title: Quantifying the sequence-function relation in gene silencing by bacterial small RNAs.
abstract: Sequence-function relations for small RNA (sRNA)-mediated gene silencing were quantified for the sRNA RyhB and some of its mRNA targets in Escherichia coli. Numerous mutants of RyhB and its targets were generated and their in vivo functions characterized at various levels of target and RyhB expression. Although a core complementary region is required for repression by RyhB, variations in the complementary sequences of the core region gave rise to a continuum of repression strengths, correlated exponentially with the computed free energy of RyhB-target duplex formation. Moreover, sequence variations in the linker region known to interact with the RNA chaperone Hfq also gave rise to a continuum of repression strengths, correlated exponentially with the computed energy cost of keeping the linker region open. These results support the applicability of the thermodynamic model in predicting sRNA-mRNA interaction and suggest that sequences at these locations may be used to fine-tune the degree of repression. Surprisingly, a truncated RyhB without the Hfq-binding region is found to repress multiple targets of the wild-type RyhB effectively, both in the presence and absence of Hfq, even though the former is required for the activity of wild-type RyhB itself. These findings challenge the commonly accepted model concerning the function of Hfq in gene silencing-both in providing stability to the sRNAs and in catalyzing the target mRNAs to take on active conformations-and raise the intriguing question of why many endogenous sRNAs subject their functions to Hfq-dependences.
authors: Institute of Theoretical Physics and Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
authors: Yue
authors: Y
authors: Hao
authors: Zhongge J
authors: ZJ
authors: Zhang
authors: David W
authors: DW
authors: Erickson
authors: Min
authors: M
authors: Huang
authors: Yingwu
authors: Y
authors: Huang
authors: Junbai
authors: J
authors: Li
authors: Terence
authors: T
authors: Hwa
authors: Hualin
authors: H
authors: Shi
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D004734:Energy Metabolism; D048168:Escherichia coli K12 / Q000235:genetics* / Q000378:metabolism; D020868:Gene Silencing; D005798:Genes, Bacterial; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009690:Nucleic Acid Conformation; D012323:RNA Processing, Post-Transcriptional; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D022661:RNA, Untranslated / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D013482:Superoxide Dismutase / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial; D022661:RNA, Untranslated; C087504:SodB protein, Bacteria; D013482:Superoxide Dismutase