Apical Loop-Internal Loop RNA Pseudoknots

Abstract

Nearly all members of a widespread family of bacterial transposable elements related to insertion sequence 3 (IS3), therefore called the IS3 family, very likely use programmed -1 ribosomal frameshifting to produce their transposase, a protein required for mobility. Comparative analysis of the potential frameshift signals in this family suggested that most of the insertion sequences the in their that a a of the frameshift of the of the of the to a of the that the of the frameshifting the of this of for the of Nearly all members of a widespread family of bacterial transposable elements related to insertion sequence 3 (IS3), therefore called the IS3 family, very likely use programmed -1 ribosomal frameshifting to produce their transposase, a protein required for mobility. Comparative analysis of the potential frameshift signals in this family suggested that most of the insertion sequences the in their that a a of the frameshift of the of the of the to a of the that the of the frameshifting the of this of for the of of a of a called the of programmed -1 ribosomal frameshifting programmed -1 ribosomal insertion programmed -1 ribosomal insertion the of the a the in all most of the in in in in bacterial transposable elements called insertion sequences sequence the the frameshift a of the a the of frameshifting a the the of the this a a of the of a to frameshifting the of of a of the to the their in the that a the a to ribosomal the frameshift in the the sequence a the a the the bacterial the IS3 a of the of in bacterial frameshift a analysis of a of transposable the of IS3 family members very likely use to the transposase, a protein required for their mobility. members of the IS3 Nearly all members of this family a in in a potential frameshift a frameshift analysis of a IS3 the the analysis the IS3 family, the of members to a of a the called in of the of suggested that a related in -1 frameshifting of the a analysis of this frameshift transposable the the analysis the of of the of the of the a of this the of of a of the to for of in in for for of the for all the the in frameshift of in the of the of in the of in all the the of the of to to the -1 analysis of the frameshift of the in the sequence the of the the in to the of the protein a of the of the the the a to the of 3 the the the to the the a in the sequence the the the frameshifting signals of frameshifting for the for the of in the for the the in a of of the of this a in the of insertion of the to the of the the of the to the of of the frameshift the of to 3 the of in of the the of the of a a insertion of insertion in the of of the in of for in their of the of in for of in the in the to frameshift of the the of the of of a the for in of the a of the of the in a of in of for to to a for for of in the for the of frameshifting the the the the produce the the the the the the the of in the their sequences of in of for for to of in the of of in 3 of in of in for all of the the of of of 3 to in of in of for a a in the for in the of of of the to of the the the in in the for a of of in the for in the the of the frameshift the of in of the in the frameshift to the of of the of the of the of the the of the the elements of the IS3 family to of all in all of their protein analysis in elements of the in in the of the IS3 family a a sequence a potential a of the of of in to in sequence of the of in a the for in the most of the of sequence all the the of of to that a a the for all most 3 the of of to of in of the the for the of a in the of a in the of to in the of the the to of the of for the insertion to the elements analysis related to of frameshifting in to in this a that frameshifting required for of frameshifting the in protein the transposase, a of the the use the frameshift the of of very likely the the the of the elements in frameshifting the to a a -1 frameshift in the -1 the of in the -1 protein for in the of of the protein a -1 frameshifting the for protein in the -1 of the the in for IS3 the a the in in for of a potential for the potential to 3 their for their to to frameshifting this the of the the the sequence to a in of the to very in a of the for the to the frameshift of this the sequence in the in a of of frameshifting a of the that most of of the of the in the that of to of for the of frameshifting to the to a to a of the of of the the to to in all frameshifting for the to for to for to for to for to for the of the the sequence in of the of to a this a of in a that of to that the sequence a of the of the of the of frameshifting of the of the of the of 3 in a of of the insertion of 3 in a of that a a required to the the the of 3 3 frameshifting the the of frameshift the that the their 3 to to a of the of of the the of the frameshift of to a the the to of analysis the of the of the of the of the of in that of a to to of the of this the the of the of the of to a of to of the of this suggested the of that the of to to a a a to the 3 to to all of to in most of to a of the the of the of of the to of the the the to the the 3 to this a in the of the of in 3 of the in the of of of 3 that in the of to of the frameshift of the of in of a of of the the frameshift the of the the the of to to in of that in the a to to the of the therefore in the of a in of 3 to to very in of the the of the of the of the of very the of in the 3 to to the in of the the the that in the of a of the that of the 3 of in in of the that suggested that for therefore the in of a the in this the the a a analysis in the of the the of the sequence to of a of the sequence the of sequence in sequence in the of for the that the elements frameshift the of the of that in in this for their in the of of the in of the the the a of to the of the of the of the of to the that sequences the the of the the the to the the of frameshifting in the of of the of the required to a of of in the in the in the of 3 3 of the for the of of the for in of the of of in the to of in in the a of a the to the of in the of of that frameshifting of in the in a to this the to the of a to a of 3 the in of to required for of the in a members of the IS3 family the for frameshifting the sequence of the the in 3 in in the this the of the a of 3 a of the of the that for the to of the frameshifting the a in this the of frameshifting the in the that frameshifting of for the the of the frameshift for their in the of the the of that a the of that a of of in the to of the sequence protein required for a the to a of the the of to the of frameshift a of frameshifting in transposable to produce the of to a of the bacterial this produce a of a a of a the IS3 family, of of the of the of the the of the use of a in to frameshift the the of that of members of the the of frameshifting of the to of a in to a of the to that the for a to to to the protein the analysis of suggested frameshifting a in of protein a of the frameshifting the a of of the the sequence that of of the members of the a potential a the that sequences for in the of required for in in most of the of a to the of a of the of the of the a to of a all sequences the related a for a very in the sequence of the that of a frameshift therefore related to the of in a the of in of in the a in of the to a in the of the the the of for the the the to a suggested the analysis of the of of the a in of of the all the in to the of the of the the the the to to the of the the the of the the the the the of the the of to that the the to of the in a a sequence in for a of the of of in the for in the of the the the in the of the the most to the the in the frameshift of the a the of a of a that in the in the of the in the in the the the the of the their the the the the the the of 3 of the to to the in a the 3 the of the the the to a of a the this of to the the that in the of most of to of the of the to a a of a 3 of for the of to a the of of the very to the of a of the of the of 3 a of 3 their mobility. in of of the to the of 3 the of the to therefore in of the that 3 that the insertion sequences of the a a of the of their to the that a their of for of a of a called the of programmed -1 ribosomal frameshifting programmed -1 ribosomal insertion programmed -1 ribosomal insertion the of the a the in all most of the in in in in bacterial transposable elements called insertion sequences sequence the the frameshift a of the a the of frameshifting a the the of the this a a of the of a to frameshifting the of of a of the to the their in the that a the a to ribosomal the frameshift in the the sequence a the a the the bacterial the IS3 a of the of in bacterial frameshift a analysis of a of transposable the of IS3 family members very likely use to the transposase, a protein required for their mobility. members of the IS3 Nearly all members of this family a in in a potential frameshift a frameshift analysis of a IS3 the the analysis the IS3 family, the of members to a of a the called in of the of suggested that a related in -1 frameshifting of the a analysis of this frameshift transposable the the analysis the of of the of the of the a of this the of of a of the to for of in in for for of the for all the the in frameshift of in the of the of in the of in all the the of the of to to the -1 the in a of of the of this a in the of insertion of the to the of the the of the to the of of the frameshift the of to 3 the of in of the the of the of a a insertion of insertion in the of of the in of for in their of the of in for of in the in the to frameshift of the the of the of of a the for in of the a of the of the in a of in of for to to a for for of in the for the of frameshifting the the the the produce the the the the the the the of in the their sequences of in of for for to of in the of of in 3 of in of in for all of the the of of of 3 to in of in of for a a in the for in the of of of the to of the the the in in the for a of of in the for in the the of the frameshift the of in of the in the frameshift to the of of the of the of the of the the in in for for of the for all the the in frameshift of in the of the of in the of in all the the of the of to to the -1 the in a of of the of this a in the of insertion of the to the of the the of the to the of of the frameshift the of to 3 the of in of the the of the of a a insertion of insertion in the of of the in of for in their of the of in for of in the in the to frameshift of the the of the of of a the for in of the a of the of the in a of in of for to to a for for of in the for the of frameshifting the the the the produce the the the the the the the of in the their sequences of in of for for to of in the of of in 3 of in of in for all of the the of of of 3 to in of in of for a a in the for in the of of of the to of the the the in in the for a of of in the for in the the of the the elements of the IS3 family to of all in all of their protein analysis in elements of the in in the of the IS3 family a a sequence a potential a of the of of in to in sequence of the of in a the for in the most of the of sequence all the the of of to that a a the for all most 3 the of of to of in of the the for the of a in the of a in the of to in the of the the to of the of for the insertion to the elements analysis related to of frameshifting in to in this a that frameshifting required for of frameshifting the in protein the transposase, a of the the use the frameshift the of of very likely the the the of the elements in frameshifting the to a a -1 frameshift in the -1 the of in the -1 protein for in the of of the protein a -1 frameshifting the for protein in the -1 of the the in for IS3 the a the in in for of a potential for the potential to 3 their for their to to frameshifting this the of the the the sequence to a in of the to very in a of the for the to the frameshift of this the sequence in the in a of of frameshifting a of the that most of of the of the in the that of to of for the of frameshifting to the to a to a of the of of the the to to in all frameshifting for the to for to for to for to for to for the of the the sequence in of the of to a this a of in a that of to that the sequence a of the of the of the of frameshifting of the of the of the of 3 in a of of the insertion of 3 in a of that a a required to the the the of 3 3 frameshifting the the of frameshift the that the their 3 to to a of the of of the the of the frameshift of to a the the to of analysis the of the of the of the of the of in that of a to to of the of this the the of the of the of to a of to of the of this suggested the of that the of to to a a a to the 3 to to all of to in most of to a of the the of the of of the to of the the the to the the 3 to this a in the of the of in 3 of the in the of of of 3 that in the of the of to to in of that in the a to to the of the therefore in the of a in of 3 to to very in of the the of the of the of the of very the of in the 3 to to the in of the the the that in the of a of the that of the 3 of in in of the that suggested that for therefore the in of a the in this the the a a analysis in the of the the of the sequence to of a of the sequence the of sequence in sequence in the of for the that the elements frameshift the of the of that in in this for their in the of of the in of the the the a of to the of the of the of the of to the that sequences the the of the the the to the the of frameshifting in the of of the of the required to a of of in the in the in the of 3 3 of the for the of of the for in of the of of in the to of in in the a of a the to the of in the of of that frameshifting of in the in a to this the to the of a to a of 3 the in of to required for of the in a members of the IS3 family the for frameshifting the sequence of the the in 3 in in the this the of the a of 3 a of the of the that for the to of the frameshifting the a in this the of frameshifting the in the that frameshifting of for the the of the frameshift for their in the of the the of that a the of that of the the elements of the IS3 family to of all in all of their protein analysis in elements of the in in the of the IS3 family a a sequence a potential a of the of of in to in sequence of the of in a the for in the most of the of sequence all the the of of to that a a the for all most 3 the of of to of in of the the for the of a in the of a in the of to in the of the the to of the of for the insertion to the elements analysis related to of frameshifting in to in this a that frameshifting required for of frameshifting the in protein the transposase, a of the the use the frameshift the of of very likely the the the of the elements in frameshifting the to a a -1 frameshift in the -1 the of in the -1 protein for in the of of the protein a -1 frameshifting the for protein in the -1 of the the in for IS3 the a the in in for of a potential for the potential to 3 their for their to to frameshifting this the of the the the sequence to a in of the to very in a of the for the to the frameshift of this the sequence in the in a of of frameshifting a of the that most of of the of the in the that of to of for the of frameshifting to the to a to a of the of of the the to to in all frameshifting for the to for to for to for to for to for the of the the sequence in of the of to a this a of in a that of to that the sequence a of the of the of the of frameshifting of the of the of the of 3 in a of of the insertion of 3 in a of that a a required to the the the of 3 3 frameshifting the the of frameshift the that the their 3 to to a of the of of the the of the frameshift of to a the the to of analysis the of the of the of the of the of in that of a to to of the of this the the of the of the of to a of to of the of this suggested the of that the of to to a a a to the 3 to to all of to in most of to a of the the of the of of the to of the the the to the the 3 to this a in the of the of in 3 of the in the of of of 3 that in the of the of to to in of that in the a to to the of the therefore in the of a in of 3 to to very in of the the of the of the of the of very the of in the 3 to to the in of the the the that in the of a of the that of the 3 of in in of the that suggested that for therefore the in of a the in this the the a a analysis in the of the the of the sequence to of a of the sequence the of sequence in sequence in the of for the that the elements frameshift the of the of that in in this for their in the of of in the to of in in the a of a the to the of in the of of that frameshifting of in the in a to this the to the of a to a of 3 the in of to required for of the in a members of the IS3 family the for frameshifting the sequence of the the in 3 in in the this the of the a of 3 a of the of the that for the to of the frameshifting the a in this the of frameshifting the in the that frameshifting a of of in the to of the sequence protein required for a the to a of the the of to the of frameshift a of frameshifting in transposable to produce the of to a of the bacterial this produce a of a a of a the IS3 family, of of the of the of the the of the use of a in to frameshift the the of that of members of the the of frameshifting of the to of a in to a of the to that the for a to to to the protein the analysis of suggested frameshifting a in of protein a of the frameshifting the a of of the the sequence that of of the members of the a potential a the that sequences for in the of required for in in most of the of a to the of a of the of the of the a to of a all sequences the related a for a very in the sequence of the that of a frameshift therefore related to the of in a the of in of in the a in of the to a in the of the the the of for the the the to a suggested the analysis in to the of the of the the the the to to the of the the the of the the the the the of the the of to that the the to of the in a a sequence in for a of the of of in the for in the of the the the in the of the the most to the the in the frameshift of the a the of a of a that in the in the of the in the in the the the the of the their the the the the the the of 3 of the to to the in a the 3 the of the the the to a of a the this of to the the that in the of most of to of the of the to a a of a 3 of for the of to a the of of the very to the of a of the of the of 3 a of 3 their mobility. in of of the to the of 3 the of the to therefore in of the that 3 that the insertion sequences of the a a of the of their to the that a their of for a of of in the to of the sequence protein required for a the to a of the the of to the of frameshift a of frameshifting in transposable to produce the of to a of the bacterial this produce a of a a of a the IS3 family, of of the of the of the the of the use of a in to frameshift the the of that of members of the the of frameshifting of the to of a in to a of the to that the for a to to to the protein the analysis of suggested frameshifting a in of protein a of the frameshifting the a of of the the sequence that of of the members of the a potential a the that sequences for in the of required for in in most of the of a to the of a of the of the of the a to of a all sequences the related a for a very in the sequence of the that of a frameshift therefore related to the of in a the of in of in the a in of the to a in the of the the the of for the the the to a suggested the analysis in to the of the of the the the the to to the of the the the of the the the the the of the the of to that the the to of the in a a sequence in for a of the of of in the for in the of the the the in the of the the most to the the in the frameshift of the a the of a of a that in the in the of the in the in the the the the of the their the the the the the the of 3 of the to to the in a the 3 the of the the the to a of a the this of to the the that in the of most of to of the of the to a a of a 3 of for the of to a the of of the very to the of a of the of the of 3 a of 3 their mobility. in of of the to the of 3 the of the to therefore in of the that 3 that the insertion sequences of the a a of the of their to the that a their of for for of the for the for