NDLI: Quantifying the sequence–function relation in gene silencing by bacterial small RNAs

Content Provider	PubMed Central
Author	Hao, Yue Zhang, Zhongge J. Erickson, David W. Huang, Min Huang, Yingwu Li, Junbai Hwa, Terence Shi, Hualin
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.
Related Links	http://dx.doi.org/10.1073/pnas.1100432108
Starting Page	12473
File Format	PDF
ISSN	10916490
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	30
Volume Number	108
Language	English
Publisher	National Academy of Sciences
Publisher Date	2011-07-26
Access Restriction	Open
Rights Holder	National Academy of Sciences
Subject Keyword	Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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

Translational repression is sufficient for gene silencing by bacterial small noncoding RNAs in the absence of mRNA destruction

Genomewide view of gene silencing by small interfering RNAs

Genomewide view of gene silencing by small interfering RNAs.

Small RNAs in transcriptional gene silencing and genome defence

High molecular weight RNAs and small interfering RNAs induce systemic posttranscriptional gene silencing in plants

Sense- and antisense-mediated gene silencing in tobacco is inhibited by the same viral suppressors and is associated with accumulation of small RNAs

Robust gene silencing mediated by antisense small RNAs in the pathogenic protist Entamoeba histolytica

Specific gene silencing by artificial trans-encoded small noncoding RNAs in bacteria

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

Similar Documents

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

Translational repression is sufficient for gene silencing by bacterial small noncoding RNAs in the absence of mRNA destruction

Genomewide view of gene silencing by small interfering RNAs

Genomewide view of gene silencing by small interfering RNAs.

Small RNAs in transcriptional gene silencing and genome defence

High molecular weight RNAs and small interfering RNAs induce systemic posttranscriptional gene silencing in plants

Sense- and antisense-mediated gene silencing in tobacco is inhibited by the same viral suppressors and is associated with accumulation of small RNAs

Robust gene silencing mediated by antisense small RNAs in the pathogenic protist Entamoeba histolytica

Specific gene silencing by artificial trans-encoded small noncoding RNAs in bacteria

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