A Highly Coupled Network of Tertiary Interactions in the SAM-I Riboswitch and Their Role in Regulatory Tuning

Journal of Molecular Biology
Christopher WostenbergRobert T Batey

Abstract

RNA folding in vivo is significantly influenced by transcription, which is not necessarily recapitulated by Mg(2+)-induced folding of the corresponding full-length RNA in vitro. Riboswitches that regulate gene expression at the transcriptional level are an ideal system for investigating this aspect of RNA folding as ligand-dependent termination is obligatorily co-transcriptional, providing a clear readout of the folding outcome. The folding of representative members of the SAM-I family of riboswitches has been extensively analyzed using approaches focusing almost exclusively upon Mg(2+) and/or S-adenosylmethionine (SAM)-induced folding of full-length transcripts of the ligand binding domain. To relate these findings to co-transcriptional regulatory activity, we have investigated a set of structure-guided mutations of conserved tertiary architectural elements of the ligand binding domain using an in vitro single-turnover transcriptional termination assay, complemented with phylogenetic analysis and isothermal titration calorimetry data. This analysis revealed a conserved internal loop adjacent to the SAM binding site that significantly affects ligand binding and regulatory activity. Conversely, most single point mutations throug...Continue Reading

References

Apr 11, 2001·Proceedings of the National Academy of Sciences of the United States of America·P NissenT A Steitz
Aug 3, 2001·The EMBO Journal·D J KleinT A Steitz
Mar 11, 2003·Proceedings of the National Academy of Sciences of the United States of America·Brooke A Murphy McDanielTina M Henkin
Aug 12, 2003·Nature Structural Biology·Wade C WinklerRonald R Breaker
Sep 21, 2004·Bioinformatics·Sam Griffiths-Jones
Oct 23, 2004·Science·UNKNOWN ENCODE Project Consortium
Mar 24, 2005·Journal of the American Chemical Society·Edward J MerinoKevin M Weeks
Apr 6, 2005·Molecular Cell·J Kenneth WickiserDonald M Crothers
Jul 1, 2006·Nature·Rebecca K Montange, Robert T Batey
Sep 7, 2007·Cell·Charles E DannWade C Winkler
Jan 5, 2008·Science·William J GreenleafSteven M Block
Jan 22, 2008·Biochemistry·Benoit Heppell, Daniel A Lafontaine
Jun 25, 2008·Annual Review of Biophysics·Rebecca K Montange, Robert T Batey
Oct 25, 2008·Methods : a Companion to Methods in Enzymology·Irina Artsimovitch, Tina M Henkin
Oct 28, 2008·Nucleic Acids Research·Paul P GardnerAlex Bateman
Nov 15, 2008·Journal of Molecular Biology·Andrea L Edwards, Robert T Batey
Jan 20, 2009·Bioinformatics·Andrew M WaterhouseGeoffrey J Barton
Mar 21, 2009·Annual Review of Biochemistry·Adam Roth, Ronald R Breaker
Dec 17, 2009·Journal of Molecular Biology·Rebecca K MontangeRobert T Batey
Jun 22, 2010·RNA·Kersten T SchroederDavid M J Lilley
Jun 29, 2010·Angewandte Chemie·Andrew C StelzerHashim M Al-Hashimi
Jul 20, 2010·Structure·Colby D StoddardRobert T Batey
Nov 26, 2010·Nucleic Acids Research·Scott P Hennelly, Karissa Y Sanbonmatsu
Nov 26, 2010·Cold Spring Harbor Perspectives in Biology·Ronald R Breaker
May 3, 2011·Nature Chemical Biology·Benoit HeppellDaniel A Lafontaine
Sep 7, 2011·Structure·Kersten T SchroederDavid M J Lilley
Apr 17, 2012·Cell·Reza BehrouziSarah A Woodson
Jul 10, 2012·Journal of Molecular Biology·Andrew D GarstRobert T Batey
Aug 2, 2012·Quarterly Reviews of Biophysics·Robert T Batey
Oct 23, 2012·Science·Kirsten L Frieda, Steven M Block
Feb 1, 2013·RNA Biology·Peter DaldropDavid M J Lilley
Mar 15, 2013·Journal of Molecular Biology·Colby D StoddardRobert T Batey
Mar 19, 2013·Cell·Pedro J Batista, Howard Y Chang
Sep 4, 2013·Nucleic Acids Research·Pablo CeresRobert T Batey
Oct 1, 2013·Nucleic Acids Research·Gal NechooshtanShoshy Altuvia

❮ Previous
Next ❯

Citations

Oct 30, 2019·The Journal of Biological Chemistry·Debapratim Dutta, Joseph E Wedekind
May 18, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Michal M MatyjasikRobert T Batey
Mar 27, 2020·The Journal of Biological Chemistry·Divyaa BhagdikarTina M Henkin
Jan 4, 2020·Cold Spring Harbor Perspectives in Biology·Marie Teng-Pei Wu, Victoria D'Souza
Aug 17, 2020·Nucleic Acids Research·Roman S Iwasaki, Robert T Batey

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Cold Spring Harbor Symposia on Quantitative Biology
Sunny D GilbertRobert T Batey
Proceedings of the National Academy of Sciences of the United States of America
Jeremiah J TrauschRobert T Batey
© 2021 Meta ULC. All rights reserved