RecO is essential for DNA damage repair in Deinococcus radiodurans.

Here we present direct evidence for the vital role of RecO in Deinococcus radiodurans's radioresistance. A recO null mutant was constructed using a deletion replacement method. The mutant exhibited a growth defect and extreme sensitivity to irradiation with gamma rays and UV light.

Structural and functional diversity of Nudix fold.

Nudix hydrolases catalyze the hydrolysis of nucleoside diphosphates linked to other moieties X, and contain the sequence motif or Nudix box, GX5EX7REUXEEXGU. The mechanisms of Nudix hydrolases are highly diverse in the position on the substrate. In this paper, we examined the sequences and structures of the MutT/Nudix superfamily.

DrRRA: a novel response regulator essential for the extreme radioresistance of Deinococcus radiodurans.

Two-component systems are predominant signal transduction pathways in prokaryotes, and also exist in many archaea as well as some eukaryotes. A typical TCS consists of a histidine kinase and a cognate response regulator. In this study, a novel gene encoding a response regulator (we designate it drRRA) is identified to be essential for the extreme radioresistance of Deinococcus radiodurans.

[Construction of a dps mutant and its functional analysis in Deinococcus radiodurans].

Dps (DNA protection during starvation) is a member of the iron-binding protein family in prokaryotes. It has been shown previously that Dps possesses ferroxidase activity and the ability to sequester iron that seems to protect DNA from oxidative damage. Based on the method of Polymerase Chain Reaction and homologous genetic recombination in vivo, the gene (DRB0092) encoding a Dps protein homology in the extremely radioresistant bacterium Deinococcus radiodurans was deleted from the wild type strain R1 genome.

Identification and functional analysis of a phytoene desaturase gene from the extremely radioresistant bacterium Deinococcus radiodurans.

The phytoene-related desaturases are the key enzymes in the carotenoid biosynthetic pathway. The gene encoding phytoene desaturase in the deinoxanthin synthesis pathway of Deinococcus radiodurans was identified and characterized. Two putative phytoene desaturase homologues (DR0861 and DR0810) were identified by analysis of conserved amino acid regions, and the former displayed the highest identity (68 %) with phytoene desaturase of the cyanobacterium Gloeobacter violaceus.

Chemiluminescence analysis of the prooxidant and antioxidant effects of epigallocatechin-3-gallate.

The aim of this study was to investigate the mechanism of antioxidant and prooxidant effects of epigallocatechin-3-gallate (EGCG) using chemiluminescence analysis. Results showed that EGCG scavenged superoxide radical and H2O22 in a dose dependent manner. EGCG scavenged 50% of superoxide radical at 0.

Evaluation of the antioxidant effects of carotenoids from Deinococcus radiodurans through targeted mutagenesis, chemiluminescence, and DNA damage analyses.

Deinococcus radiodurans is highly resistant to reactive oxygen species (ROS). The antioxidant effect of carotenoids in D. radiodurans was investigated by using a targeted mutation of the phytoene synthase gene to block the carotenoid synthesis pathway and by evaluating the survival of cells under environmental stresses.

TNF-alpha-induced NF-kappaB/RelA Ser(276) phosphorylation and enhanceosome formation is mediated by an ROS-dependent PKAc pathway.

Tumor necrosis factor-alpha (TNF-alpha) is a potent mediator of inflammation, inducing expression of a gene network mediated by NF-kappaB. Previously we found that TNF-alpha-induced reactive oxygen species (ROS) production is required for NF-kappaB action because antioxidants inhibited TNF-alpha-inducible IL-8 expression without affecting its nuclear translocation. Here, we further investigated this ROS pathway controlling NF-kappaB/RelA dependent gene expression.

Three tandem HRDC domains have synergistic effect on the RecQ functions in Deinococcus radiodurans.

The RecQ family of DNA helicases performs essential functions in the maintenance of genomic stability in all organisms. In Deinococcus radiodurans, DR1289 is a special member of RecQ family with unique arrangement of three tandem HRDC domains in the C-terminus. A dr1289 mutant is hypersensitive to gamma-irradiation, UV, H2O2 and mitomycin C.

Evolutionary pathways of an ancient gene recX.

RecX is a regulator of RecA activity by interacting with RecA protein or RecA filaments. Genes encoding RecX were found in genomes of a wide diversity of bacteria and some plants (e.g.

[Effects of PprI and RecX on antioxidant activity of Deinococcus radiodurans].

Effects of mutations of Pprl (Dr0167) and RecX (Dr1310), which are relative to radioresistance, on reactive oxygen species scavenging activities in Deinococcus radiodurans were investigated using gene mutation, chemiluminescence measurement and enzyme activity analysis. Their possible regulating functions on the activities of antioxidant enzymes was evaluated. Results show that mutant that lacks PprI is remarkably sensitive to reactive oxygen species and its enzyme activities of catalase and superoxide dismutase decrease significantly.

[Construction and functional analysis of the crtl gene disruptant in Deinococcus radiodurans].

With the method of Polymerase Chain Reaction and homologous genetic recombination in vivo, the key gene encoding bacterial-type phytoene desaturase (Crtl) which controls the carotenoids biosynthesis pathway in the non-photosynthetic and extremely radioresistant bacterium Deinococcus radiodurans was deleted from the genome. The colorless mutant obtained was designated as M61. Survival rates of mutant strain and wild type strain were investigated under different doses of gamma-radiation and hydrogen peroxide.

Functional analysis of helicase and three tandem HRDC domains of RecQ in Deinococcus radiodurans.

RecQ is a highly conserved helicase necessary for maintaining genome stability in all organisms. Genome comparison showed that a homologue of RecQ in Deinococcus radiodurans designated as DR1289 is a member of RecQ family with unusual domain arrangement: a helicase domain, an RecQ C-terminal domain, and surprisingly three HRDC domain repeats, whose function, however, remains obscure currently. Using an insertion deletion, we discovered that the DRRecQ mutation causes an increase in gamma radiation, hydroxyurea and mitomycine C and UV sensitivity.

Identification of an NF-kappaB-dependent gene network in cells infected by mammalian reovirus.

Reovirus infection activates NF-kappaB, which leads to programmed cell death in cultured cells and in the murine central nervous system. However, little is known about how NF-kappaB elicits this cellular response. To identify host genes activated by NF-kappaB following reovirus infection, we used HeLa cells engineered to express a degradation-resistant mutant of IkappaBalpha (mIkappaBalpha) under the control of an inducible promoter.

Two-step cross-linking method for identification of NF-kappaB gene network by chromatin immunoprecipitation.

The chromatin immunoprecipitation (ChIP) assay has recently been exploited as a powerful and versatile technique for probing protein-DNA interactions within the chromatin environment. In this method, intact cells are fixed with a reversible DNA-protein cross-linking agent (formaldehyde), and associated DNA is enriched by immunoprecipitating a target DNA binding protein. The bound DNA in the immune complexes is then used to identify that specific DNA binding protein's endogenous genomic targets.

A TNF-induced gene expression program under oscillatory NF-kappaB control.

Background: The cytokine tumor necrosis factor (TNF) initiates tissue inflammation, a process mediated by the NF-kappaB transcription factor. In response to TNF, latent cytoplasmic NF-kappaB is activated, enters the nucleus, and induces expression of inflammatory and anti-apoptotic gene expression programs. Recently it has been shown that NF-kappaB displays two distinct activation modes, monophasic and oscillatory, depending on stimulus duration.

RecX is involved in antioxidant mechanisms of the radioresistant bacterium Deinococcus radiodurans.

Deinococcus radiodurans shows remarkable resistance to reactive oxygen species (ROS), generated by irradiation. Disruption of recX (dr1310) in D. radiodurans using targeted mutagenesis method enhanced its ROS scavenging activity, and recX overexpression in this bacterium repressed its antioxidant activity significantly.

[Raman analysis of conformation changes of insulin solvent after being exposed to ELF pulsed electric field].

Raman spectra of insulin solvents are presented before and after being exposed to the pulsed electric field with extremely low frequency 50 Hz (ELF). The covalences of the molecule were not affected and the changes of some secondary bonds such as hydrogen bonds and salt bonds were observed. Detailed analysis of these spectra indicates that the alpha-helix of insulin molecule was destroyed after the exposure, which is proved by the shift of the peak of the amide I region toward higher wave number and by the appearance of several new peaks: 1561 and 1594 cm(-1).

Identification of direct genomic targets downstream of the nuclear factor-kappaB transcription factor mediating tumor necrosis factor signaling.

Tumor necrosis factor (TNF) is a pro-inflammatory cytokine that controls expression of inflammatory genetic networks. Although the nuclear factor-kappaB (NF-kappaB) pathway is crucial for mediating cellular TNF responses, the complete spectrum of NF-kappaB-dependent genes is unknown. In this study, we used a tetracycline-regulated cell line expressing an NF-kappaB inhibitor to systematically identify NF-kappaB-dependent genes.

LexA analog (dra0074) is a regulatory protein that is irrelevant to recA induction.

The protein DRA0074 is suggested to be another LexA in Deinococcus radiodurans, having similar motifs and RecA-mediated cleavage activity to D. radiodurans LexA (dra0344). However, its function has not been studied.

Stochastic effects of multiple regulators on expression profiles in eukaryotes.

The stochastic nature of gene regulation still remains not fully understood. In eukaryotes, the stochastic effects are primarily attributable to the binary nature of genes, which are considered either switched "on" or "off" due to the action of the transcription factors binding to the promoter. In the time period when the gene is activated, bursts of mRNA transcript are produced.

[Relationship between antibacterial activity of aloe and its anthaquinone compounds].

Objective: To investigate the relationship between the antibacterial activity of aloe and its contents of anthaquinone compounds, measure and compale antibacterial activities of aloin and aloe-emodin, and analyse the effect of glycoside on the antibacterial activity of aloin.

Method: The antibacterial activities of the extracts from the outer leaf of Aloe saponaria Haw, aloin and aloe-emodin against three Gram-negative and two Gram-positive bacteria were investigated with the method of agar diffusion. The antibacterial effect of aloin on E.

Chemiluminescence assay for reactive oxygen species scavenging activities and inhibition on oxidative damage of DNA in Deinococcus radiodurans.

Free radical scavenging effects of the cellular protein extracts from two strains of Deinococcus radiodurans and Escherichia coli against O2-, H2O2 and *OH were investigated by chemiluminescence (CL) methods. The cellular protein extracts of D. radiodurans R1 and KD8301 showed higher scavenging effects on O2- than that of E.

Expression of Deinococcus radiodurans PprI enhances the radioresistance of Escherichia coli.

PprI, a newly identified gene switch responsible for extreme radioresistance of Deinococcus radiodurans, plays a central regulatory role in multiple DNA damage repair and protection pathways in response to radiation stress [Biochem. Biophy. Res.

PprI: a general switch responsible for extreme radioresistance of Deinococcus radiodurans.

Deinococcus radiodurans exhibits an extraordinary ability to withstand the lethal and mutagenic effects of DNA damaging agents, particularly, ionizing radiation. Available evidence indicates that efficient repair of DNA damage and protection of the chromosomal structure are mainly responsible for the radioresistance. Little is known about the biochemical basis for this phenomenon.