Identification of target transcripts regulated by small RNA RyhB homologs in Salmonella: RyhB-2 regulates motility phenotype

Microbiological Research

Volumn 168, Issue 10, 2013, Pages 621-629

  Kim, Jeong Nam ^a,b   Kwon, Young Min ^a  

^a UNIVERSITY OF ARKANSAS   (United States)

^b UNIVERSITY OF FLORIDA   (United States)

Author keywords

Microarray analysis; Motility; RyhB; Salmonella; Small RNAs

Indexed keywords

CELLULAR PATHWAY; MICROARRAY ANALYSIS; MOTILITY; POST-TRANSCRIPTIONAL; REGULATORY NETWORK; RYHB; SALMONELLA TYPHIMURIUM; SMALL RNA;

BIOCHEMISTRY; GENES; MICROARRAYS; NUCLEIC ACIDS; TRANSCRIPTION;

SALMONELLA;

BACTERIUM; BIOASSAY; CHEMOTAXIS; GENE; MOTILITY; PHENOTYPE; RNA;

SALMONELLA; SALMONELLA TYPHIMURIUM;

BACTERIAL RNA; RYHB; SMALL UNTRANSLATED RNA;

ARTICLE; GENE DELETION; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; LOCOMOTION; METABOLISM; MICROARRAY ANALYSIS; MOTILITY; PHENOTYPE; PHYSIOLOGY; RNA INTERFERENCE; SALMONELLA; SALMONELLA TYPHIMURIUM; SMALL RNAS;

MICROARRAY ANALYSIS; MOTILITY; RYHB; SALMONELLA; SMALL RNAS;

GENE DELETION; GENE EXPRESSION; GENE EXPRESSION REGULATION, BACTERIAL; GENE REGULATORY NETWORKS; LOCOMOTION; MICROARRAY ANALYSIS; PHENOTYPE; RNA INTERFERENCE; RNA, BACTERIAL; RNA, SMALL UNTRANSLATED; SALMONELLA TYPHIMURIUM;

EID: 84884987724     PISSN: 09445013     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.micres.2013.06.002     Document Type: Article

References (31)

1. Alice A.F., Naka H., Crosa J.H. Global gene expression as a function of the iron status of the bacterial cell: influence of differentially expressed genes in the virulence of the human pathogen Vibrio vulnificus. Infect Immun 2008, 76(9):4019-4037.
2. Andrews S.C., Robinson A.K., Rodriguez-Quinones F. Bacterial iron homeostasis. FEMS Microbiol Rev 2003, 27(2-3):215-237.
3. Blair D.F. How bacteria sense and swim. Annu Rev Microbiol 1995, 49:489-522.
4. Darwin K.H., Miller V.L. Type III secretion chaperone-dependent regulation: activation of virulence genes by SicA and InvF in Salmonella typhimurium. EMBO J 2001, 20(8):1850-1862.
5. Datsenko K.A., Wanner B.L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA 2000, 97(12):6640-6645.
6. Djordjevic S., Stock A.M. Structural analysis of bacterial chemotaxis proteins: components of a dynamic signaling system. J Struct Biol 1998, 124(2-3):189-200.
7. Ellermeier J.R., Slauch J.M. Fur regulates expression of the Salmonella pathogenicity island 1 type III secretion system through HilD. J Bacteriol 2008, 190(2):476-486.
8. Falke J.J., Bass R.B., Butler S.L., Chervitz S.A., Danielson M.A. The two-component signaling pathway of bacterial chemotaxis: a molecular view of signal transduction by receptors, kinases, and adaptation enzymes. Annu Rev Cell Dev Biol 1997, 13:457-512.
9. Girgis H.S., Liu Y., Ryu W.S., Tavazoie S. A comprehensive genetic characterization of bacterial motility. PLoS Genet 2007, 3(9):1644-1660.
10. Harshey R.M., Matsuyama T. Dimorphic transition in Escherichia coli and Salmonella typhimurium: surface-induced differentiation into hyperflagellate swarmer cells. Proc Natl Acad Sci USA 1994, 91(18):8631-8635.
11. Inoue T., Shingaki R., Hirose S., Waki K., Mori H., Fukui K. Genome-wide screening of genes required for swarming motility in Escherichia coli K-12. J Bacteriol 2007, 189(3):950-957.
12. Kihara M., Minamino T., Yamaguchi S., Macnab R.M. Intergenic suppression between the flagellar MS ring protein FliF of Salmonella and FlhA, a membrane component of its export apparatus. J Bacteriol 2001, 183(5):1655-1662.
13. Kim J.N., Kwon Y.M. Genetic and phenotypic characterization of the RyhB regulon in Salmonella Typhimurium. Microbiol Res 2013, 168(1):41-49.
14. Kubori T., Shimamoto N., Yamaguchi S., Namba K., Aizawa S. Morphological pathway of flagellar assembly in Salmonella typhimurium. J Mol Biol 1992, 226(2):433-446.
15. Lease R.A., Smith D., McDonough K., Belfort M. The small noncoding DsrA RNA is an acid resistance regulator in Escherichia coli. J Bacteriol 2004, 186(18):6179-6185.
16. Liu W.T., Karavolos M.H., Bulmer D.M., Allaoui A., Hormaeche R.D., Lee J.J., Khan C.M. Role of the universal stress protein UspA of Salmonella in growth arrest, stress and virulence. Microb Pathog 2007, 42(1):2-10.
17. Macnab R.M. Flagella and motility. Escherichia coli and Salmonella: cellular and molecular biology 1996, 123-145. ASM Press, Washington, DC. F.C. Neidhardt, R. Curtiss, J.L. Ingraham, E.C.C. Lin, K.B. Low, B. Magasanik, W.S. Reznikoff, M. Riley, M. Schaechter, H.E. Umbarger (Eds.).
18. Masse E., Gottesman S. A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc Natl Acad Sci USA 2002, 99(7):4620-4625.
19. Masse E., Vanderpool C.K., Gottesman S. Effect of RyhB small RNA on global iron use in Escherichia coli. J Bacteriol 2005, 187(20):6962-6971.
20. Mey A.R., Craig S.A., Payne S.M. Characterization of Vibrio cholerae RyhB: the RyhB regulon and role of ryhB in biofilm formation. Infec Immun 2005, 73(9):5706-5719.
21. Murphy E.R., Payne S.M. RyhB an iron-responsive small RNA molecule, regulates Shigella dysenteriae virulence. Infect Immun 2007, 75(7):3470-3477.
22. Nambu T., Minamino T., Macnab R.M., Kutsukake K. Peptidoglycan-hydrolyzing activity of the FlgJ protein, essential for flagellar rod formation in Salmonella typhimurium. J Bacteriol 1999, 181(5):1555-1561.
23. Oglesby A.G., Farrow J.M., Lee J.H., Tomaras A.P., Greenberg E.P., Pesci E.C., Vasil M.L. The influence of iron on Pseudomonas aeruginosa physiology: a regulatory link between iron and quorum sensing. J Biol Chem 2008, 283(23):15558-15567.
24. Padalon-Brauch G., Hershberg R., Elgrably-Weiss M., Baruch K., Rosenshine I., Margalit H., Altuvia S. Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence. Nucleic Acids Res 2008, 36(6):1913-1927.
25. Papenfort K., Pfeiffer V., Mika F., Lucchini S., Hinton J.C., Vogel J. SigmaE-dependent small RNAs of Salmonella respond to membrane stress by accelerating global omp mRNA decay. Mol Microbiol 2006, 62(6):1674-1688.
26. Ratledge C., Dover L.G. Iron metabolism in pathogenic bacteria. Annu Rev Microbiol 2000, 54:881-941.
27. Robinson V.L., Buckler D.R., Stock A.M. A tale of two components: a novel kinase and a regulatory switch. Nat Struct Biol 2000, 7(8):626-633.
28. Tang Y., Guest J.R., Artymiuk P.J., Read R.C., Green J. Post-transcriptional regulation of bacterial motility by aconitase proteins. Mol Microbiol 2004, 51(6):1817-1826.
29. Tjaden B., Goodwin S.S., Opdyke J.A., Guillier M., Fu D.X., Gottesman S., Storz G. Target prediction for small, noncoding RNAs in bacteria. Nucleic Acids Res 2006, 34(9):2791-2802.
30. Vogel J., Sharma C.M. How to find small non-coding RNAs in bacteria. Biol Chem 2005, 386(12):1219-1238.
31. Wooldridge K.G., Williams P.H. Iron uptake mechanisms of pathogenic bacteria. FEMS Microbiol Rev 1993, 12(4):325-348.