Abstract: RecA is a highly conserved bacterial protein that plays crucial roles in many cellular processes and hence is a potential target in the chemotherapy of bacterial infections. An understanding of the functional similarity between RecA proteins from different bacterial species should yield further insights into the biochemistry of RecA protein, along with the potential for new approaches to facilitate the improvement of RecA-targeted drugs. In this technical note, the authors present an in silico method based on tri-oligonucleotide usage correlations (TOUC) to predict the functional similarity between two RecA orthologs. The TOUC values analyzed in this study are in good agreement with the available experimental results. This method should prove useful in guiding future experimental efforts aimed at furthering our understanding of the biochemistry of RecA proteins and subsequent development of new drugs that modulate RecA biological activities in bacteria.
Abstract: AIM: To assess esterase profiling of members of Geodermatophilaceae isolated from desert stones and monuments in Tunisia and Egypt. METHODS AND RESULTS: Members of Geodermatophilaceae family isolated from desert stones and monuments in Tunisia and Egypt were characterized by partial 16S rRNA sequences. Twenty-five strains were clustered in three dissimilar groups of the genera Geodermatophilus (12 strains), Blastococcus (5 strains) and Modestobacter (3 strains). Isolates were also screened and typed based on major groups of esterase hydrolytic activity. Their esterase patterns were determined and compared to those of ten reference strains belonging to Geodermatophilaceae family. Strains exhibited a diverse and complex pattern of electrophoretic esterase bands, and 31 haplotypes were obtained for the 35 investigated strains. Esterases produced by members of Geodermatophilaceae family have an optimal activity around 40 degrees C and at pH 8. Esterases from Geodermatophilus strains display a high resistance to thermal inactivation and alkaline pH and retaining 30 and 20% of activity after heating for 20 min at 120 degrees C and at pH 12, respectively, and were completely inactivated after 30 min at 120 degrees C. Enzyme activity has been strongly activated in the presence of Ca(2+)and Mg(2+) ions and moderately by Zn(2+) and was markedly inhibited by Cu(2+) and Co(2+) ions. CONCLUSIONS: Geodermatophilaceae isolates share a rich and particular pool of esterase activities that could be directly linked to harsh conditions characterizing their ecological habitat including high level of aridity, temperature, ionic strength and low nutrient availability. SIGNIFICANCE AND IMPACT OF THE STUDY: Esterase could be considered as enzymatic signature that outlines adaptability of Geodermatophilaceae in arid area.
Abstract: Deinococcus radiodurans possesses a DNA damage response mechanism that acts via the PprI protein to induce RecA and PprA proteins, both of which are necessary in conferring extreme radioresistance. In an effort to further delineate the nature of the DNA damage response mechanism in D. radiodurans, we set out to identify novel components of the PprI-dependent signal transduction pathway in response to radiation stress. Here we demonstrate the discovery of a novel regulatory protein, PprM (a modulator of the PprI-dependent DNA damage response), which is a homolog of cold shock protein (Csp). Disruption of the pprM gene rendered D. radiodurans significantly sensitive to gamma-rays. PprM regulates the induction of PprA but not that of RecA. PprM belongs in a distinct clade of a subfamily together with Csp homologs from D. geothermalis and Thermus thermophilus. Purified PprM is present as a homodimer under physiological conditions, as the case with Escherichia coli CspD. The pprA pprM double-disruptant strain exhibited higher sensitivity than the pprA or pprM single disruptant strains, suggesting that PprM regulates other hitherto unknown protein(s) important for radioresistance besides PprA. This study strongly suggests that PprM is involved in the radiation response mediated by PprI in D. radiodurans.
Abstract: Interactomes of proteins under positive selection from ionizing-radiation-resistant bacteria (IRRB) might be a part of the answer to the question as to how IRRB, particularly Deinococcus radiodurans R1 (Deira), resist ionizing radiation. Here, using the Database of Interacting Proteins (DIP) and the Protein Structural Interactome (PSI)-base server for PSI map, we have predicted novel interactions of orthologs of the 58 proteins under positive selection in Deira and other IRRB, but which are absent in IRSB. Among these, 18 domains and their interactomes have been identified in DNA checkpoint and repair; kinases pathways; energy and nucleotide metabolisms were the important biological processes that were found to be involved. This finding provides new clues to the cellular pathways that can to be important for ionizing-radiation resistance in Deira.
Abstract: BACKGROUND: Ionizing-radiation-resistant bacteria (IRRB) show a surprising capacity for adaptation to ionizing radiation and desiccation. Positive Darwinian selection is expected to play an important role in this trait, but no data are currently available regarding the role of positive adaptive selection in resistance to ionizing-radiation and tolerance of desiccation. We analyzed the four known genome sequences of IRRB (Deinococcus geothermalis, Deinococcus radiodurans, Kineococcus radiotolerans, and Rubrobacter xylanophilus) to determine the role of positive Darwinian selection in the evolution of resistance to ionizing radiation and tolerance of desiccation. RESULTS: We used the programs MultiParanoid and DnaSP to deduce the sets of orthologs that potentially evolved due to positive Darwinian selection in IRRB. We find that positive selection targets 689 ortholog sets of IRRB. Among these, 58 ortholog sets are absent in ionizing-radiation-sensitive bacteria (IRSB: Escherichia coli and Thermus thermophilus). The most striking finding is that all basal DNA repair genes in IRRB, unlike many of their orthologs in IRSB, are subject to positive selection. CONCLUSION: Our results provide the first in silico prediction of positively selected genes with potential roles in the molecular basis of resistance to gamma-radiation and tolerance of desiccation in IRRB. Identification of these genes provides a basis for future experimental work aimed at understanding the metabolic networks in which they participate.
Abstract: All theories related to the evolution of Deinococcus radiodurans have a common denominator: the strong positive correlation between ionizing-radiation resistance and desiccation tolerance. Currently, the widespread hypothesis is that D. radiodurans' ionizing-radiation resistance is a consequence of this organism's adaptation to desiccation (desiccation adaptation hypothesis). Here, we draw attention to major discrepancy that has emerged between the "desiccation adaptation hypothesis" and recent findings in computational biology, experimental research, and terrestrial subsurface surveys. We explain why the alternative hypothesis, suggesting that D. radiodurans' desiccation tolerance could be a consequence of this organism's adaptation to ionizing radiation (radiation adaptation hypothesis), should be considered on equal basis with the "desiccation adaptation hypothesis".
Abstract: The extremely radioresistant bacterium Deinococcus radiodurans contains two LexA homologues (LexA1 and LexA2) that are possible transcriptional regulators associated with the DNA damage response. In this study, resequencing revealed that there was an additional cytosine nucleotide (nucleotide position 612) in the D. radiodurans lexA2 gene. Purified LexA2 possessed proteolytic activity that could be stimulated by RecA. In an effort to gain an insight into the role of LexA2 in the radiation response mechanism, recA, lexA1 and lexA2 disruptant strains were generated and investigated. The intracellular level of RecA increased in lexA1 and lexA2 disruptant strains following gamma-irradiation as in the wild-type strain. These results indicated that the two LexA homologues did not possess functional overlap regarding the induction of RecA. The lexA2 disruptant strains exhibited a much higher resistance to gamma-rays than the wild-type strain. Furthermore, a luciferase assay showed that pprA promoter activation was enhanced in the lexA2 disruptant strain following gamma-irradiation. The pprA gene encoding the novel radiation-inducible protein PprA plays a critical role in the radioresistance of D. radiodurans. The increase in radioresistance of the lexA2 disruptant strain is explained in part by the enhancement of pprA promoter activation.
Abstract: Catalase plays a key role in protecting cells against toxic reactive oxygen species. Here we report on the cloning, purification and characterization of a catalase (KatA, DR1998) from the extremely radioresistant bacterium Deinococcus radiodurans. The size of purified D. radiodurans KatA monomer was 65 kDa while gel filtration revealed that the size of the enzyme was 240 kDa, suggesting that KatA formed a homotetramer in solution. Purified KatA displayed a final specific activity of 68,800 U/mg of protein. The catalase activity of KatA was inhibited by sodium azide, sodium cyanide and 3-amino-1,2,4-triazole. The absorption spectrum of KatA exhibited a Soret band at 408 nm. The position of the spectral peak remained unchanged following reduction of KatA with dithionite. No peroxidase activity was found for KatA. These results demonstrate that D. radiodurans KatA is a typical monofunctional heme-containing catalase. The stability of KatA with respect to H2O2 stress was superior to that of commercially available Aspergillus niger and bovine liver catalases. The relative abundance of KatA in cells in addition to the H2O2 resistance property may play a role in the survival strategy of D. radiodurans against oxidative damage.
Abstract: Molecular chaperones are a wide group of unrelated protein families whose role is to assist others proteins. Comparably, under environmental stress, stress proteins behave as biocatalysts of protein stabilization. Stress proteins include a large class of proteins that were originally termed heat shock proteins (HSPs) due to their initial discovery in tissues exposed to elevated temperatures. Many, but not all, stress proteins and HSPs are molecular chaperones. Moreover, not all HSPs are derivable from stress. HSPs are structurally diversified by the contribution of various domains having specific roles. HSPs have been grouped, mainly on the basis of their molecular masses, into specific families that include small HSPs (sHSPs)/alpha-crystallins, HSP10s, HSP40s, HSP60s, HSP70s, HSP90s, HSP100s and HSP110s. The names of these major families are historical artefacts with limited information content. Using the current databases, names and proteic domains of many molecular chaperones in different species were analyzed. Although traditional names of HSPs are trivial, it is unrealistic to suggest replacing them, because they are preferred and widely used. Here we suggest that these traditional names be chaperoned, in silico, by a systematic nomenclature. Thus, for example, with the same intent of use of [trioxygen: O3] for ozone, we propose here C7HSP70[Ehsa]ER-P11021 for GRP78 (78 kDa endoplasmic Human molecular chaperone in HSP70 superfamily with P11021 as its accession number in the database of the National Center for Biotechnology Information (NCBI)). The proposed systematic computer-oriented naming and classification method is designed for HSPs and also their partners based on the number of amino acids, domain structure, phylogenetic domain, localization in the cell and accession number as stated in the NCBI. Arabidopsis thaliana was analyzed as a model, because it contains a large number of various HSPs localized in several organelles. Overall, this naming system helps in building, optimizing and managing a novel online database entirely devoted to HSPs. The purported taxonomy, coupled with the newly constructed database, can contribute to studies involving large amounts of stored data on HSPs.
