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Bacterial Cyclopropane Fatty Acid Synthase mRNA is targeted by activating and repressing small RNAs

Bianco, C.M., Fröhlich, K.S., and Vanderpool, C.K. 

J. Bacteriol. 2019 Jul 

doi: 10.1128/JB.00461-19

Altering membrane protein and lipid composition is an important strategy for maintaining membrane integrity during environmental stress. Many bacterial small RNAs (sRNAs) control membrane protein production, but sRNA-mediated regulation of membrane fatty acid composition is less well understood. The sRNA RydC was previously shown to stabilize cfa (cyclopropane fatty acid synthase) mRNA, resulting in higher levels of cyclopropane fatty acids in the cell membrane. Here, we report that additional sRNAs, ArrS and CpxQ, also directly regulate cfa post-transcriptionally. RydC and ArrS act through masking an RNase E cleavage site in the cfa mRNA 5' untranslated region (UTR), and both sRNAs post-transcriptionally activate cfa In contrast, CpxQ binds to a different site in the cfa mRNA 5' UTR and represses cfa expression. Alteration of membrane lipid composition is a key mechanism for bacteria to survive low pH environments, and we show that cfa translation increases in an sRNA-dependent manner when cells are subjected to mild acid stress. This work suggests an important role for sRNAs in the acid stress response through regulation of cfa mRNA.

 

 

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KEY PUBLICATIONS

Bobrovskyy, M., Azam, M.S., Frandsen, J.K., Zhang, J., Poddar, A., Ma, X., Henkin, T.M., Ha, T., and Vanderpool, C.K. 2019. Determinants of target prioritization and regulatory hierarchy for the bacterial small RNA SgrS. Mol Microbiol. 2019 Jul 24. doi: 10.1111/mmi.14355.

 

King, A.M., Vanderpool, C.K., and Degnan, P.H. 2019. sRNA Target Prediction Organizing Tool (SPOT) Integrates Computational and Experimental Data To Facilitate Functional Characterization of Bacterial Small RNAs. mSphere. 2019 Jan 30;4(1). doi: 10.1128/mSphere.00561-18.  

Kim, K., Palmer, A.D., Vanderpool, C.K., and Slauch, J.M. 2019. The sRNA PinT contributes to PhoP-mediated regulation of the SPI1 T3SS in Salmonella enterica serovar Typhimurium. J Bacteriol. 2019 Jul 1. pii: JB.00312-19. doi: 10.1128/JB.00312-19.

Bianco, C.M., Fröhlich, K.S., and Vanderpool, C.K. 2019. Bacterial  Cyclopropane  Fatty  Acid  Synthase  mRNA  is  targeted by activating and repressing small RNAs. J Bacteriol. 2019 Jul 15. pii: JB.00461-19. doi: 10.1128/JB.00461-19.

Papenfort, K., Sun, Y., Miyakoshi, M., Vanderpool, C.K., and Vogel, J. 2013. Regulation of glucose homeostasis by small RNA mediated suboperonic mRNA stabilization. Cell 153:426. doi: 10.1016/j.cell.2013.03.003.

Rice, J. B., Balasubramanian, D., and Vanderpool, C.K. 2012. Small RNA binding site multiplicity involved in translational regulation of a polycistronic mRNA. Proc. Natl. Acad. Sci. U.S.A. 109:E2691. doi: 10.1073/pnas.1207927109.

Richards, G. R. and Vanderpool, C.K. 2012. Induction of the Pho regulon suppresses the growth defect of an Escherichia coli sgrS mutant, connecting phosphate metabolism to the glucose-phosphate stress response. J. Bact. 194:2520. 
doi: 10.1128/JB.00009-12.

Rice, J. B. and Vanderpool, C.K. 2011. The small RNA SgrS controls sugar-phosphate accumulation by regulating multiple PTS genes. Nucl. Acids Res. 39:3806. doi: 10.1093/nar/gkq1219.

Sun, Y. and Vanderpool, C.K. 2011. Regulation and function of Escherichia coli sugar efflux transporter A (SetA) during glucose-phosphate stress. J. Bact. 193:143. doi: 10.1128/JB.01008-10.

Horler, R. S. P. and Vanderpool, C.K. 2009.  Homologs of the small RNA SgrS are broadly distributed in enteric bacteria but have diverged in size and sequence.  Nucl. Acids Res.  37:5465. doi: 10.1093/nar/gkp501.

Wadler, C. S. and Vanderpool, C.K.  2009.  Characterization of homologs of the small RNA SgrS reveals diversity in function.  Nucl. Acids Res.  37:5477. doi: 10.1093/nar/gkp591.

Wadler, C. S. and Vanderpool, C.K.  2007.  A novel dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide.  Proc. Natl. Acad. Sci. U.S.A. 104:20454-20459. doi: 10.1073/pnas.0708102104.

Vanderpool, C. K.  2007.  Physiological consequences of small RNA-mediated regulation of glucose-phosphate stress.  Curr. Opin. Microbiol. 10:146-151. doi: 10.1016/j.mib.2007.03.011.

Vanderpool, C.K. and Gottesman, S. 2004. Involvement of a novel transcriptional activator and small RNA in post-transcriptional regulation of the glucose phosphoenolpyruvate phosphotransferase system. Mol Microbiol., 54(4):1076–89. 

doi: 10.1111/j.1365-2958.2004.04348.x.

 

PREPRINTS

Ragunathan P.T. and Vanderpool, C.K. Cryptic prophage-encoded small protein DicB protects Escherichia coli from phage infection by inhibiting inner membrane receptor proteins. doi: https://doi.org/10.1101/708461