tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence

Combining recombinant ribonuclease U2 and protein phosphatase for RNA modification mapping by liquid chromatography–mass spectrometry

(2015) Whitney M. Houser et al.   ANALYTICAL BIOCHEMISTRY

Codon Bias as a Means to Fine-Tune Gene Expression

(2015) Tessa E.F. Quax et al.   MOLECULAR CELL

Biogenesis and growth phase-dependent alteration of 5-methoxycarbonylmethoxyuridine in tRNA anticodons

(2015) Yusuke Sakai et al.   NUCLEIC ACIDS RESEARCH

RoboOligo: software for mass spectrometry data to support manual and de novo sequencing of post-transcriptionally modified ribonucleic acids

(2015) Paul J. Sample et al.   NUCLEIC ACIDS RESEARCH

Determinants of the CmoB carboxymethyl transferase utilized for selective tRNA wobble modification

(2015) Jungwook Kim et al.   NUCLEIC ACIDS RESEARCH

Trm9-Catalyzed tRNA Modifications Regulate Global Protein Expression by Codon-Biased Translation

(2015) Wenjun Deng et al.   PLoS Genetics

Label-Free Absolute Quantitation of Oligosaccharides Using Multiple Reaction Monitoring

(2014) Qiuting Hong et al.   ANALYTICAL CHEMISTRY

A System of RNA Modifications and Biased Codon Use Controls Cellular Stress Response at the Level of Translation

(2014) Peter C. Dedon et al.   CHEMICAL RESEARCH IN TOXICOLOGY

tRNA modifications regulate translation during cellular stress

(2014) Chen Gu et al.   FEBS LETTERS

Characterization of nucleic acids by tandem mass spectrometry - The second decade (2004-2013): From DNA to RNA and modified sequences

(2014) Stefan Schürch   MASS SPECTROMETRY REVIEWS

Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry

(2014) Dan Su et al.   Nature Protocols

Mycobacterial RNA isolation optimized for non-coding RNA: high fidelity isolation of 5S rRNA from Mycobacterium bovis BCG reveals novel post-transcriptional processing and a complete spectrum of modified ribonucleosides

(2014) Fabian Hia et al.   NUCLEIC ACIDS RESEARCH

The global identification of tRNA isoacceptors by targeted tandem mass spectrometry

(2013) Collin Wetzel et al.   ANALYST

Sulfur Amino Acids Regulate Translational Capacity and Metabolic Homeostasis through Modulation of tRNA Thiolation

(2013) Sunil Laxman et al.   CELL

Integrated Analysis of Transcriptomic and Proteomic Data

(2013) Saad Haider et al.   CURRENT GENOMICS

The Mycobacterium tuberculosis regulatory network and hypoxia

(2013) James E. Galagan et al.   NATURE

Environmental perturbations lift the degeneracy of the genetic code to regulate protein levels in bacteria

(2013) A. R. Subramaniam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HowMycobacterium tuberculosisgoes to sleep: the dormancy survival regulator DosR a decade later

(2012) Calvin Boon et al.   Future Microbiology

Urease Activity Represents an Alternative Pathway for Mycobacterium tuberculosis Nitrogen Metabolism

(2012) Wenwei Lin et al.   INFECTION AND IMMUNITY

Dynamic changes in translational efficiency are deduced from codon usage of the transcriptome

(2012) Hila Gingold et al.   NUCLEIC ACIDS RESEARCH

Appropriate DevR (DosR)-Mediated Signaling Determines Transcriptional Response, Hypoxic Viability and Virulence of Mycobacterium tuberculosis

(2012) Shyamasree De Majumdar et al.   PLoS One

Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins

(2012) Clement T.Y. Chan et al.   Nature Communications

The gene-specific codon counting database: a genome-based catalog of one-, two-, three-, four- and five-codon combinations present in Saccharomyces cerevisiae genes

(2012) Sudheer Tumu et al.   Database-The Journal of Biological Databases and Curation

Identification of N6,N6-Dimethyladenosine in Transfer RNA from Mycobacterium bovis Bacille Calmette-Guérin

(2011) Clement Chan et al.   MOLECULES

Absolute quantification of protein and post-translational modification abundance with stable isotope–labeled synthetic peptides

(2011) Arminja N Kettenbach et al.   Nature Protocols

Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift

(2011) P. Shah et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Separation and identification of oligonucleotides by hydrophilic interaction liquid chromatography (HILIC)—inductively coupled plasma mass spectrometry (ICPMS)

(2010) Renee N. Easter et al.   ANALYST

Letting Sleeping dos Lie: Does Dormancy Play a Role in Tuberculosis?

(2010) Michael C. Chao et al.   Annual Review of Microbiology

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

Synonymous but not the same: the causes and consequences of codon bias

(2010) Joshua B. Plotkin et al.   NATURE REVIEWS GENETICS

DosR-regulon genes induction in Mycobacterium bovis BCG under aerobic conditions

(2010) Mario Alberto Flores Valdez et al.   TUBERCULOSIS

A Quantitative Systems Approach Reveals Dynamic Control of tRNA Modifications during Cellular Stress

(2010) Clement T. Y. Chan et al.   PLoS Genetics

Hypoxia: a window intoMycobacterium tuberculosislatency

(2009) Tige R. Rustad et al.   CELLULAR MICROBIOLOGY

Deciphering synonymous codons in the three domains of life: Co-evolution with specific tRNA modification enzymes

(2009) Henri Grosjean et al.   FEBS LETTERS

The Mycobacterium tuberculosis DosR Regulon Assists in Metabolic Homeostasis and Enables Rapid Recovery from Nonrespiring Dormancy

(2009) R. L. Leistikow et al.   JOURNAL OF BACTERIOLOGY

The DosR regulon of M. tuberculosis and antibacterial tolerance

(2009) I.L. Bartek et al.   TUBERCULOSIS

Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications

(2008) Paul F Agris   EMBO REPORTS

Tuberculous Granulomas Are Hypoxic in Guinea Pigs, Rabbits, and Nonhuman Primates

(2008) L. E. Via et al.   INFECTION AND IMMUNITY

Cooperative Binding of Phosphorylated DevR to Upstream Sites Is Necessary and Sufficient for Activation of the Rv3134c-devRS Operon in Mycobacterium tuberculosis: Implication in the Induction of DevR Target Genes

(2008) S. Chauhan et al.   JOURNAL OF BACTERIOLOGY

The Enduring Hypoxic Response of Mycobacterium tuberculosis

(2008) Tige R. Rustad et al.   PLoS One