Identifying Hfq-binding small RNA targets in Escherichia coli

2006 ◽  
Vol 343 (3) ◽  
pp. 950-955 ◽  
Author(s):  
Yong Zhang ◽  
Shiwei Sun ◽  
Tao Wu ◽  
Jie Wang ◽  
Changning Liu ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Small Rna ◽  
Rna Targets

scholarly journals Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth

RNA Biology ◽  
2017 ◽  
Vol 14 (2) ◽  
pp. 206-218 ◽  
Author(s):  
Emiko Noro ◽  
Masaru Mori ◽  
Gakuto Makino ◽  
Yuki Takai ◽  
Sumiko Ohnuma ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Small Rna ◽  
Coli Growth

scholarly journals CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets

2008 ◽  
Vol 25 (1) ◽  
pp. 130-131 ◽  
Author(s):  
C. Addo-Quaye ◽  
W. Miller ◽  
M. J. Axtell
Keyword(s):  
Small Rna ◽  
Rna Targets

Metabolic remodeling in Escherichia coli   MG 1655. A prophage e14‐encoded small RNA ,  co293 , post‐transcriptionally regulates transcription factors HcaR and FadR

FEBS Journal ◽  
2020 ◽  
Vol 287 (21) ◽  
pp. 4767-4782
Author(s):  
Ashok Kumar Madikonda ◽  
Akbarpasha Shaikh ◽  
Sonali Khanra ◽  
Harshita Yakkala ◽  
Sailu Yellaboina ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Transcription Factors ◽  
Small Rna ◽  
Metabolic Remodeling

scholarly journals RyhB small RNA modulates the free intracellular iron pool and is essential for normal growth during iron limitation in Escherichia coli

2006 ◽  
Vol 62 (4) ◽  
pp. 1181-1190 ◽  
Author(s):  
Jean-François Jacques ◽  
Soojin Jang ◽  
Karine Prévost ◽  
Guillaume Desnoyers ◽  
Maxime Desmarais ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Small Rna ◽  
Normal Growth ◽  
Iron Limitation ◽  
Intracellular Iron ◽  
Iron Pool

scholarly journals The small RNA GlmY acts upstream of the sRNA GlmZ in the activation of glmS expression and is subject to regulation by polyadenylation in Escherichia coli

2008 ◽  
Vol 36 (8) ◽  
pp. 2570-2580 ◽  
Author(s):  
Birte Reichenbach ◽  
Alexandre Maes ◽  
Falk Kalamorz ◽  
Eliane Hajnsdorf ◽  
Boris Görke
Keyword(s):  
Escherichia Coli ◽  
Small Rna

Artificial small RNA-mediated growth inhibition in Escherichia coli and Salmonella enterica serovar Typhimurium

2020 ◽  
Vol 521 (3) ◽  
pp. 577-583 ◽  
Author(s):  
Mitsuoki Kawano ◽  
Shota Morohashi ◽  
Kohei Oda ◽  
Masataka Ishikawa ◽  
Shouta Fujita ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Growth Inhibition ◽  
Small Rna ◽  
Salmonella Enterica ◽  
Salmonella Enterica Serovar Typhimurium ◽  
Serovar Typhimurium

scholarly journals StarScan: a web server for scanning small RNA targets from degradome sequencing data

2015 ◽  
Vol 43 (W1) ◽  
pp. W480-W486 ◽  
Author(s):  
Shun Liu ◽  
Jun-Hao Li ◽  
Jie Wu ◽  
Ke-Ren Zhou ◽  
Hui Zhou ◽  
...  
Keyword(s):  
Small Rna ◽  
Web Server ◽  
Sequencing Data ◽  
Degradome Sequencing ◽  
Rna Targets

scholarly journals GadY, a Small-RNA Regulator of Acid Response Genes in Escherichia coli

2004 ◽  
Vol 186 (20) ◽  
pp. 6698-6705 ◽  
Author(s):  
Jason A. Opdyke ◽  
Ju-Gyeong Kang ◽  
Gisela Storz
Keyword(s):  
Escherichia Coli ◽  
Stationary Phase ◽  
Small Rna ◽  
Acid Resistance ◽  
Base Pairs ◽  
Gene Encoding ◽  
Mrna Accumulation ◽  
Long Form ◽  
Genes Encoding ◽  
Opposite Strand

ABSTRACT A previous bioinformatics-based search for small RNAs in Escherichia coli identified a novel RNA named IS183. The gene encoding this small RNA is located between and on the opposite strand of genes encoding two transcriptional regulators of the acid response, gadX (yhiX) and gadW (yhiW). Given that IS183 is encoded in the gad gene cluster and because of its role in regulating acid response genes reported here, this RNA has been renamed GadY. We show that GadY exists in three forms, a long form consisting of 105 nucleotides and two processed forms, consisting of 90 and 59 nucleotides. The expression of this small RNA is highly induced during stationary phase in a manner that is dependent on the alternative sigma factor σS. Overexpression of the three GadY RNA forms resulted in increased levels of the mRNA encoding the GadX transcriptional activator, which in turn caused increased levels of the GadA and GadB glutamate decarboxylases. A promoter mutation which abolished gadY expression resulted in a reduction in the amount of gadX mRNA during stationary phase. The gadY gene was shown to overlap the 3′ end of the gadX gene, and this overlap region was found to be necessary for the GadY-dependent accumulation of gadX mRNA. We suggest that during stationary phase, GadY forms base pairs with the 3′-untranslated region of the gadX mRNA and confers increased stability, allowing for gadX mRNA accumulation and the increased expression of downstream acid resistance genes.

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