The structure of fadL mRNA and its interactions with RybB sRNA
Abstract
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 structure probing of a 95-nt long fragment of Salmonella fadL mRNA showed that the annealing of sRNA RybB to the coding sequence of fadL induced local rearrangements in mRNA structure. The filter retention data showed that Hfq bound RybB and fadL with tight affinities. Moreover, Hfq increased the rate of RybB annealing to fadL mRNA. Overall, the data showed that the Hfq protein directly participates in RybB interactions with fadL mRNA.
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, http://www.ncbi.nlm.nih.gov/pubmed/20979336
Beisel CL, Updegrove TB, Janson BJ, Storz G (2012) Multiple factors dictate target selection by Hfq-binding small RNAs, EMBO J 31: 1961-1974, http://www.ncbi.nlm.nih.gov/pubmed/22388518
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, http://www.ncbi.nlm.nih.gov/pubmed/22458297
Lease RA, Woodson SA (2004) Cycling of the Sm-like protein Hfq on the DsrA small regulatory RNA, J Mol Biol 344: 1211-1223, http://www.ncbi.nlm.nih.gov/pubmed/15561140
Link TM, Valentin-Hansen P, Brennan RG (2009) Structure of Escherichia coli Hfq bound to polyriboadenylate RNA, Proc Natl Acad Sci U S A 106: 19292-19297, http://www.ncbi.nlm.nih.gov/pubmed/19889981
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, http://www.ncbi.nlm.nih.gov/pubmed/3684574
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, http://www.ncbi.nlm.nih.gov/pubmed/21510661
Otaka H, Ishikawa H, Morita T, Aiba H (2011) PolyU tail of rho-independent terminator of bacterial small RNAs is essential for Hfq action, Proc Natl Acad Sci U S A 108: 13059-13064, http://www.ncbi.nlm.nih.gov/pubmed/21788484
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, http://www.ncbi.nlm.nih.gov/pubmed/23771143
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, http://www.ncbi.nlm.nih.gov/pubmed/21059903
Papenfort K, Pfeiffer V, Mika F, Lucchini S, Hinton JC, Vogel J (2006) SigmaE-dependent small RNAs of Salmonella respond to membrane stress by accelerating global omp mRNA decay, Mol Microbiol 62: 1674-1688, http://www.ncbi.nlm.nih.gov/pubmed/17427289
Peng Y, Soper TJ, Woodson SA (2014a) Positional effects of AAN motifs in rpoS regulation by sRNAs and Hfq, J Mol Biol 426: 275-285, http://www.ncbi.nlm.nih.gov/pubmed/24051417
Peng Y, Curtis JE, Fang X, Woodson SA (2014b) Structural model of an mRNA in complex with the bacterial chaperone Hfq, Proc Natl Acad Sci U S A 111: 17134-17139, http://www.ncbi.nlm.nih.gov/pubmed/25404287
Reuter JS, Mathews DH (2010) RNAstructure: software for RNA secondary structure prediction and analysis, BMC Bioinformatics 11: 129, http://www.ncbi.nlm.nih.gov/pubmed/20230624
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, http://www.ncbi.nlm.nih.gov/pubmed/23510801
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, http://www.ncbi.nlm.nih.gov/pubmed/22661574
Sauer E, Weichenrieder O (2011) Structural basis for RNA 3'-end recognition by Hfq, Proc Natl Acad Sci U S A 108: 13065-13070, http://www.ncbi.nlm.nih.gov/pubmed/21737752
Sauer E, Schmidt S, Weichenrieder O (2012) Small RNA binding to the lateral surface of Hfq hexamers and structural rearrangements upon mRNA target recognition, Proc Natl Acad Sci U S A 109: 9396-9401, http://www.ncbi.nlm.nih.gov/pubmed/22645344
Schu DJ, Zhang A, Gottesman S, Storz G (2015) Alternative Hfq-sRNA interaction modes dictate alternative mRNA recognition, EMBO J 34: 2557-2573, http://www.ncbi.nlm.nih.gov/pubmed/26373314
Soper T, Mandin P, Majdalani N, Gottesman S, Woodson SA (2010) Positive regulation by small RNAs and the role of Hfq, Proc. Natl. Acad. Sci. U.S.A., http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20457943
Soper TJ, Woodson SA (2008) The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA, RNA 14: 1907-1917, http://www.ncbi.nlm.nih.gov/pubmed/18658123
Soper TJ, Doxzen K, Woodson SA (2011) Major role for mRNA binding and restructuring in sRNA recruitment by Hfq, RNA 17: 1544-1550, http://www.ncbi.nlm.nih.gov/pubmed/21705431
Updegrove TB, Zhang A, Storz G (2016) Hfq: the flexible RNA matchmaker, Curr Opin Microbiol 30: 133-138, http://www.ncbi.nlm.nih.gov/pubmed/26907610
Waters LS, Storz G (2009) Regulatory RNAs in bacteria, Cell 136: 615-628, http://www.ncbi.nlm.nih.gov/pubmed/19239884
Wroblewska Z, Olejniczak M (2016) Hfq assists small RNAs in binding to the coding sequence of ompD mRNA and in rearranging its structure, RNA, http://www.ncbi.nlm.nih.gov/pubmed/27154968
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, http://www.ncbi.nlm.nih.gov/pubmed/23318956
Acta Biochimica Polonica is an OpenAccess quarterly and publishes four issues a year. All contents are distributed under the Creative Commons Attribution-ShareAlike 4.0 International (CC BY 4.0) license. Everybody may use the content following terms: Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
Copyright for all published papers © stays with the authors.
Copyright for the journal: © Polish Biochemical Society.
