TY - JOUR
T1 - Positive regulation by small RNAs and the role of Hfq
AU - Soper, Toby
AU - Mandin, Pierre
AU - Majdalani, Nadim
AU - Gottesman, Susan
AU - Woodson, Sarah A.
PY - 2010/5/25
Y1 - 2010/5/25
N2 - Bacterial small noncoding RNAs carry out both positive and negative. Escherichia coli, this regulation often requires the RNA chaperone Hfq. Three small regulatory RNAs (sRNAs), DsrA, RprA, and ArcZ, positively regulate translation of the sigma factor RpoS, each pairing with the 5′ leader to open up an inhibitory hairpin. In vitro, rpoS interaction with sRNAs depends upon an (AAN)4 Hfq-binding site upstream of the pairing region. Here we show that both Hfq and this Hfq binding site are required for RprA or ArcZ to act in vivo and to form a stable complex with rpoS mRNA in vitro; both were partially dispensable for DsrA at 37°C. ArcZ sRNA is processed from 121 nt to a stable 56 nt species that contains the pairing region; only the 56 nt ArcZ makes a strong Hfq-dependent complex with rpoS. For each of these sRNAs, the stability of the sRNA • mRNA complexes, rather than their rate of formation, best predicted in vivo activity. These studies demonstrate that binding of Hfq to the rpoS mRNA is critical for sRNA regulation under normal conditions, but if the stability of the sRNA • mRNA complex is sufficiently high, the requirement for Hfq can be bypassed.
AB - Bacterial small noncoding RNAs carry out both positive and negative. Escherichia coli, this regulation often requires the RNA chaperone Hfq. Three small regulatory RNAs (sRNAs), DsrA, RprA, and ArcZ, positively regulate translation of the sigma factor RpoS, each pairing with the 5′ leader to open up an inhibitory hairpin. In vitro, rpoS interaction with sRNAs depends upon an (AAN)4 Hfq-binding site upstream of the pairing region. Here we show that both Hfq and this Hfq binding site are required for RprA or ArcZ to act in vivo and to form a stable complex with rpoS mRNA in vitro; both were partially dispensable for DsrA at 37°C. ArcZ sRNA is processed from 121 nt to a stable 56 nt species that contains the pairing region; only the 56 nt ArcZ makes a strong Hfq-dependent complex with rpoS. For each of these sRNAs, the stability of the sRNA • mRNA complexes, rather than their rate of formation, best predicted in vivo activity. These studies demonstrate that binding of Hfq to the rpoS mRNA is critical for sRNA regulation under normal conditions, but if the stability of the sRNA • mRNA complex is sufficiently high, the requirement for Hfq can be bypassed.
KW - RNA-protein interactions
KW - Sigma 38
KW - Sm-like protein
KW - Translational control
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U2 - 10.1073/pnas.1004435107
DO - 10.1073/pnas.1004435107
M3 - Article
C2 - 20457943
AN - SCOPUS:77953090678
SN - 0027-8424
VL - 107
SP - 9602
EP - 9607
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
IS - 21
ER -