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1. chinaXiv:201605.00998 [pdf]

Quantifying the sequence-function relation in gene silencing by bacterial small RNAs

Yue Hao; Zhongge J. Zhang; David W. Erickson; Min Huang; Yingwu Huang; Junbai Li; Terence Hwa; hualin shi
Subjects: Physics >> Interdisciplinary Physics and Related Areas of Science and Technology

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?inthe?linker region known to interact with?the?RNA chaperone Hfq also gave rise to a continuum of repression strengths, correlated exponentially with?thecomputed 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-bothin?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.

submitted time 2016-05-08 Hits1986Downloads802 Comment 0

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