Multiple target regulation by small noncoding RNAs rewires gene expression at the post-transcriptional level.

PubWeight™: 1.46‹?› | Rank: Top 5%

🔗 View Article (PMID 19366629)

Published in Res Microbiol on April 12, 2009

Authors

Kai Papenfort1, Jörg Vogel

Author Affiliations

1: Max Planck Institute for Infection Biology, RNA Biology Group, Charitéplatz 1, 10117 Berlin, Germany.

Articles citing this

Hfq and its constellation of RNA. Nat Rev Microbiol (2011) 4.94

Bacterial antisense RNAs: how many are there, and what are they doing? Annu Rev Genet (2010) 2.47

Identification of regulatory RNAs in Bacillus subtilis. Nucleic Acids Res (2010) 1.99

Structural basis for RNA 3'-end recognition by Hfq. Proc Natl Acad Sci U S A (2011) 1.73

A dynamic and intricate regulatory network determines Pseudomonas aeruginosa virulence. Nucleic Acids Res (2012) 1.70

Evidence for an autonomous 5' target recognition domain in an Hfq-associated small RNA. Proc Natl Acad Sci U S A (2010) 1.69

Small RNA binding to the lateral surface of Hfq hexamers and structural rearrangements upon mRNA target recognition. Proc Natl Acad Sci U S A (2012) 1.51

Reprogramming of anaerobic metabolism by the FnrS small RNA. Mol Microbiol (2010) 1.46

Structural insights into the dynamics and function of the C-terminus of the E. coli RNA chaperone Hfq. Nucleic Acids Res (2011) 1.30

Rapid binding and release of Hfq from ternary complexes during RNA annealing. Nucleic Acids Res (2011) 1.30

Staphylococcus aureus RNAIII binds to two distant regions of coa mRNA to arrest translation and promote mRNA degradation. PLoS Pathog (2010) 1.27

A Staphylococcus aureus small RNA is required for bacterial virulence and regulates the expression of an immune-evasion molecule. PLoS Pathog (2010) 1.26

Defining a role for Hfq in Gram-positive bacteria: evidence for Hfq-dependent antisense regulation in Listeria monocytogenes. Nucleic Acids Res (2009) 1.25

An upstream Hfq binding site in the fhlA mRNA leader region facilitates the OxyS-fhlA interaction. PLoS One (2010) 1.20

Structure and RNA-binding properties of the bacterial LSm protein Hfq. RNA Biol (2013) 1.16

E. coli DNA associated with isolated Hfq interacts with Hfq's distal surface and C-terminal domain. Biochim Biophys Acta (2010) 1.07

TargetRNA2: identifying targets of small regulatory RNAs in bacteria. Nucleic Acids Res (2014) 1.04

Requirement of upstream Hfq-binding (ARN)x elements in glmS and the Hfq C-terminal region for GlmS upregulation by sRNAs GlmZ and GlmY. Nucleic Acids Res (2012) 1.03

Identification of two small regulatory RNAs linked to virulence in Brucella abortus 2308. Mol Microbiol (2012) 1.01

Evolutionary dynamics of small RNAs in 27 Escherichia coli and Shigella genomes. Genome Biol Evol (2012) 0.96

Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation. RNA Biol (2014) 0.96

The small regulatory RNA SyR1/PsrR1 controls photosynthetic functions in cyanobacteria. Plant Cell (2014) 0.93

An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains. Nucleic Acids Res (2012) 0.93

A small RNA controls a protein regulator involved in antibiotic resistance in Staphylococcus aureus. Nucleic Acids Res (2014) 0.92

Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium. Genome Biol (2012) 0.91

Requirement of the CsdA DEAD-box helicase for low temperature riboregulation of rpoS mRNA. RNA Biol (2010) 0.91

Myofibril-inducing RNA (MIR) is essential for tropomyosin expression and myofibrillogenesis in axolotl hearts. J Biomed Sci (2009) 0.90

Proteome-wide alterations in Escherichia coli translation rates upon anaerobiosis. Mol Cell Proteomics (2010) 0.89

Thermodynamic and kinetic analysis of an RNA kissing interaction and its resolution into an extended duplex. Biophys J (2012) 0.88

Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria. BMC Genomics (2014) 0.87

Transcriptome complexity and riboregulation in the human pathogen Helicobacter pylori. Front Cell Infect Microbiol (2012) 0.86

RNA regulators of host immunity and pathogen adaptive responses in the oral cavity. Microbes Infect (2015) 0.84

Genome-wide analyses in bacteria show small-RNA enrichment for long and conserved intergenic regions. J Bacteriol (2014) 0.83

Small RNA modules confer different stabilities and interact differently with multiple targets. PLoS One (2013) 0.83

Identification of novel sRNAs involved in biofilm formation, motility, and fimbriae formation in Escherichia coli. Sci Rep (2015) 0.82

Two separate modules of the conserved regulatory RNA AbcR1 address multiple target mRNAs in and outside of the translation initiation region. RNA Biol (2014) 0.81

Identifying and characterizing Hfq-RNA interactions. Methods (2013) 0.81

Benzoate mediates repression of C(4)-dicarboxylate utilization in "Aromatoleum aromaticum" EbN1. J Bacteriol (2011) 0.80

Multi-target regulation by small RNAs synchronizes gene expression thresholds and may enhance ultrasensitive behavior. PLoS One (2012) 0.80

Genome-wide analyses of small non-coding RNAs in streptococci. Front Genet (2015) 0.78

Benzoate mediates the simultaneous repression of anaerobic 4-methylbenzoate and succinate utilization in Magnetospirillum sp. strain pMbN1. BMC Microbiol (2014) 0.77

The target spectrum of SdsR small RNA in Salmonella. Nucleic Acids Res (2016) 0.76

Cis-Antisense Transcription Gives Rise to Tunable Genetic Switch Behavior: A Mathematical Modeling Approach. PLoS One (2015) 0.76

Identification of the base-pairing requirements for repression of hctA translation by the small RNA IhtA leads to the discovery of a new mRNA target in Chlamydia trachomatis. PLoS One (2015) 0.76

Identification and validation of sRNAs in Edwardsiella tarda S08. PLoS One (2017) 0.75

Twins, quadruplexes, and more: functional aspects of native and engineered RNA self-assembly in vivo. Front Life Sci (2013) 0.75

Use of siRNA molecular beacons to detect and attenuate mycobacterial infection in macrophages. World J Exp Med (2015) 0.75

Early Transcriptome Response of Lactococcus lactis to Environmental Stresses Reveals Differentially Expressed Small Regulatory RNAs and tRNAs. Front Microbiol (2017) 0.75

Articles by these authors

CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature (2011) 17.38

The primary transcriptome of the major human pathogen Helicobacter pylori. Nature (2010) 7.70

Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet (2008) 5.23

Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell (2011) 4.68

Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput Biol (2009) 4.24

The RNA chaperone Hfq is essential for the virulence of Salmonella typhimurium. Mol Microbiol (2006) 3.35

SigmaE-dependent small RNAs of Salmonella respond to membrane stress by accelerating global omp mRNA decay. Mol Microbiol (2006) 3.07

Translational control and target recognition by Escherichia coli small RNAs in vivo. Nucleic Acids Res (2007) 3.06

Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA. Genes Dev (2005) 2.93

Small RNA binding to 5' mRNA coding region inhibits translational initiation. Mol Cell (2008) 2.88

An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803. Proc Natl Acad Sci U S A (2011) 2.84

Two seemingly homologous noncoding RNAs act hierarchically to activate glmS mRNA translation. PLoS Biol (2008) 2.61

Processing-independent CRISPR RNAs limit natural transformation in Neisseria meningitidis. Mol Cell (2013) 2.52

A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites. Genes Dev (2007) 2.44

Regulatory RNA in bacterial pathogens. Cell Host Microbe (2010) 2.41

The role of Hfq in bacterial pathogens. Curr Opin Microbiol (2010) 2.40

The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium. Proc Natl Acad Sci U S A (2012) 2.39

Dual RNA-seq of pathogen and host. Nat Rev Microbiol (2012) 2.32

Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation. Nat Struct Mol Biol (2009) 2.25

Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome. Nucleic Acids Res (2009) 2.20

An atlas of Hfq-bound transcripts reveals 3' UTRs as a genomic reservoir of regulatory small RNAs. EMBO J (2012) 2.10

Activation of gene expression by small RNA. Curr Opin Microbiol (2009) 2.04

Analysis of the host microRNA response to Salmonella uncovers the control of major cytokines by the let-7 family. EMBO J (2011) 2.03

Identification of regulatory RNAs in Bacillus subtilis. Nucleic Acids Res (2010) 1.99

An antisense RNA inhibits translation by competing with standby ribosomes. Mol Cell (2007) 1.97

Experimental approaches for the discovery and characterization of regulatory small RNA. Curr Opin Microbiol (2009) 1.92

A new Vibrio cholerae sRNA modulates colonization and affects release of outer membrane vesicles. Mol Microbiol (2008) 1.83

Identification of cyanobacterial non-coding RNAs by comparative genome analysis. Genome Biol (2005) 1.82

Experimental approaches to identify non-coding RNAs. Nucleic Acids Res (2006) 1.80

Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA. Mol Microbiol (2009) 1.77

A small non-coding RNA of the invasion gene island (SPI-1) represses outer membrane protein synthesis from the Salmonella core genome. Mol Microbiol (2007) 1.72

Evidence for an autonomous 5' target recognition domain in an Hfq-associated small RNA. Proc Natl Acad Sci U S A (2010) 1.69

Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability. Proc Natl Acad Sci U S A (2009) 1.66

Pervasive post-transcriptional control of genes involved in amino acid metabolism by the Hfq-dependent GcvB small RNA. Mol Microbiol (2011) 1.64

Characterization of the role of ribonucleases in Salmonella small RNA decay. Nucleic Acids Res (2007) 1.62

Systematic deletion of Salmonella small RNA genes identifies CyaR, a conserved CRP-dependent riboregulator of OmpX synthesis. Mol Microbiol (2008) 1.62

RelA protein stimulates the activity of RyhB small RNA by acting on RNA-binding protein Hfq. Proc Natl Acad Sci U S A (2012) 1.54

The seed region of a small RNA drives the controlled destruction of the target mRNA by the endoribonuclease RNase E. Mol Cell (2012) 1.49

Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism. Nucleic Acids Res (2010) 1.49

The primary transcriptome of barley chloroplasts: numerous noncoding RNAs and the dominating role of the plastid-encoded RNA polymerase. Plant Cell (2012) 1.47

Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon. Proc Natl Acad Sci U S A (2011) 1.46

Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes. RNA Biol (2009) 1.42

Small RNA-mediated activation of sugar phosphatase mRNA regulates glucose homeostasis. Cell (2013) 1.39

Comparative genomics boosts target prediction for bacterial small RNAs. Proc Natl Acad Sci U S A (2013) 1.29

Superfolder GFP reporters validate diverse new mRNA targets of the classic porin regulator, MicF RNA. Mol Microbiol (2012) 1.29

Noncoding RNA control of the making and breaking of sugars. Genes Dev (2008) 1.28

The mammalian microRNA response to bacterial infections. RNA Biol (2012) 1.27

Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions. Nucleic Acids Res (2011) 1.25

A conserved small RNA promotes discoordinate expression of the glmUS operon mRNA to activate GlmS synthesis. J Mol Biol (2007) 1.24

A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD. Nucleic Acids Res (2011) 1.23

Global regulatory functions of the Staphylococcus aureus endoribonuclease III in gene expression. PLoS Genet (2012) 1.17

The transcriptional landscape of Chlamydia pneumoniae. Genome Biol (2011) 1.16

Differential activation and functional specialization of miR-146 and miR-155 in innate immune sensing. Nucleic Acids Res (2012) 1.16

In vivo expression and purification of aptamer-tagged small RNA regulators. Nucleic Acids Res (2009) 1.15

RNA-mediated regulation in pathogenic bacteria. Cold Spring Harb Perspect Med (2013) 1.11

Photooxidative stress-induced and abundant small RNAs in Rhodobacter sphaeroides. Mol Microbiol (2009) 1.10

Targeted decay of a regulatory small RNA by an adaptor protein for RNase E and counteraction by an anti-adaptor RNA. Genes Dev (2013) 1.07

Contribution of Hfq to photooxidative stress resistance and global regulation in Rhodobacter sphaeroides. Mol Microbiol (2011) 1.05

The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair. Proc Natl Acad Sci U S A (2012) 1.04

The cyanobacterial homologue of the RNA chaperone Hfq is essential for motility of Synechocystis sp. PCC 6803. Microbiology (2008) 1.02

A small RNA activates CFA synthase by isoform-specific mRNA stabilization. EMBO J (2013) 1.02

Helicobacter pylori interferes with an embryonic stem cell micro RNA cluster to block cell cycle progression. Silence (2011) 0.98

The csgD mRNA as a hub for signal integration via multiple small RNAs. Mol Microbiol (2012) 0.95

Acid stress activation of the sigma(E) stress response in Salmonella enterica serovar Typhimurium. Mol Microbiol (2009) 0.93

Investigating CRISPR RNA Biogenesis and Function Using RNA-seq. Methods Mol Biol (2015) 0.89

Sensory and regulatory RNAs in prokaryotes: a new German research focus. RNA Biol (2007) 0.88

Use of aptamer tagging to identify in vivo protein binding partners of small regulatory RNAs. Methods Mol Biol (2012) 0.88

A candidate approach implicates the secreted Salmonella effector protein SpvB in P-body disassembly. PLoS One (2011) 0.88

Small RNAs promote mRNA stability to activate the synthesis of virulence factors. Mol Microbiol (2010) 0.85

A green fluorescent protein (GFP)-based plasmid system to study post-transcriptional control of gene expression in vivo. Methods Mol Biol (2009) 0.84

Regulatory RNAs in prokaryotes: here, there and everywhere. Mol Microbiol (2009) 0.83

Same same but different: new structural insight into CRISPR-Cas complexes. Mol Cell (2013) 0.83

Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their analysis. RNA Biol (2012) 0.81

Experimental tools to identify RNA-protein interactions in Helicobacter pylori. RNA Biol (2012) 0.80

A small RNA serving both the Hfq and CsrA regulons. Genes Dev (2013) 0.78

Bacterial regulatory mechanisms: the gene and beyond. Curr Opin Microbiol (2013) 0.77

CRISPRs extending their reach: prokaryotic RNAi protein Cas9 recruited for gene regulation. EMBO J (2013) 0.77

Analysis of A to I editing of miRNA in macrophages exposed to Salmonella. RNA Biol (2010) 0.77

Large scale biomimetic membrane arrays. Anal Bioanal Chem (2009) 0.77

Recent advances in the expression, evolution, and dynamics of prokaryotic genomes. J Bacteriol (2007) 0.76

A glimpse at the evolution of virulence control. Cell Host Microbe (2008) 0.76

Alexander Böhm (1971-2012). Mol Microbiol (2013) 0.76

Correction: Gifsy-1 Prophage IsrK with Dual Function as Small and Messenger RNA Modulates Vital Bacterial Machineries. PLoS Genet (2017) 0.75

Sweet business: Spot42 RNA networks with CRP to modulate catabolite repression. Mol Cell (2011) 0.75

Biomimetic membrane arrays on cast hydrogel supports. Langmuir (2011) 0.75

Microbes at their best: first Mol Micro Meeting Würzburg. Mol Microbiol (2011) 0.75