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Quantifying the sequence-function relation in gene silencing by bacterial small RNAs
Hao, Yue2; Zhang, Zhongge J.1; Erickson, David W.4,5; Huang, Min2; Huang, Yingwu6; Li, Junbai3; Hwa, Terence1,4,5; Shi, Hualin2
2011-07-26
Source PublicationPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
ISSN0027-8424
Volume108Issue:30Pages:12473-12478
AbstractSequence-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.
KeywordGene Regulation Noncoding Rna Posttranscriptional Control Quantitative Biology Rna Interaction
DOI10.1073/pnas.1100432108
Indexed BySCI
Language英语
WOS IDWOS:000293129900056
PublisherNATL ACAD SCIENCES
Citation statistics
Cited Times:37[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.iccas.ac.cn/handle/121111/72646
Collection中国科学院化学研究所
Corresponding AuthorShi, Hualin
Affiliation1.Univ Calif San Diego, Div Biol Sci, Mol Biol Sect, La Jolla, CA 92093 USA
2.Chinese Acad Sci, Inst Theoret Phys, Beijing 100190, Peoples R China
3.Chinese Acad Sci, Inst Chem, Beijing 100190, Peoples R China
4.Univ Calif San Diego, Ctr Theoret Biol Phys, La Jolla, CA 92093 USA
5.Univ Calif San Diego, Dept Phys, La Jolla, CA 92093 USA
6.Tsinghua Univ, Dept Biol Sci & Biotechnol, Beijing 100084, Peoples R China
Recommended Citation
GB/T 7714
Hao, Yue,Zhang, Zhongge J.,Erickson, David W.,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, Yue.,Zhang, Zhongge J..,Erickson, David W..,Huang, Min.,Huang, Yingwu.,...&Shi, Hualin.(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, Yue,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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