DR2417, a hypothetical protein characterized as a novel β-CASP family nuclease in radiation resistant bacterium, Deinococcus radiodurans

Das, Anubrata; Misra, Hari S.

doi:10.1016/j.bbagen.2012.03.014

Cited by 19 publications

(16 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These include the DR1131 mutant, inactivated for the hemZ gene involved in heme biosynthesis, the mutant for DR1207 of unknown function, the DR2374 mutant, inactivated for a ribonucleotide reductase of archeal type, and the mutant for DR2417m , encoding DncA, a novel essential β-CASP family nuclease contributing to the radiation resistance of D . radiodurans ([ 58 ] and S1 Table ). The low fraction of oxidative stress mutants identified in our library may also be due to the non-viable status of the Tn 5 -insertions into the genes essential for oxidative stress recovery in response to high level of radiations.…”

Section: Resultsmentioning

confidence: 99%

Identification of New Genes Contributing to the Extreme Radioresistance of Deinococcus radiodurans Using a Tn5-Based Transposon Mutant Library

et al. 2015

View full text Add to dashboard Cite

Here, we have developed an extremely efficient in vivo Tn5-based mutagenesis procedure to construct a Deinococcus radiodurans insertion mutant library subsequently screened for sensitivity to genotoxic agents such as γ and UV radiations or mitomycin C. The genes inactivated in radiosensitive mutants belong to various functional categories, including DNA repair functions, stress responses, signal transduction, membrane transport, several metabolic pathways, and genes of unknown function. Interestingly, preliminary characterization of previously undescribed radiosensitive mutants suggests the contribution of cyclic di-AMP signaling in the recovery of D. radiodurans cells from genotoxic stresses, probably by modulating several pathways involved in the overall cell response. Our analyses also point out a new transcriptional regulator belonging to the GntR family, encoded by DR0265, and a predicted RNase belonging to the newly described Y family, both contributing to the extreme radioresistance of D. radiodurans. Altogether, this work has revealed new cell responses involved either directly or indirectly in repair of various cell damage and confirmed that D. radiodurans extreme radiation resistance is determined by a multiplicity of pathways acting as a complex network.

show abstract

Section: Resultsmentioning

confidence: 99%

Identification of New Genes Contributing to the Extreme Radioresistance of Deinococcus radiodurans Using a Tn5-Based Transposon Mutant Library

et al. 2015

View full text Add to dashboard Cite

show abstract

“…In fact, this leaderless expression has previously been utilized to pinpoint unannotated start sites and to identify (small) proteins in Deinococcus desertii (de Groot et al 2014). We also observed several, erroneous gene interruptions due to sequencing errors, such as in case of dncA ( Figure 8C), which was in fact experimentally corrected (Das and Misra 2012). Taken together, systematic (re-)analysis of proteomic and high-throughput sequencing datasets can provide strong annotation potential.…”

Section: Discussionmentioning

confidence: 64%

“…mRNA-seq coverage clearly indicates a bp deletion ( Figure 8C, zoomed region), giving rise to an interrupted CDS. In fact, this sequencing error was pointed out earlier experimentally and the correctly reconstituted DncA was characterized as an essential nuclease involved in growth and radiation resistance of Deinoccocus radiodurans (Das and Misra 2012). Despite this reported finding, the NCBI RefSeq NP_296138.1 CDS is incorrectly translated due to the sequencing error persisting in the original genome sequence.…”

Section: Proteogenomics Test Case: Deinococcus Radioduransmentioning

confidence: 96%

Lost and found: re-searching and re-scoring proteomics data aids the discovery of bacterial proteins and improves proteome coverage

Willems

Fijałkowski

Damme

2019

Preprint

View full text Add to dashboard Cite

Prokaryotic genome annotation is heavily dependent on automated gene annotation pipelines that are prone to propagate errors and underestimate genome complexity. We describe an optimized proteogenomic workflow that uses ribo-seq and proteomic data of Salmonella Typhiumurium to identify unannotated proteins or alternative protein forms raised upon alternative translation initiation (i.e. N-terminal proteoforms). This data analysis encompasses the searching of cofragmenting peptides and post-processing with extended peptide-to-spectrum quality features including comparison to predicted fragment ion intensities. When applying this strategy, an enhanced proteome-depth is achieved as well as greater confidence for unannotated peptide hits.We demonstrate the general applicability of our pipeline by re-analyzing public Deinococcus radiodurans datasets. Taken together, systematic re-analysis using available prokaryotic (proteome) datasets holds great promise to assist in experimentally-based genome annotation.

show abstract

“…Seems to be essential for growth and γ radiation resistance in D. radiodurans Das and Misra (2012) Mn 2+ ions, PprI cleaves DdrO, hence suppressing its function. The cleavage site seems to be the same in D. radiodurans and D. deserti.…”

Section: Proteins Involved In Genome Preservation and Dna Repair Mechmentioning

confidence: 99%

Recent progress in understanding the molecular mechanisms of radioresistance in Deinococcus bacteria

2015

View full text Add to dashboard Cite

The deleterious effects of ionizing radiation are a major concern of the modern world. In the last decades, outstanding interest has been given to developing new therapeutic tools designed for protection against the toxic effects of ionizing radiation. Deinococcus spp. are among the most radioresistant organisms on Earth, being able to survive extreme doses of radiation, 1000-fold higher than most vertebrates. The molecular mechanisms underlying DNA repair and biomolecular protection, which are responsible for the remarkable radioresistance of Deinococcus bacteria, have been a debatable subject for the last 60 years. This paper is focused on the most recent findings regarding the molecular background of radioresistance and on Deinococcus bacteria response to oxidative stress. Novel proteins and genes involved in the highly regulated DNA repair processes, and enzymatic and non- enzymatic antioxidant systems are presented. In addition, a recently proposed mechanism that may contribute to oxidative damage protection in Deinococcus bacteria is discussed. A better understanding of these molecular mechanisms may draw future perspectives for counteracting radiation-related toxicity.

show abstract

DR2417, a hypothetical protein characterized as a novel β-CASP family nuclease in radiation resistant bacterium, Deinococcus radiodurans

Cited by 19 publications

References 47 publications

Identification of New Genes Contributing to the Extreme Radioresistance of Deinococcus radiodurans Using a Tn5-Based Transposon Mutant Library

Identification of New Genes Contributing to the Extreme Radioresistance of Deinococcus radiodurans Using a Tn5-Based Transposon Mutant Library

Lost and found: re-searching and re-scoring proteomics data aids the discovery of bacterial proteins and improves proteome coverage

Recent progress in understanding the molecular mechanisms of radioresistance in Deinococcus bacteria

Contact Info

Product

Resources

About