A defect in menadione biosynthesis induces global changes in gene expression in Staphylococcus aureus

Both the high-resolution two-dimensional protein gel electrophoresis technique and full-genome DNA microarrays were used for identification of Staphylococcus aureus genes whose expression was changed by a mutation in menD. Because the electron transport chain is interrupted, the mutant should be unable to use oxygen and nitrate as terminal electron acceptors. Consistent with this, a mutation in menD was found to cause a gene expression pattern typically detected under anaerobic conditions in wild-type cells: proteins involved in glycolytic as well as in fermentation pathways were upregulated, whereas tricarboxylic acid (TCA) cycle enzymes were significantly downregulated. Moreover, the expression of genes encoding enzymes for nitrate respiration and the arginine deiminase pathway was strongly increased in the mutant strain. These results indicate that the menD mutant, just as the site-directed S. aureus hemB mutant, generates ATP from glucose or fructose mainly by substrate phosphorylation and might be defective in utilizing a variety of carbon sources, including TCA cycle intermediates and compounds that generate ATP only via electron transport phosphorylation. Of particular interest is that there are also differences in the gene expression patterns between hemB and menD mutants. While some anaerobically active enzymes were present in equal amounts in both strains (Ldh1, SACOL2535), other classically anaerobic enzymes seem to be present in higher amounts either in the hemB mutant (e.g., PflB, Ald1, IlvA1) or in the menD mutant (arc operon). Only genes involved in nitrate respiration and the ald1 operon seem to be additionally regulated by a depletion of oxygen in the hemB and/or menD mutant.     

The expression and anaerobic induction of alcohol dehydrogenase in cotton

The alcohol dehydrogenase (ADH) system in cotton is characterized, with an emphasis on the cultivated allotetraploid speciesGossypium hirsutum cv. Siokra. A high level of ADH activity is present in seed of Siokra but quickly declines during germination. When exposed to anaerobic stress the level of ADH activity can be induced several fold in both roots and shoots of seedlings. Unlike maize andArabidopsis, ADH activity can be anaerobically induced in mature green leaves. Three major ADH isozymes were resolved in Siokra, and it is proposed that two genes,Adh1 andAdh2, are coding for these three isozymes. The genes are differentially expressed. ADH1 is predominant in seed and aerobically grown roots, while ADH2 is prominent in roots only after anaerobic stress. Biochemical analysis demonstrated that the ADH enzyme has a native molecular weight of approximately 81 kD and a subunit molecular weight of approximately 42 kD, thus establishing that ADH in cotton is able to form and is active as dimers. Comparisons of ADH activity levels and isozyme patterns between Siokra and other allotetraploid cottons showed that the ADH system is highly conserved among these varieties. In contrast, the diploid species of cotton all had unique isozyme patterns.This work was generously supported by an Australian Cotton Research Council Postgraduate Studentship.     

Zn++ stimulation of the induction of alcohol dehydrogenase by anaerobiosis in roots of Zea mays L.

Summary Zn⁺⁺ at an optimum concentration of 5×10^–4 M caused a two fold stimulation in the level of alcohol dehydrogenase (ADH) induced by anaerobic conditions. Isozymes specified by different genes and alleles show disproportionate increases in activity, such that, unequal representation of gene products while not eliminated, is invariably reduced by Zn⁺⁺ treatment. Thus in the case of alleles at the Adh-1 locus, there was a greater increase in the protein subunit specified by the Adh-1S allele. From previous work (Fischer and Schwartz, 1973) this protein is known to have a reduced affinity for Zn⁺⁺. This suggests that zinc availability during ADH induction is limiting and may provide an alternative to the cis-linked regulatory gene model proposed by Schwartz (1971) to explain the unequal expression of genes and alleles.     

Gene and Enhancer Trap Transposable Elements Reveal Oxygen Deprivation-regulated Genes and their Complex Patterns of Expression in Arabidopsis

Transposon tagging with modified maize Ds–GUS constructswas used to isolate genes induced by oxygen deprivation in Arabidopsisthaliana. Seedlings of 800 gene-trap (DsG) and 600 enhancer-trap(DsE) lines were grown on vertically positioned plates for 1 week,oxygen deprived for up to 24 h and stained for GUS activity.Oxygen deprivation induced intricate patterns of gene expressionin seedlings of 65 lines. The insertion site and phenotypesof 15 lines were examined. Surprisingly, none of the insertionswere into genes that encode known anaerobic polypeptides. Insertionswere identified within or adjacent to genes encoding proteinsof regulatory, enzymatic, mitochondrial protein import and unknownfunction, as well as adjacent to genes encoding a putative receptor-likekinase and putative sensor-histidine kinase. Four lines hadsignificantly lower ADH activity after 24 h of oxygen deprivationand three of these showed reduced stress tolerance. Two lineswith wild-type levels of ADH were low-oxygen intolerant. Paradoxically,several lines had significantly higher ADH activity after 12 hof oxygen deprivation but reduced stress tolerance. Caffeinetreatment, which increased ADH specific activity in wild-typeseedlings under aerobic conditions, was sufficient to increaseGUS staining in seven of the 15 lines, providing evidence thatthese genes may be regulated by cytosolic calcium levels. Theseresults demonstrate the effectiveness of the Ds–GUS taggingsystem in the identification of genes that are regulated inresponse to oxygen deprivation and a calcium second messenger.     

人体肝癌细胞急性低氧及低氧习服差异表达基因分析

本文分析了人体肝癌细胞(HepG2)急性低氧处理以及低氧习服处理后基因表达谱的改变。急性低氧处理为细胞在1％氧气中培养48h,低氧习服处理为细胞在1％氧气中培养24h,常氧培养24h,以此作为一个周期,重复6个周期。联合应用抑制消减杂交技术和cDNA芯片技术,筛选HepG2细胞经急性低氧处理与正常培养细胞相比差异表达的基因,以及经低氧习服处理细胞与正常培养细胞相比差异表达的基因。结果显示,HepG2细胞经急性低氧处理与在常氧条件下培养相比,差异表达的基因有37个,表达水平全部表现为下调,其中包括参与细胞周期、细胞应激、细胞信号转导、细胞骨架形成、转录相关蛋白及细胞代谢相关蛋白的基因,1个未知基因序列、4个EST序列、5个线粒体蛋白基因,另外有功能不明的蛋白质基因12个。低氧习服处理的细胞与常氧条件下培养的细胞相比,差异表达的基因有6个,其中包括两个线粒体蛋白基因、金属蛋白酶1基因、转铁蛋白基因、Thymosin ．beta-4和TPT1基因。其中线粒体蛋白ND4、转铁蛋白、Thymosin.beta-4和TPT1基因的表达呈上调,线粒体NDl及金属蛋白酶1基因的表达水平呈下调。经低氧习服处理后,细胞低氧耐受力提高,低氧习服处理细胞基因的表达与急性低氧处理细胞和正常培养细胞的基因表达不同,这种变化可能与低氧习服细胞低氧耐受力的增强有关。     

Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function

The major regulator controlling the physiological switch between aerobic and anaerobic growth conditions in Escherichia coli is the DNA binding protein FNR. To identify genes controlled by FNR, we used Affymetrix Antisense GeneChips to compare global gene expression profiles from isogenic MG1655 wild-type and Deltafnr strains grown in glucose minimal media under aerobic or anaerobic conditions. We found that 297 genes contained within 184 operons were regulated by FNR and/or by O2 levels. The expression of many genes known to be involved in anaerobic respiration and fermentation was increased under anaerobic growth conditions, while that of genes involved in aerobic respiration and the tricarboxylic acid cycle were repressed as expected. The expression of nine operons associated with acid resistance was also increased under anaerobic growth conditions, which may reflect the production of acidic fermentation products. Ninety-one genes with no presently defined function were also altered in expression, including seven of the most highly anaerobically induced genes, six of which we found to be directly regulated by FNR. Classification of the 297 genes into eight groups by k-means clustering analysis indicated that genes with common gene expression patterns also had a strong functional relationship, providing clues for studying the function of unknown genes in each group. Six of the eight groups showed regulation by FNR; while some expression groups represent genes that are simply activated or repressed by FNR, others, such as those encoding functions for chemotaxis and motility, showed a more complex pattern of regulation. A computer search for FNR DNA binding sites within predicted promoter regions identified 63 new sites for 54 genes. We suggest that E. coli MG1655 has a larger metabolic potential under anaerobic conditions than has been previously recognized.     

The ArcA regulon and oxidative stress resistance in Haemophilus influenzae

Haemophilus influenzae transits between niches within the human host that are predicted to differ in oxygen levels. The ArcAB two-component signal transduction system controls gene expression in response to respiratory conditions of growth and has been implicated in bacterial pathogenesis, yet the mechanism is not understood. We undertook a genome-scale study to identify genes of the H. influenzae ArcA regulon. Deletion of arcA resulted in increased anaerobic expression of genes of the respiratory chain and of H. influenzae's partial tricarboxylic acid cycle, and decreased anaerobic expression levels of genes of polyamine metabolism, and iron sequestration. Deletion of arcA also conferred a susceptibility to transient exposure to hydrogen peroxide that was greater following anaerobic growth than after aerobic growth. Array data revealed that the dps gene, not previously assigned to the ArcA modulon in bacteria, exhibited decreased expression in the arcA mutant. Deletion of dps resulted in hydrogen peroxide sensitivity and complementation restored resistance, providing insight into the previously uncharacterized mechanism of arcA-mediated H(2)O(2) resistance. The results indicate a role for H. influenzae arcA and dps in pre-emptive defence against transitions from growth in low oxygen environments to aerobic exposure to hydrogen peroxide, an antibacterial oxidant produced by phagocytes during infection.     

Reactive Oxygen Species Production and Antioxidant Enzyme Expression after Epstein–Barr Virus Lytic Cycle Induction in Raji Cell Line

In a previous study, we have described oxidative stress during Epstein-Barr virus lytic cycle induction. Oxidative stress was evidenced by the observed high MDA levels and the decreased activities of antioxidant enzymes. We hypothesised that the lower activities of the antioxidant enzymes decrease were the result of either the excessive production of reactive oxygen radical species (ROS) or a negative regulation of the antioxidant enzyme gene expressions. In an attempt to clarify this situation, EBV lytic cycle was induced in Raji cell line by a non-stressing dose of 12-0-tetradecanoylphorbol-13-acetate. BZLF-1, superoxide dismutase, and catalase gene expressions were then analysed using semi-quantitative RT-PCR, simultaneously at a kinetic of 6, 12, 24, 36, and 48?h. ROS production was evaluated by chemiluminescence. A study was conducted to establish whether ROS production, BZLF-1, and the expression of antioxidant genes were inter-correlated. Induction of the lytic cycle resulted in increased expressions of the genes of superoxide dismutase and catalase, which began at 24?h (p?相似文献   

Protein Synthesis in Maize during Anaerobic and Heat Stress

Protein accumulation and protein synthesis were investigated during anaerobic stress and heat shock in maize seedlings (Zea mays L.). Antibodies against alcohol dehydrogenase (ADH) and cytosolic glyceraldehyde-3-phosphate dehydrogenase (GAPC) were used to investigate the expression of the genes encoding these proteins during stress treatment. ADH1 protein accumulation is shown to increase about 10-fold in the root after 24 hours of anaerobic treatment. The Gpc gene products are separable into two size classes: the slow mobility GAPC1 and GAPC2 (GAPC1/2), and the faster GAPC3 and GAPC4 (GAPC3/4). The GAPC1/2 antigen did not increase at all, whereas the GAPC3/4 antigen increased less than fourfold. The proteins synthesized in the root during aerobic and anaerobic conditions were compared, and GAPC3/4 was identified as an anaerobic polypeptide. In vitro translations were used to estimate the levels of different mRNAs in roots following anaerobiosis, recovery from anaerobiosis, and heat shock. This was compared with the in vivo protein synthesis rates in roots labeled under identical conditions. In vivo labeling indicates that GAPC and ADH are not heat shock proteins. Although both GAPC3/4- and ADH1-translatable mRNA levels increase about 10-fold during anaerobiosis, in vivo labeling of these proteins (relative to total protein synthesis) is further enhanced, leading to a selective translation effect for ADH1 of threefold, and for GAPC3/4 of sixfold. In contrast, anoxia causes no change in GAPC1/2-translatable mRNA levels or in vivo labeling. As an additional comparison, β-glucosidase mRNA levels are found to be constant during anoxia, but in vivo synthesis decreases.