Chapter 15, Problem 27P

Great variation exists in the mechanisms by which RNAs can mediate gene regulation. In one recently discovered example shown in the following diagram, the genes CsrA and CsrB are global regulators of suites of target genes that are involved in the use of carbon atoms. The product of CsrA is the CsrA protein, which binds to the ribosome binding site (RBS) of target gene mRNA, preventing target gene expression. The product of the CsrB

gene is the CsrB RNA, which contains 22 binding sites for CsrA protein. CsrB RNA can thus compete with target mRNAs for CsrA protein binding. In the presence of high CsrB RNA concentrations, CsrA protein cannot bind to mRNA binding sites, so expression of the target genes is turned on.

a. For the CsrA and CsrB genes, indicate what kind of molecule the gene product is (DNA, RNA, protein, small molecule), whether it acts as a positive or negative regulator, what stage of gene expression it affects, and whether it acts in cis or in trans. (It will be interesting to compare your answers to those for Problem 26.)

b. CsrA/CsrB regulate glycogen biosynthesis and breakdown; glycogen is a polymer of glucose and a major source of stored energy in the human body. CsrA/CsrB are negative regulators of glycogen biosynthesis and positive regulators of glycogen breakdown. To what environmental factor do you think that the CsrA/CsrB system is most likely to respond? Suggest a possible way that this system might be repressible, and then suggest a different hypothesis for how this system might be inducible. (Assume in both cases that CsrB expression is modulated.) Which of your hypotheses would be most consistent with the target genes being involved in glycogen biosynthesis (an anabolic pathway), and which is most consistent with glycogen breakdown (a catabolic pathway)? Explain.