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

Subjects: Physics >> Interdisciplinary Physics and Related Areas of Science and Technology submitted time 2016-05-08

Yue Hao Zhongge J. Zhang David W. Erickson Min Huang Yingwu Huang Junbai Li Terence Hwa hualin shi

Abstract： Sequence-function爎elations for爏mall燫NA (sRNA)-mediated爂ene爏ilencing爓ere quantified for爐he爏RNA RyhB and some of its mRNA targets爄n燛scherichia coli. Numerous mutants of RyhB and its targets were generated and their爄n爒ivo functions characterized at various levels of target and RyhB expression. Although a core complementary region is required for repression燽y燫yhB, variations爄n爐he燾omplementary sequences of爐he燾ore region gave rise to a continuum of repression strengths, correlated exponentially with爐he燾omputed free energy of RyhB-target duplex formation. Moreover,爏equence爒ariations爄nthe爈inker region known to interact with爐he燫NA chaperone Hfq also gave rise to a continuum of repression strengths, correlated exponentially with爐hecomputed energy cost of keeping爐he爈inker region open. These results support爐he燼pplicability of爐he爐hermodynamic model爄n爌redicting sRNA-mRNA interaction and suggest that sequences at these locations may be used to fine-tune爐he燿egree of repression. Surprisingly, a truncated RyhB without爐he燞fq-binding region is found to repress multiple targets of爐he爓ild-type RyhB effectively, both爄n爐he爌resence and absence of Hfq, even though爐he爁ormer is required for爐he燼ctivity of wild-type RyhB itself. These findings challenge爐he燾ommonly accepted model concerning爐he爁unction爋f Hfq爄n爂ene爏ilencing-bothin爌roviding stability to爐he爏RNAs and爄n燾atalyzing爐he爐arget mRNAs to take on active conformations-and raise爐he爄ntriguing question of why many endogenous sRNAs subject their functions to Hfq-dependences.

Peer Review Status:Awaiting Review

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