Abstract
RNase III is a double-stranded RNA-specific endoribonuclease that processes and degrades numerous mRNA molecules in Escherichia coli. A previous genome-wide analysis of E. coli transcripts showed that steady-state levels of mltD mRNA, which encodes membrane-bound lytic murein transglycosylase D, was most affected by changes in cellular concentration of RNase III. Consistent with this observation, in vitro and in vivo analyses of mltD mRNA revealed RNase III cleavage sites in the coding region of mltD mRNA. Introduction of a nucleotide substitution at the identified RNase III cleavage sites inhibited RNase III cleavage activity on mltD mRNA, resulting in, consequently, approximately two-fold increase in the steady-state level of the mRNA. These findings reveal an RNase III-mediated regulatory pathway that modulates mltD expression in E. coli.
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References
Amarasinghe AK, Calin-Jageman I, Harmouch A, Sun W, Nicholson AW (2001) Escherichia coli ribonuclease III: affinity purification of hexahistidine-tagged enzyme and assays for substrate binding and cleavage. Methods Enzymol 342:143–158
Bateman A, Bycroft M (2000) The structure of a LysM domain from Escherichia coli membrane-bound lytic murein transglycosylase D (mltD). J Mol Biol 299:1113–1119
Bram RJ, Young RA, Steitz JA (1980) The ribonuclease III site flanking 23S sequences in the 30S ribosomal precursor RNA of Escherichia coli. Cell 19:393–401
Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA 97:6640–6645
de Boer HA, Comstock LJ, Vasser M (1983) The tac promoter: a functional hybrid derived from the trp and lac promoters. Proc Natl Acad Sci USA 80:21–25
Dijkstra AJ, Keck W (1996) Identification of new members of the lytic transglycosylase family in Haemophilus influenzae and Escherichia coli. Microb Drug Resist 2:141–145
Kim k, Sim S, Jeon C, Lee Y, Lee K (2011) Base substitutions at scissile bond sites are sufficient to alter RNA-binding and cleavage activity of RNase III. FEMS Microbiol Lett 315:30–37
Lee M, Jun SY, Yoon BY, Song S, Lee K, Ha NC (2012) Membrane fusion proteins of type I secretion system and tripartite efflux pumps share a binding motif for TolC in gram-negative bacteria. PLoS One 7:e40460
Lim B, Sim SH, Sim M, Kim K, Jeon CO, Lee Y, Ha NC, Lee K (2012) RNase III controls the degradation of corA mRNA in Escherichia coli. J Bacteriol 194:2214–2220
Pei XY, Hinchliffe P, Symmons MF, Koronakis E, Benz R, Hughes C, Koronakis V (2011) Structures of sequential open states in a symmetrical opening transition of the TolC exit duct. Proc Natl Acad Sci USA 108:2112–2117
Sim SH, Yeom JH, Shin C, Song WS, Shin E, Kim HM, Cha CJ, Han SH et al (2010) Escherichia coli ribonuclease III activity is downregulated by osmotic stress: consequences for the degradation of bdm mRNA in biofilm formation. Mol Microbiol 75:413–425
Takiff HE, Chen SM, Court DL (1989) Genetic analysis of the rnc operon of Escherichia coli. J Bacteriol 171:2581–2590
Thunnissen AM, Dijkstra AJ, Kalk KH, Rozeboom HJ, Engel H, Keck W, Dijkstra BW (1994) Doughnut-shaped structure of a bacterial muramidase revealed by X-ray crystallography. Nature 367:750–753
Xu Z, Wang Y, Han Y, Chen J, Zhang XH (2011) Mutation of a novel virulence-related gene mltD in Vibrio anguillarum enhances lethality in zebra fish. Res Microbiol 162:144–150
Yeom JH, Go H, Shin E, Kim HL, Han SH, Moore CJ, Bae J, Lee K (2008) Inhibitory effects of RraA and RraB on RNase E-related enzymes imply conserved functions in the regulated enzymatic cleavage of RNA. FEMS Microbiol Lett 285:10–15
Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415
Acknowledgments
This work was supported by NRF Grant (2011-0028553) funded by the Ministry of Education, Science, and Technology and the Next-Generation BioGreen 21 Program (SSAC, Grant No.: PJ009025), Rural Development Administration, Republic of Korea.
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Boram Lim and Sangmi Ahn contributed equally to this work.
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Lim, B., Ahn, S., Sim, M. et al. RNase III Controls mltD mRNA Degradation in Escherichia coli . Curr Microbiol 68, 518–523 (2014). https://doi.org/10.1007/s00284-013-0504-5
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DOI: https://doi.org/10.1007/s00284-013-0504-5