A GntR-type transcriptional repressor controls sialic acid utilization in Bifidobacterium breve UCC2003

FEMS Microbiology Letters

Volumn 362, Issue 4, 2015, Pages

  Egan, Muireann ^a   O'Connell Motherway, Mary ^a   van Sinderen, Douwe ^a  

^a UNIVERSITY COLLEGE CORK   (Ireland)

Author keywords

Bifidobacteria; Human milk oligosaccharides; Mucin; Neuraminic acid; Transcriptional repression

Indexed keywords

SIALIC ACID; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR NANR; TRANSCRIPTOME; UNCLASSIFIED DRUG; BACTERIAL DNA; BACTERIAL PROTEIN; N ACETYLNEURAMINIC ACID; REPRESSOR PROTEIN;

ARTICLE; BACTERIAL CELL; BACTERIAL GENE; BACTERIAL STRAIN; BIFIDOBACTERIUM BREVE; CARBOHYDRATE METABOLISM; CONTROLLED STUDY; ESCHERICHIA COLI; GENE CLUSTER; INVERTED REPEAT; NANR GENE; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DETERMINATION; PROTEIN DNA BINDING; PROTEIN EXPRESSION; PROTEIN FUNCTION; RNA ANALYSIS; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION REGULATION; UPREGULATION; BIFIDOBACTERIUM; CHEMISTRY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MULTIGENE FAMILY; OPERATOR GENE; REGULATORY SEQUENCE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

BACTERIAL PROTEINS; BIFIDOBACTERIUM; DNA, BACTERIAL; ESCHERICHIA COLI; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; MULTIGENE FAMILY; MUTAGENESIS, INSERTIONAL; N-ACETYLNEURAMINIC ACID; OPERATOR REGIONS, GENETIC; PROMOTER REGIONS, GENETIC; REGULATORY ELEMENTS, TRANSCRIPTIONAL; REPRESSOR PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

EID: 84954290113     PISSN: 03781097     EISSN: 15746968     Source Type: Journal    
DOI: 10.1093/femsle/fnu056     Document Type: Article

References (44)

1. Altschul SF, Gish W, MillerW, et al. Basic local alignment search tool. J Mol Biol 1990;215:403-10.
2. Alvarez-Martin P, O'Connell MotherwayM, Turroni F, et al. A twocomponent regulatory system controls autoregulated serpin expression in Bifidobacterium breve UCC2003. Appl Environ Microb 2012;78:7032-41.
3. Aá lvarez-Martáin P, O'Connell-Motherway M, van Sinderen D, et al. Functional analysis of the pBC1 replicon from Bifidobacterium catenulatum L48. Appl Microbiol Biot 2007;76: 1395-402.
4. Bordoni A, Amaretti A, Leonardi A, et al. Cholesterol-lowering probiotics: in vitro selection and in vivo testing of bifidobacteria.Appl Microbiol Biot 2013;97:8273-81.
5. Bottacini F, O'Connell Motherway M, Kuczynski J, et al. Comparative genomics of the Bifidobacterium breve taxon. BMC Genomics 2014;15:170.
6. Cohn M, Horibata K. Inhibition by glucose of the induced synthesis of the beta-galactoside-enzyme system of Escherichia coli. Analysis of maintenance. J Bacteriol 1959;78:601-12.
7. Egan M, O'Connell Motherway M, Ventura M, et al. Metabolism of sialic acid by Bifidobacterium breve UCC2003. Appl Environ Microb 2014;80:4414-26.
8. Finn RD, Mistry J, Tate J, et al. The Pfam protein families database.Nucleic Acids Res 2010;38:D211-22.
9. Fujita Y, Fujita T. The gluconate operon gnt of Bacillus subtilis encodes its own transcriptional negative regulator. P Natl Acad Sci USA 1987;84:4524-8.
10. Gorke B, Stulke J. Carbon catabolite repression in bacteria: many ways to make the most out of nutrients. Nat Rev Microbiol 2008;6:613-24.
11. Goujon M, McWilliam H, Li W, et al. A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res 2010;38: W695-9.
12. Hamoen LW, Van Werkhoven AF, Bijlsma JJE, et al. The competence transcription factor of Bacillus subtilis recognizes short A/T-rich sequences arranged in a unique, flexible pattern along the DNA helix. Gene Dev 1998;12:1539-50.
13. Haydon DJ, Guest JR. A new family of bacterial regulatory proteins.FEMS Microbiol Lett 1991;79:291-6.
14. Hoskisson PA, Rigali S. Variation in form and function: the helixturn- helix regulators of the GntR superfamily. Adv Appl Microbiol 2009;69:1-22.
15. Hwang J, Kim BS, Jang SY, et al. Structural insights into the regulation of sialic acid catabolism by the Vibrio vulnificus transcriptional repressor NanR. P Natl Acad Sci USA 2013;110:E2829-37.
16. Kalivoda KA, Steenbergen SM, Vimr ER, et al. Regulation of sialic acid catabolism by the DNA binding protein NanR in Escherichia coli. J Bacteriol 2003;185:4806-15.
17. Kim BS,Hwang J, Kim MH, et al. Cooperative regulation of the Vibrio vulnificus nan gene cluster by NanR protein, cAMP receptor protein, and N-acetylmannosamine 6-phosphate. J Biol Chem 2011;286:40889-99.
18. Law J, Buist G, Haandrikman A, et al. A system to generate chromosomal mutations in Lactococcus lactis which allows fast analysis of targeted genes. J Bacteriol 1995;177:7011-8.
19. LeBlanc JG, Milani C, de Giori GS, et al. Bacteria as vitamin suppliers to their host: a gut microbiota perspective. Curr Opin Biotech 2013;24:160-8.
20. Lee J-H, O'Sullivan D. Genomic insights into bifidobacteria. Microbiol Mol Biol R 2010;74:378-416.
21. Lugli GA, Milani C, Turroni F, et al. Investigation of the evolutionary development of the genus Bifidobacterium by comparative genomics. Appl Environ Microb 2014;80:6383-94.
22. Maze A, O'Connell-Motherway M, Fitzgerald G, et al. Identification and characterization of a fructose phosphotransferase system in Bifidobacterium breve UCC2003. Appl Environ Microb 2007;73:545-53.
23. Milani C, Lugli GA, Duranti S, et al. Genome encyclopaedia of type strains of the genus Bifidobacterium. Appl Environ Microb 2014;80:6290-302
24. O'Connell KJ, O'Connell MotherwayM, Liedtke A, et al. Transcription of two adjacent carbohydrate utilization gene clusters in Bifidobacterium breve UCC2003 is controlled by LacI- and repressor open reading frame kinase (ROK)-type regulators.Appl Environ Microb 2014;80:3604-14.
25. O'Connell Motherway M, Fitzgerald GF, van Sinderen D. Metabolism of a plant derived galactose-containing polysaccharide by Bifidobacterium breve UCC2003. Microb Biotechnol 2011a;4:403-16.
26. O'Connell Motherway M, O'Driscoll J, Fitzgerald GF, et al. Overcoming the restriction barrier to plasmid transformation and targeted mutagenesis in Bifidobacterium breve UCC2003. Microb Biotechnol 2009;2:321-32.
27. O'Connell Motherway M, Zomer A, Leahy SC, et al. Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor. P Natl Acad Sci USA 2011b;108:11217-22.
28. OlsonME, King JM, Yahr TL, et al. Sialic acid catabolism in Staphylococcus aureus. J Bacteriol 2013;195:1779-88.
29. Plumbridge J, Vimr E. Convergent pathways for utilization of the amino sugars N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminic acid by Escherichia coli. J Bacteriol 1999;181:47-54.
30. Pokusaeva K, Neves AR, Zomer A, et al. Ribose utilization by the human commensal Bifidobacterium breve UCC2003. Microb Biotechnol 2010;3:311-23.
31. Pokusaeva K, O'Connell MM, Zomer A, et al. Cellodextrin utilization by Bifidobacterium breve UCC2003. Appl Environ Microb 2011;77:1681-90.
32. Rigali S, Derouaux A, Giannotta F, et al. Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA Subfamilies. J Biol Chem 2002;277:12507-15.
33. Riordan O. Studies on antimicrobial activity and genetic diversity of Bifidobacterium species: molecular characterization of a 5.75 kb plasmid and a chromosomally encoded recA gene homologue from Bifidobacterium breve. Ph.D. Thesis. National University of Ireland Cork 1998.
34. Rutherford K, Parkhill J, Crook J, et al. Artemis: sequence visualization and annotation. Bioinformatics 2000;16:944-5.
35. Sambrook J, Fritsch EF, Maniatis T. Molecular Cloning a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory, 1989.
36. Schell M, Karmirantzou M, Snel B, et al. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. P Natl Acad Sci USA 2002;99:14422-7.
37. Sela DA, Chapman J, Adeuya A, et al. The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infantmicrobiome. P Natl Acad Sci USA 2008;105:18964-9.
38. Servin AL. Antagonistic activities of lactobacilli and bifidobacteria against microbial pathogens. FEMS Microbiol Rev 2004;28:405-40.
39. van Aalten DMF, DiRusso CC, Knudsen J, et al. Crystal structure of FadR, a fatty acid-responsive transcription factor with a novel acyl coenzyme A-binding fold. EMBO J 2000;19:5167-77
40. Ventura M, Canchaya C, Fitzgerald G, et al. Genomics as a means to understand bacterial phylogeny and ecological adaptation: the case of bifidobacteria. Anton van Leeuw 2007;91:351- 72
41. Ventura M, Zink R, Fitzgerald GF, et al. Gene structure and transcriptional organization of the dnaK operon of Bifidobacterium breve UCC2003 and application of the operon in bifidobacterial tracing. Appl Environ Microb 2005;71:487-500.
42. White R. Control of amino sugar metabolism in Escherichia coli and isolation of mutants unable to degrade amino sugars.Biochem J 1968;106:847-58.
43. Xu Y, Heath RJ, Li Z, et al. The FadR˙DNA Complex: transcriptional control of fatty acid metabolism in Escherichia coli. J Biol Chem 2001;276:17373-9.
44. Zomer A, Fernandez M, Kearney B, et al. An interactive regulatory network controls stress response in Bifidobacterium breve UCC2003. J Bacteriol 2009;191:7039-49.