Selective translation of leaderless mRNAs by specialized ribosomes generated by MazF in Escherichia coli.

Escherichia coli (E. coli) mazEF is a stress-induced toxin-antitoxin (TA) module. The toxin MazF is an endoribonuclease that cleaves single-stranded mRNAs at ACA sequences. Here, we show that MazF cleaves at ACA sites at or closely upstream of the AUG start codon of some specific mRNAs and thereby generates leaderless mRNAs. Moreover, we provide evidence that MazF also targets 16S rRNA within 30S ribosomal subunits at the decoding center, thereby removing 43 nucleotides from the 3' terminus. As this region comprises the anti-Shine-Dalgarno (aSD) sequence that is required for translation initiation on canonical mRNAs, a subpopulation of ribosomes is formed that selectively translates the described leaderless mRNAs both in vivo and in vitro. Thus, we have discovered a modified translation machinery that is generated in response to MazF induction and that probably serves for stress adaptation in Escherichia coli.

Correction to: Reprogramming of gene expression in Escherichia coli cultured on pyruvate versus glucose.

The article Reprogramming of.

Reprogramming of gene expression in Escherichia coli cultured on pyruvate versus glucose.

Previous studies revealed important roles of small RNAs (sRNAs) in regulation of bacterial metabolism, stress responses and virulence. However, only a minor fraction of sRNAs is well characterized with respect to the spectra of their targets, conditional expression profiles and actual mechanisms they use to regulate gene expression to control particular biological pathways. To learn more about the specific contribution of sRNAs to the global regulatory network controlling the Escherichia coli central carbon metabolism (CCM), we employed microarray analysis and compared transcriptome profiles of E. coli cells grown on two alternative minimal media supplemented with either pyruvate or glucose, respectively. Microarray analysis revealed that utilization of these alternative carbon sources led to profound differences in gene expression affecting all major gene clusters associated with CCM as well as expression of several known (CyaR, RyhB, GcvB and RyeA) and putative (C0652) sRNAs. To assess the impact of transcriptional reprogramming of gene expression on E. coli protein abundance, we also employed two-dimensional protein gel electrophoresis. Our experimental data made it possible to determine the major pathways for pyruvate assimilation when it is used as a sole carbon source and reveal the impact of other key processes (i.e., energy production, molecular transport and cell resistance to stress) associated with the CCM in E. coli. Moreover, some of these processes were apparently controlled by GcvB, RyhB and CyaR at the post-transcriptional level, thus indicating the complexity and interconnection of the regulatory networks that control CCM in bacteria.

An unexpected type of ribosomes induced by kasugamycin: a look into ancestral times of protein synthesis?

Translation of leaderless mRNAs, lacking ribosomal recruitment signals other than the 5'-terminal AUG-initiating codon, occurs in all three domains of life. Contemporary leaderless mRNAs may therefore be viewed as molecular fossils resembling ancestral mRNAs. Here, we analyzed the phenomenon of sustained translation of a leaderless mRNA in the presence of the antibiotic kasugamycin. Unexpected from the known in vitro effects of the drug, kasugamycin induced the formation of stable approximately 61S ribosomes in vivo, which were proficient in selectively translating leaderless mRNA. 61S particles are devoid of more than six proteins of the small subunit, including the functionally important proteins S1 and S12. The lack of these proteins could be reconciled with structural changes in the 16S rRNA. These studies provide in vivo evidence for the functionality of ribosomes devoid of multiple proteins and shed light on the evolutionary history of ribosomes.

Isolation of Pseudomonas fluorescens species highly resistant to pentachlorobenzene.

Polychlorinated aromatic compounds, including pentachlorobenzenes and hexachlorobenzenes, are recalcitrant industrial pollutants that cause adverse effects on living cells. In this paper, the isolation of Pseudomonas fluorescens species with high resistance to pentachlorobenzene (PeCB) is reported. It was found that, in contrast to its slightly negative effect on P. fluorescens growth, PeCB readily inhibited the cell growth of Serratia spp. and Escherichia coli strains, thus indicating that inhibition of bacterial growth by PeCB is species-dependent. Analysis of a P. fluorescens isolate revealed that the exposure to PeCB induced production of reactive oxygen species and led to an increase in the level of alkyl hydroperoxide reductase C (AhpC), an important enzyme enhancing the cell tolerance to organic hydroperoxides usually accumulated under oxidative stress. The putative mechanism conferring PeCB resistance to P. fluorescens and the potential use of P. fluorescens in bioremediation are discussed.