Question

How does the 6S RNA promote global changes in gene expression?

Provide examples of how small RNAs can promote RNA degradation?

What is a molecular mechanism by which small RNAs promote translation? Provide an example where this may regulate a virulence factor.

What is a molecular mechanism by which small RNAs inhibit translation? Provide an example where this may regulate a virulence factor.

What is the function of Hfq and what role does it play in various mechanisms of post-transcriptional regulation?

How does RNAIII function to promote S. aureus pathogenesis in response to quorum sensing signals?

Answer 1

1) 6S RNA is a small RNA regulator of RNA polymerase that is present throughout the bacterial kingdom. Studies in Escherichia coli revealed that 6S RNA forms a complex with RNA polymerase resulting in regulation of transcription and cells lacking 6S RNA have altered survival phenotypes. The physiological role of 6S RNA of atleast in E. coli is to contribute to regulation in gene expression response to poor nutrient environment. 6S RNA also regulates widely different gene depending upon growth phase. The interaction between 6S RNA and Rsd and show widespread expression changes in a strain lacking both regulators. The identification of 6S RNAs in diverse bacterial species, the details of 6S RNA-RNA polymerase interaction, the identification of promoters regulated by 6S RNA, the physiological consequences of 6S RNA dependent regulation and the impact of pRNA synthesis.

2) Small RNA plays a major role in the post transcriptional regulation of gene expression. Active RNA degradation system in cells tgat can transcribe more RNA than accumulates. Small RNAs induced mRNA degradation occurs through binding of an sRNA to a target mRNA concomitant action of RNA degradosome, which induces an endoribonuclease E dependent cleavage and degradation of targeted mRNA. RNA degradation in eukaryotic cell is a key modulator of gene expression. In eukaryotic cell RNA degradation relies on a set of enzymes that carry specific ribonuclease activity. RNAs are degraded by the exoribonucleolytic reaction in the 5'-3' or 3'-5' direction. The 5'-3' exoribonucleases in eukaryotic cells are localized in the cytoplasm and nucleus. The 3'-5' exonuclease activities are contained in a complex called exosomes present in nuclear and cytoplasmic campartments.

3) sRNAs in gram positive bacteria are still plentiful although the detailed gene regulation mechanism. Strict virulence control is critical for a pathogen's survival an many sRNAs have been found to be involved in that process. The mechanism of transacting sRNAs involved in virulence regulation in various gram positive pathogen. The function of trans acting sRNAs are to regulate translation initiation and RNA stability. The role of most sRNAs is to control translation. These control occurs by three different steps. 1) sRNAs directly bind and block the ribosome binding site and inhibit translation. 2) sRNAs binds to induce structural changes of the RBS to inhibit or promote translation. 3) sRNAs binds in order to block a ribosome standby site to promote translation.

4) Hfq is a RNA binding protein involved in translational activation and inhibition. It show high sequence conservation across the different prokaryotes and across sm protein which are eukaryotic protein involved in mRNA splicing. The major role of Hfq is to stimulate basepairing between sRNAs and target mRNAs by binding both RNAs through three RNA binding surface. The post transcriptional network exerted by Hfq and its associated sRNAs, it is important to the cellular concentration of Hfq is regulated. Characterisation of sRNAs - target mRNA interaction in C. crescentus and suggest that Hfq independent processes could be an important aspect of post-transcriptional gene regulation in this organism.

5) Quorum sensing is the regulation of gene expression in response to fluctuations in cell population density. Quorum sensing bacteria releases and produces chemical signal molecule called autoinducers that increase in the concentration of cell density. Staphylococcus aureus RNAlll is one of the main intracellular effectors of the quorum sensing system. It is multifunctional RNA that encodes a small peptide and its non coding parts act as antisense RNAs to regukate the translation or the stability of mRNA encoding transcriptional regulators, major virulence factors, cell wall metabolism enzymes. The agar locus contains two transcriptional units RNAll & RNAlll under the transcriptional control of promoters. RNAlll modulate gene expression to facilitate adaptation in specific environment.