Folding of the SAM aptamer is determined by the formation of a K-turn-dependent pseudoknot

Biochemistry
Benoit Heppell, Daniel A Lafontaine

Abstract

The S-adenosylmethionine (SAM) riboswitch is one of the most recurrent riboswitches found in bacteria and has three known different natural aptamers. The Bacillus subtilis yitJ SAM riboswitch aptamer is organized around a four-way junction which is characterized by the presence of a pseudoknot and a K-turn motif. By replacing the adenine involved in a Watson-Crick base pair at position 138 in the core region of the aptamer with the fluorescent analogue 2-aminopurine (2AP), we show that the ligand-induced reorganization of the aptamer strongly attenuates 2AP fluorescence. The fluorescence quenching process is specific to SAM on the basis of the observation that the structural analogue S-adenosylhomocysteine does not promote a similar effect. We find that the pseudoknot is important for the reorganization of the core domain and that the K-turn motif also has a marked influence on the core domain reorganization, most probably through its important role in pseudoknot formation. Finally, we show that SAM riboswitch ligand binding is facilitated by the L7Ae K-turn binding protein, which suggests that K-turn motifs may be protein anchor sites used by riboswitches to promote RNA folding.

References

Feb 12, 2000·Journal of Molecular Biology·A C Déclais, D M Lilley
Jun 29, 2000·Annual Review of Biochemistry·P B Moore
Aug 3, 2001·The EMBO Journal·D J KleinT A Steitz
Oct 9, 2002·Journal of Molecular Biology·Daniel A LafontaineDavid M J Lilley
Jul 26, 2003·The EMBO Journal·Gerard J OstheimerAlice Barkan
Jan 20, 2004·Trends in Biochemical Sciences·Evgeny Nudler, Alexander S Mironov
May 3, 2005·FEBS Letters·Takahiro YamauchiNaoki Sugimoto
May 3, 2006·Journal of Molecular Biology·Sunny D GilbertRobert T Batey
Nov 23, 2006·Journal of Molecular Biology·Jan LipfertSebastian Doniach

❮ Previous
Next ❯

Citations

May 15, 2013·Bioorganic & Medicinal Chemistry·Lea BüttnerClaudia Höbartner
Aug 2, 2012·Quarterly Reviews of Biophysics·Robert T Batey
Sep 3, 2011·Journal of the American Chemical Society·Marie F SoulièreRonald Micura
Jan 25, 2013·Journal of the American Chemical Society·Kelly KarnsAmy E Herr
Nov 28, 2008·Nucleic Acids Research·Luc JaegerCody Geary
Sep 29, 2009·Nucleic Acids Research·Kersten T Schroeder, David M J Lilley
Nov 26, 2010·Nucleic Acids Research·Scott P Hennelly, Karissa Y Sanbonmatsu
Dec 21, 2010·Nucleic Acids Research·Simon BlouinDaniel A Lafontaine
Dec 22, 2012·Nucleic Acids Research·Scott P HennellyKarissa Y Sanbonmatsu
Oct 15, 2010·Cold Spring Harbor Perspectives in Biology·Andrew D GarstRobert T Batey
Feb 23, 2012·RNA·Nathan J BairdAdrian R Ferré-D'Amaré
Jun 22, 2010·RNA·Kersten T SchroederDavid M J Lilley
Dec 18, 2009·Nature Chemical Biology·Adrian R Ferré-D'Amaré
May 3, 2011·Nature Chemical Biology·Benoit HeppellDaniel A Lafontaine
Sep 8, 2015·Journal of Molecular Biology·Christopher WostenbergRobert T Batey
May 15, 2012·Current Opinion in Structural Biology·Alexander Serganov, Dinshaw J Patel
Mar 24, 2009·Current Opinion in Structural Biology·Alexander Serganov
May 28, 2014·Biochimica Et Biophysica Acta·Patrick St-PierreD A Lafontaine
May 28, 2014·Biochimica Et Biophysica Acta·Ian R PriceAilong Ke
Dec 23, 2008·Chembiochem : a European Journal of Chemical Biology·Simon BlouinDaniel A Lafontaine
Jun 24, 2014·Biochimica Et Biophysica Acta·Karissa Y Sanbonmatsu
May 7, 2014·Biochimica Et Biophysica Acta·David M J Lilley
Sep 15, 2012·Wiley Interdisciplinary Reviews. RNA·David M J Lilley
Oct 1, 2011·Wiley Interdisciplinary Reviews. RNA·Robert T Batey
Nov 7, 2013·Chemistry : a European Journal·Christoph KrönerClemens Richert
Feb 6, 2010·Chembiochem : a European Journal of Chemical Biology·Falk Wachowius, Claudia Höbartner
Aug 4, 2015·The Journal of Chemical Physics·Sha GongWenbing Zhang
Feb 18, 2012·RNA Biology·Sébastien H EschbachDaniel A Lafontaine
Sep 7, 2011·Structure·Kersten T SchroederDavid M J Lilley
May 3, 2011·Bioorganic & Medicinal Chemistry Letters·Young Wan HamDaniel L Dayton
Jul 20, 2010·Structure·Colby D StoddardRobert T Batey
Oct 29, 2015·PloS One·Corinna TheisJan Gorodkin
Aug 11, 2016·Nanoscale·Lin Huang, David M J Lilley
Sep 8, 2017·Chembiochem : a European Journal of Chemical Biology·Shun NakanoTakashi Morii

❮ 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.