(Q33556640)

28 July 2017

title

RNA sequencing and proteogenomics reveal the importance of leaderless mRNAs in the radiation-tolerant bacterium Deinococcus deserti (English)

1 reference

28 July 2017

0 references

Deinococcus deserti

1 reference

Arjan de Groot

0 references

Laurence Blanchard

0 references

David Vallenet

0 references

David Pignol

0 references

Jean Armengaud

0 references

David Roche

1 reference

28 July 2017

Bernard Fernandez

series ordinal

1 reference

28 July 2017

Monika Ludanyi

series ordinal

1 reference

28 July 2017

Stéphane Cruveiller

series ordinal

1 reference

28 July 2017

publication date

1 April 2014

1 reference

Genome Biology and Evolution

28 July 2017

published in

1 reference

28 July 2017

1 reference

28 July 2017

1 reference

28 July 2017

page(s)

932-948

1 reference

Comparative proteomics reveals key proteins recruited at the nucleoid of Deinococcus after irradiation-induced DNA damage.

28 July 2017

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Genome-wide mapping of transcriptional start sites defines an extensive leaderless transcriptome in Mycobacterium tuberculosis

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RNA at 92 °C: the non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi

21 June 2018

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Biology of extreme radiation resistance: the way of Deinococcus radiodurans

21 June 2018

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Proteogenomic insights into salt tolerance by a halotolerant alpha-proteobacterium isolated from an Andean saline spring.

21 June 2018

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Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti 1021.

21 June 2018

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Major soluble proteome changes in Deinococcus deserti over the earliest stages following gamma-ray irradiation

21 June 2018

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Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features

21 June 2018

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21 June 2018

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21 June 2018

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The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium.

21 June 2018

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21 June 2018

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The Pseudomonas aeruginosa transcriptome in planktonic cultures and static biofilms using RNA sequencing

21 June 2018

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Extreme anti-oxidant protection against ionizing radiation in bdelloid rotifers

21 June 2018

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Death by protein damage in irradiated cells

21 June 2018

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Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions

21 June 2018

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DNA binding is essential for PprI function in response to radiation damage in Deinococcus radiodurans

21 June 2018

1 reference

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Intrinsically disordered proteins as molecular shields

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

cis-antisense RNA, another level of gene regulation in bacteria.

21 June 2018

1 reference

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Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Oxidative Stress Resistance inDeinococcus radiodurans

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

A Major Role for Nonenzymatic Antioxidant Processes in the Radioresistance of Halobacterium salinarum

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

RtcB is the RNA ligase component of an Escherichia coli RNA repair operon

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Translation initiation: variations in the mechanism can be anticipated

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Differential expression analysis for sequence count data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Proximity of the Start Codon to a Leaderless mRNA's 5′ Terminus Is a Strong Positive Determinant of Ribosome Binding and Expression in Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Studying bacterial transcriptomes using RNA-seq

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Small-Molecule Antioxidant Proteome-Shields in Deinococcus radiodurans

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Unstructured hydrophilic sequences in prokaryotic proteomes correlate with dehydration tolerance and host association

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Protein damage and death by radiation in Escherichia coli and Deinococcus radiodurans

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Structural and operational complexity of the Geobacter sulfurreducens genome.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

The primary transcriptome of the major human pathogen Helicobacter pylori

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Cysteine residues exposed on protein surfaces are the dominant intramitochondrial thiol and may protect against oxidative damage

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

A single-base resolution map of an archaeal transcriptome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Proteomics-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Next generation sequencing of microbial transcriptomes: challenges and opportunities.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Mutagenic lesion bypass and two functionally different RecA proteins in Deinococcus deserti

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Begin at the beginning: evolution of translational initiation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

DdrB protein, an alternative Deinococcus radiodurans SSB induced by ionizing radiation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

The Sequence Alignment/Map format and SAMtools

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

A toolbox for validation of mass spectrometry peptides identification and generation of database: IRMa

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Protein structure prediction on the Web: a case study using the Phyre server

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

An unexpected type of ribosomes induced by kasugamycin: a look into ancestral times of protein synthesis?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Crystal structure of the IrrE protein, a central regulator of DNA damage repair in deinococcaceae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Differentiating protein-coding and noncoding RNA: challenges and ambiguities

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Deinococcus radiodurans PprI switches on DNA damage response and cellular survival networks after radiation damage

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Ribosomes bind leaderless mRNA in Escherichia coli through recognition of their 5'-terminal AUG

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Antioxidant activity of proteins and peptides.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Protein oxidation: key to bacterial desiccation resistance?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Experimental characterization of Cis-acting elements important for translation and transcription in halophilic archaea

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Hydrophilic protein associated with desiccation tolerance exhibits broad protein stabilization function

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Protein oxidation implicated as the primary determinant of bacterial radioresistance

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Reactive cysteine in proteins: protein folding, antioxidant defense, redox signaling and more

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Deinococcus deserti sp. nov., a gamma-radiation-tolerant bacterium isolated from the Sahara Desert.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Deinococcus radiodurans - the consummate survivor

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

A ring-like nucleoid is not necessary for radioresistance in the Deinococcaceae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Analysis of Deinococcus radiodurans's transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Translation initiation with 70S ribosomes: an alternative pathway for leaderless mRNAs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

AMIGene: Annotation of MIcrobial Genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Ringlike structure of the Deinococcus radiodurans genome: a key to radioresistance?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Leaderless mRNAs bind 70S ribosomes more strongly than 30S ribosomal subunits in Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

The IrrE protein of Deinococcus radiodurans R1 is a novel regulator of recA expression

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

SSAHA: a fast search method for large DNA databases

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

The initiation codon affects ribosome binding and translational efficiency in Escherichia coli of cI mRNA with or without the 5' untranslated leader

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Selective stimulation of translation of leaderless mRNA by initiation factor 2: evolutionary implications for translation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Base-Calling of Automated Sequencer Traces UsingPhred. I. Accuracy Assessment

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

AGAINST ALL ODDS: The Survival Strategies of Deinococcus radiodurans

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Radioresistance of Deinococcus radiodurans: functions necessary to survive ionizing radiation are also necessary to survive prolonged desiccation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Fitting a mixture model by expectation maximization to discover motifs in biopolymers

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Identification of common molecular subsequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Attenuation in the control of expression of bacterial operons

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4007540

Deinococcus radiodurans: What Belongs to the Survival Kit?

21 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU069

Proteogenomic definition of biomarkers for the large Roseobacter clade and application for a quick screening of new environmental isolates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU069

Accumulation of Mn(II) in Deinococcus radiodurans facilitates gamma-radiation resistance.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU069

A novel mechanism for translation initiation operates in haloarchaea

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU069

PprI: a general switch responsible for extreme radioresistance of Deinococcus radiodurans.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU069

A comparative proteomic approach to better define Deinococcus nucleoid specificities.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU069

Evidence for the translation initiation of leaderless mRNAs by the intact 70 S ribosome without its dissociation into subunits in eubacteria.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU069

An AUG initiation codon, not codon-anticodon complementarity, is required for the translation of unleadered mRNA in Escherichia coli

21 January 2018

1 reference

12 December 2020

Transcription attenuation in bacteria: theme and variations

1 reference

12 December 2020

Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity

1 reference

12 December 2020

Optimized rapid amplification of cDNA ends (RACE) for mapping bacterial mRNA transcripts

1 reference

12 December 2020

MoxR AAA+ ATPases: a novel family of molecular chaperones?

1 reference

12 December 2020

Identifiers

DOI

10.1093/GBE/EVU069

1 reference

28 July 2017

1 reference

28 July 2017

1 reference