Role of Conserved Surface Amino Acids in Binding of SmpB Protein to SsrA RNA

Abstract

Bacteria possess a unique salvage mechanism for rescuing ribosomes stalled on aberrant mRNAs. A complex of SmpB protein and SsrA RNA orchestrates this salvage process. The specific and direct binding of SmpB facilitates recognition and delivery of SsrA RNA to stalled ribosomes. The SmpB protein is conserved throughout the bacterial kingdom and contains several conserved amino acid sequence motifs. We present evidence to demonstrate amino acid and conserved and of the a the process. the SmpB is to to the delivery of SsrA RNA to stalled ribosomes. present evidence to demonstrate the of is to SsrA binding present evidence to demonstrate and for the SsrA binding of SmpB the of the demonstrate for the for the demonstrate the of this of conserved SmpB binding to SsrA a for recognition of SsrA Bacteria possess a unique salvage mechanism for rescuing ribosomes stalled on aberrant mRNAs. A complex of SmpB protein and SsrA RNA orchestrates this salvage process. The specific and direct binding of SmpB facilitates recognition and delivery of SsrA RNA to stalled ribosomes. The SmpB protein is conserved throughout the bacterial kingdom and contains several conserved amino acid sequence motifs. We present evidence to demonstrate amino acid and conserved and of the a the process. the SmpB is to to the delivery of SsrA RNA to stalled ribosomes. present evidence to demonstrate the of is to SsrA binding present evidence to demonstrate and for the SsrA binding of SmpB the of the demonstrate for the for the demonstrate the of this of conserved SmpB binding to SsrA a for recognition of SsrA of RNA and protein RNA RNA RNA and RNA the of protein to a of and on for the and and and is a RNA is unique sequence and is and The for SsrA SsrA RNA stalled the and to the The to the of a to the of and unique bacterial is of SsrA RNA protein The of SmpB specific binding to SsrA RNA and and of the complex stalled ribosomes the of SmpB protein SsrA ribosomes. SmpB to the of SsrA the of SsrA of the complex to for recognition and of stalled SmpB protein is conserved of SmpB bacterial the of several conserved and to a of the and of conserved amino of SmpB We on a of conserved on of the SmpB We and evidence for the of amino the RNA complex of the and demonstrate the to the binding of SmpB protein to SsrA the this of the of is conserved bacterial and SmpB the for SsrA RNA a for a of the SmpB and protein of SmpB amino acid to of and A and for to and for a of the a and for The ribosomes of of and of ribosomes a The for and the to ribosomes and for and RNA for and of RNA to and a SsrA of ribosomes and the on SmpB protein and a of SmpB of the of to of and for and and the of of for to to the of the SmpB for SmpB protein and of The of SmpB for the and of of the SmpB and The protein for to the The of and and the binding to for The acid to a and of of The protein A and a A of A to the SmpB SmpB of for the SmpB and for the SmpB and The a and a The and to a sequence RNA RNA the and the and on and SmpB protein to the protein the of RNA a the specific SsrA of RNA to and for on a and to the RNA and to binding for and SmpB a protein of to to and the of the SmpB and the the is the of RNA is a the of the specific and is the of SmpB the of SmpB protein is a of the process. several specific binding to SsrA recognition of stalled and of SsrA the of SmpB protein the of a of amino acid conserved bacterial the of conserved amino a of of the SmpB to the of conserved to SmpB We on the of a of conserved amino acid the of the SmpB protein this on several conserved amino acid and and conserved of the protein We for a the the The a the and a of the The to acid and the of to SmpB the of on the this the a of We of the and on The of of the conserved SmpB and a on the of SmpB to of of SmpB and a and the of SmpB a a for conserved of the SmpB the of a of of SmpB and of the of the to of and a protein the of and a a of demonstrate several conserved and of the of SmpB a the the of protein of the and of the of the SmpB SmpB SmpB a and a SmpB a of for the of the the conserved and a to the to a of the SmpB to of the complex stalled ribosomes. We the SmpB protein is for of SsrA RNA ribosomes the of the ribosomes SmpB of and and the of SmpB protein of the and SmpB of SmpB protein ribosomes The and the the of SmpB and SmpB ribosomes The SmpB the ribosomes is on of of protein the and of the of SmpB SmpB SmpB a and a SmpB a for the the to of SmpB protein to SsrA RNA and ribosomes. this the of protein and the We the and present the We the and to of present and demonstrate the to to a the of SmpB protein present the of conserved of the SmpB protein of the of SmpB the of SmpB present the of the of the of protein SmpB is for of SsrA RNA stalled for the of SsrA RNA the for SmpB the of SsrA RNA SmpB The the of SsrA RNA and A and to the of the of the SmpB and the the of SsrA RNA for the the SsrA to SsrA of the to demonstrate of The SmpB the ribosomes is on the and of the of SsrA RNA ribosomes the SmpB of SmpB SsrA RNA is the binding of SmpB protein to SsrA of a complex is for the delivery of SsrA RNA to stalled ribosomes. the of SmpB to SsrA to stalled ribosomes is to the binding and of SmpB protein for SsrA this of SmpB protein and of amino acid and of the for SmpB protein and the to The of protein for and binding and the is the of RNA is a the of the specific and is the of SmpB The binding the of and RNA to the of and binding the for SmpB protein to for for for and for the binding the binding the binding and the binding of the amino and to the binding of SmpB protein to SsrA RNA acid to the binding SmpB and to complex SsrA conserved the protein SsrA binding for SmpB protein and a the SsrA binding of several SmpB and and binding and for and amino acid SsrA binding of the of specific the binding the binding and the binding The of binding and of and A and and The binding to demonstrate the conserved amino acid and to binding of SmpB protein to SsrA RNA and the of the complex stalled binding SmpB the binding of and for The of and SsrA RNA on the is to the of protein The of the is is of of the SmpB A to the of SmpB SsrA RNA protein and SsrA RNA conserved is to the specific the binding of SmpB protein to SsrA RNA the of SmpB and SsrA bacterial the of this the of SmpB protein SsrA this and SmpB protein The of SmpB protein is a of and The SmpB protein to We to the binding of protein for SsrA RNA to the for of the contains the a a to of binding SsrA RNA a of The binding the of and The of a and a of RNA the SmpB SsrA and binding for SmpB protein and a binding SmpB a of a the binding of to of the A to for binding to SsrA of SmpB SsrA the for SmpB protein and SsrA to and to and of to binding of SmpB protein to SsrA this and of SmpB and of the SmpB the for SmpB The to The of protein for the SsrA RNA and binding and for the SmpB a binding of this amino acid a to binding and of SmpB binding binding the conserved amino acid to the SsrA binding of the a this binding of SmpB protein to SsrA RNA The for SmpB protein to for the a of binding to a binding of acid to SmpB binding for SsrA RNA binding for SsrA RNA demonstrate the conserved of SmpB to the SmpB a binding of SmpB protein to SsrA binding SmpB the binding of and for of of the SmpB A to the for of SsrA RNA to the of conserved amino acid to the of SmpB The conserved and of amino and of SmpB protein amino conserved for a of is amino a SmpB binding to SsrA is conserved The of the and of the complex for the of this is for stalled ribosomes and protein to for the of the and SsrA is for the to a of to to the and and of a of this unique and bacterial the of specific of to a of the mechanism of SmpB protein SsrA RNA and the and of stalled ribosomes. the amino acid of SmpB of for the the SmpB and a of and of the of the SmpB protein to the of of the of to SmpB the to the and of and acid and conserved SmpB and to the of the SmpB of ribosomes the the of the the SmpB The the of SmpB protein and SsrA RNA to the the and to to SsrA RNA to stalled ribosomes for the specific SsrA of specific the SmpB binding for SsrA RNA and the delivery of SsrA RNA to stalled ribosomes. this the SsrA binding is to SmpB the SsrA binding the the of SmpB protein stalled ribosomes is on and SsrA of the amino and the binding of SmpB protein for SsrA a RNA binding is present SmpB protein to SsrA binding amino acid and of the of of specific SmpB and the to SsrA binding conserved SmpB SmpB amino and and to SsrA binding of SmpB the conserved SmpB and of specific bacterial a of and the of a of conserved and amino acid SmpB protein The protein and on of the SmpB protein a and for We the of of the of amino to the of SmpB SmpB of RNA binding a of the protein a the the of the of to the SmpB the of sequence of specific amino and to for the SmpB protein a of SmpB and SsrA of SmpB protein and a of SmpB complex the of SsrA The SmpB is The and on SmpB protein and complex the and of and to and on of the protein The to the of SsrA the of the of amino acid to the SsrA binding of SmpB protein The direct of the and of conserved amino acid to of SmpB protein SsrA the the and evidence for the conserved and binding of SmpB protein to SsrA of RNA and protein RNA RNA RNA and RNA the of protein to a of and on for the and and SsrA and is a RNA is unique sequence and is and The for SsrA SsrA RNA stalled the and to the The to the of a to the of and unique bacterial is of SsrA RNA protein The of SmpB specific binding to SsrA RNA and and of the complex stalled ribosomes the of SmpB protein SsrA ribosomes. SmpB to the of SsrA the of SsrA of the complex to for recognition and of stalled ribosomes. The SmpB protein is conserved of SmpB bacterial the of several conserved and to a of the and of conserved amino of SmpB We on a of conserved on of the SmpB We and evidence for the of amino the RNA complex of the and demonstrate the to the binding of SmpB protein to SsrA the this of the of is conserved bacterial and SmpB the for SsrA RNA a for a of the SmpB and protein of SmpB amino acid to of and A and for to and for a of the a and for The ribosomes of of and of ribosomes a The for and the to ribosomes and for and RNA for and of RNA to and a SsrA of ribosomes and the on SmpB protein and a of SmpB of the of to of and for and and the of of for to to the of the SmpB for SmpB protein and of The of SmpB for the and of of the SmpB and The protein for to the The of and and the binding to for The acid to a and of of The protein A and a A of A to the SmpB SmpB of for the SmpB and for the SmpB and The a and a The and to a sequence RNA RNA the and the and on and SmpB protein to the protein the of RNA a the specific SsrA of RNA to and for on a and to the RNA and to binding for and SmpB a protein of to to and the of the SmpB and the the is the of RNA is a the of the specific and is the of and SmpB the for SsrA RNA a for a of the SmpB and protein of SmpB amino acid to of and A and for to and for a of the a and for The ribosomes of of and of ribosomes a The for and the to ribosomes and for and RNA for and of RNA to and a SsrA of ribosomes and the on SmpB protein and a of SmpB of the of to of and for and and the of of for to to the of the SmpB for SmpB protein and of The of SmpB for the and of of the SmpB and The protein for to the The of and and the binding to for The acid to a and of of The protein A and a A of A to the SmpB SmpB of for the SmpB and for the SmpB and The a and a The and to a sequence RNA RNA the and the and on and SmpB protein to the protein the of RNA a the specific SsrA of RNA to and for on a and to the RNA and to binding for and SmpB a protein of to to and the of the SmpB and the the is the of RNA is a the of the specific and is the of SmpB the of SmpB protein is a of the process. several specific binding to SsrA recognition of stalled and of SsrA the of SmpB protein the of a of amino acid conserved bacterial the of conserved amino a of of the SmpB to the of conserved to SmpB We on the of a of conserved amino acid the of the SmpB protein this on several conserved amino acid and and conserved of the protein We for a the the The a the and a of the The to acid and the of to SmpB the of on the this the a of We of the and on The of of the conserved SmpB and a on the of SmpB to of of SmpB and a and the of SmpB a a for conserved of the SmpB the of a of of SmpB and of the of the to of and a protein the of and a a of demonstrate several conserved and of for the of the the conserved and a to the to a of the SmpB to of the complex stalled ribosomes. We the SmpB protein is for of SsrA RNA ribosomes the of the ribosomes SmpB of and and the of SmpB protein of the and SmpB of SmpB protein ribosomes The and the the of SmpB and SmpB ribosomes The SmpB the ribosomes is on of of protein the and of the of SmpB SmpB SmpB a and a SmpB a for the the to of SmpB protein to SsrA RNA and ribosomes. this the of protein and the We the and present the We the and to of present and demonstrate the to to a the of SmpB protein present the of conserved of the SmpB protein of the of SmpB the of SmpB present the of the of the of protein SmpB is for of SsrA RNA stalled for the of SsrA RNA the for SmpB the of SsrA RNA SmpB The the of SsrA RNA and A and to the of the of the SmpB and the the of SsrA RNA for the the SsrA to SsrA of the to demonstrate of The SmpB the ribosomes is on the and of the of SsrA RNA ribosomes the SmpB of SmpB SsrA RNA is the binding of SmpB protein to SsrA of a complex is for the delivery of SsrA RNA to stalled ribosomes. the of SmpB to SsrA to stalled ribosomes is to the binding and of SmpB protein for SsrA this of SmpB protein and of amino acid and of the for SmpB protein and the to The of protein for and binding and the is the of RNA is a the of the specific and is the of SmpB The binding the of and RNA to the of and binding the for SmpB protein to for for for and for the binding the binding the binding and the binding of the amino and to the binding of SmpB protein to SsrA RNA acid to the binding SmpB and to complex SsrA conserved the protein SsrA binding for SmpB protein and a the SsrA binding of several SmpB and and binding and for and amino acid SsrA binding of the of specific the binding the binding and the binding The of binding and of and A and and The binding to demonstrate the conserved amino acid and to binding of SmpB protein to SsrA RNA and the of the complex stalled binding SmpB the binding of and for The of and SsrA RNA on the is to the of protein The of the is is of of the SmpB A to the of SmpB SsrA RNA protein and SsrA RNA conserved is to the specific the binding of SmpB protein to SsrA RNA the of SmpB and SsrA bacterial the of this the of SmpB protein SsrA this and SmpB protein The of SmpB protein is a of and The SmpB protein to We to the binding of protein for SsrA RNA to the for of the contains the a a to of binding SsrA RNA a of The binding the of and The of a and a of RNA the SmpB SsrA and binding for SmpB protein and a binding SmpB a of a the binding of to of the A to for binding to SsrA of SmpB SsrA the for SmpB protein and SsrA to and to and of to binding of SmpB protein to SsrA this and of SmpB and of the SmpB the for SmpB The to The of protein for the SsrA RNA and binding and for the SmpB a binding of this amino acid a to binding and of SmpB binding binding the conserved amino acid to the SsrA binding of the a this binding of SmpB protein to SsrA RNA The for SmpB protein to for the a of binding to a binding of acid to SmpB binding for SsrA RNA binding for SsrA RNA demonstrate the conserved of SmpB to the SmpB a binding of SmpB protein to SsrA binding SmpB the binding of and for of of the SmpB A to the for of SsrA RNA SmpB the of SmpB protein is a of the process. several specific binding to SsrA recognition of stalled and of SsrA the of SmpB protein the of a of amino acid conserved bacterial the of conserved amino a of of the SmpB to the of conserved to SmpB We on the of a of conserved amino acid the of the SmpB protein this on several conserved amino acid and and conserved of the protein We for a the the The a the and a of the The to acid and the of to SmpB the of on the this the a of We of the and on The of of the conserved SmpB and a on the of SmpB to of of SmpB and a and the of SmpB a a for conserved of the SmpB the of a of of SmpB and of the of the to of and a protein the of and a a of demonstrate several conserved and of for the of the the conserved and a to the to a of the SmpB to of the complex stalled ribosomes. We the SmpB protein is for of SsrA RNA ribosomes the of the ribosomes SmpB of and and the of SmpB protein of the and SmpB of SmpB protein ribosomes The and the for the the to of SmpB protein to SsrA RNA and ribosomes. this the of protein and the We the and present the We the and to of present and demonstrate the to to a the of SmpB protein present the of conserved of the SmpB protein ribosomes. SmpB is for of SsrA RNA stalled for the of SsrA RNA the for SmpB the of SsrA RNA SmpB The the of SsrA RNA and A and to the of the of the SmpB and the the of SsrA RNA for the the of SmpB SsrA RNA is the binding of SmpB protein to SsrA of a complex is for the delivery of SsrA RNA to stalled ribosomes. the of SmpB to SsrA to stalled ribosomes is to the binding and of SmpB protein for SsrA this of SmpB protein and of amino acid and of the for SmpB protein and the to The of protein for and binding and the is the of RNA is a the of the specific and is the of SmpB The binding the of and RNA to the of and binding The the for SmpB protein to for for for and for the binding the binding the binding and the binding of the amino and to the binding of SmpB protein to SsrA RNA acid to the binding SmpB and to complex SsrA conserved the protein SsrA the SsrA binding of several SmpB and and binding and for and amino acid SsrA binding of the of specific the binding the binding and the binding The of binding and of and A and and The binding to demonstrate the conserved amino acid and to binding of SmpB protein to SsrA RNA and the of the complex stalled ribosomes. SmpB SsrA RNA protein and SsrA RNA conserved is to the specific the binding of SmpB protein to SsrA RNA the of SmpB and SsrA bacterial the of this the of SmpB protein SsrA this and SmpB protein The of SmpB protein is a of and The SmpB protein to We to the binding of protein for SsrA RNA to the for of the contains the a a to of binding SsrA RNA a of The binding the of and The of a and a of RNA the SmpB SsrA and of SmpB SsrA the for SmpB protein and SsrA to and to and of to binding of SmpB protein to SsrA this and of SmpB and of the SmpB the for SmpB The to The of protein for the SsrA RNA and binding and for the SmpB a binding of this amino acid a to binding and of SmpB binding binding the conserved amino acid to the SsrA binding of the a this binding of SmpB protein to SsrA RNA The for SmpB protein to for the a of binding to a binding of acid to SmpB binding for SsrA RNA binding for SsrA RNA demonstrate the conserved of SmpB to the SmpB a binding of SmpB protein to SsrA to the of conserved amino acid to the of SmpB The conserved and of amino and of SmpB protein amino conserved for a of is amino a SmpB binding to SsrA is conserved The of the and of the complex for the of this is for stalled ribosomes and protein to for the of the and SsrA is for the to a of to to the and and of a of this unique and bacterial the of specific of to a of the mechanism of SmpB protein SsrA RNA and the and of stalled ribosomes. the amino acid of SmpB of for the the SmpB and a of and of the of the SmpB protein to the of of the of to SmpB the to the and of and acid and conserved SmpB and to the of the SmpB of ribosomes the the of the the SmpB The the of SmpB protein and SsrA RNA to the the and to to SsrA RNA to stalled ribosomes for the specific SsrA of specific the SmpB binding for SsrA RNA and the delivery of SsrA RNA to stalled ribosomes. this the SsrA binding is to SmpB the SsrA binding the the of SmpB protein stalled ribosomes is on and SsrA of the amino and the binding of SmpB protein for SsrA a RNA binding is present SmpB protein to SsrA binding amino acid and of the of of specific SmpB and the to SsrA binding conserved SmpB SmpB amino and and to SsrA binding of SmpB the conserved SmpB and of specific bacterial a of and the of a of conserved and amino acid SmpB protein The protein and on of the SmpB protein a and for We the of of the of amino to the of SmpB SmpB of RNA binding a of the protein a the the of the of to the SmpB the of sequence of specific amino and to for the SmpB protein a of SmpB and SsrA of SmpB protein and a of SmpB complex the of SsrA The SmpB is The and on SmpB protein and complex the and of and to and on of the protein The to the of SsrA the of the of amino acid to the SsrA binding of SmpB protein The direct of the and of conserved amino acid to of SmpB protein SsrA the the and evidence for the conserved and binding of SmpB protein to SsrA to the of conserved amino acid to the of SmpB The conserved and of amino and of SmpB protein amino conserved for a of is amino a SmpB binding to SsrA The is conserved The of the and of the complex for the of this is for stalled ribosomes and protein to for the of the and SsrA is for the to a of to to the and and of a of this unique and bacterial the of specific The of to a of the mechanism of SmpB protein SsrA RNA and the and of stalled ribosomes. the amino acid of SmpB of for the the SmpB and a of and of the of the SmpB protein to the of of the of to SmpB the to the and of and acid and conserved SmpB and to the of the SmpB of ribosomes the the of the the SmpB The the of SmpB protein and SsrA RNA to the the and to to SsrA RNA to stalled ribosomes for the specific SsrA of specific the SmpB binding for SsrA RNA and the delivery of SsrA RNA to stalled ribosomes. this the SsrA binding is to SmpB the SsrA binding the the of SmpB protein stalled ribosomes is on and SsrA of the amino and the binding of SmpB protein for SsrA a RNA binding is present SmpB protein to SsrA binding amino acid and of the of of specific SmpB and the to SsrA binding conserved SmpB SmpB amino and and to SsrA binding of SmpB the conserved SmpB and of specific bacterial a of and the of a of conserved and amino acid SmpB protein The protein and on of the SmpB protein a and for We the of of the of amino to the of SmpB SmpB of RNA binding a of the protein a the the of the of to the SmpB the of sequence of specific amino and to for the SmpB protein a of SmpB and SsrA of SmpB protein and a of SmpB complex the of SsrA The SmpB is The and on SmpB protein and complex the and of and to and on of the protein The to the of SsrA the of the of amino acid to the SsrA binding of SmpB protein The direct of the and of conserved amino acid to of SmpB protein SsrA the the and evidence for the conserved and binding of SmpB protein to SsrA We and for on the We of the for and We to and of The for for