Reversible interconversion of the functional state of the gene regulator FNR from Escherichia coli in vivo by O2 and iron availability

FNR, the gene regulator of anaerobic respiratory genes of Escherichia coli is converted in vivo by O₂ and by chelating agents to an inactive state. The interconversion process was studied in vivo in a strain with temperature controlled synthesis of FNR by measuring the expression of the frd (fumarate reductase) operon and the reactivity of FNR with the alkylating agent iodoacetic acid. FNR from aerobic bacteria is, after arresting FNR synthesis and shifting to anaerobic conditions, able to activate frd expression and behaves in the alkylation assay like anaerobic FNR. After shift from anaerobic to aerobic conditions, FNR no longer activates the expression of frd and reacts similar to aerobic FNR in the alkylation assay. The conversion of aerobic (inactive) to anaerobic (active) FNR occurs in the presence of chloramphenicol, an inhibitor of protein synthesis. Anaerobic FNR can also be converted post-translationally to inactive, metal-depleted FNR by growing the bacteria in the presence of chelating agents. The reverse is also possible by incubating metal-depleted bacteria with Fe²⁺. From the experiments it is concluded that the aerobic and the metal-depleted form of FNR can be transferred post-translationally and reversibly to the anaerobic (active) form. The response of FNR to changes in O₂ supply therefore occurs at the FNR protein level in a reversible mode.Abbreviation BV_red = reduced benzyl viologen     

Regulatory O2 tensions for the synthesis of fermentation products in Escherichia coli and relation to aerobic respiration

In an oxystat, the synthesis of the fermentation products formate, acetate, ethanol, lactate, and succinate of Escherichia coli was studied as a function of the O₂ tension (pO₂) in the medium. The pO₂ values that gave rise to half-maximal synthesis of the products (pO_0.5) were 0.2–0.4 mbar for ethanol, acetate, and succinate, and 1 mbar for formate. The pO_0.5 for the expression of the adhE gene encoding alcohol dehydrogenase was approximately 0.8 mbar. Thus, the pO₂ for the onset of fermentation was distinctly lower than that for anaerobic respiration (pO_0.5≤ 5 mbar), which was determined earlier. An essential role for quinol oxidase bd in microaerobic growth was demonstrated. A mutant deficient for quinol oxidase bd produced lactate as a fermentation product during growth at microoxic conditions (approximately 10 mbar O₂), in contrast to the wild-type or a quinol-oxidase-bo-deficient strain. In the presence of nitrate, the amount of lactate was largely decreased. Therefore, under microoxic conditions, the pO₂ appears to be too high for (mixed acid) fermentation to function and too low for aerobic respiration by quinol oxidase bo. Received: 7 February 1997 / Accepted: 2 May 1997     

Aerobic and anaerobic metabolism in a facultative anaerobe Ep01 lacking cytochrome, quinone and catalase

Abstract A facultative anaerobe, strain Ep01 produced a mixture of pyruvate, formate, acetate and ethanol from glucose anaerobically, and acetate and pyruvate aerobically. Cell extract of anaerobic-grown cells contained active pyruvate formatelyase, aldehyde dehydrogenase and alcohol dehydrogenase, while cell extract of aerobic grown cells contained an active pyruvate dehydrogenase system, NaDH oxidase and NADH peroxidase. Levels of acetate kinase and phosphate acetyltransferase activities were not significantly different in cells grown under either condition. Based on the metabolic products and the emzyme activities, we propose the presence of two metabolic pathways in strain Ep01, namely, a pathway to form formate, acetate and ethanol under anaerobic conditions, and a pathway to form under aerobic conditions. This explains why strain Ep01 can grow well both under strictly anaerobic conditions and well-aerated conditions.     

Members of the genus Arthrobacter grow anaerobically using nitrate ammonification and fermentative processes: anaerobic adaptation of aerobic bacteria abundant in soil

Members of the genus Arthrobacter are usually regarded as obligate aerobic bacteria. The anaerobic growth and energy metabolism of two Arthrobacter species were investigated. Arthrobacter globiformis utilized both nitrate ammonification and lactate, acetate and ethanol producing fermentation processes for anaerobic growth. Only nitrate supported anaerobic growth of Arthrobacter nicotianae. Anaerobically induced respiratory nitrate reductase activity was detected in both strains. Neither of the tested strains used the alternative electron acceptors fumarate, dimethylsulfoxide or trimethylamine-N-oxide.     

厌氧氨氧化菌内含物——糖原颗粒

厌氧氨氧化菌(anaerobic ammonium-oxidizing bacteria, AnAOB)是分类学上新近建立的细菌类群。由于生长缓慢,培养困难,迄今没有获得纯培物。与已知细菌类群相比,AnAOB具有诸多特异性细胞结构和功能。AnAOB是化能自养型细菌,但在其细胞内经常可见贮藏性的内含物——糖原颗粒。探讨这种糖原颗粒的性状与动态,可深化人们对AnAOB的认识。本文结合文献报道及前期研究基础,对厌氧氨氧化菌糖原颗粒的结构、代谢和功能特性进行了探讨,分析认为AnAOB糖原颗粒分布于核糖细胞质内,且处于多途径合成与多位点消耗的动态平衡中;此外,糖原颗粒具有提供能量、碳架和应激保护等能力,对逆境下AnAOB的生存具有重要意义。本综述可为厌氧氨氧化菌的深入研究和工程应用提供支撑。     

Metabolism of alkylbenzenes, alkanes, and other hydrocarbons in anaerobic bacteria

Aromatic and aliphatic hydrocarbons are the main constituents of petroleum and its refined products. Whereas degradation of hydrocarbons by oxygen-respiring microorganisms has been known for about a century, utilization of hydrocarbons under anoxic conditions has been investigated only during the past decade. Diverse strains of anaerobic bacteria have been isolated that degrade toluene anaerobically, using nitrate, iron(III), or sulfate as electron acceptors. Also, other alkylbenzenes such as m-xylene or ethylbenzene are utilized by a number of strains. The capacity for anaerobic utilization of alkylbenzenes has been observed in members of the -, -, - and -subclasses of the Proteobacteria. Furthermore, denitrifying bacteria and sulfate-reducing bacteria with the capacity for anaerobic alkane degradation have been isolated, which are members of the - and -subclass, respectively. The mechanism of the activation of hydrocarbons as apolar molecules in the absence of oxygen is of particular interest.The biochemistry of anaerobic toluene degradation has been studied in detail. Toluene is activated by addition to fumarate to yield benzylsuccinate, which is then further metabolized via benzoyl-CoA. The toluene-activating enzyme presents a novel type of glycine radical protein. Another principle of anaerobic alkylbenzene activation has been observed in the anaerobic degradation of ethylbenzene. Ethylbenzene in denitrifying bacteria is dehydrogenated to 1-phenylethanol and further to acetophenone; the latter is also metabolized to benzoyl-CoA. Naphthalene is presumably activated under anoxic conditions by a carboxylation reaction. Investigations into the pathway of anaerobic alkane degradation are only at the beginning. The saturated hydrocarbons are mostlikely activated by addition of a carbon compound rather than by desaturation and hydration, as speculated about in some early studies. An anaerobic oxidation of methane with sulfate as electron acceptor has been documented in aquatic sediments. The process is assumed to involve a reversal of methanogenesis catalyzed by Archaea, and scavenge of an electron-carrying metabolite by sulfate-reducing bacteria. Among unsaturated non-aromatic hydrocarbons, anaerobic bacterial degradation has been demonstrated and investigated with n-alkenes, alkenoic terpenes and the alkyne, acetylene.     

Respiratory metabolism and gene expression during seed germination

Oxygen uptake and carbon dioxide release rapidly increase in seeds during imbibition. The oxygen uptake is associated with oxidative phosphorylation through cytochrome oxidase. During the early stage of germination substrate level phosphorylation may also contribute to ATP production. All indications suggest that this route of ATP production is insignificant during aerobic germination. However, during oxygen stress, substrate level phosphorylation does significantly contribute to ATP production in some species. Carbohydrate oxidation plays a significant role in the germination process. Up to two thirds of the carbon from carbohydrate breakdown enters the tricarboxylic acid cycle through the phosphoenolpyruvate carboxylase reaction. This anapleurotic input into the Krebs cycle most probably reflects the high demand on intermediates from the cycle for biosynthesis. The extent to which other substrates are utilized for respiration is uncertain. Information regarding the levels of key metabolites and enzymes, as well as their cellular distribution is limited. The involvement of gene expression in the regulation of respiratory metabolism is poorly characterised. Several genes which have been cloned are only expressed during germination. With the exception of the early methionine labeled polypeptide, little is known about the function of these genes.     

Photosynthetic electron transport and anaerobic metabolism in purple non-sulfur phototrophic bacteria

Purple non-sulfur phototrophic bacteria, exemplifed byRhodobacter capsulatus andRhodobacter sphaeroides, exhibit a remarkable versatility in their anaerobic metabolism. In these bacteria the photosynthetic apparatus, enzymes involved in CO₂ fixation and pathways of anaerobic respiration are all induced upon a reduction in oxygen tension. Recently, there have been significant advances in the understanding of molecular properties of the photosynthetic apparatus and the control of the expression of genes involved in photosynthesis and CO₂ fixation. In addition, anaerobic respiratory pathways have been characterised and their interaction with photosynthetic electron transport has been described. This review will survey these advances and will discuss the ways in which photosynthetic electron transport and oxidation-reduction processes are integrated during photoautotrophic and photoheterotrophic growth.     

Anaerobic dechlorination and degradation of hexachlorocyclohexane isomers by anaerobic and facultative anaerobic bacteria

Screening studies with strict and facultative anaerobic bacteria showed that Clostridium app. and several other representatives of Bacillaceae and Enterobacteriaceae actively degraded -hexachlorocyclohexane (-HCH) under anaerobic conditions. Representatives of Lactobacillaceae and Propronibacterium were inactive. With ³⁶Cl-labelled -HCH a nearly complete dechlorination was shown to occur in 4–6 days by Clostridium butyricum, C. pasteurianum and Citrobacter freundii, while other facultative anaerobic species were less active.Aerobically grown facultative anaerobes also dechlorinated actively -HCH during subsequent anaerobic incubation with glucose, pyruvate or formate as substrates. The -, - and -HCH isomers were also, but more slowly, dechlorinated (>>-HCH). All species active in anaerobic degradation of -HCH formed -tetrachlorocyclohexene (TCH) as the main intermediate metabolite and no -pentachlorocyclohexene (PCH) or other isomers of TCH or PCH have been found. Small amounts of tri- and tetrachlorinated benzenes have been found too. The mechanism of dechlorination is discussed.Non-Common Abbreviations Used -HCH -hexachlorocyclohexane - -TCH -2,3,4,5-tetrachlorocyclohexene - -PCH -1,2,3,4,5-pentachlorocyclohexene - GLC gas liquid chromatography     

Divergent roles of RpoS in Escherichia coli under aerobic and anaerobic conditions

Escherichia coli exhibited different levels of rpoS expression and general stress resistance under aerobiosis and anaerobiosis. Expression measured using reporter gene fusions and protein levels was lower under anaerobic conditions. Consistent with earlier findings, rpoS mutants were selected in aerobic nutrient-limited cultures but rpoS mutants were not enriched under anaerobiosis. This result suggested that, despite its decreased level, RpoS had a function under anaerobic conditions not essential under aerobiosis. Competition experiments between rpoS(+) and rpoS bacteria confirmed the advantage conferred by RpoS under anaerobiosis. In contrast, stress resistance assays suggested RpoS made a greater contribution to general stress resistance under aerobiosis than anaerobiosis. These results indicate a significant, but different role of RpoS in aerobic and anaerobic environments.     

Symbiosis regulation in a facultatively symbiotic temperate coral: zooxanthellae division and expulsion

Zooxanthellae mitotic index (MI) and expulsion rates were measured in the facultatively symbiotic scleractinian Astrangia poculata during winter and summer off the southern New England coast, USA. While MI was significantly higher in summer than in winter, mean expulsion rates were comparable between seasons. Corals therefore appear to allow increases in symbiont density when symbiosis is advantageous during the warm season, followed by a net reduction during the cold season when zooxanthellae may draw resources from the coral. Given previous reports that photosynthesis in A. poculata symbionts does not occur below approximately 6°C, considerable zooxanthellae division at 3°C and in darkness suggests that zooxanthellae are heterotrophic at low seasonal temperatures. Finally, examination of expulsion as a function of zooxanthellae density revealed that corals with very low zooxanthellae densities export a significantly greater proportion of their symbionts, apparently allowing them to persist in a stable azooxanthellate state.     

The rnf gene products in Rhodobacter capsulatus play an essential role in nitrogen fixation during anaerobic DMSO-dependent growth in the dark

The rnf genes in Rhodobacter capsulatus are essential for nitrogen fixation in the light. Because R. capsulatus grows readily on N₂ in the dark by anaerobic respiration with dimethylsulfoxide, the diazotrophic capacities of various strains in the dark were examined. No rnf mutants tested grew diazotrophically, and a nonpolar fdxN-null mutant showed decreased diazotrophic growth in the dark, suggesting that the Rnf and FdxN proteins form the primary electron donor pathway to nitrogenase in the dark as well as in the light. Nonphotosynthetic mutants lacking the component of cyclic electron transport grew diazotrophically and the levels of Rnf proteins were similar to those of the wild-type. These results indicate that rnf gene products play an essential role in nitrogen fixation without any functional link to the cyclic electron transport system. Received: 19 August 1997 / Accepted: 20 January 1998     

Rate-determining steps in penicillopepsin-catalysed reactions

FNR regulates the expression of target genes in response to anaerobiosis. It resembles the catabolite gene activator or cAMP-receptor protein (CRP) except for the presence of an N-terminal cysteine cluster, which may form a redox-sensing iron-binding site. Site-directed mutagenesis has shown that 3 of the 4 cysteine residues in the N-terminal cluster (Cys-20, -23 and -29, but not Cys-16) and the only other cysteine residue (Cys-122), are essential for the normal activation and repression of PNR-dependent promoters. Deletion of residues Pro-3-Arg-9 (inclusive) had no effect, but FNR was inactivated by a frameshift extending through the C-terminal DNA-binding domain. Four independent in vivo mutants contained identical Gly-96→Asp substitutions, which may inactivate FNR by distorting a sharp turn between β-strands in the predicted structure.     

高等植物赤霉素2-氧化酶基因的克隆、表达及其调控

赤霉素(GA)是一类重要的植物激素,对高等植物整个生命周期的生长发育起关键作用。调控赤霉素生物合成和代谢途径中的关键酶基因的表达可以控制植物体内赤霉素的含量。GA2-氧化酶是调节赤霉素合成和代谢的关键酶之一,使活性GA失活。本文主要对GA2-氧化酶基因的克隆、表达调控及其在植物基因工程中的应用等方面进行综述,为通过基因工程技术调控植物体内活性赤霉素的含量从而得到改良品种提供思路。     

Indirect and suboptimal control of gene expression is widespread in bacteria

Gene regulation in bacteria is usually described as an adaptive response to an environmental change so that genes are expressed when they are required. We instead propose that most genes are under indirect control: their expression responds to signal(s) that are not directly related to the genes’ function. Indirect control should perform poorly in artificial conditions, and we show that gene regulation is often maladaptive in the laboratory. In Shewanella oneidensis MR‐1, 24% of genes are detrimental to fitness in some conditions, and detrimental genes tend to be highly expressed instead of being repressed when not needed. In diverse bacteria, there is little correlation between when genes are important for optimal growth or fitness and when those genes are upregulated. Two common types of indirect control are constitutive expression and regulation by growth rate; these occur for genes with diverse functions and often seem to be suboptimal. Because genes that have closely related functions can have dissimilar expression patterns, regulation may be suboptimal in the wild as well as in the laboratory.     

An alternative method to determine maximal accumulated O2 deficit in runners

An accepted measure of anaerobic capacity is the maximal O2 deficit. But it is not feasible to use O2 deficit if > or =10 submaximal runs are needed to extrapolate the O2 demand of high velocity running (Medb? et al. 1988). Recently, an alternative method to determine O2 deficit was proposed (Hill 1996) using only results of supramaximal cycle ergometer tests. The purpose of this study was to evaluate this alternative method with data from treadmill tests. Twenty-six runners ran at 95%, 100%, 105%, and 110% of their velocity at VO2max. Times to exhaustion, velocity, and accumulated oxygen uptake (VO2) from each individual's four tests were fit to the following equation using iterative nonlinear regression: accumulated VO2 = (O2 demand x velocity x time)-O2 deficit. The mean value s derived for O2 demand and O2 deficit were 0.198+/-0.031 ml x kg(-1) x m(-1) and 42+/-22 ml x kg(-1). SEE for the parameters were 0.007+/-0.007 ml x kg(-1) x m(-1) and 8+/-10 ml x kg(-1), respectively. Mean R2 was 0.998+/-0.003. It was concluded that O2 deficit can be determined from all-out treadmill tests without the need to perform submaximal tests.     

Production and consumption of nitric oxide by denitrifying bacteria under anaerobic and aerobic conditions

Abstract: Pseudomonas aeruginosa, P. stutzeri and Azospirillum brasilense showed highest NO production rates and NO consumption rate constants when anaerobically grown cells were tested under anaerobic conditions. Aerobic assay conditions resulted in 20–75-fold lower NO production rates. NO consumption rate constants, however, decreased by less than a factor of four. NO consumption activity was observed even in aerobically grown P. aeruginosa , provided the assay was done under anaerobic conditions. Obviously, NO consumption was less O₂-sensitive than NO production so that compensation between production and consumption occurred at lower NO mixing ratios under aerobic than under anaerobic conditions.