Ionizing-radiation-resistant Kocuria rhizophila PT10 isolated from the Tunisian Sahara xerophyte Panicum turgidum: Polyphasic characterization and proteogenomic arsenal.

A new strain belonging to the genus Kocuria, designed PT10, was isolated from irradiated roots of the xerophyte Panicum turgidum. Isolate PT10 is a Gram-positive, coccoid, aerobic and ionizing-radiation (IR)-resistant actinobacterium. PT10 has shown an ability to survive under extreme conditions, such as gamma irradiation, desiccation and high concentration of hydrogen peroxide. Phenotypic, chemotaxonomic and comparative genome analyses support the assignment of strain PT10 (LMG 31102 = DSM 108617) as Kocuria rhizophila. The complete genome sequence of PT10 consists of one chromosome (2,656,287 bps), with a 70.7% G + C content and comprises 2481 protein-coding sequences. A total of 1487 proteins were identified by LC-MS/MS profiling. In silico analyses revealed that the proteome of the oxidation-tolerant PT10 possesses several features explaining its IR-resistant phenotype and many adaptive pathways implicated in response to environmental pressures - desiccation, cold, reactive oxygen species and other stressors.

Draft genome sequence of Promicromonospora panici sp. nov., a novel ionizing-radiation-resistant actinobacterium isolated from roots of the desert plant Panicum turgidum.

A novel strain of the genus Promicromonospora, designated PT9T, was recovered from irradiated roots of the xerophyte Panicum turgidum collected from the Ksar Ghilane oasis in southern Tunisia. Strain PT9T is aerobic, non-spore-forming, Gram- positive actinomycete that produces branched hyphae and forms white to yellowish-white colonies. Chemotaxonomic features, including fatty acids, whole cell sugars and polar lipid profiles, support the assignment of PT9T to the genus Promicromonospora. The genomic relatedness indexes based on DNA-DNA hybridization and average nucleotide identity values revealed a significant genomic divergence between strain PT9T and all sequenced type strains of the taxon. Phylogenomic analysis showed that isolate PT9T was most closely related to Promicromonospora soli CGMCC 4.7398T. Phenotypic and phylogenomic analyses suggest that isolate PT9T represents a novel species of the genus Promicromonospora, for which the name Promicromonospora panici sp. nov. is proposed. The type strain is PT9T (LMG 31103T = DSM 108613T).The isolate PT9T is an ionizing-radiation-resistant actinobacterium (D10 value = 2.6 kGy), with resistance to desiccation and hydrogen peroxide. The complete genome sequence of PT9T consists of 6,582,650 bps with 71.2% G+C content and 6291 protein-coding sequences. This genome will help to decipher the microbial genetic bases for ionizing-radiation resistance mechanisms including the response to oxidative stress.

Effect of gamma irradiation on the proteogenome of cold-acclimated Kocuria rhizophila PT10.

The effects of ionizing radiation (IR) on the protein dynamics of cold-stressed cells of a radioresistant actinobacterium, Kocuria rhizophila PT10, isolated from the rhizosphere of the desert plant Panicum turgidum were investigated using a shotgun methodology based on nanoflow liquid chromatography coupled to tandem mass spectrometry. Overall, 1487 proteins were certified, and their abundances were compared between the irradiated condition and control. IR of cold-acclimated PT10 triggered the over-abundance of proteins involved in (1) a strong transcriptional regulation, (2) amidation of peptidoglycan and preservation of cell envelope integrity, (3) detoxification of reactive electrophiles and regulation of the redox status of proteins, (4) base excision repair and prevention of mutagenesis and (5) the tricarboxylic acid (TCA) cycle and production of fatty acids. Also, one of the more significant findings to emerge from this study is the SOS response of stressed PT10. Moreover, a comparison of top hits radio-modulated proteins of cold-acclimated PT10 with proteomics data from gamma-irradiated Deinococcus deserti showed that stressed PT10 has a specific response characterised by a high over-abundance of NemA, GatD, and UdgB.

Roots of the xerophyte Panicum turgidum host a cohort of ionizing-radiation-resistant biotechnologically-valuable bacteria.

Bacterial communities associated with roots of Panicum turgidum, exposed to arid conditions, were investigated with a combination of cultural and metataxonomic approaches. Traditional culture-based techniques were used and 32 isolates from the irradiated roots were identified as belonging to Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria phyla. Four actinobacterial strains were shown to be ionizing-radiation (IR)-resistant: Microbacterium sp. PT8 (4.8 kGy (kGy)), Micrococcus sp. PT11 (4.4 kGy), Kocuria rhizophila PT10 (2.9 kGy) and Promicromonospora panici PT9T (2.6 kGy), based on the D10 dose necessary for a 90% reduction in colony forming units (CFU). Concerning the investigation of microbial communities in situ, metataxonomic analyses of the diversity of IR-resistant microorganisms associated with irradiated roots revealed a marked dominance of Actinobacteria (46.6%) and Proteobacteria (31.5%) compared to Bacteroidetes (4.6%) and Firmicutes (3.2%). Gamma irradiation not only changed the structure of bacterial communities, but also affected their functional properties. Comparative analyses of metabolic profiles indicated the induction of several pathways related to adaptation to oxidative stress in irradiated roots, such as DNA repair, secondary metabolites synthesis, reactive oxygen species (ROS)-mitigating enzymes, etc. P. turgidum is emblematic of desert-adapted plants. Until now, there is no other work that has focused on the microbial profile of irradiated roots of this xerophyte.

Effect of Gamma Irradiation on Enhanced Biological Activities of Exopolysaccharide from Halomonas desertis G11: Biochemical and Genomic Insights.

In this work, a native exopolysaccharide (nEPS) produced by Halomonas desertis G11 isolated from a Tunisian extreme environment was modified by gamma irradiation. Characterization as well as the antioxidant and antitumor activities of nEPS and its gamma-irradiated derivatives (iEPSs) were comparatively evaluated. In vitro and in vivo antioxidant potentials were determined by using different methods and through different antioxidant enzymes. The antitumor activity was checked against a human colon cancer cell line. Analyses of the complete genome sequence were carried out to identify genes implicated in the production of nEPS. Thus, the genomic biosynthesis pathway and the export mechanism of nEPS were proposed. Analyses of irradiation data showed that iEPSs acquired new functional groups, lower molecular weights, and gained significantly (p < 0.05) higher antioxidant and antitumor abilities compared with nEPS. These findings provide a basis for using iEPSs as novel pharmaceutical agents for human therapies.

Polyphenolic extracts from the xerophyte Rhamnus lycioides as a radiation biodosimeter.

The majority of dosimeters currently in use are synthetic and very expensive. Therefore, the study of the dosimetric characteristics of polyphenolic extracts of xerophytes is useful because drought stress causes an increase in the production of these cheap and natural compounds containing benzene rings. Here, the polyphenolic compounds were extracted from Rhamnus lycioides which was collected from Bou-Hedma National Park in Tunisia and identified using liquid chromatography-mass spectrometry (LC-MS). We investigated the impact of cobalt-60 (60Co) irradiation (0-30 kilogray (kGy)) on the color parameters of polyphenolic extracts of R. lycioides using the Konica Minolta CR 300 portable colorimeter and UV-Visible spectroscopy. The structural and morphological characteristics of the irradiated extracts were assessed using Fourier transform infrared (FT-IR) spectroscopy, X-ray diffraction (XRD) technique and scanning electron microscopy (SEM). Overall, our results suggest that exposure to ionizing radiation (IR) of the polyphenolic components of the xerophyte R. lycioides has produced significant dose-dependent changes in their optical and morphological properties. Thus, these extracts can be valorized as biodosimeters in the dose range from 5 to 25 kGy.

Radiation-inducible radioprotective exopolysaccharides of Bacillus siamensis CV5 from irradiated roots of Cistanche violacea to decrease free radical damage produced by ionizing radiation.

Purpose: To assess exopolysaccharides (EPS) of Bacillus siamensis CV5, isolated from irradiated roots of Cistanche violacea, for their induction by ionizing radiation (IR) and their antioxidant and radioprotective power.Materials and methods: Isolated bacteria from the roots of C. violacea were screened for EPS production. The most EPS-producing bacterium was selected and the response surface methodology (RSM) was applied to elucidate the IR dose effects on EPS production. Gamma irradiation effects on the morphology and functional groups of EPS were studied using microscopy and Fourier transform infra-red (FT-IR). The radioprotective potential of EPS on the survival of B. siamensis CV5 following IR was evaluated using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Free radicals scavenging potentialities (FRSP) of non-irradiated and irradiated EPS were evaluated through 2, 2--diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid (ABTS) and ferric reducing ability of plasma (FRAP) assays.Results: Twenty strains, isolated from irradiated roots of C. violacea, were screened for their EPS production. IR-resistant B. siamensis CV5 was the most EPS-producing strain. Its purified EPS contained rhamnose, fructose, mannose and glucose. RSM indicated that EPS of CV5 (CV5-EPS) are radiation inducible. Micrographs of CV5-EPS suggested an increase in the total area and a decrease in the Feret's statistical diameter following exposure to IR. FT-IR spectra of these EPS revealed an increase of various functional groups. The MTT survival assay demonstrated a positive correlation between the added quantity of CV5-EPS and the viability of irradiated CV5 (p < .01). DPPH, ABTS and FRAP assays indicated that the antioxidant activities of CV5-EPS increased significantly with the irradiation dose (p < .01).Conclusions: CV5-EPS were demonstrated as radiation-inducible and radioprotective biomolecules. This radioprotective potential of CV5-EPS could be associated with their antioxidant activities. In the future, irradiated EPS could be tested as a gel in cancer radiotherapy for minimizing the damage caused by rays to surrounding healthy tissues.

The PEG-responding desiccome of the alder microsymbiont Frankia alni.

Actinorhizal plants are ecologically and economically important. Symbiosis with nitrogen-fixing bacteria allows these woody dicotyledonous plants to colonise soils under nitrogen deficiency, water-stress or other extreme conditions. However, proteins involved in xerotolerance of symbiotic microorganisms have yet to be identified. Here we characterise the polyethylene glycol (PEG)-responding desiccome from the most geographically widespread Gram-positive nitrogen-fixing plant symbiont, Frankia alni, by next-generation proteomics, taking advantage of a Q-Exactive HF tandem mass spectrometer equipped with an ultra-high-field Orbitrap analyser. A total of 2,052 proteins were detected and quantified. Under osmotic stress, PEG-grown F. alni cells increased the abundance of envelope-associated proteins like ABC transporters, mechano-sensitive ion channels and Clustered Regularly Interspaced Short Palindromic Repeats CRISPR-associated (cas) components. Conjointly, dispensable pathways, like nitrogen fixation, aerobic respiration and homologous recombination, were markedly down-regulated. Molecular modelling and docking simulations suggested that the PEG is acting on Frankia partly by filling the inner part of an up-regulated osmotic-stress large conductance mechanosensitive channel.