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2016 | 63 | 4 | 835-840
Article title

The structure of fadL mRNA and its interactions with RybB sRNA

Content
Title variants
Languages of publication
EN
Abstracts
EN
Small bacterial RNAs (sRNAs) regulate translation by pairing with complementary sequences in their target mRNAs, in a process which is often dependent on the Hfq protein. Here, the secondary structure of a 95-nt long fragment of Salmonella fadL mRNA containing RybB sRNA binding site in the coding region was analyzed. The data indicated local rearrangements in this mRNA structure after the annealing of RybB. The filter retention data had shown that Hfq bound both RybB and the fadL mRNA fragment with tight affinities. Moreover, Hfq increased the rate of RybB annealing to fadL mRNA. These data indicate that Hfq directly participates in RybB interactions with the fadL mRNA.
Keywords
EN
Hfq   sRNA   mRNA   RybB   fadL   coding sequence  
Publisher

Year
Volume
63
Issue
4
Pages
835-840
Physical description
Dates
published
2016
received
2016-06-06
revised
2016-10-21
accepted
2016-10-24
(unknown)
2016-11-25
Contributors
  • Department of Biochemistry, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
  • Department of Biochemistry, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
  • Department of Biochemistry, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
References
  • Balbontin R, Fiorini F, Figueroa-Bossi N, Casadesus J, Bossi L (2010) Recognition of heptameric seed sequence underlies multi-target regulation by RybB small RNA in Salmonella enterica. Mol Microbiol 78: 380-394. https://doi.org/10.1111/j.1365-2958.2010.07342.x.
  • Black PN, Said B, Ghosn CR, Beach JV, Nunn WD (1987) Purification and characterization of an outer membrane-bound protein involved in long-chain fatty acid transport in Escherichia coli. J Biol Chem 262: 1412-1419. http://www.ncbi.nlm.nih.gov/pubmed/3027089.
  • Bouvier M, Sharma CM, Mika F, Nierhaus KH, Vogel J (2008) Small RNA binding to 5' mRNA coding region inhibits translational initiation. Mol Cell 32: 827-837. https://doi.org/10.1016/j.molcel.2008.10.027.
  • Chen S, Zhang A, Blyn LB, Storz G (2004) MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli. J Bacteriol 186: 6689-6697. https://doi.org/10.1128/JB.186.20.6689-6697.2004.
  • Ciesiolka J, Wrzesinski J, Gornicki P, Podkowinski J, Krzyzosiak WJ (1989) Analysis of magnesium, europium and lead binding sites in methionine initiator and elongator tRNAs by specific metal-ion-induced cleavages. Eur J Biochem 186: 71-77. https://doi.org/10.1111/j.1432-1033.1989.tb15179.x.
  • Corcoran CP, Podkaminski D, Papenfort K, Urban JH, Hinton JC, Vogel J (2012) Superfolder GFP reporters validate diverse new mRNA targets of the classic porin regulator, MicF RNA. Mol Microbiol 84: 428-445. https://doi.org/10.1111/j.1365-2958.2012.08031.x.
  • Figueroa-Bossi N, Valentini M, Malleret L, Fiorini F, Bossi L (2009) Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target. Genes Dev 23: 2004-2015. https://doi.org/10.1101/gad.541609.
  • Guo MS, Updegrove TB, Gogol EB, Shabalina SA, Gross CA, Storz G (2014) MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein. Genes Dev 28: 1620-1634. https://doi.org/10.1101/gad.243485.114.
  • Jorgensen MG, Thomason MK, Havelund J, Valentin-Hansen P, Storz G (2013) Dual function of the McaS small RNA in controlling biofilm formation. Genes Dev 27: 1132-1145. https://doi.org/10.1101/gad.214734.113.
  • Lease RA, Woodson SA (2004) Cycling of the Sm-like protein Hfq on the DsrA small regulatory RNA. J Mol Biol 344: 1211-1223. https://doi.org/10.1016/j.jmb.2004.10.006.
  • Malecka EM, Strozecka J, Sobanska D, Olejniczak M (2015) Structure of bacterial regulatory RNAs determines their performance in competition for the chaperone protein Hfq. Biochemistry 54: 1157-1170. https://doi.org/10.1021/bi500741d.
  • Milligan JF, Groebe DR, Witherell GW, Uhlenbeck OC (1987) Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res 15: 8783-8798. https://doi.org/10.1093/nar/15.21.8783.
  • Nunn WD, Simons RW (1978) Transport of long-chain fatty acids by Escherichia coli: mapping and characterization of mutants in the fadL gene. Proc Natl Acad Sci U S A 75: 3377-3381. http://www.ncbi.nlm.nih.gov/pubmed/356053.
  • Olejniczak M (2011) Despite similar binding to the Hfq protein regulatory RNAs widely differ in their competition performance. Biochemistry 50: 4427-4440. https://doi.org/10.1021/bi102043f.
  • Panja S, Santiago-Frangos A, Schu DJ, Gottesman S, Woodson SA (2015) Acidic residues in the Hfq chaperone increase the selectivity of sRNA binding and annealing. J Mol Biol 427: 3491-3500. https://doi.org/10.1016/j.jmb.2015.07.010.
  • Panja S, Schu DJ, Woodson SA (2013) Conserved arginines on the rim of Hfq catalyze base pair formation and exchange. Nucleic Acids Res 41: 7536-7546. https://doi.org/10.1093/nar/gkt521.
  • Papenfort K, Bouvier M, Mika F, Sharma CM, Vogel J (2010) Evidence for an autonomous 5' target recognition domain in an Hfq-associated small RNA. Proc Natl Acad Sci U S A 107: 20435-20440. https://doi.org/10.1073/pnas.1009784107.
  • Papenfort K, Vogel J (2010) Regulatory RNA in bacterial pathogens. Cell Host Microbe 8: 116-127. 10.1016/j.chom.2010.06.008.
  • Parker A, Gottesman S (2016) Small RNA Regulation of TolC, the outer membrane component of bacterial multidrug transporters. J Bacteriol 198: 1101-1113. https://doi.org/10.1128/JB.00971-15.
  • Peng Y, Curtis JE, Fang X, Woodson SA (2014a) Structural model of an mRNA in complex with the bacterial chaperone Hfq. Proc Natl Acad Sci U S A 111: 17134-17139. https://doi.org/10.1073/pnas.1410114111.
  • Peng Y, Soper TJ, Woodson SA (2014b) Positional effects of AAN motifs in rpoS regulation by sRNAs and Hfq. J Mol Biol 426: 275-285. https://doi.org/10.1016/j.jmb.2013.08.026.
  • Pfeiffer V, Papenfort K, Lucchini S, Hinton JC, Vogel J (2009) Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation. Nat Struct Mol Biol 16: 840-846. https://doi.org/10.1038/nsmb.1631.
  • Reuter JS, Mathews DH (2010) RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics 11: 129. https://doi.org/10.1186/1471-2105-11-129.
  • Ross JA, Ellis MJ, Hossain S, Haniford DB (2013) Hfq restructures RNA-IN and RNA-OUT and facilitates antisense pairing in the Tn10/IS10 system. RNA 19: 670-684. https://doi.org/10.1261/rna.037747.112.
  • Salim NN, Faner MA, Philip JA, Feig AL (2012) Requirement of upstream Hfq-binding (ARN)x elements in glmS and the Hfq C-terminal region for GlmS upregulation by sRNAs GlmZ and GlmY. Nucleic Acids Res 40: 8021-8032. https://doi.org/10.1093/nar/gks392.
  • Santiago-Frangos A, Kavita K, Schu DJ, Gottesman S, Woodson SA (2016) C-terminal domain of the RNA chaperone Hfq drives sRNA competition and release of target RNA. Proc Natl Acad Sci U S A 113: E6089-E6096. https://doi.org/10.1073/pnas.1613053113.
  • Schu DJ, Zhang A, Gottesman S, Storz G (2015) Alternative Hfq-sRNA interaction modes dictate alternative mRNA recognition. EMBO J 34: 2557-2573. https://doi.org/10.15252/embj.201591569.
  • Soper TJ, Doxzen K, Woodson SA (2011) Major role for mRNA binding and restructuring in sRNA recruitment by Hfq. RNA 17: 1544-1550. https://doi.org/10.1261/rna.2767211.
  • Soper TJ, Woodson SA (2008) The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA. RNA 14: 1907-1917. https://doi.org/10.1261/rna.1110608.
  • Tree JJ, Granneman S, McAteer SP, Tollervey D, Gally DL (2014) Identification of bacteriophage-encoded anti-sRNAs in pathogenic Escherichia coli. Mol Cell 55: 199-213. https://doi.org/10.1016/j.molcel.2014.05.006.
  • Updegrove TB, Zhang A, Storz G (2016) Hfq: the flexible RNA matchmaker. Curr Opin Microbiol 30: 133-138. https://doi.org/10.1016/j.mib.2016.02.003.
  • Wagner EG, Romby P (2015) Small RNAs in bacteria and archaea: who they are, what they do, and how they do it. Adv Genet 90: 133-208. https://doi.org/10.1016/bs.adgen.2015.05.001.
  • Waters LS, Storz G (2009) Regulatory RNAs in bacteria. Cell 136: 615-628. https://doi.org/10.1016/j.cell.2009.01.043.
  • Wroblewska Z, Olejniczak M (2016a) Contributions of the Hfq protein to translation regulation by small noncoding RNAs binding to the mRNA coding sequence Acta Biochim Pol 63: 701-707. https://doi.org/10.18388/abp.2016_1362.
  • Wroblewska Z, Olejniczak M (2016b) Hfq assists small RNAs in binding to the coding sequence of ompD mRNA and in rearranging its structure. RNA 22: 979-994. https://doi.org/10.1261/rna.055251.115.
  • Zhang A, Schu DJ, Tjaden BC, Storz G, Gottesman S (2013) Mutations in interaction surfaces differentially impact E. coli Hfq association with small RNAs and their mRNA targets. J Mol Biol 425: 3678-3697. https://doi.org/10.1016/j.jmb.2013.01.006.
  • Zheng A, Panja S, Woodson SA (2016) Arginine patch predicts the RNA annealing activity of Hfq from gram-negative and gram-positive bacteria. J Mol Biol 428: 2259-2264. https://doi.org/10.1016/j.jmb.2016.03.027.
Document Type
Publication order reference
Identifiers
YADDA identifier
bwmeta1.element.bwnjournal-article-abpv63p835kz
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