Hierarchical mechanism of amino acid sensing by the T-box riboswitch

Nature Communications
Krishna C SuddalaNils G Walter

Abstract

In Gram-positive bacteria, T-box riboswitches control gene expression to maintain the cellular pools of aminoacylated tRNAs essential for protein biosynthesis. Co-transcriptional binding of an uncharged tRNA to the riboswitch stabilizes an antiterminator, allowing transcription read-through, whereas an aminoacylated tRNA does not. Recent structural studies have resolved two contact points between tRNA and Stem-I in the 5' half of the T-box riboswitch, but little is known about the mechanism empowering transcriptional control by a small, distal aminoacyl modification. Using single-molecule fluorescence microscopy, we have probed the kinetic and structural underpinnings of tRNA binding to a glycyl T-box riboswitch. We observe a two-step mechanism where fast, dynamic recruitment of tRNA by Stem-I is followed by ultra-stable anchoring by the downstream antiterminator, but only without aminoacylation. Our results support a hierarchical sensing mechanism wherein dynamic global binding of the tRNA body is followed by localized readout of its aminoacylation status by snap-lock-based trapping.

References

Oct 11, 1972·Biochimica Et Biophysica Acta·D HentzenJ P Garel
May 16, 2001·Journal of Molecular Biology·J A Pleiss, O C Uhlenbeck
Aug 19, 2003·RNA·Mary R YousefTina M Henkin
Jan 20, 2004·RNA·Terry A GoodyDavid M J Lilley
Sep 28, 2004·Nature Structural & Molecular Biology·Scott C BlanchardJoseph D Puglisi
Apr 6, 2005·Molecular Cell·J Kenneth WickiserDonald M Crothers
Oct 4, 2005·Methods : a Companion to Methods in Enzymology·James R CollettAndrew D Ellington
Nov 14, 2007·Genome Biology·Jeffrey E Barrick, Ronald R Breaker
Feb 5, 2008·Methods : a Companion to Methods in Enzymology·Caroline Köhrer, Uttam L Rajbhandary
Mar 25, 2008·RNA·Alexey G VitreschakMikhail S Gelfand
May 31, 2008·Nature Methods·Rahul RoyTaekjip Ha
Oct 2, 2008·Methods in Molecular Biology·Feng Qin
Jul 15, 2009·Biochimica Et Biophysica Acta·Andrew D Garst, Robert T Batey
Nov 26, 2009·FEBS Letters·Nicholas J GreenTina M Henkin
Mar 23, 2010·Nature Structural & Molecular Biology·John AbelsonNils G Walter
Jun 29, 2010·Methods in Enzymology·Mario Blanco, Nils G Walter
Feb 22, 2011·Journal of Molecular Biology·Jiachen Wang, Edward P Nikonowicz
Mar 1, 2013·Protein Engineering, Design & Selection : PEDS·Maxim ChudaevWlodek Mandecki
Apr 17, 2013·Proceedings of the National Academy of Sciences of the United States of America·Jason C GriggAilong Ke
Jul 31, 2013·Nature·Jinwei Zhang, Adrian R Ferré-D'Amaré
Nov 19, 2013·Nature Structural & Molecular Biology·Ramya KrishnanNils G Walter
May 13, 2014·Biochimica Et Biophysica Acta·Tina M Henkin
Nov 30, 2014·Methods in Enzymology·Krishna C Suddala, Nils G Walter
Jan 15, 2015·Proceedings of the National Academy of Sciences of the United States of America·Anna V SherwoodTina M Henkin
May 12, 2015·Wiley Interdisciplinary Reviews. RNA·Jinwei Zhang, Adrian R Ferré-D'Amaré
Sep 30, 2015·Nature·John A HoweTerry Roemer
Nov 3, 2015·Journal of Molecular Biology·Lin Huang, David M J Lilley
Feb 26, 2016·Angewandte Chemie·Mark A BoernekeThomas Hermann
Apr 5, 2016·Biomolecules·Jinwei Zhang, Adrian R Ferré-DAmaré
Apr 20, 2016·Methods : a Companion to Methods in Enzymology·Lorena ParleaBruce A Shapiro
Nov 1, 2016·Nature Reviews. Microbiology·Lionello Bossi, Nara Figueroa-Bossi
Oct 28, 2016·Microbiology and Molecular Biology Reviews : MMBR·Ruben A T MarsJan Maarten van Dijl
Feb 16, 2017·Nature Reviews. Molecular Cell Biology·Stanislaw A GorskiJennifer A Doudna
Apr 12, 2017·RNA·Phillip J McCownRonald R Breaker
May 23, 2017·Nucleic Acids Research·Bhaskar Chetnani, Alfonso Mondragón

❮ Previous
Next ❯

Citations

Jul 10, 2019·Nucleic Acids Research·Anoja MegalathanSoma Dhakal
Dec 4, 2019·Nature Structural & Molecular Biology·Krishna C Suddala, Jinwei Zhang
Nov 20, 2019·Nature Structural & Molecular Biology·Shuang LiJinwei Zhang
Jun 6, 2019·Methods and Protocols·Dalton R GibbsSoma Dhakal
Mar 7, 2020·Nature Communications·Jhonatan A Hernandez-ValdesOscar P Kuipers
Feb 26, 2021·The Journal of Physical Chemistry. B·Anoja MegalathanSoma Dhakal
May 28, 2021·Chembiochem : a European Journal of Chemical Biology·Hannah DepmeierStephanie Kath-Schorr
Oct 18, 2020·Bioorganic & Medicinal Chemistry·Ian ArmstrongJennifer V Hines
Jun 3, 2020·ACS Nano·Xiuhai MaoXiaolei Zuo
Feb 21, 2019·ACS Sensors·Anisa KaurSoma Dhakal

❮ Previous
Next ❯

Methods Mentioned

BETA
FRET
aminoacylation
isothermal titration calorimetry
electrophoresis
electrophoretic mobility shift assay
fluorescence coincidence assay
NMR
its
in vitro transcription
filter binding

Software Mentioned

KARTS
QuB
ImageQuant
Exiqon
SiM
Matlab
smFRET
OriginLab

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.