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 sRNA 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 demonstrated that the LPS modification is under control of the sRNA. 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. In addition, a second small RNA regulator of the eptB gene was 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 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. Deletion of dsrA decreases biofilm production, although our results suggest this may reflect multiple effects of the sRNA. 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, we have screened multiple other transcriptional regulators for sRNA regulation. We find that only a subset of regulators are subject to sRNA effects, and we are investigating the physiological significance of this extra level of regulation. 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. 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 with multiple sRNA:mRNA reporters in vivo;the results demonstrate that some mutants are defective only for some sRNA/mRNA pairs, suggesting that there are multiple modes for Hfq to bind and act to stimulate pairing. In addition, the role of individual subunits in the hexamer had not been examined. We have created genes encoding covalently linked multimers of Hfq, allowing us to place mutations in given subunits. Initial studies suggest that some sites within Hfq need only be present on alternating subunits for full function, while others are needed on all subunits. 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. Among the mutations isolated were changes in conserved and essential amino acids in hfq and 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.

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Keefer, Andrea B; Asare, Eugenia K; Pomerantsev, Andrei P et al. (2017) In vivo characterization of an Hfq protein encoded by the Bacillus anthracis virulence plasmid pXO1. BMC Microbiol 17:63
Parker, Ashley; Cureoglu, Suanur; De Lay, Nicholas et al. (2017) Alternative pathways for Escherichia coli biofilm formation revealed by sRNA overproduction. Mol Microbiol 105:309-325
Sedlyarova, Nadezda; Shamovsky, Ilya; Bharati, Binod K et al. (2016) sRNA-Mediated Control of Transcription Termination in E. coli. Cell 167:111-121.e13
Lee, Hyun-Jung; Gottesman, Susan (2016) sRNA roles in regulating transcriptional regulators: Lrp and SoxS regulation by sRNAs. Nucleic Acids Res 44:6907-23
Brosse, Anaïs; Korobeinikova, Anna; Gottesman, Susan et al. (2016) Unexpected properties of sRNA promoters allow feedback control via regulation of a two-component system. Nucleic Acids Res :
Parker, Ashley; Gottesman, Susan (2016) Small RNA Regulation of TolC, the Outer Membrane Component of Bacterial Multidrug Transporters. J Bacteriol 198:1101-13
Chen, Jiandong; Gottesman, Susan (2016) Spot 42 sRNA regulates arabinose-inducible araBAD promoter activity by repressing synthesis of the high-affinity low-capacity arabinose transporter. J Bacteriol :
Santiago-Frangos, Andrew; Kavita, Kumari; Schu, Daniel J et al. (2016) C-terminal domain of the RNA chaperone Hfq drives sRNA competition and release of target RNA. Proc Natl Acad Sci U S A 113:E6089-E6096
Panja, Subrata; Santiago-Frangos, Andrew; Schu, Daniel J et al. (2015) Acidic Residues in the Hfq Chaperone Increase the Selectivity of sRNA Binding and Annealing. J Mol Biol 427:3491-3500
Gottesman, Susan; Storz, Gisela (2015) RNA reflections: converging on Hfq. RNA 21:511-2

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