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Quantifying the sequence-function relation in gene silencing by bacterial small RNAs
Hao, Y; Zhang, ZJ; Erickson, DW; Huang, M; Huang, YW; Li, JB; Hwa, T; Shi, HL; Shi, HL (reprint author), Univ Calif San Diego, Div Biol Sci, Mol Biol Sect, La Jolla, CA 92093 USA.
2011
发表期刊PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
ISSN0027-8424
卷号108期号:30页码:12473-12478
摘要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.
部门归属[Zhang, Zhongge J.; Hwa, Terence] Univ Calif San Diego, Div Biol Sci, Mol Biol Sect, La Jolla, CA 92093 USA; [Hao, Yue; Huang, Min; Shi, Hualin] Chinese Acad Sci, Inst Theoret Phys, Beijing 100190, Peoples R China; [Li, Junbai] Chinese Acad Sci, Inst Chem, Beijing 100190, Peoples R China; [Erickson, David W.; Hwa, Terence] Univ Calif San Diego, Ctr Theoret Biol Phys, La Jolla, CA 92093 USA; [Erickson, David W.; Hwa, Terence] Univ Calif San Diego, Dept Phys, La Jolla, CA 92093 USA; [Huang, Yingwu] Tsinghua Univ, Dept Biol Sci & Biotechnol, Beijing 100084, Peoples R China
关键词Small Regulatory Rnas Small Noncoding Rnas Messenger-rna Escherichia-coli Binding-sites Soluble-rna Translational Initiation Vibrio-cholerae Outer-membrane Hfq-binding
学科领域Physics
资助者National Institutes of Health [R01-GM77298]; National Natural Science Foundation of China [10428409, 90403140]; National Basic Research Program of China [2007CB814800] ; National Institutes of Health [R01-GM77298]; National Natural Science Foundation of China [10428409, 90403140]; National Basic Research Program of China [2007CB814800] ; National Institutes of Health [R01-GM77298]; National Natural Science Foundation of China [10428409, 90403140]; National Basic Research Program of China [2007CB814800] ; National Institutes of Health [R01-GM77298]; National Natural Science Foundation of China [10428409, 90403140]; National Basic Research Program of China [2007CB814800] ; National Institutes of Health [R01-GM77298]; National Natural Science Foundation of China [10428409, 90403140]; National Basic Research Program of China [2007CB814800] ; National Institutes of Health [R01-GM77298]; National Natural Science Foundation of China [10428409, 90403140]; National Basic Research Program of China [2007CB814800] ; National Institutes of Health [R01-GM77298]; National Natural Science Foundation of China [10428409, 90403140]; National Basic Research Program of China [2007CB814800] ; National Institutes of Health [R01-GM77298]; National Natural Science Foundation of China [10428409, 90403140]; National Basic Research Program of China [2007CB814800]
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收录类别SCI
语种英语
资助者National Institutes of Health [R01-GM77298]; National Natural Science Foundation of China [10428409, 90403140]; National Basic Research Program of China [2007CB814800] ; National Institutes of Health [R01-GM77298]; National Natural Science Foundation of China [10428409, 90403140]; National Basic Research Program of China [2007CB814800] ; National Institutes of Health [R01-GM77298]; National Natural Science Foundation of China [10428409, 90403140]; National Basic Research Program of China [2007CB814800] ; National Institutes of Health [R01-GM77298]; National Natural Science Foundation of China [10428409, 90403140]; National Basic Research Program of China [2007CB814800] ; National Institutes of Health [R01-GM77298]; National Natural Science Foundation of China [10428409, 90403140]; National Basic Research Program of China [2007CB814800] ; National Institutes of Health [R01-GM77298]; National Natural Science Foundation of China [10428409, 90403140]; National Basic Research Program of China [2007CB814800] ; National Institutes of Health [R01-GM77298]; National Natural Science Foundation of China [10428409, 90403140]; National Basic Research Program of China [2007CB814800] ; National Institutes of Health [R01-GM77298]; National Natural Science Foundation of China [10428409, 90403140]; National Basic Research Program of China [2007CB814800]
WOS记录号WOS:000293129900056
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被引频次:36[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/14315
专题理论物理所SCI论文
通讯作者Shi, HL (reprint author), Univ Calif San Diego, Div Biol Sci, Mol Biol Sect, La Jolla, CA 92093 USA.
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Hao, Y,Zhang, ZJ,Erickson, DW,et al. Quantifying the sequence-function relation in gene silencing by bacterial small RNAs[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA,2011,108(30):12473-12478.
APA Hao, Y.,Zhang, ZJ.,Erickson, DW.,Huang, M.,Huang, YW.,...&Shi, HL .(2011).Quantifying the sequence-function relation in gene silencing by bacterial small RNAs.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA,108(30),12473-12478.
MLA Hao, Y,et al."Quantifying the sequence-function relation in gene silencing by bacterial small RNAs".PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 108.30(2011):12473-12478.
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