Deinococcus radiodurans

Top PDF Deinococcus radiodurans:

Natural Transformation in Deinococcus radiodurans: A Genetic Analysis Reveals the Major Roles of DprA, DdrB, RecA, RecF, and RecO Proteins

Natural Transformation in Deinococcus radiodurans: A Genetic Analysis Reveals the Major Roles of DprA, DdrB, RecA, RecF, and RecO Proteins

Horizontal gene transfer is a major driver of bacterial evolution and adaptation to environmental stresses, occurring notably via transformation of naturally competent organisms. The Deinococcus radiodurans bacterium, characterized by its extreme radioresistance, is also naturally competent. Here, we investigated the role of D. radiodurans players involved in different steps of natural transformation. First, we identified the factors (PilQ, PilD, type IV pilins, PilB, PilT, ComEC-ComEA, and ComF) involved in DNA uptake and DNA translocation across the external and cytoplasmic membranes and showed that the DNA-uptake machinery is similar to that described in the Gram negative bacterium Vibrio cholerae. Then, we studied the involvement of recombination and DNA repair proteins, RecA, RecF, RecO, DprA, and DdrB into the DNA processing steps of D. radiodurans transformation by plasmid and genomic DNA. The transformation frequency of the cells devoid of DprA, a highly conserved protein among competent species, strongly decreased but was not completely abolished whereas it was completely abolished in 1dprA 1recF, 1dprA 1recO, and 1dprA 1ddrB double mutants. We propose that RecF and RecO, belonging to the recombination mediator complex, and DdrB, a specific deinococcal DNA binding protein, can replace a function played by DprA, or alternatively, act at a different step of recombination with DprA. We also demonstrated that a 1dprA mutant is as resistant as wild type to various doses of γ-irradiation, suggesting that DprA, and potentially transformation, do not play a major role in D. radiodurans radioresistance.
En savoir plus

17 En savoir plus

Variabilité génétique chez la bactérie radiorésistante Deinococcus radiodurans : la recombinaison entre séquences répétées et la transformation naturelle

Variabilité génétique chez la bactérie radiorésistante Deinococcus radiodurans : la recombinaison entre séquences répétées et la transformation naturelle

Résumé La bactérie Deinococcus radiodurans est connue pour sa capacité à résister à un grand nombre de traitements génotoxiques parmi lesquels on peut citer l’exposition aux rayons ionisants, aux ultra- violets, à la mitomycine C, à la dessication et au stress oxydant. Elle est capable lors d’une exposition à des doses extrêmes de rayons γ générant des centaines de cassures de l’ADN de reconstituer un génome intact en seulement 2 à 3 heures via un mécanisme original, l’ESDSA, impliquant une synthèse massive d’ADN pendant la phase de réparation des cassures de l’ADN. En plus de mécanismes efficaces de réparation de l’ADN, elle possède un kit de survie comprenant une compaction importante du nucléoïde, des mécanismes de protection des protéines contre l’oxydation, une réponse originale aux lésions de l’ADN et des protéines spécifiques induites après irradiation. Tous ces facteurs contribuent au maintien de l’intégrité du génome et à la survie de la cellule lors de l’exposition à différents agents génotoxiques. Souvent considéré comme un organisme ayant une stabilité génomique exceptionnelle, cette bactérie possède dans son génome un grand nombre de séquences répétées et des éléments mobiles et est par ailleurs naturellement compétente. Ce sont autant de facteurs pouvant participer à la variabilité génétique de cette espèce. Je me suis donc intéressée lors de ma thèse à deux processus pouvant participer à l’instabilité génétique chez D. radiodurans : la recombinaison entre séquences répétées et la transformation naturelle.
En savoir plus

268 En savoir plus

PprA : une protéine clé dans la radiorésistance chez Deinococcus radiodurans

PprA : une protéine clé dans la radiorésistance chez Deinococcus radiodurans

a b s t r a c t Deinococcus radiodurans, one of the most radioresistant organisms known to date is able to reconstruct an intact genome from hundreds of DNA fragments. Here, we investigate the in vivo role of PprA, a radiation- induced Deinococcus specific protein. We report that DNA double strand break repair in cells devoid of PprA and exposed to 3800 Gy ␥-irradiation takes place efficiently with a delay of only 1 h as compared to the wild type, whereas massive DNA synthesis begins 90 min after irradiation as in the wild type, a phenotype insufficient to explain the severe radiosensitivity of the pprA mutant. We show that the slow kinetics of reassembly of DNA fragments in a pprA recA double mutant was the same as that observed in a recA single mutant demonstrating that PprA does not play a major role in DNA repair through RecA- independent pathways. Using a tagged PprA protein and immunofluorescence microscopy, we show that PprA is recruited onto the nucleoid after ␥-irradiation before DNA double strand break repair completion, and then is found as a thread across the septum in dividing cells. Moreover, whereas untreated cells devoid of PprA displayed a wild type morphology, they showed a characteristic cell division abnormality after irradiation not found in other radiosensitive mutants committed to die, as DNA is present equally in the two daughter cells but not separated at the division septum. We propose that PprA may play a crucial role in the control of DNA segregation and/or cell division after DNA double strand break repair.
En savoir plus

210 En savoir plus

Intrinsically disordered regions may lower the hydration free energy in proteins: a case study of nudix hydrolase in the bacterium Deinococcus radiodurans.

Intrinsically disordered regions may lower the hydration free energy in proteins: a case study of nudix hydrolase in the bacterium Deinococcus radiodurans.

sequence entropy, and lack of the so-called order-promoting amino acids and bulky hydrophobic residues. Based on such features, several bioinformatics tools have been developed that can reliably predict the level of intrinsic disorder in a given sequence [11,20]. Moreover, using mostly NMR, small-angle X-ray scattering, and different spectroscopic methods [5,7,25], basic structural features of IDPs have been elucidated, including their molecular size, level of structural heterogeneity, role of transient structure in coupled binding-and-folding events, aggregation tendencies and presence of persistent structure [6,7,25]. In particular, a combination of computer simulation and experimen- tally-determined restraints has provided some of the first ensemble-level pictures of IDPs [13,25,26]. However, compared with our knowledge of the structure and mechanism of ordered proteins, our understanding of IDPs is still extremely rudimentary and incomplete, primarily because of their structural and dynamic complexity. In the present study, we use molecular dynamics simulations and free energy calculations to focus on the role of IDPs in an extremophile bacterium: Deinococcus radiodurans.
En savoir plus

11 En savoir plus

Nanoscale surface structures of DNA bound to Deinococcus radiodurans HU unveiled by atomic force microscopy.

Nanoscale surface structures of DNA bound to Deinococcus radiodurans HU unveiled by atomic force microscopy.

The Deinococcus radiodurans protein HU (DrHU) was shown to be critical for nucleoid activities, yet its functional and structural properties remain largely unexplored. We have applied atomic force microscopy (AFM) imaging to study DrHU binding to pUC19-DNA in vitro and analyzed the topographic structures formed at the nanoscale. At the single-molecule level, AFM imaging allows visualization of super-helical turns on naked DNA surfaces and characterization of free DrHU molecules observed as homodimers. When enhancing the molecular surface structures of AFM images by the Laplacian weight filter, the distri- bution of bound DrHUs was visibly varied as a function of the DrHU/DNA molar ratio. At a low molar ratio, DrHU binding was found to reduce the volume of condensed DNA con figuration by about 50%. We also show that DrHU is capable of bridging distinct DNA segments. Moreover, at a low molar ratio, the binding orientation of individual DrHU dimers could be perceived on partially “open” DNA configuration. At a high molar ratio, DrHU sti ffened the DNA molecule and enlarged the spread of the open DNA configuration. Furthermore, a lattice-like pattern could be seen on the surface of DrHU –DNA complex, indicating that DrHU multimerization had occurred leading to the formation of a higher order architecture. Together, our results show that the functional plasticity of DrHU in mediating DNA organization is subject to both the conformational dynamics of DNA molecules and protein abundance.
En savoir plus

12 En savoir plus

PprA Protein Is Involved in Chromosome Segregation via Its Physical and Functional Interaction with DNA Gyrase in Irradiated Deinococcus radiodurans Bacteria

PprA Protein Is Involved in Chromosome Segregation via Its Physical and Functional Interaction with DNA Gyrase in Irradiated Deinococcus radiodurans Bacteria

Tandem mass spectrometry and proteomic data interpretation. The protein samples obtained by coimmunoprecipitation with the PprA::HA protein were heated at 95°C for 5 min and then loaded onto a 10% NuPAGE gel (Invitrogen) for a short electrophoresis in MOPS (morpholinepropanesulfonic acid) buffer. The proteins were briefly stained with Coomassie blue safe stain (Invitrogen). Polyacrylamide bands containing the whole enriched subproteomes were processed as previously described for further destaining and iodoacetamide treatments (57). Samples were subjected for 4 h to proteolysis at 37°C with 10 ng/ ␮l of sequencing-grade trypsin (Roche) in 50 mM NH 4 HCO 3 and 0.01% ProteaseMAX surfactant (Promega) to maximize peptide recovery as described previously (58). The reactions were stopped with 0.5% (final) trifluoroacetic acid. The resulting peptides (10 ␮l of the 40 ␮l generated with the procedure) were analyzed with an LTQ-Orbitrap XL hybrid mass spectrometer (Thermo Fisher) coupled to an UltiMate 3000 NanoLC system (Dionex-LC Packings) operating a reverse-phase Acclaim PepMap100 C 18 ␮-precolumn (5 ␮m, 100 Å, 300-␮m inner diameter by 5 mm; Dionex) and a nanoscale Acclaim PepMap100 C 18 capillary column (3 ␮m, 100 Å, 75 ␮m-inner diameter by 15 cm; Dionex) as described previously (59). Peptide mixtures (10 ␮l) were desalted on-line and then resolved at a flow rate of 0.3 ␮l per min using a 90-min gradient from 5 to 60% solvent B (0.1% HCOOH–80% CH 3 CN) with 0.1% HCOOH–100% H 2 O as solvent A. The linear trap quadrupole (LTQ)-Orbitrap XL mass spectrometer was recalibrated internally in real time with polydimethylcyclosiloxane ions generated from ambient air in the electrospray process {monoprotonated [(CH 3 ) 2 SiO] 6 with m/z of 445.120024} and operated in data- dependent mode using the TOP3 strategy as described previously (60). In brief, a scan cycle was initiated with a full scan of high mass accuracy from m/z 300 to 1,800 in the Orbitrap analyzer at a resolution of 30,000, followed by MS-MS scans in the LTQ linear ion trap on the three most abundant precursor ions, with dynamic exclusion of previously selected ions. Peak lists were generated using the Mascot Daemon software (Matrix Science), and MS-MS spectra were assigned with the MASCOT search engine (version 2.2.04; Matrix Science) as described previously (58). The in-house D. radiodurans protein sequence database (36) comprised 3,311 polypeptide sequences, totaling 1,006,757 amino acids. Peptides were identified with a P value threshold below 0.05. Protein spectral counts were normalized as described in Liu et al. (61) by systematically adding one spectral count to all experimental values. These normalized values were then compared with the Tfold or the ACfold modules of the PatternLab software (62).
En savoir plus

18 En savoir plus

Cell morphology and nucleoid dynamics in dividing Deinococcus radiodurans

Cell morphology and nucleoid dynamics in dividing Deinococcus radiodurans

Nucleoid conformations were assessed in Syto9 and Nile Red- stained wild-type D. radiodurans cells and representative shapes of nucleoids were retrieved for each phase of the cell cycle (Fig. 3 ). In addition, time-lapse 3D imaging of either Syto9-stained nucleoids (Supplementary Movie 2) or HU-mCherry-expressing D. radiodurans (Supplementary Movie 3) was performed during a complete cell cycle to determine the chronological order in which these different conformations appeared. These videos clearly highlight the dynamic nature of the nucleoids. In Phases 1 and 2, a majority of nucleoids (respectively 52% and 42%) adopted toroidal shapes with an average diameter of 0.95 ± 0.10 µm (Supplementary Fig. 2). In addition, in Phase 1, a substantial fraction (28%) of nucleoids were found to form condensed, undefined structures, which were seen to be short-lived (minutes) in our time-lapses and rapidly became toroids, which appeared to be more stable and long-lasting. Due to the reduced resolution of the spinning-disk images in the Z-axis, we cannot rule out that these undefined structures may correspond to top views of toroids with an interior ring size below the resolution limit of the images. In Phase 2, 16% of nucleoids presented a square configuration with bright vertices and a significant fraction (21%) also adopted a more open configuration (open ring or crescent). In Phase 3, these two nucleoid configurations were found to be the most prevalent (respectively 25% and 30%) and the crescent-shaped nucleoids were positioned with their convex sides facing the S -1
En savoir plus

14 En savoir plus

Experimental and statistical analysis of nutritional requirements for the growth of the extremophile Deinococcus geothermalis DSM 11300

Experimental and statistical analysis of nutritional requirements for the growth of the extremophile Deinococcus geothermalis DSM 11300

provide carbon and nitrogen sources, phosphorous and sulfur, salts, oligo-elements and sometimes growth factors like vitamin(s) etc. Few results concerning nutritional requirements of Deinococcus geothermalis have been published to date (Ferreira et al. 1997 ; Brim et al. 2003 ; Kongpol et al. 2008 ). A multifactorial statistical analysis was chosen to compare the compo- sition of the different defined media described for the culture of several strains of Deinococcus radiodurans, Deinococcus geothermalis and Micrococcus. Initially, D. radiodurans was named M. radiodurans because of its similarity to strains of the genus Micrococcus. In 1981, research on M. radiodurans properties showed that this strain had to be renamed and classified in a new genus, Deinococcus (Brooks and Murray 1981 ). D. radiodurans is the main mesophile strain of Dei- nococcus and is the most studied strain of Deinococc- aceae. Most of the chemically defined medium has been designed for the growth of D. radiodurans. As described previously, PCA was chosen for this statis- tical analysis. PCA helped providing a graphical rep- resentation of the data and evaluating the main factors (defined medium components) that had a significant influence on the growth of Deinococcus and Micro- coccus strains.
En savoir plus

14 En savoir plus

Proteomics-based Refinement of Deinococcus deserti Genome Annotation Reveals an Unwonted Use of Non-canonical Translation Initiation Codons

Proteomics-based Refinement of Deinococcus deserti Genome Annotation Reveals an Unwonted Use of Non-canonical Translation Initiation Codons

Mathieu Baudet‡, Philippe Ortet§¶ 储, Jean-Charles Gaillard‡, Bernard Fernandez‡, Philippe Gue´rin‡, Christine Enjalbal**, Gilles Subra**, Arjan de Groot§¶ 储, Mohamed Barakat§¶ 储, Alain Dedieu‡, and Jean Armengaud‡ ‡‡ Deinococcaceae are a family of extremely radiation-toler- ant bacteria that are currently subjected to numerous studies aimed at understanding the molecular mecha- nisms for such radiotolerance. To achieve a comprehen- sive and accurate annotation of the Deinococcus deserti genome, we performed an N terminus-oriented charac- terization of its proteome. For this, we used a labeling reagent, N-tris(2,4,6-trimethoxyphenyl)phosphonium acetyl succinimide, to selectively derivatize protein N termini. The large scale identification of N-tris(2,4,6-trimethoxy- phenyl)phosphonium acetyl succinimide-modified N-ter- minal-most peptides by shotgun liquid chromatography- tandem mass spectrometry analysis led to the validation of 278 and the correction of 73 translation initiation codons in the D. deserti genome. In addition, four new genes were detected, three located on the main chromo- some and one on plasmid P3. We also analyzed signal peptide cleavages on a genome-wide scale. Based on comparative proteogenomics analysis, we propose a set of 137 corrections to improve Deinococcus radiodurans and Deinococcus geothermalis gene annotations. Some of these corrections affect important genes involved in DNA repair mechanisms such as polA, ligA, and ddrB. Surprisingly, experimental evidences were obtained indi- cating that DnaA (the protein involved in the DNA replica- tion initiation process) and RpsL (the S12 ribosomal con- served protein) translation is initiated in Deinococcaceae
En savoir plus

13 En savoir plus

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

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

damage including double-strand breaks, which are the most deleterious to the organism (Mattimore & Battista, 1996). Bacteria belonging to the genus Deinococcus, in particular the well-studied Deinococcus radiodurans, have the dis- tinctive feature of being the most radiation-tolerant of vegetative cells. D. radiodurans can withstand doses of radiation a thousand times higher than a human can. It can survive doses of radiation that do not exist naturally on Earth. Therefore, it is likely that this radiation tolerance is related to the bacterial response to natural non-radioactive DNA-damaging conditions such as desiccation (Makarova et al., 2001). At the time of writing, eight recognized species belong to the genus Deinococcus (Ferreira et al., 1997; Rainey et al., 1997; Suresh et al., 2004). Three other species have been described very recently, ‘Deinococcus frigens’, ‘Deino- coccus saxicola’ and ‘Deinococcus marmoris’ (Hirsch et al., 2004). Only D. radiodurans R 1 T has been studied extensively.
En savoir plus

7 En savoir plus

Quantitative Characterization of the Growth of Deinococcus geothermalis DSM-11302: Effect of Inoculum Size, Growth Medium and Culture Conditions

Quantitative Characterization of the Growth of Deinococcus geothermalis DSM-11302: Effect of Inoculum Size, Growth Medium and Culture Conditions

Keywords: Deinococcus geothermalis; strain variability; physiology; growth performances 1. Introduction Bacteria belonging to the Deinococcaceae family possess very interesting properties as they are well-known for being the most radiation-resistant bacteria. Deinococcus species can survive and repair their genome even after an exposition to high radiation levels [1,2] or other environmental stress agents including ultraviolet light, oxidative stress and desiccation [3–5]. Their ability to tolerate high temperatures, a broad range of pH and chemicals compounds make Deinococcaceae good candidates for production of bioenergy products such as bioethanol and metabolites derivatives [6]. To implement biological processes involving Deinococcus strains, a better understanding of their physiology in a bioreactor culture on a minimal medium is required. The most studied strains of Deinococcaceae are the mesophile one, Deinococcus radiodurans and the thermophilic one, Deinococcus geothermalis.
En savoir plus

24 En savoir plus

Crystal structure of the transcriptional repressor DdrO: insight into the metalloprotease/repressor-controlled radiation response in Deinococcus

Crystal structure of the transcriptional repressor DdrO: insight into the metalloprotease/repressor-controlled radiation response in Deinococcus

Exposure to harmful conditions such as radiation and desiccation induce oxidative stress and DNA damage. In radiation-resistant Deinococcus bacteria, the radiation /desiccation response is controlled by two proteins: the XRE family transcriptional repres- sor DdrO and the COG2856 metalloprotease IrrE. The latter cleaves and inactivates DdrO. Here, we report the biochemical characterization and crystal struc- ture of DdrO, which is the first structure of a XRE protein targeted by a COG2856 protein. DdrO is com- posed of two domains that fold independently and are separated by a flexible linker. The N-terminal do- main corresponds to the DNA-binding domain. The C-terminal domain, containing three alpha helices ar- ranged in a novel fold, is required for DdrO dimeriza- tion. Cleavage by IrrE occurs in the loop between the last two helices of DdrO and abolishes dimeriza- tion and DNA binding. The cleavage site is hidden in the DdrO dimer structure, indicating that IrrE cleaves DdrO monomers or that the interaction with IrrE in- duces a structural change rendering accessible the cleavage site. Predicted COG2856 /XRE regulatory protein pairs are found in many bacteria, and avail- able data suggest two different molecular mecha- nisms for stress-induced gene expression: COG2856
En savoir plus

16 En savoir plus

Structural Investigation of the Thermostability and Product Specificity of Amylosucrase from the Bacterium Deinococcus geothermalis

Structural Investigation of the Thermostability and Product Specificity of Amylosucrase from the Bacterium Deinococcus geothermalis

AS that were characterized so far are produced by various species from the genus Neisseria (4), Deinococcus (14, 15), and Alteromonas (16). However, Neisseria polysaccharea amylosu- crase (NpAS) is the only AS for which several structures, alone or in complex with sucrose substrate or products, are available to date (17–20). The three-dimensional structure of NpAS is organized in five domains, namely A, B, C, N, and B ⬘. B⬘ and N domains are only found in AS, whereas the three other domains are conserved among GH13 enzymes. Although the potential of NpAS for glycodiversification is large, this enzyme suffers from a low catalytic efficiency and a weak thermostability, limiting its industrial development (15). Directed evolution has been attempted to improve NpAS catalytic efficiency and thermosta- bility (21). Searching for more thermostable and efficient enzymes in the natural diversity is another alternative that has motivated the biochemical characterization of the amylosu- crases from Deinococcus geothermalis (DgAS) (15), Deinococ-
En savoir plus

14 En savoir plus

Growth of the extremophilic Deinococcus geothermalis DSM 11302 using co-substrate fed-batch culture

Growth of the extremophilic Deinococcus geothermalis DSM 11302 using co-substrate fed-batch culture

Abstract Deinococcus geothermalis metabolism has been scarcely studied to date, although new developments on its utilization for bioremediation have been carried out. So, large- scale production of this strain and a better understanding of its physiology are required. A fed-batch experiment was con- ducted to achieve a high cell density non-limiting culture of D. geothermalis DSM 11302. A co-substrate nutritional strat- egy using glucose and yeast extract was carried out in a 20-L bioreactor in order to maintain a non-limited growth at a maximal growth rate of 1 h −1 at 45 °C. Substrate supplies
En savoir plus

11 En savoir plus

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

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

increase of their translation and/or to protein-protein or protein-DNA interactions that increase their stability. We have shown that DdrB and SSB are clearly accu- mulating in large quantities in the very earliest stages after irradiation, at least in our experimental conditions. These two single-stranded DNA binding proteins are probably of high importance to protect ssDNA that is formed after massive DNA damage and/or to initiate genome reconstitution by recruitment of other DNA re- pair proteins. That they are both up-regulated at the same early stage may indicate that they work concomi- tantly. Interestingly, Xu et al. [19] have recently shown that both proteins interact in vitro. Another recent study reported that DdrB is involved in DNA repair through a single-strand annealing (SSA) process that precedes the Extended Synthesis-Dependent Strand Annealing (ESDSA) [12]. Finally, the specific post-translational modifications of GyrA detected from irradiated samples raises the importance of post-translational modifications of the Deinococcus proteome upon DNA damages. Whether the resulting heterogeneity impacts the cellular response is an open question.
En savoir plus

15 En savoir plus

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

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

prediction error in D. deserti (Figure 2A). Deide_19980 was first predicted on the forward strand. As four identified peptides correspond exactly to the polypeptide encoded on the reverse strand at the same locus, we corrected the orientation of this gene and replaced Deide_19980 with Deide_19972 in the opposite orientation. Remarkably, comparative genomics with D. radio- durans and D. geothermalis suggests various prediction errors in these species as well (Table 2). For example, we found four different peptides substantiating the existence of Deide_15980, initially thought to be a D. deserti-specific protein (Figure S1). However, protein sequences highly homologous to Deide_15980 are found when DR_0869 (D. radiodurans) and Dgeo_0511 (D. geothermalis) are translated in the reverse direction. Therefore, DR_0869 and Dgeo_0511 should be reassessed, possibly reversing their orienta- tion. D. deserti’s genome was further manually scrutinized for such errors. For 35 D. deserti genes, previously unpredicted homologs were identified in D. radiodurans and/or D. geothermalis, and these include nine additional instances of reversal of gene orientation (Table 2). Twenty-six of the conserved but differently annotated loci are present in each of the three sequenced Deinococcus genomes. Interestingly, two of these correspond to DNAdamage response genes ddrC (DR_0003; Dgeo_0047) and ddrH (DR_0438). Their gene products have not been characterized, but DR_0003 has been inactivated, resulting in decreased radiation resistance [11]. Homologs of the reported DdrC and DdrH proteins were not found in the D. deserti protein database. However, when the orientations of DR_0003 and Dgeo_0047 are reversed, proteins highly homologous to Deide_23280 are found (Figures 2B and S2). The data strongly suggest that DR_0003 and Dgeo_0047 were incorrectly annotated and that Deide_23280 and its homologs are the correct genes. Indeed, Deide_23280 and homologs are much more similar to each other than the DR_0003 homologs (Figure S2); specific RT-PCR experiments showed that Deide_23280 is transcribed in D. deserti (Figure S3); and a palindromic motif identified in the upstream regions of genes that are induced upon radiation/desiccation [8] is present upstream of Deide_23280 and its two homologs (Figure 2B). For ddrH, a homolog of DR_0438 was not found in D. geothermalis [8]. However, if DR_0438 is transcribed from the opposite DNA strand, homologs are found in D. geothermalis (Dgeo_0322) and D. deserti (Deide_20641). These protein similarities suggest that Deide_20641 and Dgeo_0322 are the correctly annotated ddrH (Figure S4). The sequences of the bona fide DdrC, DdrH and the other newly recognized Deinococcus-specific proteins (Table 2) do not contain any described domain or motif. Characterization of their function and structure requires further experimental analysis.
En savoir plus

13 En savoir plus

Show all 16 documents...