Conformational heterogeneity of the SAM-I riboswitch transcriptional ON state: a chaperone-like role for S-adenosyl methionine.

Journal of Molecular Biology
Wei HuangFareed Aboul-ela

Abstract

Riboswitches are promising targets for the design of novel antibiotics and engineering of portable genetic regulatory elements. There is evidence that variability in riboswitch properties allows tuning of expression for genes involved in different stages of biosynthetic pathways by mechanisms that are not currently understood. Here, we explore the mechanism for tuning of S-adenosyl methionine (SAM)-I riboswitch folding. Most SAM-I riboswitches function at the transcriptional level by sensing the cognate ligand SAM. SAM-I riboswitches orchestrate the biosynthetic pathways of cysteine, methionine, SAM, and so forth. We use base-pair probability predictions to examine the secondary-structure folding landscape of several SAM-I riboswitch sequences. We predict different folding behaviors for different SAM-I riboswitch sequences. We identify several "decoy" base-pairing interactions involving 5' riboswitch residues that can compete with the formation of a P1 helix, a component of the ligand-bound "transcription OFF" state, in the absence of SAM. We hypothesize that blockage of these interactions through SAM contacts contributes to stabilization of the OFF state in the presence of ligand. We also probe folding patterns for a SAM-I rib...Continue Reading

References

Jul 11, 1990·Nucleic Acids Research·A A Yolov, Z A Shabarova
Jun 26, 1989·Nucleic Acids Research·J Yon, M Fried
Jan 1, 1986·Annual Review of Biochemistry·T Platt
Nov 1, 1995·Journal of Biomolecular NMR·F DelaglioA Bax
Jan 1, 1996·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·M A HuynenP F Stadler
Aug 3, 2001·The EMBO Journal·D J KleinT A Steitz
Sep 27, 2002·Chemistry & Biology·Ali NahviRonald R Breaker
Mar 11, 2003·Proceedings of the National Academy of Sciences of the United States of America·Brooke A Murphy McDanielTina M Henkin
Apr 19, 2003·Proceedings of the National Academy of Sciences of the United States of America·Vitaly EpshteinEvgeny Nudler
Aug 12, 2003·Nature Structural Biology·Wade C WinklerRonald R Breaker
Oct 3, 2003·Proceedings of the National Academy of Sciences of the United States of America·Frank J GrundyTina M Henkin
Apr 21, 2004·Journal of Molecular Biology·Alastair I H MurchieJonathan Karn
Apr 6, 2005·Molecular Cell·J Kenneth WickiserDonald M Crothers
Oct 6, 2005·Biochemistry·J Kenneth WickiserDonald M Crothers
Jul 1, 2006·Nature·Rebecca K Montange, Robert T Batey
Dec 5, 2006·Nature Chemical Biology·Kenneth F BlountRonald R Breaker
Dec 13, 2006·Nature Biotechnology·Kenneth F Blount, Ronald R Breaker
May 8, 2007·Journal of the American Chemical Society·Shana Topp, Justin P Gallivan
May 23, 2007·Nucleic Acids Research·Andrea RentmeisterMichael Famulok
Jun 19, 2007·Bioinformatics·Eva FreyhultPeter Clote
Sep 12, 2007·Nature Reviews. Genetics·Alexander Serganov, Dinshaw J Patel
Nov 14, 2007·Genome Biology·Jeffrey E Barrick, Ronald R Breaker
Dec 27, 2007·Molecular Cell·Vitaly EpshteinEvgeny Nudler
Jan 12, 2008·Journal of the American Chemical Society·Changbong Hyeon, D Thirumalai
Jan 22, 2008·Biochemistry·Benoit Heppell, Daniel A Lafontaine
May 27, 2008·Bioorganic & Medicinal Chemistry Letters·Rajaneesh AnupamJennifer V Hines
Jun 25, 2008·Annual Review of Biophysics·Rebecca K Montange, Robert T Batey
Jul 8, 2008·Chembiochem : a European Journal of Chemical Biology·Markus Wieland, Jörg S Hartig
Nov 6, 2008·Current Opinion in Microbiology·Julius B LucksAdam P Arkin
Dec 23, 2008·Chembiochem : a European Journal of Chemical Biology·Simon BlouinDaniel A Lafontaine
Jan 27, 2009·Biophysical Journal·Paul C WhitfordKevin Y Sanbonmatsu
Mar 21, 2009·Annual Review of Biochemistry·Adam Roth, Ronald R Breaker
Mar 24, 2009·Current Opinion in Structural Biology·Alexander Serganov
Aug 4, 2009·Nature Biotechnology·John E DueberJay D Keasling

❮ Previous
Next ❯

Citations

May 25, 2013·PLoS Computational Biology·Wei HuangFareed Aboul-ela
May 28, 2014·Biochimica Et Biophysica Acta·Patrick St-PierreD A Lafontaine
Aug 4, 2015·The Journal of Chemical Physics·Sha GongWenbing Zhang
Jul 14, 2017·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Sha GongWenbing Zhang
Sep 19, 2017·Nature Chemical Biology·Christoph ManzG Ulrich Nienhaus
Mar 29, 2020·Journal of Computational Chemistry·Osama Alaidi, Fareed Aboul-Ela
Nov 11, 2018·World Journal of Microbiology & Biotechnology·Jean Paul SinumvayoPhilibert Tuyishime
Dec 23, 2020·Chembiochem : a European Journal of Chemical Biology·Abdallah S AbdelsattarFareed Aboul-Ela

❮ Previous
Next ❯

Related Concepts

Related Feeds

Antifungals

An antifungal, also known as an antimycotic medication, is a pharmaceutical fungicide or fungistatic used to treat and prevent mycosis such as athlete's foot, ringworm, candidiasis, cryptococcal meningitis, and others. Discover the latest research on antifungals here.

Antifungals (ASM)

An antifungal, also known as an antimycotic medication, is a pharmaceutical fungicide or fungistatic used to treat and prevent mycosis such as athlete's foot, ringworm, candidiasis, cryptococcal meningitis, and others. Discover the latest research on antifungals here.