10.1128/JB.185.20.6016-6024.2003, 225023, 14526012.
22. Del Nobile MA, Altieri C, Corbo MR, Sinigaglia M, La Notte E. Development of a structured model for batch cultures of lactic acid bacteria. J Ind Microbiol Biotechnol 2003, 30(7):421-426. 10.1007/s10295-003-0066-9, 12937997.
23. Kleerebezem M, Boekhorst J, van Kranenburg R, Molenaar D, Kuipers OP, Leer R, Tarchini R, Peters SA, Sandbrink HM, Fiers MW, et al. Complete genome sequence of Lactobacillus plantarum WCFS1. Proc Natl Acad Sci USA 2003, 100(4):1990-1995. 10.1073/pnas.0337704100, 149946, 12566566.
24. Guzzo J, Jobin MP, Delmas F, Fortier LC, Garmyn D, Tourdot-Marechal R, Lee B, Divies C. Regulation of stress response in Oenococcus oeni as a function of environmental changes and growth phase. Int J Food Microbiol 2000, 55(1-3):27-31. 10.1016/S0168-1605(00)00209-9, 10791713.
25. Ma Y, Curran TM, Marquis RE. Rapid procedure for acid adaptation of oral lactic-acid bacteria and further characterization of the response. Can J Microbiol 1997, 43(2):143-148. 10.1139/m97-019, 9090104.
26. de Vos WM, Vaughan EE. Genetics of lactose utilization in lactic acid bacteria. FEMS Microbiol Rev 1994, 15(2-3):217-237.
27. Desvaux M, Hebraud M, Talon R, Henderson IR. Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue. Trends Microbiol 2009, 17(4):139-145. 10.1016/j.tim.2009.01.004, 19299134.
28. Rodriguez-Ortega MJ, Norais N, Bensi G, Liberatori S, Capo S, Mora M, Scarselli M, Doro F, Ferrari G, Garaguso I, et al. Characterization and identification of vaccine candidate proteins through analysis of the group A Streptococcus surface proteome. Nat Biotechnol 2006, 24(2):191-197. 10.1038/nbt1179, 16415855.
29. Toomey N, Monaghan A, Fanning S, Bolton D. Transfer of antibiotic resistance marker genes between lactic acid bacteria in model rumen and plant environments. Appl Environ Microbiol 2009, 75(10):3146-3152. 10.1128/AEM.02471-08, 2681641, 19270126.
30. Buck BL, Altermann E, Svingerud T, Klaenhammer TR. Functional Analysis of Putative Adhesion Factors in Lactobacillus acidophilus NCFM. Appl Environ Microbiol 2005, 71(12):8344-8351. 10.1128/AEM.71.12.8344-8351.2005, 16332821.
31. Kawai R, Igarashi K, Samejima M. Gene Cloning and Heterologous Expression of Glycoside Hydrolase Family 55 β-1,3-Glucanase from the Basidiomycete Phanerochaete Chrysosporium. Biotechnology Letters 2006, 28(6):365-371. 10.1007/s10529-005-6179-7, 16614901.
32. Roos S, Jonsson H. A high-molecular-mass cell-surface protein from Lactobacillus reuteri 1063 adheres to mucus components. Microbiology 2002, 148(Pt 2):433-442.
33. Quadri LE. Regulation of antimicrobial peptide production by autoinducer-mediated quorum sensing in lactic acid bacteria. Antonie Van Leeuwenhoek 2002, 82(1-4):133-145. 10.1023/A:1020624808520, 12369185.
34. Raimann E, Schmid B, Stephan R, Tasara T. The alternative sigma factor sigma(L) of L. monocytogenes promotes growth under diverse environmental stresses. Foodborne Pathog Dis 2009, 6(5):583-591. 10.1089/fpd.2008.0248, 19422306.
35. Vesterlund S, Karp M, Salminen S, Ouwehand AC. Staphylococcus aureus adheres to human intestinal mucus but can be displaced by certain lactic acid bacteria. Microbiology 2006, 152(Pt 6):1819-1826. 10.1099/mic.0.28522-0, 16735744.
36. Vesterlund S, Paltta J, Karp M, Ouwehand AC. Adhesion of bacteria to resected human colonic tissue: quantitative analysis of bacterial adhesion and viability. Res Microbiol 2005, 156(2):238-244. 10.1016/j.resmic.2004.08.012, 15748990.
37. Kovalenko NK, Podgorskii VS, Kasumova SA. [Adhesion of lactic acid bacteria to epithelium of different cavities of the human organism]. Mikrobiol Z 2004, 66(4):62-68.
38. Zhou M, Boekhorst J, Francke C, Siezen R. LocateP: Genome-scale subcellular-location predictor for bacterial proteins. BMC Bioinformatics 2008, 9(1):173. 10.1186/1471-2105-9-173, 2375117, 18371216.
39. Sprenger J, Fink JL, Teasdale RD. Evaluation and comparison of mammalian subcellular localization prediction methods. BMC Bioinformatics 2006, 7(Suppl 5):S3. 10.1186/1471-2105-7-S5-S3, 1764480, 17254308.
40. Nakai K, Horton P. Computational prediction of subcellular localization. Methods Mol Biol 2007, 390:429-466. full_text, 17951705.
41. Chou KC, Shen HB. Large-scale predictions of gram-negative bacterial protein subcellular locations. J Proteome Res 2006, 5(12):3420-3428. 10.1021/pr060404b, 17137343.
42. Kassahn KS, Dang VT, Wilkins SJ, Perkins AC, Ragan MA. Evolution of gene function and regulatory control after whole-genome duplication: comparative analyses in vertebrates. Genome Res 2009, 19(8):1404-1418. 10.1101/gr.086827.108, 2720184, 19439512.
43. Makarova KS, Koonin EV. Evolutionary genomics of lactic acid bacteria. J Bacteriol 2007, 189(4):1199-1208. 10.1128/JB.01351-06, 1797341, 17085562.
44. Masson S, Kern T, Le Gouellec A, Giustini C, Simorre JP, Callow P, Vernet T, Gabel F, Zapun A. Central domain of DivIB caps the C-terminal regions of the FtsL/DivIC coiled-coil rod. J Biol Chem 2009, 284(40):27687-27700. 10.1074/jbc.M109.019471, 2785697, 19635793.
45. Le Gouellec A, Roux L, Fadda D, Massidda O, Vernet T, Zapun A. Roles of pneumococcal DivIB in cell division. J Bacteriol 2008, 190(13):4501-4511. 10.1128/JB.00376-08, 2446777, 18441058.
46. Bennett JA, Aimino RM, McCormick JR. Streptomyces coelicolor genes ftsL and divIC play a role in cell division but are dispensable for colony formation. J Bacteriol 2007, 189(24):8982-8992. 10.1128/JB.01303-07, 2168613, 17951394.
47. Noirclerc-Savoye M, Le Gouellec A, Morlot C, Dideberg O, Vernet T, Zapun A. In vitro reconstitution of a trimeric complex of DivIB, DivIC and FtsL, and their transient co-localization at the division site in Streptococcus pneumoniae. Mol Microbiol 2005, 55(2):413-424. 10.1111/j.1365-2958.2004.04408.x, 15659160.
48. Robson SA, Michie KA, Mackay JP, Harry E, King GF. The Bacillus subtilis cell division proteins FtsL and DivIC are intrinsically unstable and do not interact with one another in the absence of other septasomal components. Mol Microbiol 2002, 44(3):663-674. 10.1046/j.1365-2958.2002.02920.x, 11994149.
49. Sievers J, Errington J. The Bacillus subtilis cell division protein FtsL localizes to sites of septation and interacts with DivIC. Mol Microbiol 2000, 36(4):846-855. 10.1046/j.1365-2958.2000.01895.x, 10844672.
50. Katis VL, Wake RG. Membrane-bound division proteins DivIB and DivIC of Bacillus subtilis function solely through their external domains in both vegetative and sporulation division. J Bacteriol 1999, 181(9):2710-2718. 93709, 10217758.
51. Daniel RA, Harry EJ, Katis VL, Wake RG, Errington J. Characterization of the essential cell division gene ftsL(yIID) of Bacillus subtilis and its role in the assembly of the division apparatus. Mol Microbiol 1998, 29(2):593-604. 10.1046/j.1365-2958.1998.00954.x, 9720875.
52. Katis VL, Harry EJ, Wake RG. The Bacillus subtilis division protein DivIC is a highly abundant membrane-bound protein that localizes to the division site. Mol Microbiol 1997, 26(5):1047-1055. 10.1046/j.1365-2958.1997.6422012.x, 9426141.
53. Levin PA, Losick R. Characterization of a cell division gene from Bacillus subtilis that is required for vegetative and sporulation septum formation. J Bacteriol 1994, 176(5):1451-1459. 205212, 8113187.
54. Siezen R, Boekhorst J, Muscariello L, Molenaar D, Renckens B, Kleerebezem M. Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria. BMC Genomics 2006, 7:126. 10.1186/1471-2164-7-126, 16723015.
55. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
56. Berger B, Pridmore RD, Barretto C, Delmas-Julien F, Schreiber K, Arigoni F, Brüssow H. Similarity and Differences in the Lactobacillus acidophilus Group Identified by Polyphasic Analysis and Comparative Genomics▽, †. J Bacteriol 2007, 189(4):1311-1321. 10.1128/JB.01393-06, 1797336, 17142402.
57. Canchaya C, Claesson MJ, Fitzgerald GF, van Sinderen D, O'Toole PW. Diversity of the genus Lactobacillus revealed by comparative genomics of five species. Microbiology 2006, 152(Pt 11):3185-3196. 10.1099/mic.0.29140-0, 17074890.
58. Claesson MJ, van Sinderen D, O'Toole PW. The genus Lactobacillus--a genomic basis for understanding its diversity. FEMS Microbiol Lett 2007, 269(1):22-28. 10.1111/j.1574-6968.2006.00596.x, 17343688.
59. Ventura M, Jankovic I, Walker DC, Pridmore RD, Zink R. Identification and Characterization of Novel Surface Proteins in Lactobacillus johnsonii and Lactobacillus gasseri. Appl Environ Microbiol 2002, 68(12):6172-6181. 10.1128/AEM.68.12.6172-6181.2002, 134427, 12450842.
60. Callanan M, Kaleta P, O'Callaghan J, O'Sullivan O, Jordan K, McAuliffe O, Sangrador-Vegas A, Slattery L, Fitzgerald GF, Beresford T, et al. Genome sequence of Lactobacillus helveticus, an organism distinguished by selective gene loss and insertion sequence element expansion. J Bacteriol 2008, 190(2):727-735. 10.1128/JB.01295-07, 2223680, 17993529.
61. Makarova K, Slesarev A, Wolf Y, Sorokin A, Mirkin B, Koonin E, Pavlov A, Pavlova N, Karamychev V, Polouchine N, et al. Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci USA 2006, 103(42):15611-15616. 10.1073/pnas.0607117103, 1622870, 17030793.
62. Khaleghi M, Kermanshahi RK, Yaghoobi MM, Zarkesh-Esfahani SH, Baghizadeh A. Assessment of Bile Salt Effects on S-Layer Production, slp Gene Expression and Some Physicochemical Properties of Lactobacillus acidophilus ATCC 4356. J Microbiol Biotechnol 2010, 20(4):749-756.
63. Goh YJ, Azcarate-Peril MA, O'Flaherty S, Durmaz E, Valence F, Jardin J, Lortal S, Klaenhammer TR. Development and application of a upp-based counterselective gene replacement system for the study of the S-layer protein SlpX of Lactobacillus acidophilus NCFM. Appl Environ Microbiol 2009, 75(10):3093-3105. 10.1128/AEM.02502-08, 2681627, 19304841.
64. Buck BL, Altermann E, Svingerud T, Klaenhammer TR. Functional analysis of putative adhesion factors in Lactobacillus acidophilus NCFM. Appl Environ Microbiol 2005, 71(12):8344-8351. 10.1128/AEM.71.12.8344-8351.2005, 1317474, 16332821.
65. Avall-Jaaskelainen S, Hynonen U, Ilk N, Pum D, Sleytr UB, Palva A. Identification and characterization of domains responsible for self-assembly and cell wall binding of the surface layer protein of Lactobacillus brevis ATCC 8287. BMC Microbiol 2008, 8:165. 10.1186/1471-2180-8-165, 2571106, 18828902.
66. Prado Acosta M, Mercedes Palomino M, Allievi MC, Sanchez Rivas C, Ruzal SM. Murein hydrolase activity in the surface layer of Lactobacillus acidophilus ATCC 4356. Appl Environ Microbiol 2008, 74(24):7824-7827. 10.1128/AEM.01712-08, 2607185, 18931300.
67. Konstantinov SR, Smidt H, de Vos WM, Bruijns SC, Singh SK, Valence F, Molle D, Lortal S, Altermann E, Klaenhammer TR, et al. S layer protein A of Lactobacillus acidophilus NCFM regulates immature dendritic cell and T cell functions. Proc Natl Acad Sci USA 2008, 105(49):19474-19479. 10.1073/pnas.0810305105, 2592362, 19047644.
68. Chen X, Xu J, Shuai J, Chen J, Zhang Z, Fang W. The S-layer proteins of Lactobacillus crispatus strain ZJ001 is responsible for competitive exclusion against Escherichia coli O157:H7 and Salmonella typhimurium. Int J Food Microbiol 2007, 115(3):307-312. 10.1016/j.ijfoodmicro.2006.11.007, 17289201.
69. Sanders ME, Klaenhammer TR. Invited review: the scientific basis of Lactobacillus acidophilus NCFM functionality as a probiotic. J Dairy Sci 2001, 84(2):319-331. 10.3168/jds.S0022-0302(01)74481-5, 11233016.
70. Azcarate-Peril MA, Altermann E, Goh YJ, Tallon R, Sanozky-Dawes RB, Pfeiler EA, O'Flaherty S, Buck BL, Dobson A, Duong T, et al. Analysis of the genome sequence of Lactobacillus gasseri ATCC 33323 reveals the molecular basis of an autochthonous intestinal organism. Appl Environ Microbiol 2008, 74(15):4610-4625. 10.1128/AEM.00054-08, 2519322, 18539810.
71. Boekhorst J, Helmer Q, Kleerebezem M, Siezen RJ. Comparative analysis of proteins with a mucus-binding domain found exclusively in lactic acid bacteria. Microbiology 2006, 152(Pt 1):273-280. 10.1099/mic.0.28415-0, 16385136.
72. van Pijkeren JP, Canchaya C, Ryan KA, Li Y, Claesson MJ, Sheil B, Steidler L, O'Mahony L, Fitzgerald GF, van Sinderen D, et al. Comparative and functional analysis of sortase-dependent proteins in the predicted secretome of Lactobacillus salivarius UCC118. Appl Environ Microbiol 2006, 72(6):4143-4153. 10.1128/AEM.03023-05, 1489637, 16751526.
73. MacKenzie DA, Tailford LE, Hemmings AM, Juge N. Crystal structure of a mucus-binding protein repeat reveals an unexpected functional immunoglobulin binding activity. J Biol Chem 2009, 284(47):32444-32453. 10.1074/jbc.M109.040907, 2781659, 19758995.
74. Gendrot F, Foucaud-Scheunemann C, Ferchichi M, Hemme D. Characterization of amino acid transport in the dairy strain Leuconostoc mesenteroides subsp. mesenteroides CNRZ 1273. Lett Appl Microbiol 2002, 35(4):291-295. 10.1046/j.1472-765X.2002.01191.x, 12358690.
75. Dudley E, Steele J. Lactococcus lactis LM0230 contains a single aminotransferase involved in aspartate biosynthesis, which is essential for growth in milk. Microbiology 2001, 147(Pt 1):215-224.
76. Juillard V, Guillot A, Le Bars D, Gripon JC. Specificity of milk peptide utilization by Lactococcus lactis. Appl Environ Microbiol 1998, 64(4):1230-1236. 106134, 9546157.
77. Mierau I, Kunji ER, Leenhouts KJ, Hellendoorn MA, Haandrikman AJ, Poolman B, Konings WN, Venema G, Kok J. Multiple-peptidase mutants of Lactococcus lactis are severely impaired in their ability to grow in milk. J Bacteriol 1996, 178(10):2794-2803. 178013, 8631666.
78. Florez AB, Delgado S, Mayo B. Antimicrobial susceptibility of lactic acid bacteria isolated from a cheese environment. Can J Microbiol 2005, 51(1):51-58. 10.1139/w04-114, 15782234.
79. Chirica LC, Guray T, Gurakan GC, Bozoglu TF. Characterization of extracellular beta-lactamases from penicillin G-resistant cells of Streptococcus thermophilus. J Food Prot 1998, 61(7):896-898.
80. Coque JJ, Liras P, Martin JF. Genes for a beta-lactamase, a penicillin-binding protein and a transmembrane protein are clustered with the cephamycin biosynthetic genes in Nocardia lactamdurans. Embo J 1993, 12(2):631-639. 413247, 8440253.
81. Yamamura A, Okada A, Kameda Y, Ohtsuka J, Nakagawa N, Ebihara A, Nagata K, Tanokura M. Structure of TTHA1623, a novel metallo-beta-lactamase superfamily protein from Thermus thermophilus HB8. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009, 65(Pt 5):455-459. 10.1107/S174430910901361X, 19407375.
82. Korycka-Dahl M, Richardson T, Bradley RL. Use of microbial beta-lactamase to destroy penicillin added to milk. J Dairy Sci 1985, 68(8):1910-1916. 10.3168/jds.S0022-0302(85)81049-3, 3930584.
83. Kao SM, Olmsted SB, Viksnins AS, Gallo JC, Dunny GM. Molecular and genetic analysis of a region of plasmid pCF10 containing positive control genes and structural genes encoding surface proteins involved in pheromone-inducible conjugation in Enterococcus faecalis. J Bacteriol 1991, 173(23):7650-7664. 212534, 1938961.
84. Ruhfel RE, Manias DA, Dunny GM. Cloning and characterization of a region of the Enterococcus faecalis conjugative plasmid, pCF10, encoding a sex pheromone-binding function. J Bacteriol 1993, 175(16):5253-5259. 204993, 8349565.
85. Hirt H, Manias DA, Bryan EM, Klein JR, Marklund JK, Staddon JH, Paustian ML, Kapur V, Dunny GM. Characterization of the pheromone response of the Enterococcus faecalis conjugative plasmid pCF10: complete sequence and comparative analysis of the transcriptional and phenotypic responses of pCF10-containing cells to pheromone induction. J Bacteriol 2005, 187(3):1044-1054. 10.1128/JB.187.3.1044-1054.2005, 545727, 15659682.
86. Kirillova Iu M, Mikhailova EO, Balaban NP, Mardanova AM, Rudenskaia GN, Kostrov SV, Sharipova MR. [Growth conditions and production of the Bacillus intermedius subtilisin-like serine proteinase by the recombinant Bacillus subtilis strain]. Mikrobiologiia 2006, 75(2):172-178.
87. Mikhailova EO, Mardanova AM, Balaban NP, Rudenskaya GN, Ilyinskaya ON, Sharipova MR. Biochemical properties of Bacillus intermedius subtilisin-like proteinase secreted by a Bacillus subtilis recombinant strain in its stationary phase of growth. Biochemistry (Mosc) 2009, 74(3):308-315. 10.1134/S0006297909030109, 19364326.
88. Siezen RJ, Bruinenberg PG, Vos P, van Alen-Boerrigter I, Nijhuis M, Alting AC, Exterkate FA, de Vos WM. Engineering of the substrate-binding region of the subtilisin-like, cell-envelope proteinase of Lactococcus lactis. Protein Eng 1993, 6(8):927-937. 10.1093/protein/6.8.927, 8309942.
89. Srivastava R, Liu JX, Howell SH. Proteolytic processing of a precursor protein for a growth-promoting peptide by a subtilisin serine protease in Arabidopsis. Plant J 2008, 56(2):219-227. 10.1111/j.1365-313X.2008.03598.x, 2667306, 18643977.
90. Goh YJ, Klaenhammer TR. Functional roles of aggregation-promoting-like factor in stress tolerance and adherence of Lactobacillus acidophilus NCFM. Appl Environ Microbiol 2010,
91. Jankovic I, Ventura M, Meylan V, Rouvet M, Elli M, Zink R. Contribution of aggregation-promoting factor to maintenance of cell shape in Lactobacillus gasseri 4B2. J Bacteriol 2003, 185(11):3288-3296. 10.1128/JB.185.11.3288-3296.2003, 155393, 12754226.
92. Marcotte H, Ferrari S, Cesena C, Hammarstrom L, Morelli L, Pozzi G, Oggioni MR. The aggregation-promoting factor of Lactobacillus crispatus M247 and its genetic locus. J Appl Microbiol 2004, 97(4):749-756. 10.1111/j.1365-2672.2004.02364.x, 15357724.
93. Schneewind O, Jones KF, Fischetti VA. Sequence and structural characteristics of the trypsin-resistant T6 surface protein of group A streptococci. J Bacteriol 1990, 172(6):3310-3317. 209141, 2188957.
94. Fischetti VA, Pancholi V, Schneewind O. Conservation of a hexapeptide sequence in the anchor region of surface proteins from gram-positive cocci. Mol Microbiol 1990, 4(9):1603-1605. 10.1111/j.1365-2958.1990.tb02072.x, 2287281.
95. Kleerebezem M, Hols P, Bernard E, Rolain T, Zhou M, Siezen RJ, Bron PA. The extracellular biology of the lactobacilli. FEMS Microbiol Rev 2010, 34(2):199-230. 10.1111/j.1574-6976.2009.00208.x, 20088967.
96. Boekhorst J, de Been MW, Kleerebezem M, Siezen RJ. Genome-wide detection and analysis of cell wall-bound proteins with LPxTG-like sorting motifs. J Bacteriol 2005, 187(14):4928-4934. 10.1128/JB.187.14.4928-4934.2005, 1169495, 15995208.
97. Bae T, Schneewind O. The YSIRK-G/S motif of staphylococcal protein A and its role in efficiency of signal peptide processing. J Bacteriol 2003, 185(9):2910-2919. 10.1128/JB.185.9.2910-2919.2003, 154403, 12700270.
98. DeDent A, Bae T, Missiakas DM, Schneewind O. Signal peptides direct surface proteins to two distinct envelope locations of Staphylococcus aureus. Embo J 2008, 27(20):2656-2668. 10.1038/emboj.2008.185, 2572169, 18800056.
99. Zhang Z, Liu C, Zhu Y, Zhong Y, Zhu Y, Zheng H, Zhao GP, Wang SY, Guo X. Complete genome sequence of Lactobacillus plantarum JDM1. J Bacteriol 2009, 2715720, 19465650.
100. Boekhorst J, Siezen RJ, Zwahlen MC, Vilanova D, Pridmore RD, Mercenier A, Kleerebezem M, de Vos WM, Brussow H, Desiere F. The complete genomes of Lactobacillus plantarum and Lactobacillus johnsonii reveal extensive differences in chromosome organization and gene content. Microbiology 2004, 150(Pt 11):3601-3611. 10.1099/mic.0.27392-0, 15528649.
101. Savijoki K, Kahala M, Palva A. High level heterologous protein production in Lactococcus and Lactobacillus using a new secretion system based on the Lactobacillus brevis S-layer signals. Gene 1997, 186(2):255-262. 10.1016/S0378-1119(96)00717-2, 9074504.
102. De Angelis M, de Candia S, Calasso MP, Faccia M, Guinee TP, Simonetti MC, Gobbetti M. Selection and use of autochthonous multiple strain cultures for the manufacture of high-moisture traditional Mozzarella cheese. Int J Food Microbiol 2008, 125(2):123-132. 10.1016/j.ijfoodmicro.2008.03.043, 18538430.
103. Pastink MI, Teusink B, Hols P, Visser S, de Vos WM, Hugenholtz J. Genome-scale model of Streptococcus thermophilus LMG18311 for metabolic comparison of lactic acid bacteria. Appl Environ Microbiol 2009, 75(11):3627-3633. 10.1128/AEM.00138-09, 2687286, 19346354.
104. Wegmann U, O'Connell-Motherway M, Zomer A, Buist G, Shearman C, Canchaya C, Ventura M, Goesmann A, Gasson MJ, Kuipers OP, et al. Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363. J Bacteriol 2007, 189(8):3256-3270. 10.1128/JB.01768-06, 1855848, 17307855.
105. Le Bourgeois P, Mata M, Ritzenthaler P. Genome comparison of Lactococcus strains by pulsed-field gel electrophoresis. FEMS Microbiol Lett 1989, 50(1-2):65-69. 10.1016/0378-1097(89)90460-6, 2737464.
106. Petrova P, Emanuilova M, Petrov K. Amylolytic Lactobacillus strains from Bulgarian fermented beverage boza. Z Naturforsch C 2010, 65(3-4):218-224.
107. Liu M, Bayjanov JR, Renckens B, Nauta A, Siezen RJ. The proteolytic system of lactic acid bacteria revisited: a genomic comparison. BMC Genomics 2010, 11:36. 10.1186/1471-2164-11-36, 2827410, 20078865.
108. Bounaix MS, Gabriel V, Morel S, Robert H, Rabier P, Remaud-Simeon M, Gabriel B, Fontagne-Faucher C. Biodiversity of exopolysaccharides produced from sucrose by sourdough lactic acid bacteria. J Agric Food Chem 2009, 57(22):10889-10897. 10.1021/jf902068t, 19848387.
109. Cobo Molinos A, Abriouel H, Ben Omar N, Lopez RL, Galvez A. Microbial diversity changes in soybean sprouts treated with enterocin AS-48. Food Microbiol 2009, 26(8):922-926. 10.1016/j.fm.2009.06.012, 19835782.
110. De Vuyst L, Vrancken G, Ravyts F, Rimaux T, Weckx S. Biodiversity, ecological determinants, and metabolic exploitation of sourdough microbiota. Food Microbiol 2009, 26(7):666-675. 10.1016/j.fm.2009.07.012, 19747599.
111. Chao SH, Wu RJ, Watanabe K, Tsai YC. Diversity of lactic acid bacteria in suan-tsai and fu-tsai, traditional fermented mustard products of Taiwan. Int J Food Microbiol 2009, 135(3):203-210. 10.1016/j.ijfoodmicro.2009.07.032, 19700215.
112. Roh SW, Kim KH, Nam YD, Chang HW, Park EJ, Bae JW. Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing. ISME J 2010, 4(1):1-16. 10.1038/ismej.2009.83, 19587773.
113. Ouadghiri M, Vancanneyt M, Vandamme P, Naser S, Gevers D, Lefebvre K, Swings J, Amar M. Identification of lactic acid bacteria in Moroccan raw milk and traditionally fermented skimmed milk 'lben'. J Appl Microbiol 2009, 106(2):486-495. 10.1111/j.1365-2672.2008.04016.x, 19054226.
114. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Edgar R, Federhen S, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2008, (36 Database):D13-21. 2238880, 18045790.
115. O'Brien KP, Remm M, Sonnhammer EL. Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res 2005, (33 Database):D476-480. 540061, 15608241.
116. Edgar R. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004, 5(1):113. 10.1186/1471-2105-5-113, 517706, 15318951.
117. Bailey TL, Williams N, Misleh C, Li WW. MEME: discovering and analyzing DNA and protein sequence motifs. Nucl Acids Res 2006, 34(suppl_2):W369-373. 10.1093/nar/gkl198, 1538909, 16845028.
118. Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, et al. Pfam: clans, web tools and services. Nucleic Acids Res 2006, (34 Database):D247-251. 10.1093/nar/gkj149, 16381856.
119. Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, ollich V, Lassmann T, Moxon S, Marshall M, Khanna A, et al. Pfam: clans, web tools and services. Nucl Acids Res 2006, 34(suppl_1):D247-251. 10.1093/nar/gkj149, 1347511, 16381856.
120. Sonnhammer E, Eddy S, Birney E, Bateman A, Durbin R. Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucl Acids Res 1998, 26(1):320-322. 10.1093/nar/26.1.320, 147209, 9399864.
121. Bateman A, Birney E, Durbin R, Eddy SR, Finn RD, Sonnhammer EL. Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Res 1999, 27(1):260-262. 10.1093/nar/27.1.260, 148151, 9847196.
122. Boekhorst J, Wels M, Kleerebezem M, Siezen RJ. The predicted secretome of Lactobacillus plantarum WCFS1 sheds light on interactions with its environment. Microbiology 2006, 152(Pt 11):3175-3183. 10.1099/mic.0.29217-0, 17074889.
123. Siezen R, Boekhorst J, Muscariello L, Molenaar D, Renckens B, Kleerebezem M. Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria. BMC Genomics 2006, 7(1):126. 10.1186/1471-2164-7-126, 1534035, 16723015.
124. Kerkhoven R, van Enckevort FH, Boekhorst J, Molenaar D, Siezen RJ. Visualization for genomics: the Microbial Genome Viewer. Bioinformatics 2004, 20(11):1812-1814. 10.1093/bioinformatics/bth159, 14988111.
125. Eddy SR. A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation. PLoS Comput Biol 2008, 4(5):e1000069. 10.1371/journal.pcbi.1000069, 2396288, 18516236.
126. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25(1):25-29. 10.1038/75556, 10802651.
127. Snel B, Bork P, Huynen MA. The identification of functional modules from the genomic association of genes. Proc Natl Acad Sci USA 2002, 99(9):5890-5895. 10.1073/pnas.092632599, 122872, 11983890.
128. Tatusov RL, Natale D, A N, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, et al. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucl Acids Res 2001, 29(1):22-28. 10.1093/nar/29.1.22, 29819, 11125040.
129. Tatusov RL, Koonin EV, Lipman DJ. A Genomic Perspective on Protein Families. Science 1997, 278(5338):631-637. 10.1126/science.278.5338.631, 9381173.
130. Boekhorst J, Snel B. Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties. BMC Bioinformatics 2007, 8:356. 10.1186/1471-2105-8-356, 2048517, 17888146.
131. Bendtsen JD, Kiemer L, Fausboll A, Brunak S. Non-classical protein secretion in bacteria. BMC Microbiol 2005, 5:58. 10.1186/1471-2180-5-58, 1266369, 16212653.
132. Hubert P, Sawma P, Duneau JP, Khao J, Henin J, Bagnard D, Sturgis J. Single-spanning transmembrane domains in cell growth and cell-cell interactions: More than meets the eye?. Cell Adh Migr 2010, 4(2).