SRNA Expedites Polycistronic MRNA Decay in

Overview

Journal Front Mol Biosci

Specialty Biology

Date 2023 Mar 20

PMID 36936984

Authors

Heung Jin Jeon

Yonho Lee

Monford Paul Abishek N

Changjo Kang

Heon M Lim

Affiliations

Soon will be listed here.

Abstract

In bacteria, most small RNA (sRNA) elicits RNase E-mediated target mRNA degradation by binding near the translation initiation site at the 5' end of the target mRNA. Spot 42 is an sRNA that binds in the middle of the operon near the translation initiation site of , the third gene of four, but it is not clear whether this binding causes degradation of mRNA. In this study, we measured the decay rate of mRNA using Northern blot and found that Spot 42 binding caused degradation of only a specific group of mRNA that shares their 3' end with full-length mRNA. The results showed that in the MG1655Δ strain in which the Spot 42 gene was removed, the half-life of each mRNA in the group increased by about 200% compared to the wild type. Since these mRNA species are intermediate mRNA molecules created by the decay process of the full-length mRNA, these results suggest that sRNA accelerates the mRNA decaying processes that normally operate, thus revealing an unprecedented role of sRNA in mRNA biology.

References

Callaghan A, Marcaida M, Stead J, McDowall K, Scott W, Luisi B . Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover. Nature. 2005; 437(7062):1187-91. DOI: 10.1038/nature04084. View

Beisel C, Storz G . The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli. Mol Cell. 2011; 41(3):286-97. PMC: 3072601. DOI: 10.1016/j.molcel.2010.12.027. View

Desnoyers G, Morissette A, Prevost K, Masse E . Small RNA-induced differential degradation of the polycistronic mRNA iscRSUA. EMBO J. 2009; 28(11):1551-61. PMC: 2693151. DOI: 10.1038/emboj.2009.116. View

Belasco J, Beatty J, ADAMS C, von Gabain A, Cohen S . Differential expression of photosynthesis genes in R. capsulata results from segmental differences in stability within the polycistronic rxcA transcript. Cell. 1985; 40(1):171-81. DOI: 10.1016/0092-8674(85)90320-4. View

Schmittgen T . Real-time quantitative PCR. Methods. 2002; 25(4):383-5. DOI: 10.1006/meth.2001.1260. View

Updegrove T, Zhang A, Storz G . Hfq: the flexible RNA matchmaker. Curr Opin Microbiol. 2016; 30:133-138. PMC: 4821791. DOI: 10.1016/j.mib.2016.02.003. View

Adhya S . Suboperonic regulatory signals. Sci STKE. 2003; 2003(185):pe22. DOI: 10.1126/stke.2003.185.pe22. View

Mackie G . Ribonuclease E is a 5'-end-dependent endonuclease. Nature. 1998; 395(6703):720-3. DOI: 10.1038/27246. View

Jiang X, Belasco J . Catalytic activation of multimeric RNase E and RNase G by 5'-monophosphorylated RNA. Proc Natl Acad Sci U S A. 2004; 101(25):9211-6. PMC: 438955. DOI: 10.1073/pnas.0401382101. View

10.

Masse E, Gottesman S . A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc Natl Acad Sci U S A. 2002; 99(7):4620-5. PMC: 123697. DOI: 10.1073/pnas.032066599. View

11.

Livak K, Schmittgen T . Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2002; 25(4):402-8. DOI: 10.1006/meth.2001.1262. View

12.

Proshkin S, Rahmouni A, Mironov A, Nudler E . Cooperation between translating ribosomes and RNA polymerase in transcription elongation. Science. 2010; 328(5977):504-8. PMC: 2930199. DOI: 10.1126/science.1184939. View

13.

Bossi L, Schwartz A, Guillemardet B, Boudvillain M, Figueroa-Bossi N . A role for Rho-dependent polarity in gene regulation by a noncoding small RNA. Genes Dev. 2012; 26(16):1864-73. PMC: 3426764. DOI: 10.1101/gad.195412.112. View

14.

Prevost K, Desnoyers G, Jacques J, Lavoie F, Masse E . Small RNA-induced mRNA degradation achieved through both translation block and activated cleavage. Genes Dev. 2011; 25(4):385-96. PMC: 3042161. DOI: 10.1101/gad.2001711. View

15.

Jeon H, Lee Y, N M, Wang X, Chattoraj D, Lim H . sRNA-mediated regulation of gal mRNA in E. coli: Involvement of transcript cleavage by RNase E together with Rho-dependent transcription termination. PLoS Genet. 2021; 17(10):e1009878. PMC: 8577784. DOI: 10.1371/journal.pgen.1009878. View

16.

Morita T, Aiba H . RNase E action at a distance: degradation of target mRNAs mediated by an Hfq-binding small RNA in bacteria. Genes Dev. 2011; 25(4):294-8. PMC: 3042153. DOI: 10.1101/gad.2030311. View

17.

Chen J, Morita T, Gottesman S . Regulation of Transcription Termination of Small RNAs and by Small RNAs: Molecular Mechanisms and Biological Functions. Front Cell Infect Microbiol. 2019; 9:201. PMC: 6582626. DOI: 10.3389/fcimb.2019.00201. View

18.

Ullmann A, Joseph E, Danchin A . Cyclic AMP as a modulator of polarity in polycistronic transcriptional units. Proc Natl Acad Sci U S A. 1979; 76(7):3194-7. PMC: 383790. DOI: 10.1073/pnas.76.7.3194. View

19.

Hui M, Foley P, Belasco J . Messenger RNA degradation in bacterial cells. Annu Rev Genet. 2014; 48:537-59. PMC: 4431577. DOI: 10.1146/annurev-genet-120213-092340. View

20.

Waters L, Storz G . Regulatory RNAs in bacteria. Cell. 2009; 136(4):615-28. PMC: 3132550. DOI: 10.1016/j.cell.2009.01.043. View