4.6 Article

The bacterial yjdF riboswitch regulates translation through its tRNA-like fold

Related references

Note: Only part of the references are listed.
Review Biochemistry & Molecular Biology

Riboswitch control of bacterial RNA stability

Jamie Richards et al.

Summary: Riboswitches can not only regulate translation and transcription, but also control bacterial RNA lifetimes by accelerating or impeding RNA degradation. Binding of ligand can trigger endocleavage, self-cleavage, or protect RNA from degradation by blocking access to vulnerable regions, which in turn affects translation and transcription.

MOLECULAR MICROBIOLOGY (2021)

Article Biochemistry & Molecular Biology

An uncommon [K+(Mg2+)2] metal ion triad imparts stability and selectivity to the Guanidine-I riboswitch

Robert J. Trachman et al.

Summary: The ykkC-I riboswitch class shows divergent evolution, with K+ ion chelation and solvent tuning affecting ligand specificity and affinity among the riboswitches. The Burkholderia structure reveals a unique ion triad in the guanidine-binding pocket, suggesting a novel mechanism for RNA-ligand interactions. This study highlights how natural selection has shaped the versatile RNA fold of ykkC-I riboswitches.
Article Multidisciplinary Sciences

Switching at the ribosome: riboswitches need rProteins as modulators to regulate translation

Vanessa de Jesus et al.

Summary: Translational riboswitches are RNA regulators that modulate gene expression during translation initiation by interacting with 30S ribosome protein S1. The ligand-induced allosteric switch in adenine-sensing riboswitch is insufficient on its own and requires the interaction to fully open the translation initiation region.

NATURE COMMUNICATIONS (2021)

Review Microbiology

Naturally Occurring tRNAs With Non-canonical Structures

Natalie Krahn et al.

FRONTIERS IN MICROBIOLOGY (2020)

Review Cell Biology

The emerging complexity of the tRNA world: mammalian tRNAs beyond protein synthesis

Paul Schimmel

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2018)

Article Biochemistry & Molecular Biology

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

Ioanna Kalvari et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

Activation of the Stringent Response by Loading of RelA-tRNA Complexes at the Ribosomal A-Site

Kristoffer Skovbo Winther et al.

MOLECULAR CELL (2018)

Article Multidisciplinary Sciences

Riboswitches for the alarmone ppGpp expand the collection of RNA-based signaling systems

Madeline E. Sherlock et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Cell Biology

Riboswitches and Translation Control

Ronald R. Breaker

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2018)

Article Biochemistry & Molecular Biology

Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class

James W. Nelson et al.

MOLECULAR CELL (2017)

Article Biochemistry & Molecular Biology

Structural basis for high-affinity fluorophore binding and activation by RNA Mango

Robert J. Trachman et al.

NATURE CHEMICAL BIOLOGY (2017)

Article Biochemistry & Molecular Biology

Riboswitch diversity and distribution

Phillip J. McCown et al.

Article Chemistry, Multidisciplinary

ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions

D. Franke et al.

JOURNAL OF APPLIED CRYSTALLOGRAPHY (2017)

Article Biochemistry & Molecular Biology

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

Todd M. Lowe et al.

NUCLEIC ACIDS RESEARCH (2016)

Review Biochemistry & Molecular Biology

tRNA-mimicry in IRES-mediated translation and recoding

Samuel E. Butcher et al.

RNA BIOLOGY (2016)

Article Multidisciplinary Sciences

Global shape mimicry of tRNA within a viral internal ribosome entry site mediates translational reading frame selection

Hilda H. Au et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Multidisciplinary Sciences

The structural basis of transfer RNA mimicry and conformational plasticity by a viral RNA

Timothy M. Colussi et al.

NATURE (2014)

Article Biochemistry & Molecular Biology

EttA regulates translation by binding the ribosomal E site and restricting ribosome-tRNA dynamics

Bo Chen et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2014)

Review Genetics & Heredity

tRNAs as regulators of biological processes

Medha Raina et al.

FRONTIERS IN GENETICS (2014)

Review Biochemistry & Molecular Biology

A Decade of Riboswitches

Alexander Serganov et al.

Article Biochemical Research Methods

Flexizymes for genetic code reprogramming

Yuki Goto et al.

NATURE PROTOCOLS (2011)

Review Biophysics

The glmS ribozyme: use of a small molecule coenzyme by a gene-regulatory RNA

Adrian R. Ferre-D'Amare

QUARTERLY REVIEWS OF BIOPHYSICS (2010)

Article Biotechnology & Applied Microbiology

Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes

Zasha Weinberg et al.

GENOME BIOLOGY (2010)

Software Review Chemistry, Multidisciplinary

DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering

Daniel Franke et al.

JOURNAL OF APPLIED CRYSTALLOGRAPHY (2009)

Review Biochemistry & Molecular Biology

The flexizyme system: a highly flexible tRNA aminoacylation tool for the translation apparatus

Masaki Ohuchi et al.

CURRENT OPINION IN CHEMICAL BIOLOGY (2007)

Article Biochemical Research Methods

A highly flexible tRNA acylation method for non-natural potypeptide synthesis

H Murakami et al.

NATURE METHODS (2006)

Article Biochemistry & Molecular Biology

Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs

A Serganov et al.

CHEMISTRY & BIOLOGY (2004)

Article Biochemistry & Molecular Biology

Adenine riboswitches and gene activation by disruption of a transcription terminator

M Mandal et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2004)

Article Chemistry, Multidisciplinary

Automated matching of high- and low-resolution structural models

MB Kozin et al.

JOURNAL OF APPLIED CRYSTALLOGRAPHY (2001)