Characterization of the serpin-encoding gene of bifidobacterium breve 210B

Applied and Environmental Microbiology

Volumn 76, Issue 10, 2010, Pages 3206-3219

  Turroni, Francesca ^a   Foroni, Elena ^a   Motherway, Mary O'Connell ^b   Bottacini, Francesca ^a   Giubellini, Vanessa ^a   Zomer, Aldert ^b   Ferrarini, Alberto ^c   Delledonne, Massimo ^c   Zhang, Ziding ^d   Van Sinderen, Douwe ^b   Ventura, Marco ^a  

^a UNIVERSITY OF PARMA   (Italy)

^b UNIVERSITY COLLEGE CORK   (Ireland)

^c UNIVERSITY OF VERONA   (Italy)

^d CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BIFIDOBACTERIA; BIFIDOBACTERIUM; ENCODING GENES; GENOME SEQUENCES; MULTICELLULAR EUKARYOTES; PHYLOGENETIC ANALYSIS; PRIMER EXTENSION; Q-RT-PCR; QUANTITATIVE REAL TIME PCR; SERINE PROTEASE INHIBITOR; SERPINS;

AMINO ACIDS; BACTERIA; BACTERIOLOGY; ENCODING (SYMBOLS); GENE ENCODING; PHOSPHATASES; PROTEINS; TRANSCRIPTION;

ENZYME ACTIVITY;

SERINE PROTEINASE; SERINE PROTEINASE INHIBITOR;

BACTERIUM; ENZYME ACTIVITY; GENE EXPRESSION; GENOME; HYBRIDIZATION; PHYLOGENETICS; POLYMERASE CHAIN REACTION; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; BIFIDOBACTERIUM; CHEMICAL STRUCTURE; CHEMISTRY; CLASSIFICATION; DRUG EFFECT; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT;

AMINO ACID SEQUENCE; BASE SEQUENCE; BIFIDOBACTERIUM; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SERINE PROTEASES; SERPINS;

BACTERIA (MICROORGANISMS); BIFIDOBACTERIUM; BIFIDOBACTERIUM BREVE; EUKARYOTA;

EID: 77952265532     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.02938-09     Document Type: Article

References (48)

1. Barrangou, R., E. P. Briczinski, L. L. Traeger, J. R. Loquasto, M. Richards, P. Horvath, A. C. Coute-Monvoisin, G. Leyer, S. Rendulic, J. L. Steele, J. R. Broadbent, T. Oberg, E. G. Dudley, S. Schuster, D. A. Romero, and R. F. Roberts. 2009. Comparison of the complete genome sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04. J. Bacteriol. 191:4144-4151.
2. Benjamini, Y., and Y. Hochberg. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. 57: 289-300.
3. Bilban, M., L. K. Buehler, S. Head, G. Desoye, and V. Quaranta. 2002. Defining signal thresholds in DNA microarrays: exemplary application for invasive cancer. BMC Genomics 3:19. (Pubitemid 39565264)
4. Bolstad, B. M., R. A. Irizarry, M. Astrand, and T. P. Speed. 2003. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19:185-193.
5. Burg, N. D., and M. H. Pillinger. 2001. The neutrophil: function and regulation in innate and humoral immunity. Clin. Immunol. 99:7-17.
6. Elliott, P. R., J. P. Abrahams, and D. A. Lomas. 1998. Wild-type alpha 1-antitrypsin is in the canonical inhibitory conformation. J. Mol. Biol. 275: 419-425.
7. Felsenstein, J. 1997. An alternating least squares approach to inferring phylogenies from pairwise distances. Syst. Biol. 46:101-111.
8. Furrie, E., S. Macfarlane, A. Kennedy, J. H. Cummings, S. V. Walsh, D. A. O'Neil, and G. T. Macfarlane. 2005. Synbiotic therapy (Bifidobacterium longum/Synergy 1) initiates resolution of inflammation in patients with active ulcerative colitis: a randomised controlled pilot trial. Gut 54:242-249. (Pubitemid 40139241)
9. Gettins, P. G. 2002. Serpin structure, mechanism, and function. Chem. Rev. 102:4751-4804.
10. Grenier, D. 1994. Characteristics of a protease inhibitor produced by Prevotella intermedia. FEMS Microbiol. Lett. 119:13-18.
11. Huntington, J. A., R. J. Read, and R. W. Carrell. 2000. Structure of a serpin-protease complex shows inhibition by deformation. Nature 407:923-926.
12. Irving, J. A., R. N. Pike, A. M. Lesk, and J. C. Whisstock. 2000. Fhylogeny of the serpin superfamiiy: implications of patterns of amino acid conservation for structure and function. Genome Res. 10:1845-1864.
13. Irving, J. A., P. J. Steenbakkers, A. M. Lesk, H. J. Op den Camp, R. N. Pike, and J. C. Whisstock. 2002. Serpins in prokaryotes. Mol. Biol. Evol. 19:1881-1890.
14. Ivanov, D., C. Emonet, F. Foata, M. Affolter, M. Delley, M. Fisseha, S. Blum-Sperisen, S. Kochhar, and F. Arigoni. 2006. A serpin from the gut bacterium Bifidobacterium longum inhibits eukaryotic elastase-like serine proteases. J. Biol. Chem. 281:17246-17252.
15. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
16. Leahy, S. C., D. G. Higgins, G. F. Fitzgerald, and D. van Sinderen. 2005. Getting better with bifidobacteria. J. Appl. Microbiol. 98:1303-1315.
17. Lee, J. H., V. N. Karamychev, S. A. Kozyavkin, D. Mills, A. R. Pavlov, N. V. Pavlova, N. N. Polouchine, P. M. Richardson, V. V. Shakhova, A. I. Slesarev, B. Weimer, and D. J. O'Sullivan. 2008. Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth. BMC Genomics 9:247.
18. Marco, M. L., S. Pavan, and M. Kleerebezem. 2006. Towards understanding molecular modes of probiotic action. Curr. Opin. Biotechnol. 17:204-210.
19. Menard, R., and A. C. Storer. 1998. Papain. Academic Press, London, United Kingdom.
20. Mottonen, J., A. Strand, J. Symersky, R. M. Sweet, D. E. Danley, K. F. Geoghegan, R. D. Gerard, and E. J. Goldsmith. 1992. Structural basis of latency in plasminogen activator inhibitor-1. Nature 355:270-273.
21. O'Hara, A. M., and F. Shanahan. 2007. Mechanisms of action of probiotics in intestinal diseases. Sci. World J. 7:31-46.
22. O'Mahony, L., J. McCarthy, P. Kelly, G. Hurley, F. Luo, K. Chen, G. C. O'Sullivan, B. Kiely, J. K. Collins, F. Shanahan, and E. M. Quigley. 2005. Lactobacillus and bifidobacterium in irritable bowel syndrome: symptom responses and relationship to cytokine profiles. Gastroenterology 128:541-551. (Pubitemid 40585355)
23. Ouwehand, A. C., S. Salminen, and E. Isolauri. 2002. Probiotics: an overview of beneficial effects. Antonie Van Leeuwenhoek 82:279-289.
24. + flux. Nature 416:291-297.
25. Roberts, T. H., J. Hejgaard, N. F. Saunders, R. Cavicchioli, and P. M. Curmi. 2004. Serpins in unicellular Eukarya, Archaea, and Bacteria: sequence analysis and evolution. J. Mol. Evol. 59:437-447.
26. Sali, A., and T. L. Blundell. 1993. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234:779-815.
27. Sambrook, J., E. E. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
28. Sanchez, B., M. C. Champomier-Verges, P. Anglade, F. Baraige, C. G. de Los Reyes-Gavilan, A. Margolles, and M. Zagorec. 2005. Proteomic analysis of global changes in protein expression during bile salt exposure of Bifidobacterium longum NCIMB 8809. J. Bacteriol. 187:5799-5808. (Pubitemid 41134318)
29. Sansonetti, P. J. 2004. War and peace at mucosal surfaces. Nat. Rev. Immunol. 4:953-964.
30. Schell, M. A., M. Karmirantzou, B. Snel, D. Vilanova, B. Berger, G. Pessi, M. C. Zwahlen, F. Desiere, P. Bork, M. Delley, R. D. Pridmore, and F. Arigoni. 2002. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc. Natl. Acad. Sci. U. S. A. 99:14422-14427.
31. Sela, D. A., J. Chapman, A. Adeuya, J. H. Kim, F. Chen, T. R. Whitehead, A. Lapidus, D. S. Rokhsar, C. B. Lebrilla, J. B. German, N. P. Price, P. M. Richardson, and D. A. Mills. 2008. The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome. Proc. Natl. Acad. Sci. U. S. A. 105:18964-18969.
32. Shiga, Y., H. Yamagata, N. Tsukagoshi, and S. Udaka. 1995. BbrFI, an extracellular proteinase inhibitor of Bacillus brevis, protects cells from the attack of exogenous proteinase. Biosci. Biotechnol. Biochem. 59:2348-2350.
33. Silverman, G. A., P. I. Bird, R. W. Carrell, F. C. Church, P. B. Coughlin, P. G. Gettins, J. A. Irving, D. A. Lomas, C. J. Luke, R. W. Moyer, P. A. Pemberton, E. Remold-O'Donnell, G. S. Salvesen, J. Travis, and J. C. Whisstock. 2001. The serpins are an expanding superfamiiy of structurally similar but functionally diverse proteins. Evolution, mechanism of inhibition, novel functions, and a revised nomenclature. J. Biol. Chem. 276:33293-33296.
34. Smyth, G. K. 2004. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3:Article3.
35. Turroni, F., E. Foroni, P. Pizzetti, V. Giubellini, A. Ribbera, P. Merusi, P. Cagnasso, B. Bizzarri, G. L. de'Angelis, F. Shanahan, D. van Sinderen, and M. Ventura. 2009. Exploring the diversity of the bifidobacterial population in the human intestinal tract. Appl. Environ. Microbiol. 75:1534-1545.
36. Turroni, F., J. R. Marchesi, E. Foroni, M. Gueimonde, F. Shanahan, A. Margolles, D. van Sinderen, and M. Ventura. 2009. Microbiomic analysis of the bifidobacteria! population in the human distal gut. ISME J. 3:745-751.
37. Ventura, M., C. Canchaya, A. Del Casale, F. Dellaglio, E. Neviani, G. F. Fitzgerald, and D. van Sinderen. 2006. Analysis of bifidobacterial evolution using a multilocus approach. Int. J. Syst. Evol. Microbiol. 56:2783-2792.
38. Ventura, M., C. Canchaya, G. F. Fitzgerald, R. S. Gupta, and D. van Sinderen. 2007. Genomics as a means to understand bacterial phylogeny and ecological adaptation: the case of bifidobacteria. Antonie Van Leeuwenhoek 91:351-372. (Pubitemid 46681587)
39. Ventura, M., C. Canchaya, A. Tauch, G. Chandra, G. F. Fitzgerald, K. F. Chater, and D. van Sinderen. 2007. Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol. MoI. Biol. Rev. 71: 495-548.
40. Ventura, M., J. G. Kenny, Z. Zhang, G. F. Fitzgerald, and D. van Sinderen. 2005. The clpB gene of Bifidobacterium breve UCC 2003: transcriptional analysis and first insights into stress induction. Microbiology 151:2861-2872. (Pubitemid 41309561)
41. Ventura, M., S. O'Flaherty, M. J. Claesson, F. Turroni, T. R. Klaenhammer, D. van Sinderen, and P. O'Toole. 2009. Genome-scale analyses of healthpromoting bacteria: probiogenomics. Nat. Rev. Microbiol. 7:61-71.
42. Ventura, M., R. Reniero, and R. Zink. 2001. Specific identification and targeted characterization of Bifidobacterium lactis from different environmental isolates by a combined multiplex-FCR approach. Appl. Environ. Microbiol. 67:2760-2765.
43. Ventura, M., F. Turroni, A. Zomer, E. Foroni, V. Giubellini, F. Bottadni, C. Canchaya, M. J. Claesson, F. He, M. Mantzourani, L. Mulas, A. Ferrarini, B. Gao, M. Delledonne, B. Henrissat, P. Coutinho, M. Oggioni, R. S. Gupta, Z. Zhang, D. Beighton, G. F. Fitzgerald, P. W. O'Toole, and D. van Sinderen. 2009. The Bifidobacterium dentium BdI genome sequence reflects its genetic adaptation to the human oral cavity. PLoS Genet. 5:el000785.
44. Ventura, M., D. van Sinderen, G. F. Fitzgerald, and R. Zink. 2004. Insights into the taxonomy, genetics and physiology of bifidobacteria. Antonie Van Leeuwenhoek 86:205-223. (Pubitemid 39517700)
45. Ventura, M., and R. Zink. 2003. Comparative sequence analysis of the tuf and recA genes and restriction fragment length polymorphism of the internal transcribed spacer region sequences supply additional tools for discriminating Bifidobacterium lactis from Bifidobacterium animalis. Appl. Environ. Microbiol. 69:7517-7522.
46. Wagner, R. 2000. Transcription regulation in prokaryotes. Oxford University Press, New York, NY.
47. Zhang, Q., A. M. Buckle, R. H. Law, M. C. Pearce, L. D. Cabrita, G. J. Lloyd, J. A. Irving, A. I. Smith, K. Ruzyla, J. Rossjohn, S. P. Bottomley, and J. C. Whisstock. 2007. The N terminus of the serpin, tengpin, functions to trap the metastable native state. EMBO Rep. 8:658-663. (Pubitemid 47029472)
48. Zoetendal, E. G., C. C. Booijink, E. S. Klaassens, H. G. Heilig, M. Kleerebezem, H. Smidt, and W. M. de Vos. 2006. Isolation of RNA from bacterial samples of the human gastrointestinal tract. Nat. Frotoc. 1: 954-959.