4.8 Article

Pervasive translation in Mycobacterium tuberculosis

Related references

Note: Only part of the references are listed.
Article Multidisciplinary Sciences

Uncovering de novo gene birth in yeast using deep transcriptomics

William R. Blevins et al.

Summary: Recent research has identified 213 de novo originated transcripts in Saccharomyces cerevisiae, with half of them expressed from regions that already contain other genes. These transcripts show similar expression changes in response to stress and some are capable of translating small proteins.

NATURE COMMUNICATIONS (2021)

Article Cell Biology

A snapshot of translation in Mycobacterium tuberculosis during exponential growth and nutrient starvation revealed by ribosome profiling

Elizabeth B. Sawyer et al.

Summary: Research found that a large proportion of mRNA transcripts expressed in M. tuberculosis lack canonical bacterial translation initiation signals, which has important implications for fine-tuning of translation. Under conditions of nutrient starvation, patterns of ribosome recruitment vary, suggesting that regulation of translation in this pathogen is more complex than originally thought.

CELL REPORTS (2021)

Article Biochemistry & Molecular Biology

Alternative ORFs and small ORFs: shedding light on the dark proteome

Mona Wu Orr et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Multidisciplinary Sciences

Pervasive functional translation of noncanonical human open reading frames

Jin Chen et al.

SCIENCE (2020)

Article Multidisciplinary Sciences

De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences

Nikolaos Vakirlis et al.

NATURE COMMUNICATIONS (2020)

Article Biochemistry & Molecular Biology

Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome

Sezen Meydan et al.

MOLECULAR CELL (2019)

Article Biochemical Research Methods

Interactive Peptide Spectral Annotator: A Versatile Web-based Tool for Proteomic Applications

Dain R. Brademan et al.

MOLECULAR & CELLULAR PROTEOMICS (2019)

Article Genetics & Heredity

De novo gene birth

Stephen Branden Van Oss et al.

PLOS GENETICS (2019)

Article Biochemistry & Molecular Biology

Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes

Hila Sberro et al.

Article Biochemistry & Molecular Biology

A Molecular Portrait of De Novo Genes in Yeasts

Nikolaos Vakirlis et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Biochemistry & Molecular Biology

Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes

Alexandre Lomsadze et al.

GENOME RESEARCH (2018)

Article Biochemical Research Methods

Identifying New Small Proteins in Escherichia coli

Caitlin E. VanOrsdel et al.

PROTEOMICS (2018)

Article Ecology

Translation of neutrally evolving peptides provides a basis for de novo gene evolution

Jorge Ruiz-Orera et al.

NATURE ECOLOGY & EVOLUTION (2018)

Article Microbiology

Leaderless mRNAs in the Spotlight: Ancient but Not Outdated!

Heather J. Beck et al.

MICROBIOLOGY SPECTRUM (2018)

Article Biochemistry & Molecular Biology

A Comprehensive Analysis of Transcript-supported De Novo Genes in Saccharomyces sensu stricto Yeasts

Tzu-Chiao Lu et al.

MOLECULAR BIOLOGY AND EVOLUTION (2017)

Article Biochemistry & Molecular Biology

Measurements of translation initiation from all 64 codons in E. coli

Ariel Hecht et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Multidisciplinary Sciences

WhiB6 regulation of ESX-1 gene expression is controlled by a negative feedback loop in Mycobacterium marinum

Rachel E. Bosserman et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Biotechnology & Applied Microbiology

Transcriptome-scale RNase-footprinting of RNA-protein complexes

Zhe Ji et al.

NATURE BIOTECHNOLOGY (2016)

Article Cell Biology

High-Precision Analysis of Translational Pausing by Ribosome Profiling in Bacteria Lacking EFP

Christopher J. Woolstenhulme et al.

CELL REPORTS (2015)

Review Biochemistry & Molecular Biology

Small Proteins Can No Longer Be Ignored

Gisela Storz et al.

ANNUAL REVIEW OF BIOCHEMISTRY, VOL 83 (2014)

Review Microbiology

Pervasive transcription: illuminating the dark matter of bacterial transcriptomes

Joseph T. Wade et al.

NATURE REVIEWS MICROBIOLOGY (2014)

Article Biochemistry & Molecular Biology

Pervasive transcription: detecting functional RNAs in bacteria

Meghan Lybecker et al.

TRANSCRIPTION-AUSTIN (2014)

Article Biochemistry & Molecular Biology

Computational analysis of bacterial RNA-Seq data

Ryan McClure et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Biochemical Research Methods

Direct Detection of Bacterial Protein Secretion Using Whole Colony Proteomics

Matthew M. Champion et al.

MOLECULAR & CELLULAR PROTEOMICS (2012)

Article Multidisciplinary Sciences

Proto-genes and de novo gene birth

Anne-Ruxandra Carvunis et al.

NATURE (2012)

Article Biochemical Research Methods

ViennaRNA Package 2.0

Ronny Lorenz et al.

ALGORITHMS FOR MOLECULAR BIOLOGY (2011)

Article Biochemical Research Methods

Composition bias and the origin of ORFan genes

Inbal Yomtovian et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

Prodigal: prokaryotic gene recognition and translation initiation site identification

Doug Hyatt et al.

BMC BIOINFORMATICS (2010)

Article Biochemical Research Methods

Universal sample preparation method for proteome analysis

Jacek R. Wisniewski et al.

NATURE METHODS (2009)

Article Biochemical Research Methods

Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics

Paul J. Boersema et al.

NATURE PROTOCOLS (2009)

Article Multidisciplinary Sciences

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

Nicholas T. Ingolia et al.

SCIENCE (2009)

Article Biochemical Research Methods

Nonlinear fitting method for determining local false discovery rates from decoy database searches

Wilfred H. Tang et al.

JOURNAL OF PROTEOME RESEARCH (2008)

Article Biochemical Research Methods

Identifying bacterial genes and endosymbiont DNA with Glimmer

Arthur L. Delcher et al.

BIOINFORMATICS (2007)

Article Biochemistry & Molecular Biology

GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses

J Besemer et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemistry & Molecular Biology

Proteome analysis of Escherichia coli K-12 by two-dimensional native-state chromatography and MALDI-MS

MM Champion et al.

MOLECULAR MICROBIOLOGY (2003)

Article Biochemistry & Molecular Biology

Leaderless mRNAs in bacteria: surprises in ribosomal recruitment and translational control

I Moll et al.

MOLECULAR MICROBIOLOGY (2002)