RadA: A protein involved in DNA damage repair processes of Deinococcus radiodurans R1

In search of the pH limit of growth in halo-alkaliphilic cyanobacteria

Cyanobacteria have many biotechnological applications. Increasing their cultivation pH can assist in capturing carbon dioxide and avoiding invasion by other organisms. However, alkaline media may have adverse effects on cyanobacteria, such as reducing the Carbon-Concentrating Mechanism's efficiency. Here, we cultivated two halo-alkaliphilic cyanobacteria consortia in chemostats at pH 10.2-11.4. One consortium was dominated by Ca. Sodalinema alkaliphilum, the other by a species of Nodosilinea. These two cyanobacteria dominate natural communities in Canadian and Asian alkaline soda lakes. We show that increasing the pH decreased biomass yield. This decrease was caused, in part, by a dramatic increase in carbon transfer to heterotrophs. At pH 11.4, cyanobacterial growth became limited by bicarbonate uptake, which was mainly ATP dependent. In parallel, the higher the pH, the more sensitive cyanobacteria became to light, resulting in photoinhibition and upregulation of DNA repair systems.

Molecular mechanism of engineered Zymomonas mobilis to furfural and acetic acid stress

Acetic acid and furfural (AF) are two major inhibitors of microorganisms during lignocellulosic ethanol production. In our previous study, we successfully engineered Zymomonas mobilis 532 (ZM532) strain by genome shuffling, but the molecular mechanisms of tolerance to inhibitors were still unknown. Therefore, this study investigated the responses of ZM532 and its wild-type Z. mobilis (ZM4) to AF using multi-omics approaches (transcriptomics, genomics, and label free quantitative proteomics). Based on RNA-Seq data, two differentially expressed genes, ZMO_RS02740 (up-regulated) and ZMO_RS06525 (down-regulated) were knocked out and over-expressed through CRISPR-Cas technology to investigate their roles in AF tolerance. Overall, we identified 1865 and 14 novel DEGs in ZM532 and wild-type ZM4. In contrast, 1532 proteins were identified in ZM532 and wild-type ZM4. Among these, we found 96 important genes in ZM532 involving acid resistance mechanisms and survival rates against stressors. Furthermore, our knockout results demonstrated that growth activity and glucose consumption of mutant strains ZM532∆ZMO_RS02740 and ZM4∆ZMO_RS02740 decreased with increased fermentation time from 42 to 55 h and ethanol production up to 58% in ZM532 than that in ZM532∆ZMO_RS02740. Hence, these findings suggest ZMO_RS02740 as a protective strategy for ZM ethanol production under stressful conditions.

Genomic analysis of Paenibacillus sp. MDMC362 from the Merzouga desert leads to the identification of a potentially thermostable catalase

Microorganisms in hot deserts face heat and other environmental conditions, such as desiccation, UV radiation, or low nutrient availability. Therefore, this hostile environment harbour microorganisms with acquired characteristics related to survival in their habitat, which can be exploited in biotechnology. In this work, the genome of Paenibacillus sp. MDMC362 isolated from the Merzouga desert in Morocco was sequenced to understand its survival strategy's genetic basis; and to evaluate the thermostability of a catalase extracted from genomic annotation files using molecular dynamics. Paenibacillus sp. MDMC362 genome was rich in genetic elements involved in the fight against different stresses, notably temperature stress, UV radiations, osmotic stress, carbon starvation, and oxidative stress. Indeed, we could identify genes of the operons groES-groEL and hrcA-grpE-dnaK and those involved in the different stages of sporulation, which can help the bacteria to survive the high temperatures imposed by a desertic environment. We also observed the genetic components of the UvrABC system and additional mechanisms involved in DNA repair, which help overcome UV radiation damage. Other genes have been identified in the genome, like those coding for ectoine and proline, that aids fight osmotic stress and desiccation. Catalase thermostability investigation using molecular dynamics showed that the protein reached stability and conserved its compactness at temperatures up to 373.15 K. These results suggest a potential thermostability of the enzyme. Since the studied protein is a core protein, thermostability could be conserved among Paenibacillus sp. MDMC362 closely related strains; however, bacteria from harsh environments may have a slight advantage regarding protein stability.

Transcriptome analysis reveals manganese tolerance mechanisms in a novel native bacterium of Bacillus altitudinis strain HM-12

Bacillus altitudinis HM-12, isolated from ferromanganese ore tailings, can resist up to 1200 mM Mn(II) when exposed to concentrations from 50 mM to 1400 mM. HM-12 exhibited high Mn(II) removal efficiency (90.6 %). We report the transcriptional profile of HM-12 using RNA-Seq and found 423 upregulated and 536 downregulated differentially expressed genes (DEGs) compared to the control. Gene Ontology analysis showed that DEGs were mainly linked with transporter activity, binding, catalytic activity in molecular function, cellular anatomical entity in cellular component, cellular process, and metabolic process. Kyoto Encyclopedia of Genes and Genomes analysis showed that DEGs were mostly mapped to membrane transport, signal transduction, carbohydrate and amino acid metabolism, energy metabolism, and cellular community pathways. Transport analysis showed that two manganese importer systems, mntH and mntABC, were significantly downregulated. The manganese efflux genes (mneS, yceF and ykoY) exhibited significant upregulation. Manganese homeostasis seems to be subtly regulated by manganese uptake and efflux genes. Moreover, it was found that copA as a Mn(II) oxidase gene and a copper chaperone gene copZ were considerably upregulated by signal transduction analysis. csoR encoding a transcriptional repressor which can regulate the copZA operon was upregulated. The strong Mn(II) oxidizing activity of HM-12 was also confirmed by physicochemical characterization. In metabolism and environmental information processing, yjqC encoding manganese catalase was significantly upregulated, while katE and katX encoding heme catalases were significantly downregulated. The antioxidant gene pcaC was significantly upregulated, but ykuU encoding alkyl hydroperoxide reductase, yojM encoding superoxide dismutase, and perR encoding redox-sensing transcriptional repressor were downregulated. These results highlight the oxidative activity of HM-12 by regulating the transcription of oxidase, catalase, peroxidase, and superoxide dismutase to sense the cellular redox status and prevent Mn(II) intoxication. This study provides relevant information on the biological tolerance and oxidation mechanisms in response to Mn(II) stress.

The Influence of Different Forms of Silver on Selected Pathogenic Bacteria

The application of silver nanoparticles as an antibacterial agent is becoming more common. Unfortunately, their effect on microorganisms is still not fully understood. Therefore, this paper attempts to investigate the influence of silver ions, biologically synthesized silver nanoparticles and nanoparticles functionalized with antibiotics on molecular bacteria profiles. The initial stage of research was aimed at the mechanism determination involved in antibiotics sorption onto nanoparticles' surface. For this purpose, the kinetics study was performed. Next, the functionalized formulations were characterized by Fourier transform infrared spectroscopy (FT-IR), dynamic light scattering (DLS) and a zeta potential study. The results reveal that functionalization is a complex process, but does not significantly affect the stability of biocolloids. Furthermore, the antimicrobial assays, in most cases, have shown no increases in antibacterial activity after nanoparticle functionalization, which suggests that the functionalization process does not always generate the improved antimicrobial effect. Finally, the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) technique was employed to characterize the changes in the molecular profile of bacteria treated with various antibacterial agents. The recorded spectra proved many differences in bacterial lipids and proteins profiles compared to untreated cells. In addition, the statistical analysis of recorded spectra revealed the strain-dependent nature of stress factors on the molecular profile of microorganisms.

Life in High Salt Concentrations with Changing Environmental Conditions: Insights from Genomic and Phenotypic Analysis of Salinivibrio sp

Life in salt pans with varying chemical compositions require special adaptation strategies at both the physiological and molecular level. The Marakkanam salt pan in South India is characterized with a high fluctuation in salinity (19–490 ppt), Ultravioletradiation, and heavy metal concentrations. Several bacterial species have been isolated and identified in the view of phylogenetic analysis and for the subsequent production of industrially important enzymes. However, limited information exists on the genomic basis of their survival under variable environmental conditions. To this extent, we sequenced the whole genome of the Salinivibrio sp. HTSP, a moderately halophilic bacterium. We analysed the physiological and genomic attributes of Salinivibrio sp. HTSP to elucidate the strategies of adaptation under various abiotic stresses. The genome size is estimated to be 3.39 Mbp with a mean G + C content of 50.6%, including 3150 coding sequences. The genome possessed osmotic stress-related coding sequences, and genes involved in different pathways of DNA repair mechanisms and genes related to the resistance to toxic metals were identified. The periplasmic stress response genes and genes of different oxidative stress mechanisms were also identified. The tolerance capacity of the bacterial isolates to heavy metals, UV-radiation, and salinity was also confirmed through appropriate laboratory experiments under controlled conditions.

Replacing water and nutrients for ethanol production by ARTP derived biogas slurry tolerant Zymomonas mobilis strain

BACKGROUND

Reducing fresh water consumption and nutrient addition will be an effective way to reduce the whole cost of bioethanol production. On the other hand, treatment of biogas slurry derived from anaerobic digestion (AD), in which a great amount of nutrients is still left, costs too much to remove these pollutants. It would be beneficial for both digestate valorization and ethanol production if biogas slurry is used for producing bioethanol. However, both hyperosmosis and potential biotoxic components of the biogas slurry can severely inhibit fermentation.

RESULTS

In this study, two rounds of atmospheric and room temperature plasma (ARTP) mutagenesis combined with adaptive laboratory evolution (ALE) were applied to improve the adaptability and genetic stability of Zymomonas mobilis in biogas slurry. Mutants D95 and S912 were identified. Growth of the mutants was remarkably improved in biogas slurry. The highest ethanol productivity reached 0.63 g/L/h which was 61.7% higher than ZM4 (0.39 g/L/h). Genomic re-sequencing results also revealed that single nucleic variations (SNVs) and Indels occurred in the mutants, which are likely related to inhibitor in biogas slurry and low pH tolerance.

CONCLUSIONS

Our study demonstrated that these mutant strains have great potential to produce ethanol using biogas slurry to replace fresh water and nutrients.

Conservation and diversity of radiation and oxidative stress resistance mechanisms in Deinococcus species

Deinococcus bacteria are famous for their extreme resistance to ionising radiation and other DNA damage- and oxidative stress-generating agents. More than a hundred genes have been reported to contribute to resistance to radiation, desiccation and/or oxidative stress in Deinococcus radiodurans. These encode proteins involved in DNA repair, oxidative stress defence, regulation and proteins of yet unknown function or with an extracytoplasmic location. Here, we analysed the conservation of radiation resistance-associated proteins in other radiation-resistant Deinococcus species. Strikingly, homologues of dozens of these proteins are absent in one or more Deinococcus species. For example, only a few Deinococcus-specific proteins and radiation resistance-associated regulatory proteins are present in each Deinococcus, notably the metallopeptidase/repressor pair IrrE/DdrO that controls the radiation/desiccation response regulon. Inversely, some Deinococcus species possess proteins that D. radiodurans lacks, including DNA repair proteins consisting of novel domain combinations, translesion polymerases, additional metalloregulators, redox-sensitive regulator SoxR and manganese-containing catalase. Moreover, the comparisons improved the characterisation of several proteins regarding important conserved residues, cellular location and possible protein–protein interactions. This comprehensive analysis indicates not only conservation but also large diversity in the molecular mechanisms involved in radiation resistance even within the Deinococcus genus.

Genome shuffling enhances stress tolerance of Zymomonas mobilis to two inhibitors

BACKGROUND

Furfural and acetic acid are the two major inhibitors generated during lignocellulose pretreatment and hydrolysis, would severely inhibit the cell growth, metabolism, and ethanol fermentation efficiency of Zymomonas mobilis. Effective genome shuffling mediated by protoplast electrofusion was developed and then applied to Z. mobilis.

RESULTS

After two rounds of genome shuffling, 10 different mutants with improved cell growth and ethanol yield in the presence of 5.0 g/L acetic acid and 3.0 g/L furfural were obtained. The two most prominent genome-shuffled strains, 532 and 533, were further investigated along with parental strains in the presence of 7.0 g/L acetic acid and 3.0 g/L furfural. The results showed that mutants 532 and 533 were superior to the parental strain AQ8-1 in the presence of 7.0 g/L acetic acid, with a shorter fermentation time (30 h) and higher productivity than AQ8-1. Mutant 533 exhibited subtle differences from parental strain F34 in the presence of 3.0 g/L furfural. Mutations present in 10 genome-shuffled strains were identified via whole-genome resequencing, and the source of each mutation was identified as either de novo mutation or recombination of the parent genes.

CONCLUSIONS

These results indicate that genome shuffling is an efficient method for enhancing stress tolerance in Z. mobilis. The engineered strains generated in this study could be potential cellulosic ethanol producers in the future.

The Lon protease-like domain in the bacterial RecA paralog RadA is required for DNA binding and repair

Homologous recombination (HR) plays an essential role in the maintenance of genome integrity. RecA/Rad51 paralogs have been recognized as an important factor of HR. Among them, only one bacterial RecA/Rad51 paralog, RadA, is involved in HR as an accessory factor of RecA recombinase. RadA has a unique Lon protease-like domain (LonC) at its C terminus, in addition to a RecA-like ATPase domain. Unlike Lon protease, RadA's LonC domain does not show protease activity but is still essential for RadA-mediated DNA repair. Reconciling these two facts has been difficult because RadA's tertiary structure and molecular function are unknown. Here, we describe the hexameric ring structure of RadA's LonC domain, as determined by X-ray crystallography. The structure revealed the two positively charged regions unique to the LonC domain of RadA are located at the intersubunit cleft and the central hole of a hexameric ring. Surprisingly, a functional domain analysis demonstrated the LonC domain of RadA binds DNA, with site-directed mutagenesis showing that the two positively charged regions are critical for this DNA-binding activity. Interestingly, only the intersubunit cleft was required for the DNA-dependent stimulation of ATPase activity of RadA, and at least the central hole was essential for DNA repair function. Our data provide the structural and functional features of the LonC domain and their function in RadA-mediated DNA repair.

Mechanisms of Stress Resistance and Gene Regulation in the Radioresistant Bacterium Deinococcus radiodurans

The bacterium Deinococcus radiodurans reveals extraordinary resistance to ionizing radiation, oxidative stress, desiccation, and other damaging conditions. In this review, we consider the main molecular mechanisms underlying such resistance, including the action of specific DNA repair and antioxidation systems, and transcription regulation during the anti-stress response.

Identification of distinctive molecular traits that are characteristic of the phylum "Deinococcus-Thermus" and distinguish its main constituent groups

The phylum "Deinococcus-Thermus" contains two heavily researched groups of extremophilic bacteria: the highly radioresistant order Deinococcales and the thermophilic order Thermales. Very few characteristics are known that are uniquely shared by members of the phylum "Deinococcus-Thermus". Comprehensive phylogenetic and comparative analyses of >65 "Deinococcus-Thermus" genomes reported here have identified numerous molecular signatures in the forms of conserved signature insertions/deletions (CSIs) and conserved signature proteins (CSPs), which provide distinguishing characteristics of the phylum "Deinococcus-Thermus" and its main groups. We have identified 58 unique CSIs and 155 unique CSPs that delineate different phylogenetic groups within the phylum. Of these identified traits, 24 CSIs and 29 CSPs are characteristic of the phylum "Deinococcus-Thermus" and they provide novel and reliable means to circumscribe/describe this phylum. An additional 3 CSIs and 3 CSPs are characteristic of the order Deinococcales, and 6 CSIs and 51 CSPs are characteristic of the order Thermales. The remaining 25 CSIs and 72 CSPs identified in this study are distinctive traits of genus level groups within the phylum "Deinococcus-Thermus". The molecular characteristics identified in this work provide novel and independent support for the common ancestry of the members of the phylum "Deinococcus-Thermus" and provide a new means to distinguish the main constituent clades of the phylum. Additionally, the CSIs and CSPs identified in this work may play a role in the unique extremophilic adaptations of the members of this phylum and further functional analyses of these characteristics could provide novel biochemical insights into the unique adaptations found within the phylum "Deinococcus-Thermus".

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

The extremely radioresistant bacterium Deinococcus radiodurans possesses a rapid and efficient but poorly known DNA damage response mechanism that mobilizes one-third of its genome to survive lethal radiation damage. Deinococcal PprI serves as a general switch to regulate the expression of dozens of proteins from different pathways after radiation, including the DNA repair proteins RecA, PprA and SSB. However, the underlying mechanism is poorly understood. In this study, we analyzed the dynamic alteration in global transcriptional profiles in wildtype and pprI mutant strains by combining microarrays and time-course sampling. We found that PprI up-regulated transcription of at least 210 genes after radiation, including 21 DNA repair and replication-related genes. We purified PprI and a helix-turn-helix (HTH) domain mutant and found that PprI specifically bound to the promoters of recA and pprA in vitro but did not bind nonspecific double-strand DNA. Chromatin immunoprecipitation (ChIP) assays confirmed that PprI specifically interacted with the promoter DNA of recA and pprA after radiation. Finally, we showed that a DNA-binding activity-deficient pprI mutant only partially restored resistance of the pprI mutant strain to γ radiation, UV radiation, and mitomycin C. Taken together, these results indicate that DNA-binding activity is essential for PprI to program the DNA repair process and cellular survival of D. radiodurans in response to radiation damage.

Oxidative stress resistance in Deinococcus radiodurans

Deinococcus radiodurans is a robust bacterium best known for its capacity to repair massive DNA damage efficiently and accurately. It is extremely resistant to many DNA-damaging agents, including ionizing radiation and UV radiation (100 to 295 nm), desiccation, and mitomycin C, which induce oxidative damage not only to DNA but also to all cellular macromolecules via the production of reactive oxygen species. The extreme resilience of D. radiodurans to oxidative stress is imparted synergistically by an efficient protection of proteins against oxidative stress and an efficient DNA repair mechanism, enhanced by functional redundancies in both systems. D. radiodurans assets for the prevention of and recovery from oxidative stress are extensively reviewed here. Radiation- and desiccation-resistant bacteria such as D. radiodurans have substantially lower protein oxidation levels than do sensitive bacteria but have similar yields of DNA double-strand breaks. These findings challenge the concept of DNA as the primary target of radiation toxicity while advancing protein damage, and the protection of proteins against oxidative damage, as a new paradigm of radiation toxicity and survival. The protection of DNA repair and other proteins against oxidative damage is imparted by enzymatic and nonenzymatic antioxidant defense systems dominated by divalent manganese complexes. Given that oxidative stress caused by the accumulation of reactive oxygen species is associated with aging and cancer, a comprehensive outlook on D. radiodurans strategies of combating oxidative stress may open new avenues for antiaging and anticancer treatments. The study of the antioxidation protection in D. radiodurans is therefore of considerable potential interest for medicine and public health.

Proteomic and physiological responses of Kineococcus radiotolerans to copper

Copper is a highly reactive, toxic metal; consequently, transport of this metal within the cell is tightly regulated. Intriguingly, the actinobacterium Kineococcus radiotolerans has been shown to not only accumulate soluble copper to high levels within the cytoplasm, but the phenotype also correlated with enhanced cell growth during chronic exposure to ionizing radiation. This study offers a first glimpse into the physiological and proteomic responses of K. radiotolerans to copper at increasing concentration and distinct growth phases. Aerobic growth rates and biomass yields were similar over a range of Cu(II) concentrations (0–1.5 mM) in complex medium. Copper uptake coincided with active cell growth and intracellular accumulation was positively correlated with Cu(II) concentration in the growth medium (R² = 0.7). Approximately 40% of protein coding ORFs on the K. radiotolerans genome were differentially expressed in response to the copper treatments imposed. Copper accumulation coincided with increased abundance of proteins involved in oxidative stress and defense, DNA stabilization and repair, and protein turnover. Interestingly, the specific activity of superoxide dismutase was repressed by low to moderate concentrations of copper during exponential growth, and activity was unresponsive to perturbation with paraquot. The biochemical response pathways invoked by sub-lethal copper concentrations are exceptionally complex; though integral cellular functions are preserved, in part, through the coordination of defense enzymes, chaperones, antioxidants and protective osmolytes that likely help maintain cellular redox. This study extends our understanding of the ecology and physiology of this unique actinobacterium that could potentially inspire new biotechnologies in metal recovery and sequestration, and environmental restoration.

Deinococcus radiodurans: what belongs to the survival kit?

Deinococcus radiodurans, one of the most radioresistant organisms known to date, is able to repair efficiently hundreds of DNA double- and single-strand breaks as well as other types of DNA damages promoted by ionizing or ultraviolet radiation. We review recent discoveries concerning several aspects of radioresistance and survival under high genotoxic stress. We discuss different hypotheses and possibilities that have been suggested to contribute to radioresistance and propose that D. radiodurans combines a variety of physiological tools that are tightly coordinated. A complex network of regulatory proteins may be discovered in the near future that might allow further understanding of radioresistance.