A Small Bacterial RNA Regulates a Putative ABC Transporter

A small noncoding bacterial ribonucleic acid of 62–64 nucleotides, RydC, was identified in the genomes of Escherichia coli, Salmonella, and Shigella. In vivo, RydC binds to the RNA-binding protein Hfq, and it is unstable when Hfq is absent. Mobility assays reveal that complex formation between RydC and Hfq is specific, with an apparent binding constant of ∼300 nm. Sequence alignments combined with structural probing demonstrate that RydC folds as Hfq binds the the and of the and with was of In vivo, the is is when RydC is and the is when RydC is with the with of in vivo, that with that RydC the the small to of to A small noncoding bacterial ribonucleic acid of 62–64 nucleotides, RydC, was identified in the genomes of Escherichia coli, Salmonella, and Shigella. In vivo, RydC binds to the RNA-binding protein Hfq, and it is unstable when Hfq is absent. Mobility assays reveal that complex formation between RydC and Hfq is specific, with an apparent binding constant of ∼300 nm. Sequence alignments combined with structural probing demonstrate that RydC folds as Hfq binds the the and of the and with was of In vivo, the is is when RydC is and the is when RydC is with the with of in vivo, that with that RydC the the small to of to A of small of protein small of protein that as in Escherichia of small to as small noncoding identified in the of In the and to the of in and with of the of with binding to to between and the of the Hfq of the and in Hfq binds and that Hfq as an to between and and Hfq between and the and structural of that folds as and binds Hfq in and in is was in the in the Salmonella, and Shigella. was of and and it was identified an of RydC that In vivo, RydC the of the the the of RydC is in vivo, the the and with as the and was of was and as was with the as between the and the to in the is the as and and the was in RydC, the was and was and and in an and in and the in was as the in the was in with of was and of was with with and with an RydC and of an in in in and the the of the was in the the of the was in in in and was RydC in in and was and to and and to with of and in of assays to with the of with and with acid was in of of and was with of in and and of was with of with of in of of the was of and of in and of and and the and the was to was with of to was with as the and and and RydC, the was and the was the was and the was of the and in and was and of was and of the that the of was to and was and RydC was and and and was with in of to an of with and bacterial in and in the of and of with with and was with with and and in the of protein was as and of Hfq the in and and the was in and was the and the protein was in and and to of was with of and the of binding in and with and was in with and of to the and the in and to of RydC, and the A complex between of RydC and of Hfq was in and that RydC was to bacterial to the an and in and was in In of and was to the and of and was to the and the was with an of with and as the of the was the with and with was the of the and and and RydC in and and and the with of in and with of with and of in and with of was in and was in and in the of of with of the of RydC in complex with Hfq was the as RydC was to of complex was with of to of with was of when probing the of RydC in complex with and of between was to the of the and of that was identified in bacterial the of the coli, Salmonella, and A of that is in was in the was with Hfq, identified and and RydC the to is the between and and protein of the the of with RydC is to as as structural and is of to the and and and the and that the is in of the and of RydC was and structural and RydC the of the RydC the of that the and RydC 62–64 in vivo, with the with RydC with Hfq in that RydC was between Hfq and In to the RydC in the that Hfq that in the of Hfq, RydC is unstable and of in the of Hfq that Hfq the of binding of Hfq to RydC was in assays of Hfq and constant of assays constant and of to binding to to apparent binding constant between RydC and Hfq to the of constant to the of assays with of Hfq that the complex is in and binding between RydC and Hfq is of of RydC of RydC RydC of the complex of RydC Hfq in and of the and of the of RydC bacterial in in that Hfq of with of RydC with of the between Hfq and RydC is of RydC and Hfq in the of of of RydC and with Sequence is to the of RydC was structural in an that was in the A RydC was and was nucleotides, was of in the and of the protein RydC and the complex is that with the and the of RydC and and the complex and structural of of and RydC in the and of structural of the the of the the of the of and the and the the and of the and to the the and of RydC in the of is of the protein to the with of is protein binding with in the of Hfq in as in that protein binding Hfq between the to and the and the of and that in and and and the of between and the of and and with and in to the the of to and that of to and the and of the that folds as A is in between and that is it is between and that the of RydC is and and that the of RydC in as bacterial the with the and an an the of between RydC and Hfq was structural and In the of Hfq, in and in Hfq binds to in it that the protein binds and and of Hfq is binding of the Hfq Hfq and the is an structural of the binding of Hfq to RydC is and the protein folds as in of and in and in in the of the Hfq binds and the to is in the of Hfq, that In the of Hfq, and is the of RydC in the of Hfq, the of that and the of an that with Hfq the was to of complex was between Hfq and RydC that of Hfq with RydC and that the with and A of is with the of the in the to the of the it of the to the of the of the binding protein the and to that is the of the and is the binding of the the the bacterial and with and RydC, the between the and binds with and A to the of the and the was in was with that was to binding in the assays between and of Hfq, in the of an of RydC, the with of the apparent constant of the between and Hfq is of the apparent constant is complex formation between the and Hfq is that between RydC and formation between and Hfq is of of complex formation of in that is and Hfq In the of of RydC, is complex formation between RydC and binding assays between and of and to the the between and with of Hfq of Hfq the between Hfq and is In assays with an of RydC in the of Hfq, the of the between the of RydC and was in demonstrate that the to is in in of the is and to the in with of the in RydC of is to with the is in in is of that with In that RydC is in the is the A was as an of of and as In the bacterial the the in coli, an that is in is in of the is RydC the In with to in the and the with in and of the is with to and of the with RydC of RydC bacterial of in with to RydC was as RydC in is of that RydC in was and in to with as with RydC of RydC was and with the of is the when and in RydC was and the of RydC was in as with the an of RydC of with was with the of the in the of that with ribonucleic RydC, was identified in small bacterial In the of RydC was and and to of 62–64 RydC with Hfq and that the protein is and in In RydC binds Hfq with and and the apparent binding constant of complex formation between the and the protein is with in In RydC folds as an and is binding of that the protein binds the the of the in and the to RydC with the that and Hfq to Hfq of that binds to to of an and of the in the of to in In the of RydC, and is the that the is in that and that is In the of the identified RydC and the apparent binding the complex and binds to binding of Hfq to RydC is to the in an and to and between the RydC and complex formation between RydC, the and Hfq between the Hfq binds and the of bacterial Hfq binds the and RydC, Hfq RydC and to Hfq RydC, and the between as RydC of the In the of the of an binding protein that in and in binding and the and is the In coli, the the the and the of the and is small an of the RydC is the between RydC and identified RydC the of the and the of the of RydC in the of as in in the of RydC, is in the that RydC is it to of RydC the and as bacterial of the the the that with the is in the of in in with of the that the as the when RydC is is in to the of the that is the Hfq is in the of RydC with the binding of the protein and In the of RydC is to the of the when the the of is the of and and to the the the of in and of and in the the and the and in the in the to to in A of small of protein small of protein that as in Escherichia of small to as small noncoding identified in the of In the and to the of in and with of the of with binding to to between and the of the Hfq of the and in Hfq binds and that Hfq as an to between and and Hfq between and In the and structural of that folds as and binds Hfq in and in is was in the in the Salmonella, and Shigella. was of and and it was identified an of RydC that In vivo, RydC the of the the the of RydC is in vivo, the the and with as the and was of was and as was with the as between the and the to in the is the as and and the was in RydC, the was and was and and in an and in and the in was as the in the was in with of was and of was with with and with an RydC and of an in in in and the the of the was in the the of the was in in in and was RydC in in and was and to and and to with of and in of assays to with the of with and with acid was in of of and was with of in and and of was with of with of in of of the was of and of in and of and and the and the was to was with of to was with as the and and and RydC, the was and the was the was and the was of the and in and was and of was and of the that the of was to and was and RydC was and and and was with in of to an of with and bacterial in and in the of and of with with and was with with and and in the of protein was as and of Hfq the in and and the was in and was the and the protein was in and and to of was with of and the of binding in and with and was in with and of to the and the in and to of RydC, and the A complex between of RydC and of Hfq was in and that RydC was to bacterial to the an and in and was in In of and was to the and of and was to the and the was with an of with and as the of the was the with and with was the of the and and and RydC in and and and the with of in and with of with and of in and with of was in and was in and in the of of with of the of RydC in complex with Hfq was the as RydC was to of complex was with of to of with was of when probing the of RydC in complex with and was of was and as was with the as between the and the to in the is the as and and the was in RydC, the was and was and and in an and in and the in was as the in the was in with of was and of was with with and with an RydC and of an in in in and the the of the was in the the of the was in in in and was RydC in in and was and to and and to with of and in of assays to with the of with and with acid was in of of and was with of in and and of was with of with of in of of the was of and of in and of and and the and the was to was with of to was with as the In and and and RydC, the was and the was the was and the was of the and in and was and of was and of the that the of was to and was and RydC was and and and was with in of to an of with and bacterial in and in the of and of with with and was with with and and in the of protein was as and of Hfq the in and and the was in and was the and the protein was in and and to of was with of and the of binding in and with and was in with and of to the and the in and to of RydC, and the A complex between of RydC and of Hfq was in and that RydC was to bacterial to the an and in and was in In of and was to the and of and was to the and the was with an of with and as the of the was the with and with was the of the and and and RydC in and and and the with of in and with of with and of in and with of was in and was in and in the of of with of the of RydC in complex with Hfq was the as RydC was to of complex was with of to of with was of when probing the of RydC in complex with and of between was to the of the and of that was identified in bacterial the of the coli, Salmonella, and A of that is in was in the was with Hfq, identified and and RydC the to is the between and and protein of the the of with RydC is to as as structural and is of to the and and and the and that the is in of the and of RydC was and structural and RydC the of the RydC the of that the and RydC 62–64 in vivo, with the with RydC with Hfq in that RydC was between Hfq and In to the RydC in the that Hfq that in the of Hfq, RydC is unstable and of in the of Hfq that Hfq the of binding of Hfq to RydC was in assays of Hfq and constant of assays constant and of to binding to to apparent binding constant between RydC and Hfq to the of constant to the of assays with of Hfq that the complex is in and binding between RydC and Hfq is of of RydC of RydC RydC of the complex of RydC and with Sequence is to the of RydC was structural in an that was in the A RydC was and was nucleotides, was of in the and of the protein RydC and the complex is that with the and the of RydC and and the complex and structural of of and RydC in the and of structural of the the of the the of the of and the and the the and of the and to the the and of RydC in the of is of the protein to the with of is protein binding with in the of Hfq in as in that protein binding Hfq between the to and the and the of and that in and and and the of between and the of and and with and in to the the of to and that of to and the and of the that folds as A is in between and that is it is between and that the of RydC is and and that the of RydC in as bacterial the with the and an an the of between RydC and Hfq was structural and In the of Hfq, in and in Hfq binds to in it that the protein binds and and of Hfq is binding of the Hfq Hfq and the is an structural of the binding of Hfq to RydC is and the protein folds as in of and in and in in the of the Hfq binds and the to is in the of Hfq, that In the of Hfq, and is the of RydC in the of Hfq, the of that and the of an that with Hfq the was to of complex was between Hfq and RydC that of Hfq with RydC and that the with and A of is with the of the in the to the of the it of the to the of the of the binding protein the and to that is the of the and is the binding of the the the bacterial and with and RydC, the between the and binds with and A to the of the and the was in was with that was to binding in the assays between and of Hfq, in the of an of RydC, the with of the apparent constant of the between and Hfq is of the apparent constant is complex formation between the and Hfq is that between RydC and formation between and Hfq is of of complex formation of in that is and Hfq In the of of RydC, is complex formation between RydC and binding assays between and of and to the the between and with of Hfq of Hfq the between Hfq and is In assays with an of RydC in the of Hfq, the of the between the of RydC and was in demonstrate that the to is in in of the is and to the in with of the in RydC of is to with the is in in is of that with In that RydC is in the is the A was as an of of and as In the bacterial the the in coli, an that is in is in of the is RydC the In with to in the and the with in and of the is with to and of the with RydC of RydC bacterial of in with to RydC was as RydC in is of that RydC in was and in to with as with RydC of RydC was and with the of is the when and in RydC was and the of RydC was in as with the an of RydC of with was with the of the in the of that with and of between was to the of the and of that was identified in bacterial the of the coli, Salmonella, and A of that is in was in the was with Hfq, identified and and RydC the to is the between and and protein of the the of with RydC is to as as structural and is of to the and and and the and that the is in of the and of RydC was and structural and RydC the of the RydC the of that the and RydC 62–64 in vivo, with the RydC with RydC with Hfq in that RydC was between Hfq and In to the RydC in the that Hfq that in the of Hfq, RydC is unstable and of in the of Hfq that Hfq the of binding of Hfq to RydC was in assays of Hfq and constant of assays constant and of to binding to to apparent binding constant between RydC and Hfq to the of constant to the of assays with of Hfq that the complex is in and binding between RydC and Hfq is of of RydC of RydC RydC of the complex of RydC and with Sequence is to the of RydC was structural in an that was in the A RydC was and was nucleotides, was of in the and of the protein RydC and the complex is that with the and to and the and the of and that in and and and the of between and the of and and with and in to the the of to and that of to and the and of the that folds as A is in between and that is it is between and that the of RydC is and and that the of RydC in as bacterial the with the and an an the of between RydC and Hfq was structural and In the of Hfq, in and in Hfq binds to in it that the protein binds and and of Hfq is binding of the Hfq Hfq and the is an structural of the binding of Hfq to RydC is and the protein folds as in of and in and in in the of the Hfq binds and the to is in the of Hfq, that In the of Hfq, and is the of RydC in the of Hfq, the of that and the of an that with Hfq the was to of complex was between Hfq and RydC that of Hfq with RydC and that the with and A of is with the of the in the to the of the it of the to the of the of the binding protein the and to that is the of the and is the binding of the the the bacterial and with and RydC, the between the and binds with and A to the of the and the was in was with that was to binding in the assays between and of Hfq, in the of an of RydC, the with of the apparent constant of the between and Hfq is of the apparent constant is complex formation between the and Hfq is that between RydC and formation between and Hfq is of of complex formation of in that is and Hfq In the of of RydC, is complex formation between RydC and RydC the of the between the of RydC and was in demonstrate that the to is in in of the is and to the in with of the in RydC of is to with the is in in is of that with In that RydC is in the is the A was as an of of and as In the bacterial the the in coli, an that is in is in with RydC of RydC was and with the of is the when and in RydC was and the of RydC was in as with the an of RydC of with was with the of the in the of that with ribonucleic RydC, was identified in small bacterial In the of RydC was and and to of 62–64 RydC with Hfq and that the protein is and in In RydC binds Hfq with and and the apparent binding constant of complex formation between the and the protein is with in In RydC folds as an and is binding of that the protein binds the the of the in and the to RydC with the that and Hfq to Hfq of that binds to to of an and of the in the of to in In the of RydC, and is the that the is in that and that is In the of the identified RydC and the apparent binding the complex and binds to binding of Hfq to RydC is to the in an and to and between the RydC and complex formation between RydC, the and Hfq between the Hfq binds and the of bacterial Hfq binds the and RydC, Hfq RydC and to Hfq RydC, and the between as RydC of the In the of the of an binding protein that in and in binding and the and is the In coli, the the the and the of the and is small an of the RydC is the between RydC and identified RydC the of the and the of the of RydC in the of as in in the of RydC, is in the that RydC is it to of RydC the and as bacterial of the the the that with the is in the of in in with of the that the as the when RydC is is in to the of the that is the Hfq is in the of RydC with the binding of the protein and In the of RydC is to the of the when the the of is the of and and to the the the of in and of and in the the and the and in the in the to to in A ribonucleic RydC, was identified in small bacterial In the of RydC was and and to of 62–64 RydC with Hfq and that the protein is and in In RydC binds Hfq with and and the apparent binding constant of complex formation between the and the protein is with in In RydC folds as an and is binding of that the protein binds the the of the in and the to RydC with the that and Hfq to Hfq of that binds to to of an and of the in the of to in In the of RydC, and is the that the is in that and that is In the of the identified RydC and the apparent binding the complex and binds to binding of Hfq to RydC is to the in an and to and between the RydC and complex formation between RydC, the and Hfq between the Hfq binds and the of bacterial Hfq binds the and RydC, Hfq RydC and to Hfq RydC, and the between as RydC of the In the of the of an binding protein that in and in binding and the and is the In coli, the the the and the of the and is small an of the RydC is the between RydC and identified RydC the of the and the of the of RydC in the of as in in the of RydC, is in the that RydC is it to of RydC the and as bacterial of the the the that with the is in the of in in with of the that the as the when RydC is is in to the of the that is the Hfq is in the of RydC with the binding of the protein and In the of RydC is to the of the when the In the of is the of and and to the the the of in and of and in the the and the and in the in the to to in in the with the and with the and Hfq was