Browse > Article
http://dx.doi.org/10.14348/molcells.2019.0040

Mechanisms for Hfq-Independent Activation of rpoS by DsrA, a Small RNA, in Escherichia coli  

Kim, Wonkyong (Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST))
Choi, Jee Soo (Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST))
Kim, Daun (Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST))
Shin, Doohang (Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST))
Suk, Shinae (Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST))
Lee, Younghoon (Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST))
Publication Information
Molecules and Cells / v.42, no.5, 2019 , pp. 426-439 More about this Journal
Abstract
Many small RNAs (sRNAs) regulate gene expression by base pairing to their target messenger RNAs (mRNAs) with the help of Hfq in Escherichia coli. The sRNA DsrA activates translation of the rpoS mRNA in an Hfq-dependent manner, but this activation ability was found to partially bypass Hfq when DsrA is overproduced. The precise mechanism by which DsrA bypasses Hfq is unknown. In this study, we constructed strains lacking all three rpoS-activating sRNAs (i.e., ArcZ, DsrA, and RprA) in $hfq^+$ and $Hfq^-$ backgrounds, and then artificially regulated the cellular DsrA concentration in these strains by controlling its ectopic expression. We then examined how the expression level of rpoS was altered by a change in the concentration of DsrA. We found that the translation and stability of the rpoS mRNA are both enhanced by physiological concentrations of DsrA regardless of Hfq, but that depletion of Hfq causes a rapid degradation of DsrA and thereby decreases rpoS mRNA stability. These results suggest that the observed Hfq dependency of DsrA-mediated rpoS activation mainly results from the destabilization of DsrA in the absence of Hfq, and that DsrA itself contributes to the translational activation and stability of the rpoS mRNA in an Hfq-independent manner.
Keywords
DsrA; Escherichia coli; Hfq; rpoS; small RNAs;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Andrade, J.M., Dos Santos, R.F., Chelysheva, I., Ignatova, Z., and Arraiano, C.M. (2018). The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity. EMBO J. 37, e97631.   DOI
2 Andrade, J.M., Pobre, V., Matos, A.M., and Arraiano, C.M. (2012). The crucial role of PNPase in the degradation of small RNAs that are not associated with Hfq. RNA 18, 844-855.   DOI
3 Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K.A., Tomita, M., Wanner, B.L., and Mori, H. (2006). Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2, 2006.0008.   DOI
4 Bak, G., Han, K., Kim, D., and Lee, Y. (2014). Roles of rpoS-activating small RNAs in pathways leading to acid resistance of Escherichia coli. Microbiologyopen 3, 15-28.   DOI
5 Bandyra, K.J., Said, N., Pfeiffer, V., Górna, M.W., Vogel, J., and Luisi, B.F. (2012). The seed region of a small RNA drives the controlled destruction of the target mRNA by the endoribonuclease RNase E. Mol. Cell 47, 943-953.   DOI
6 Bobrovskyy, M., and Vanderpool, C.K. (2013). Regulation of bacterial metabolism by small RNAs using diverse mechanisms. Annu. Rev. Genet. 47, 209-232.   DOI
7 Brennan, R.G., and Link, T.M. (2007). Hfq structure, function and ligand binding. Curr. Opin. Microbiol. 10, 125-133.   DOI
8 Cherepanov, P.P., and Wackernagel, W. (1995). Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flpcatalyzed excision of the antibiotic-resistance determinant. Gene 158, 9-14.   DOI
9 De Lay, N., Schu, D.J., and Gottesman, S. (2013). Bacterial small RNAbased negative regulation: Hfq and its accomplices. J. Biol. Chem. 288, 7996-8003.   DOI
10 Desnoyers, G., and Masse, E. (2012). Noncanonical repression of translation initiation through small RNA recruitment of the RNA chaperone Hfq. Genes Dev. 26, 726-739.   DOI
11 Folichon, M., Arluison, V., Pellegrini, O., Huntzinger, E., Regnier, P., and Hajnsdorf, E. (2003). The poly(A) binding protein Hfq protects RNA from RNase E and exoribonucleolytic degradation. Nucleic Acids Res. 31, 7302-7310.   DOI
12 Gottesman, S., and Storz, G. (2011). Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harb. Perspect. Biol. 3, a003798.   DOI
13 Hammerle, H., Veecrek, B., Resch, A., and Blasi, U. (2013). Duplex formation between the sRNA DsrA and rpoS mRNA is not sufficient for efficient RpoS synthesis at low temperature. RNA Biol. 10, 1834-1841.   DOI
14 Hopkins, J.F., Panja, S., and Woodson, S.A. (2011). Rapid binding and release of Hfq from ternary complexes during RNA annealing. Nucleic Acids Res. 39, 5193-5202.   DOI
15 Ikeda, Y., Yagi, M., Morita, T., and Aiba, H. (2011). Hfq binding at RhlB-recognition region of RNase E is crucial for the rapid degradation of target mRNAs mediated by sRNAs in Escherichia coli. Mol. Microbiol. 79, 419-432.   DOI
16 Kim, S., Kim, H., Park, I., and Lee, Y. (1996). Mutational analysis of RNA structures and sequences postulated to affect 3' processing of M1 RNA, the RNA component of Escherichia coli RNase P. J. Biol. Chem. 271, 19330-19337.   DOI
17 Lalaouna, D., and Masse, E. (2016). The spectrum of activity of the small RNA DsrA: not so narrow after all. Curr. Genet. 62, 261-264.   DOI
18 Lease, R.A., Cusick, M.E., and Belfort, M. (1998). Riboregulation in Escherichia coli: DsrA RNA acts by RNA:RNA interactions at multiple loci. Proc. Natl. Acad. Sci. U. S. A. 95, 12456-12461.   DOI
19 Lalaouna, D., Morissette, A., Carrier, M.C., and Masse, E. (2015). DsrA regulatory RNA represses both hns and rbsD mRNAs through distinct mechanisms in Escherichia coli. Mol. Microbiol. 98, 357-369.   DOI
20 Lease, R.A., and Belfort, M. (2000). Riboregulation by DsrA RNA: trans-actions for global economy. Mol. Microbiol. 38, 667-672.   DOI
21 Lease, R.A., and Woodson, S.A. (2004). Cycling of the Sm-like protein Hfq on the DsrA small regulatory RNA. J. Mol. Biol. 344, 1211-1223.   DOI
22 Link, T.M., Valentin-Hansen, P., and Brennan, R.G. (2009). Structure of Escherichia coli Hfq bound to polyriboadenylate RNA. Proc. Natl. Acad. Sci. U. S. A. 106, 19292-19297.   DOI
23 Lorenz, C., Gesell, T., Zimmermann, B., Schoeberl, U., Bilusic, I., Rajkowitsch, L., Waldsich, C., von Haeseler, A., and Schroeder, R. (2010). Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts. Nucleic Acids Res. 38, 3794-3808.   DOI
24 Majdalani, N., Cunning, C., Sledjeski, D., Elliott, T., and Gottesman, S. (1998). DsrA RNA regulates translation of RpoS message by an antiantisense mechanism, independent of its action as an antisilencer of transcription. Proc. Natl. Acad. Sci. U. S. A. 95, 12462-12467.   DOI
25 Malecka, E.M., Strozecka, J., Sobanska, D., and Olejniczak, M. (2015). Structure of bacterial regulatory RNAs determines their performance in competition for the chaperone protein Hfq. Biochemistry 54, 1157-1170.   DOI
26 Mandin, P., and Gottesman, S. (2010). Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA. EMBO J. 29, 3094-3107.   DOI
27 Moller, T., Franch, T., Hojrup, P., Keene, D.R., Bachinger, H.P., Brennan, R.G., and Valentin-Hansen, P. (2002). Hfq: a bacterial Smlike protein that mediates RNA-RNA interaction. Mol. Cell 9, 23-30.   DOI
28 McCullen, C.A., Benhammou, J.N., Majdalani, N., and Gottesman, S. (2010). Mechanism of positive regulation by DsrA and RprA small noncoding RNAs: pairing increases translation and protects rpoS mRNA from degradation. J. Bacteriol. 192, 5559-5571.   DOI
29 Mikulecky, P.J., Kaw, M.K., Brescia, C.C., Takach, J.C., Sledjeski, D.D., and Feig, A.L. (2004). Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAs. Nat. Struct. Mol. Biol. 11, 1206-1214.   DOI
30 Milligan, J.F., and Uhlenbeck, O.C. (1989). Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol. 180, 51-62.   DOI
31 Moore, S.D. (2011). Assembling new Escherichia coli strains by transduction using phage P1. Methods Mol. Biol. 765, 155-169.   DOI
32 Muller-Hill, B. (1985). Experiments with gene fusions. Trends Genet. 1, 61.   DOI
33 Majdalani, N., Vanderpool, C.K., and Gottesman, S. (2005). Bacterial small RNA regulators. Crit. Rev. Biochem. Mol. Biol. 40, 93-113.   DOI
34 Murina, V.N., and Nikulin, A.D. (2015). Bacterial small regulatory RNAs and Hfq protein. Biochemistry (Mosc) 80, 1647-1654.   DOI
35 Panja, S., Santiago-Frangos, A., Schu, D.J., Gottesman, S., and Woodson, S.A. (2015). Acidic residues in the Hfq chaperone increase the selectivity of sRNA binding and annealing. J. Mol. Biol. 427, 3491-3500.   DOI
36 Panja, S., and Woodson, S.A. (2012). Hfq proximity and orientation controls RNA annealing. Nucleic Acids Res. 40, 8690-8697.   DOI
37 Resch, A., Afonyushkin, T., Lombo, T.B., McDowall, K.J., Blasi, U., and Kaberdin, V.R. (2008). Translational activation by the noncoding RNA DsrA involves alternative RNase III processing in the rpoS 5'-leader. RNA 14, 454-459.   DOI
38 Park, H., Bak, G., Kim, S.C., and Lee, Y. (2013). Exploring sRNAmediated gene silencing mechanisms using artificial small RNAs derived from a natural RNA scaffold in Escherichia coli. Nucleic Acids Res. 41, 3787-3804.   DOI
39 Peng, Y., Soper, T.J., and Woodson, S.A. (2014). Positional effects of AAN motifs in rpoS regulation by sRNAs and Hfq. J. Mol. Biol. 426, 275-285.   DOI
40 Repoila, F., and Gottesman, S. (2001). Signal transduction cascade for regulation of RpoS: temperature regulation of DsrA. J. Bacteriol. 183, 4012-4023.   DOI
41 Ross, J.A., Ellis, M.J., Hossain, S., and Haniford, D.B. (2013). Hfq restructures RNA-IN and RNA-OUT and facilitates antisense pairing in the Tn10/IS10 system. RNA 19, 670-684.   DOI
42 Salvail, H., Caron, M.P., Belanger, J., and Masse, E. (2013). Antagonistic functions between the RNA chaperone Hfq and an sRNA regulate sensitivity to the antibiotic colicin. EMBO J. 32, 2764-2778.   DOI
43 Santiago-Frangos, A., Kavita, K., Schu, D.J., Gottesman, S., and Woodson, S.A. (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.   DOI
44 Sauer, E., Schmidt, S., and 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.   DOI
45 Sauer, E., and Weichenrieder, O. (2011). Structural basis for RNA 3'-end recognition by Hfq. Proc. Natl. Acad. Sci. U. S. A. 108, 13065-13070.   DOI
46 Sledjeski, D.D., Gupta, A., and Gottesman, S. (1996). The small RNA, DsrA, is essential for the low temperature expression of RpoS during exponential growth in Escherichia coli. EMBO J. 15, 3993-4000.   DOI
47 Sauter, C., Basquin, J., and Suck, D. (2003). Sm-like proteins in Eubacteria: the crystal structure of the Hfq protein from Escherichia coli. Nucleic Acids Res. 31, 4091-4098.   DOI
48 Schu, D.J., Zhang, A., Gottesman, S., and Storz, G. (2015). Alternative Hfq-sRNA interaction modes dictate alternative mRNA recognition. EMBO J. 34, 2557-2573.   DOI
49 Sedlyarova, N., Shamovsky, I., Bharati, B.K., Epshtein, V., Chen, J., Gottesman, S., Schroeder, R., and Nudler, E. (2016). sRNA-mediated control of transcription termination in E. coli. Cell 167, 111-121.e13.   DOI
50 Sledjeski, D.D., Whitman, C., and Zhang, A. (2001). Hfq is necessary for regulation by the untranslated RNA DsrA. J. Bacteriol. 183, 1997-2005.   DOI
51 Soper, T., Mandin, P., Majdalani, N., Gottesman, S., and Woodson, S.A. (2010). Positive regulation by small RNAs and the role of Hfq. Proc. Natl. Acad. Sci. U. S. A. 107, 9602-9607.   DOI
52 Soper, T.J., and Woodson, S.A. (2008). The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA. RNA 14, 1907-1917.   DOI
53 Storz, G., Vogel, J., and Wassarman, K.M. (2011). Regulation by small RNAs in bacteria: expanding frontiers. Mol. Cell 43, 880-891.   DOI
54 Updegrove, T.B., Zhang, A., and Storz, G. (2016). Hfq: the flexible RNA matchmaker. Curr. Opin. Microbiol. 30, 133-138.   DOI
55 Streit, S., Michalski, C.W., Erkan, M., Kleeff, J., and Friess, H. (2009). Northern blot analysis for detection and quantification of RNA in pancreatic cancer cells and tissues. Nat. Protoc. 4, 37-43.   DOI
56 Thomason, L.C., Costantino, N., and Court, D.L. (2007). E. coli genome manipulation by P1 transduction. Curr. Protoc. Mol. Biol. Chapter 1, Unit 1.17.
57 Updegrove, T.B., and Wartell, R.M. (2011). The influence of Escherichia coli Hfq mutations on RNA binding and sRNA${\cdot}$mRNA duplex formation in rpoS riboregulation. Biochim. Biophys. Acta 1809, 532-540.   DOI
58 Vecerek, B., Beich-Frandsen, M., Resch, A., and Blasi, U. (2010). Translational activation of rpoS mRNA by the non-coding RNA DsrA and Hfq does not require ribosome binding. Nucleic Acids Res. 38, 1284-1293.   DOI
59 Vecerek, B., Rajkowitsch, L., Sonnleitner, E., Schroeder, R., and Blasi, U. (2008). The C-terminal domain of Escherichia coli Hfq is required for regulation. Nucleic Acids Res. 36, 133-143.   DOI
60 Vogel, J., and Luisi, B.F. (2011). Hfq and its constellation of RNA. Nat. Rev. Microbiol. 9, 578-589.   DOI
61 Wang, W., Wang, L., Zou, Y., Zhang, J., Gong, Q., Wu, J., and Shi, Y. (2011). Cooperation of Escherichia coli Hfq hexamers in DsrA binding. Genes Dev. 25, 2106-2117.   DOI
62 Wassarman, K.M., Zhang, A., and Storz, G. (1999). Small RNAs in Escherichia coli. Trends Microbiol. 7, 37-45.   DOI
63 Waters, L.S., and Storz, G. (2009). Regulatory RNAs in bacteria. Cell 136, 615-628.   DOI
64 Zhang, X., and Bremer, H. (1995). Control of the Escherichia coli rrnB P1 promoter strength by ppGpp. J. Biol. Chem. 270, 11181-11189.   DOI
65 Zhang, A., Schu, D.J., Tjaden, B.C., Storz, G., and 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.   DOI