Kwang-sun Kim

YmdB: a stress-responsive ribonuclease-binding regulator of E. coli RNase III activity

The broad cellular actions of RNase III family enzymes include ribosomal RNA (rRNA) processing, mRNA decay, and the generation of noncoding microRNAs in both prokaryotes and eukaryotes. Here we report that YmdB, an evolutionarily conserved 18.8-kDa protein of Escherichia coli of previously unknown function, is a regulator of RNase III cleavages. We show that YmdB functions by interacting with a site in the RNase III catalytic region, that expression of YmdB is transcriptionally activated by both cold-shock stress and the entry of cells into stationary phase, and that this activation requires the sigma-factor-encoding gene, rpoS. We discovered that down-regulation of RNase III activity occurs during both stresses and is dependent on YmdB production during cold shock; in contrast, stationary-phase regulation was unperturbed in YmdB-null mutant bacteria, indicating the existence of additional, YmdB-independent, factors that dynamically regulate RNase III actions during normal cell growth. Our results reveal the previously unsuspected role of ribonuclease-binding proteins in the regulation of RNase III activity.

Rho-dependent Termination of ssrS (6S RNA) Transcription in Escherichia coli IMPLICATION FOR 3′ PROCESSING OF 6S RNA AND EXPRESSION OF DOWNSTREAM ygfA (PUTATIVE 5-FORMYL-TETRAHYDROFOLATE CYCLO-LIGASE)

It is well known that 6S RNA, a global regulatory noncoding RNA that modulates gene expression in response to the cellular stresses in Escherichia coli, is generated by processing from primary ssrS (6S RNA) transcripts derived from two different promoters. The 5′ processing of 6S RNA from primary transcripts has been well studied; however, it remains unclear how the 3′-end of this RNA is generated although previous studies have suggested that exoribonucleolytic trimming is necessary for 3′ processing. Here, we describe several Rho-dependent termination sites located ∼90 bases downstream of the mature 3′-end of 6S RNA. Our data suggest that the 3′-end of 6S RNA is generated via exoribonucleolytic trimming, rather than endoribonucleolytic cleavage, following the transcription termination events. The termination sites identified in this study are within the open reading frame of the downstream ygfA (putative 5-formyl-tetrahydrofolate cyclo-ligase) gene, a part of the highly conserved bacterial operon ssrS-ygfA, which is up-regulated during the biofilm formation. Our findings reveal that ygfA expression, which also aids the formation of multidrug-tolerant persister cells, could be regulated by Rho-dependent termination activity in the cell.

Ribonuclease E Modulation of the Bacterial SOS Response

Plants, animals, bacteria, and Archaea all have evolved mechanisms to cope with environmental or cellular stress. Bacterial cells respond to the stress of DNA damage by activation of the SOS response, the canonical RecA/LexA-dependent signal transduction pathway that transcriptionally derepresses a multiplicity of genes–leading to transient arrest of cell division and initiation of DNA repair. Here we report the previously unsuspected role of E. coli endoribonuclease RNase E in regulation of the SOS response. We show that RNase E deletion or inactivation of temperature-sensitive RNase E protein precludes normal initiation of SOS. The ability of RNase E to regulate SOS is dynamic, as down regulation of RNase E following DNA damage by mitomycin C resulted in SOS termination and restoration of RNase E function leads to resumption of a previously aborted response. Overexpression of the RraA protein, which binds to the C-terminal region of RNase E and modulates the actions of degradosomes, recapitulated the effects of RNase E deficiency. Possible mechanisms for RNase E effects on SOS are discussed.

3′-end processing of precursor M1 RNA by the N-terminal half of RNase E

M1 RNA, the catalytic component of Escherichia coli RNase P, is derived from the 3′‐end processing of precursor M1 RNA, a major transcript of the rnpB gene. In this study, we investigated the mechanism of 3′‐end processing of M1 RNA using the recombinant N‐terminal half RNase E. The cleavage site preference of RNase E differed from that of the 40% ammonium sulfate precipitate (ASP‐40), a partially purified cell extract containing processing activity. However, the addition of a trace amount of ASP‐40 changed the cleavage site preference of RNase E to that of ASP‐40 suggesting the involvement of a soluble factor in cleavage site preference.

Structural analysis of Escherichia coli C5 protein

Structural analysis of Escherichia coli C5 protein Jae-Sun Shin, Kwang-Sun Kim, Kyoung-Seok Ryu, Kook Han, Younghoon Lee, and Byong-Seok Choi* 1Department of Chemistry, KAIST, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Korea 2 Biomedical Proteomics Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea 3 Systems and Synthetic Biology Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea 4 Biosystems and Bioengineering Program, University of Science and Technology (UST), Daejeon 305-350, Korea 5Division of Magnetic Resonance Research, Korea Basic Science Institute, Yangcheong-Ri 804-1, Ochang-Eup, Cheongwon-Gun, Chungbuk 363-883, Korea