In the last fifteen years, the important roles of small non-coding RNAs in regulation in all organisms have been recognized and begun to be studied. Our laboratory, in collaboration with others, undertook two global searches for non-coding RNAs in E. coli, contributing significantly to the more than 80 regulatory RNAs that are now identified. A large number of these small RNAs (sRNAs) bind tightly to the RNA chaperone Hfq. We and others have shown that every RNA that binds tightly to Hfq acts by pairing with target mRNAs, regulating stability and translation of the mRNA, either positively or negatively. Our lab has studied a number of these sRNAs in detail. We have found that expression of each sRNA is regulated by different stress conditions, and that the sRNA plays an important role in adapting to stress. We have also examined the mechanism by which Hfq operates to allow sRNAs to act. The lab continues to investigate the in vivo roles of small RNAs, identifying the regulatory networks they participate in and their roles in those networks. The sRNA RyhB is important for iron homeostasis, by down-regulating expression of non-essential iron binding proteins under iron limitation. Two other sRNAs remodel the outer membrane under high osmolarity conditions, while another Hfq-binding RNA, is dependent on an alternative sigma factor, Sigma E, for transcription and down-regulates outer membrane proteins. These sRNAs are characteristic of many regulatory RNAs that regulate the cell surface, possibly important during infection. Consistent with the idea that all major regulatory systems may have small RNA components, another Hfq-binding RNA, named MgrR, is regulated by PhoP and PhoQ, a two-component system important for Salmonella virulence. PhoP and PhoQ activate synthesis of the RNA under low Magnesium and low calcium conditions;the small RNA inactivates an enzyme for modification of the cell surface lipopolysaccharide, eptB, affecting the cells sensitivity to antimicrobial peptides such as polymyxin. This is the first example of regulation of an LPS modifying enzyme by sRNAs. In collaborative work, we have confirmed the effect of the sRNA in regulating LPS modification. In addition, we find that the gene for the LPS modification enzyme is positively regulated by the specialized sigma factor Sigma E, leading to expression under conditions of periplasmic stress, when this LPS barrier may be particularly important. A second small RNA regulator of the eptB gene was also identified, linking regulation to a switch between aerobic and anaerobic growth. This work as well as work in other labs underscores the variety of regulatory networks that sRNAs participate in. In addition to regulation of LPS and outer membrane proteins, we have now shown that multiple sRNAs regulate bacterial motility, many of them by regulating a critical transcriptional activator of flagellar synthesis, flhDC. Two sRNAs positively regulate motility, while at least four down-regulate motility. These provide unexpected new inputs to the well-studied regulation of flagellar synthesis. Bacteria such as E. coli are motile under some circumstances, but in some growth conditions form non-motile biofilms. Not surprisingly, we find that sRNAs play important roles in biofilm formation as well. We have initially focused on the role of DsrA, a small RNA first identified in this lab and known to positively regulate the stress sigma factor RpoS and negatively regulate the H-NS repressor. Overexpression of DsrA increases biofilm production, and this is dependent on regulation of H-NS. The downstream targets of H-NS are also being identified. Our results suggest that both flhDC, the central regulator of motility, and rpoS, encoding the stress sigma factor, act as nodes for regulation by multiple sRNAs. Using methods developed in the lab for rapidly creating translational fusions to genes of interest and screening the set of Hfq-dependent sRNAs to identify regulatory interactions, we have screened multiple other transcriptional regulators for sRNA regulation. We find that only a subset of regulators, including Lrp and SoxS, are subject to sRNA regulation, and we are investigating the physiological significance of this extra level of regulation. In another study, a small RNA was found to negatively regulate tolC, the core of multiple drug efflux pumps in E. coli. The impact of this regulation on drug resistance is being investigated. The action of these small RNAs depends on the RNA chaperone Hfq, a protein with homology to the Lsm and Sm families of eukaryotic proteins involved in RNA splicing and other functions. Hfq binds both to sRNAs and to mRNAs, and stimulates pairing, but exactly how it does this is not entirely clear. Two of the projects in the lab have focused on the mechanism of sRNA function and the role of Hfq and other proteins. Hfq is a hexamer of identical subunits. While many mutations have been created in Hfq, these have generally been studied in vitro with purified mutant protein and a very narrow set of sRNAs and model mRNAs. In collaboration with G. Storz, NICHD, interesting hfq alleles have now been studied in vivo with multiple sRNA:mRNA reporters;the results demonstrate that some mutants are defective only for specific sRNA/mRNA pairs, suggesting that there are multiple modes for Hfq to bind and act to stimulate pairing. In addition, we have found that the Hfq-dependent sRNAs fall into two classes, defined by their behavior in different Hfq mutants. All of these sRNAs depend on the known sRNA binding site on the proximal face of Hfq for in vivo stability. The larger group, called Class I, is rapidly degraded when used, most likely dependent upon pairing. Mutations in the distal face of Hfq, which disrupt target mRNA binding, stabilize the Class I sRNAs, and mutations in the rim of Hfq, implicated in pairing, destabilize the sRNAs. Class II sRNAs are generally more stable than Class I sRNAs, are not destabilized by the rim mutants, but are by the distal site mutants. These results suggest at least two distinct modes of sRNA binding to Hfq. In order to determine if factors other than Hfq are necessary for the action of these sRNAs, a genetic selection was developed to select for failure of two sRNAs to act. The mutants isolated fell into two classes;the first, expected class, had changes in conserved and essential amino acids in hfq. The second class were loss of function mutations in pnp, encoding polynucleotide phosphorylase. Polynucleotide phosphorylase (PNPase) is a 3'to 5'endonuclease that associates with the RNA degradosome, an RNAse known to be involved in degradation of sRNAs as well as their target mRNAs. pnp mutations lead to increased instability and decreased levels of multiple sRNAs, and this decreased accumulation may be sufficient to explain their failure to act. Our genetic analysis suggests that PNPase may play an unexpected role in protecting sRNAs from degradation, probably by regulating the activity of the RNA degradosome. This proposal has now been confirmed by in vitro work from B. Luisi and students at the U. of Cambridge, and we are collaborating with them to further dissect how PNPase, Hfq, and the degradosome interact. Further genetic dissection of PNPase demonstrates that the active site of PNPase is critical for protection of sRNAs;this will also be investigated in vitro. Overall, we have developed highly efficient in vivo tools for studying sRNAs and the networks they reside in. Our focus is increasingly on the role of the sRNAs in complex bacterial behavior and investigations into the mechanism of sRNA function.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Investigator-Initiated Intramural Research Projects (ZIA)
Project #
Application #
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
National Cancer Institute Division of Basic Sciences
Zip Code
Thompson, Karl M; Gottesman, Susan (2014) The MiaA tRNA modification enzyme is necessary for robust RpoS expression in Escherichia coli. J Bacteriol 196:754-61
De Lay, Nicholas; Schu, Daniel J; Gottesman, Susan (2013) Bacterial small RNA-based negative regulation: Hfq and its accomplices. J Biol Chem 288:7996-8003
Moon, Kyung; Six, David A; Lee, Hyun-Jung et al. (2013) Complex transcriptional and post-transcriptional regulation of an enzyme for lipopolysaccharide modification. Mol Microbiol 89:52-64
De Lay, Nicholas; Gottesman, Susan (2009) The Crp-activated small noncoding regulatory RNA CyaR (RyeE) links nutritional status to group behavior. J Bacteriol 191:461-76
Mandin, Pierre; Gottesman, Susan (2009) A genetic approach for finding small RNAs regulators of genes of interest identifies RybC as regulating the DpiA/DpiB two-component system. Mol Microbiol 72:551-65
Guillier, Maude; Gottesman, Susan (2008) The 5'end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator. Nucleic Acids Res 36:6781-94