Carbohydrate-active enzymes from pigmented Bacilli: A genomic approach to assess carbohydrate utilization and degradation

BMC Microbiology

Volumn 11, Issue , 2011, Pages

  Manzo, Nicola ^a   D'Apuzzo, Enrica ^a   Coutinho, Pedro M ^b   Cutting, Simon M ^c   Henrissat, Bernard ^b   Ricca, Ezio ^a  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^b AIX MARSEILLE UNIVERSITY   (France)

^c UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CARBOHYDRATE; CARBOHYDRATE ACTIVE ENZYME; CAROTENOID; ENZYME; ESTERASE; GLYCAN; GLYCOSIDASE; GLYCOSYLTRANSFERASE; LEVAN; MUCIN; POLYSACCHARIDE LYASE; UNCLASSIFIED DRUG; BACTERIAL PROTEIN;

ARTICLE; BACILLI; BACILLUS FIRMUS; BACILLUS INDICUS; BACTERIAL COLONIZATION; BACTERIAL GROWTH; BACTERIAL METABOLISM; BACTERIUM ISOLATE; BIOFILM; CARBOHYDRATE METABOLISM; ENZYME ANALYSIS; NONHUMAN; PROTEIN DOMAIN; BACILLUS; BACTERIAL GENOME; ENZYMOLOGY; GENETICS; GENOMICS; METABOLISM; MOLECULAR GENETICS; PIGMENTATION;

ANIMALIA; BACILLI (CLASS); BACILLUS (BACTERIUM); BACILLUS FIRMUS; BACILLUS INDICUS; MAMMALIA; POSIBACTERIA;

BACILLUS; BACTERIAL PROTEINS; CARBOHYDRATE METABOLISM; ENZYMES; GENOME, BACTERIAL; GENOMICS; MOLECULAR SEQUENCE DATA; PIGMENTATION;

EID: 80052603842     PISSN: 14712180     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-11-198     Document Type: Article

References (43)

1. Structure, assembly, and function of the spore surface layers. Henriques AO, Moran CP Jr, Ann Rev Microbiol 2007 61 555 588 10.1146/annurev.micro.61. 080706.093224 (Pubitemid 350058221)
2. Defining the natural habitat of Bacillus sporeformers. Hong HA, To E, Fakhry S, Baccigalupi L, Ricca E, Cutting SM, Res Microbiol 2009 160 375 379 10.1016/j.resmic.2009.06.006 19589385
3. On the fate of ingested Bacillus spores. Spinosa MR, Braccini T, Ricca E, De Felice M, Morelli L, Pozzi G, Oggioni MR, Res Microbiol 2000 151 361 368 10.1016/S0923-2508(00)00159-5 10919516 (Pubitemid 30435552)
4. Screening for Bacillus isolates in the broiler gastrointestinal tract. Barbosa TM, Serra CR, La Ragione RM, Woodward MJ, Henriques AO, Appl Environ Microbiol 2005 71 968 978 10.1128/AEM.71.2.968-978.2005 15691955 (Pubitemid 40227469)
5. Characterisation of spore forming Bacilli isolated from the human gastrointestinal tract. Fakhry S, Sorrentini I, Ricca E, De Felice M, Baccigalupi L, J Appl Microbiol 2008 105 2178 2186 10.1111/j.1365-2672.2008. 03934.x 19120663
6. Bacillus subtilis isolated from the human gastrointestinal tract. Hong HA, Khanejaa R, Nguyen I, Tam MK, Cazzato A, Tand S, Urdaci M, Brisson A, Gasbarrini A, Barnes I, Cutting SM, Res Microbiol 2009 160 134 143 10.1016/j.resmic.2008.11.002 19068230
7. Bacillus probiotics: Spore germination in the gastrointestinal tract. Casula G, Cutting SM, Appl Environ Microbiol 2002 68 2344 2352 10.1128/AEM.68.5.2344-2352.2002 11976107 (Pubitemid 34477831)
8. The intestinal life cycle of Bacillus subtilis and close relatives. Tam NK, Uyen NQ, Hong HA, Duc LH, Hoa TT, Serra CR, Henriques AO, Cutting SM, J Bacteriol 2006 188 2692 2700 10.1128/JB.188.7.2692-2700.2006 16547057
9. Oral Vaccine Delivery by Recombinant Spore Probiotics. Cutting SM, Hong HA, Baccigalupi L, Ricca E, Int Rev Immunol 2009 28 487 505 10.3109/ 08830180903215605 19954360
10. Red pigment in Bacillus megaterium spores. Mitchell C, Iyer S, Skomurski JF, Vary JC, Appl Environ Microbiol 1986 52 64 67 3089159 (Pubitemid 16064923)
11. Reclassification of bioindicator strains Bacillus subtilis DSM 675 and Bacillus subtilis DSM 2277 as Bacillus atrophaeus. Fritze D, Pukall R, Int J Syst Evol Microbiol 2001 51 35 37 11211269 (Pubitemid 32118407)
12. Bacillus indicus sp. nov., an arsenic-resistant bacterium isolated from an aquifer in West Bengal, India. Suresh K, Prabagaran SR, Sengupta S, Shivaji S, Int J Syst Evol Microbiol 2004 54 1369 1375 10.1099/ijs.0.03047-0 15280316 (Pubitemid 39139862)
13. Bacillus cibi sp. nov., isolated from jeotgal, a traditional Korean fermented seafood. Yoon JH, Lee CH, Oh TK, Int J Syst Evol Microbiol 2055 55 733 736
14. Isolation and characterisation of novel alkaliphiles from bauxite-processing waste and description of Bacillus vedderi sp. nov., a new obligate alkaliphile. Agnew MD, Koval SF, Jarrell KF, Syst Appl Microbiol 1995 18 221 230
15. Bacillus jeotgali sp. nov., isolated from jeotgal, Korean traditional fermented seafood. Yoon JH, Kang SS, Lee KC, Kho YH, Choi SH, Kang KH, Park YH, Int J Syst Evol Microbiol 2001 51 1087 1092 10.1099/00207713-51-3-1087 11411677 (Pubitemid 32499315)
16. Bacillus okuhidensis sp. nov., isolated from the Okuhida spa area of Japan. Li Z, Kawamura Y, Shida O, Yamagata S, Deguchi T, Ezaki T, Int J Syst Evol Microbiol 2002 52 1205 1209 10.1099/ijs.0.01962-0 12148629 (Pubitemid 34846418)
17. Phenetic diversity of alkaliphilic Bacillus strains: proposal for nine new species. Nielsen P, Fritze D, Priest FG, Microbiology 1995 141 1745 1761 10.1099/13500872-141-7-1745
18. DNA base composition of halophilic and nonhalophilkic Bacillus firmus strains of marine origin. Ruger HJ, Koploy JAC, Microb Ecol 1980 6 141 146 10.1007/BF02010552 (Pubitemid 10019704)
19. Carotenoids found in Bacillus. Khaneja R, Perez-Fons L, Fakhry S, Baccigalupi L, Steiger S, To E, Sandmann G, Dong TC, Ricca E, Fraser PD, Cutting SM, J. Appl. Microbiol 2010 108 1889 1902 19878522
20. Carotenoids present in halotolerant Bacillus spore formers. Duc LH, Fraser P, Cutting SM, FEMS Microbiol Lett 2006 255 215 224 10.1111/j.1574-6968. 2005.00091.x 16448498
21. The body of evidence to support a protective role for lutein and zeaxanthin in delaying chronic disease. Overview. Mares-Perlman JA, Millen AE, Ficek TL, Hankinson SE, J Nutr 2002 132 518S 524S 11880585 (Pubitemid 34208762)
22. Lycopene and prostate cancer risk. Methodological considerations in the epidemiologic literature. Giovannucci E, Pure Appl Chem 2002 74 1427 1434 10.1351/pac200274081427
23. Glycoside Hydrolases and Glycosyltransferases. Families, Modules, and Implications for Genomics. Henrissat B, Davis GJ, Plant Physiology 2000 124 1515 1519 10.1104/pp.124.4.1515 11115868 (Pubitemid 32065162)
24. A classification of nucleotide-diphospho-sugar glycosyltransferases based on amino acid sequence similarities. Campbell JA, Davies GJ, Bulone V, Henrissat B, Biochem J 1997 326 929 939 9334165 (Pubitemid 27438071)
25. Life with no sugars? Coutinho PM, Henrissat B, J Mol Microbiol Biotechnol 1999 1 307 308 10943561
26. Carbohydrate-binding modules: fine-tuning polysaccharide recognition. Boraston AB, Bolam DN, Gilbert HJ, Davies GJ, Biochem J 2004 382 769 781 10.1042/BJ20040892 15214846 (Pubitemid 39312891)
27. Evolution of Symbiotic Bacteria in the Distal Human Intestine. Xu J, Mahowald MA, Ley RE, Lozupone CA, Hamady M, Martens EC, Henrissat B, Coutinho PM, Minx P, Latreille P, Cordum H, Van Brunt A, Kim K, Fulton RS, Fulton LA, Clifton SW, Wilson RK, Knight RD, Gordon JI, PLoS Biol 2007 5 156 10.1371/journal.pbio.0050156 17579514 (Pubitemid 47105347)
28. Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Samuel BS, Hansen EE, Manchester JK, Coutinho PM, Henrissat B, Fulton R, Latreille P, Kim K, Wilson RK, Gordon JI, Proc Natl Acad Sci US 2007 104 10643 10648 10.1073/pnas.0704189104 (Pubitemid 47185718)
29. Cloning and Regulation of Erwinia herbicola Pigment Genes. Perry KL, Simonitch TA, Harrison-Lavoie KJ, Liu ST, J Bacteriol 1986 168 607 612 3023282 (Pubitemid 17172744)
30. Genetics of Eubacterial Carotenoid Biosynthesis: A Colorful Tale. Armstrong GA, Annu Rev Microbiol 1997 51 629 659 10.1146/annurev.micro.51.1.629 9343362 (Pubitemid 27433061)
31. Analysis of the Dual Regulatory Mechanisms Controlling Expression of the Vegetative Catalase Gene of Bacillus subtilis. Bol DK, Yasbin RE, J Bacteriol 1994 176 6744 6748 7961428 (Pubitemid 24338090)
32. SodA and manganese are essential for resistance to oxidative stress in growing and sporulating cells of Bacillus subtilis. Inaoka T, Matsumura Y, Tsuchido T, J Bacteriol 1999 181 1939 1943 10074093 (Pubitemid 29138632)
33. Control of cell fate by the formation of an architecturally complex bacterial community. Vlamakis H, Aguilar C, Losick R, Kolter R, Genes Dev 2008 22 945 953 10.1101/gad.1645008 18381896 (Pubitemid 351482847)
34. A major protein component of the Bacillus subtilis biofilm matrix. Branda SS, Chu F, Kearns DB, Losick R, Kolter R, Mol Microbiol 2006 59 1229 1238 10.1111/j.1365-2958.2005.05020.x 16430696
35. An accessory protein required for anchoring and assembly of amyloid fibres in B. subtilis biofilms. Romero D, Vlamakis H, Losick R, Kolter R, Mol Microbiol 2011 E-published
36. Exopolymeric substances (EPS) from Bacillus subtilis: polymers and genes encoding their synthesis. Marvasi M, Visscher PT, Casillas Martinez L, FEMS Microbiol Lett 2010 313 1 9 10.1111/j.1574-6968.2010.02085.x 20735481
37. Colonization of Mucin by Human Intestinal Bacteria and Establishment of Biofilm Communities in a Two-Stage Continuous Culture System. Macfarlane S, Woodmansey EJ, Macfarlane JT, Appl Environ Microbiol 2005 71 7483 7492 10.1128/AEM.71.11.7483-7492.2005 16269790 (Pubitemid 43194242)
38. Adhesive Properties, Extracellular Protein Production, and Metabolism in the Lactobacillus rhamnosus GG Strain when Grown in the Presence of Mucin. Borja S, Saad N, Schmitter J-M, Bressollier P, Urdaci MC, J Microbiol Biotechnol 2010 20 978 984 10.4014/jmb.0911.11007 20622495
39. Characterization of intestinal bacteria tightly bound to the human ileal epithelium. Fakhry S, Manzo N, D'Apuzzo E, Pietrini L, Sorrentini I, Ricca E, De Felice M, Baccigalupi L, Res Microbiol 2009 160 817 823 10.1016/j.resmic.2009. 09.009 19782749
40. Mucin degradation by Bifidobactrium strain isolated from human intestinal microbiota. Ruas-Madiedo P, Gueimonde M, Fernandez-Garcia M, de los Reyes-Gavilan C, Margolles A, Appl Environ Microbiol 2008 74 1936 1940 10.1128/AEM.02509-07 18223105 (Pubitemid 351400151)
41. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B, Nucleic Acids Res 2009 37 Database 233 238
42. Profile hidden Markov models. Eddy SR, Bioinformatics 1998 14 755 763 10.1093/bioinformatics/14.9.755 9918945 (Pubitemid 28552108)
43. A sensitive predictor for potential GPI lipid modification sites in fungal protein sequences and its application to genome-wide studies for Aspergillus nidulans, Candida albicans, Neurospora crassa, Saccharomyces cerevisiae and Schizosaccharomyces pombe. Eisenhaber B, Schneider G, Wildpaner M, Eisenhaber F, J Mol Biol 2004 337 243 253 10.1016/j.jmb.2004.01.025 15003443 (Pubitemid 38293395)