Formation of Complex and Unstable Chromosomal Translocations in Yeast

Genome instability, associated with chromosome breakage syndromes and most humancancers, is still poorly understood. In the yeast Saccharomycescerevisiae, numerous genes with roles in the preservation of genomeintegrity have been identified. DNA-damage-checkpoint-deficient yeast cells thatlack Sgs1, a RecQ-like DNA helicase related to the humanBloom''s-syndrome-associated helicase BLM, show an increased rate ofgenome instability, and we have previously shown that they accumulate recurringchromosomal translocations between three similar genes, CAN1,LYP1 and ALP1. Here, the chromosomallocation, copy number and sequence similarity of the translocation targetsALP1 and LYP1 were altered to gain insightinto the formation of complex translocations. Among 844 clones with chromosomalrearrangements, 93 with various types of simple and complex translocationsinvolving CAN1, LYP1 and ALP1were identified. Breakpoint sequencing and mapping showed that the formation ofcomplex translocation types is strictly dependent on the location of theinitiating DNA break and revealed that complex translocations arise via acombination of interchromosomal translocation and template-switching, as well asfrom unstable dicentric intermediates. Template-switching occurred betweensequences on the same chromosome, but was inhibited if the genes weretransferred to different chromosomes. Unstable dicentric translocationscontinuously gave rise to clones with multiple translocations in variouscombinations, reminiscent of intratumor heterogeneity in human cancers. Basesubstitutions and evidence of DNA slippage near rearrangement breakpointsrevealed that translocation formation can be accompanied by point mutations, andtheir presence in different translocation types within the same clone providesevidence that some of the different translocation types are derived from eachother rather than being formed de novo. These findings provideinsight into eukaryotic genome instability, especially the formation oftranslocations and the sources of intraclonal heterogeneity, both of which areoften associated with human cancers.     

Analysis of Respiratory Chain Regulation in Roots of Soybean Seedlings

Changes in the respiratory rate and the contribution of the cytochrome (Cyt) c oxidase and alternative oxidase (COX and AOX, respectively) were investigated in soybean (Glycine max L. cv Stevens) root seedlings using the ¹⁸O-discrimination method. In 4-d-old roots respiration proceeded almost entirely via COX, but by d 17 more than 50% of the flux occurred via AOX. During this period the capacity of COX, the theoretical yield of ATP synthesis, and the root relative growth rate all decreased substantially. In extracts from whole roots of different ages, the ubiquinone pool was maintained at 50% to 60% reduction, whereas pyruvate content fluctuated without a consistent trend. In whole-root immunoblots, AOX protein was largely in the reduced, active form at 7 and 17 d but was partially oxidized at 4 d. In isolated mitochondria, Cyt pathway and succinate dehydrogenase capacities and COX I protein abundance decreased with root age, whereas both AOX capacity and protein abundance remained unchanged. The amount of mitochondrial protein on a dry-mass basis did not vary significantly with root age. It is concluded that decreases in whole-root respiration during growth of soybean seedlings can be largely explained by decreases in maximal rates of electron transport via COX. Flux via AOX is increased so that the ubiquinone pool is maintained in a moderately reduced state.     

Circadian Regulation of Glutathione Levels and Biosynthesis in Drosophila melanogaster

Circadian clocks generate daily rhythms in neuronal, physiological, and metabolic functions. Previous studies in mammals reported daily fluctuations in levels of the major endogenous antioxidant, glutathione (GSH), but the molecular mechanisms that govern such fluctuations remained unknown. To address this question, we used the model species Drosophila, which has a rich arsenal of genetic tools. Previously, we showed that loss of the circadian clock increased oxidative damage and caused neurodegenerative changes in the brain, while enhanced GSH production in neuronal tissue conferred beneficial effects on fly survivorship under normal and stress conditions. In the current study we report that the GSH concentrations in fly heads fluctuate in a circadian clock-dependent manner. We further demonstrate a rhythm in activity of glutamate cysteine ligase (GCL), the rate-limiting enzyme in glutathione biosynthesis. Significant rhythms were also observed for mRNA levels of genes encoding the catalytic (Gclc) and modulatory (Gclm) subunits comprising the GCL holoenzyme. Furthermore, we found that the expression of a glutathione S-transferase, GstD1, which utilizes GSH in cellular detoxification, significantly fluctuated during the circadian day. To directly address the role of the clock in regulating GSH-related rhythms, the expression levels of the GCL subunits and GstD1, as well as GCL activity and GSH production were evaluated in flies with a null mutation in the clock genes cycle and period. The rhythms observed in control flies were not evident in the clock mutants, thus linking glutathione production and utilization to the circadian system. Together, these data suggest that the circadian system modulates pathways involved in production and utilization of glutathione.     

Changes in Hexokinase Activity in Echinochloa phyllopogon and Echinochloa crus-pavonis in Response to Abiotic Stress

Hexokinase (HXK; EC 2.7.1.1) regulates carbohydrate entry into glycolysis and is known to be a sensor for sugar-responsive gene expression. The effect of abiotic stresses on HXK activity was determined in seedlings of the flood-tolerant plant Echinochloa phyllopogon (Stev.) Koss and the flood-intolerant plant Echinochloa crus-pavonis (H.B.K.) Schult grown aerobically for 5 d before being subjected to anaerobic, chilling, heat, or salt stress. HXK activity was stimulated in shoots of E. phyllopogon only by anaerobic stress. HXK activity was only transiently elevated in E. crus-pavonis shoots during anaerobiosis. In roots of both species, anoxia and chilling stimulated HXK activity. Thus, HXK is not a general stress protein but is specifically induced by anoxia and chilling in E. phyllopogon and E. crus-pavonis. In both species HXK exhibited an optimum pH between 8.5 and 9.0, but the range was extended to pH 7.0 in air-grown E. phyllopogon to 6.5 in N₂-grown E. phyllopogon. At physiologically relevant pHs (6.8 and 7.3, N₂ and O₂ conditions, respectively), N₂-grown seedlings retained greater HXK activity at the lower pH. The pH response suggests that in N₂-grown seedlings HXK can function in a more acidic environment and that a specific isozyme may be important for regulating glycolytic activity during anaerobic metabolism in E. phyllopogon.     

线粒体自噬调控机制研究进展

线粒体为细胞正常生命运动提供能量和物质;然而各种因素会导致线粒体损伤,衰老及功能紊乱,它们是细胞潜在的危险因素,必需及时清除,线粒体自噬可以起到这一作用,维持细胞稳态。当细胞处于恶劣环境时,线粒体自噬可通过降解线粒体补充生命必需物质,从而度过危机维持生存。另外线粒体自噬会在某些情况下通过降解正常线粒体来维持线粒体质量和数量的平衡。不同生物中具有不同的线粒体自噬途径和机制,酵母中主要通过Atg32磷酸化调控线粒体自噬;哺乳动物中则存在分别由Parkin-PINK1、Nix、FUNDC1等不同蛋白介导的线粒体自噬调控机制;植物线粒体自噬的研究主要集中在拟南芥,其途径及具体调控机制尚不明确。综述了近年来酵母、动物和植物中线粒体自噬的作用机制及调控因子等方面的研究进展。     

Estimating the Excess Investment in Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase in Leaves of Spring Wheat Grown under Elevated CO2

Wheat (Triticum aestivum L.) was grown under CO₂ partial pressures of 36 and 70 Pa with two N-application regimes. Responses of photosynthesis to varying CO₂ partial pressure were fitted to estimate the maximal carboxylation rate and the nonphotorespiratory respiration rate in flag and preceding leaves. The maximal carboxylation rate was proportional to ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) content, and the light-saturated photosynthetic rate at 70 Pa CO₂ was proportional to the thylakoid ATP-synthase content. Potential photosynthetic rates at 70 Pa CO₂ were calculated and compared with the observed values to estimate excess investment in Rubisco. The excess was greater in leaves grown with high N application than in those grown with low N application and declined as the leaves senesced. The fraction of Rubisco that was estimated to be in excess was strongly dependent on leaf N content, increasing from approximately 5% in leaves with 1 g N m⁻² to approximately 40% in leaves with 2 g N m⁻². Growth at elevated CO₂ usually decreased the excess somewhat but only as a consequence of a general reduction in leaf N, since relationships between the amount of components and N content were unaffected by CO₂. We conclude that there is scope for improving the N-use efficiency of C₃ crop species under elevated CO₂ conditions.     

Mathematical Model for Growth Regulation of Fission Yeast Schizosaccharomyces pombe

Regulation of polarised cell growth is essential for many cellular processes including spatial coordination of cell morphology changes during the division cycle. We present a mathematical model of the core mechanism responsible for the regulation of polarised growth dynamics during the fission yeast cell cycle. The model is based on the competition of growth zones localised at the cell tips for a common substrate distributed uniformly in the cytosol. We analyse the bifurcations in this model as the cell length increases, and show that the growth activation dynamics provides an explanation for the new-end take-off (NETO) as a saddle-node bifurcation at which the cell sharply switches from monopolar to bipolar growth. We study the parameter sensitivity of the bifurcation diagram and relate qualitative changes of the growth pattern, e.g. delayed or absent NETO, to previously observed mutant phenotypes. We investigate the effects of imperfect asymmetric cell division, and show that this leads to distinct growth patterns that provide experimentally testable predictions for validating the presented competitive growth zone activation model. Finally we discuss extension of the model for describing mutant cells with more than two growth zones.     

Nitrile-specifier Proteins Involved in Glucosinolate Hydrolysis in Arabidopsis thaliana

Glucosinolates are plant secondary metabolites present in Brassicaceae plants such as the model plant Arabidopsis thaliana. Intact glucosinolates are believed to be biologically inactive, whereas degradation products after hydrolysis have multiple roles in growth regulation and defense. The degradation of glucosinolates is catalyzed by thioglucosidases called myrosinases and leads by default to the formation of isothiocyanates. The interaction of a protein called epithiospecifier protein (ESP) with myrosinase diverts the reaction toward the production of epithionitriles or nitriles depending on the glucosinolate structure. Here we report the identification of a new group of nitrile-specifier proteins (AtNSPs) in A. thaliana able to generate nitriles in conjunction with myrosinase and a more detailed characterization of one member (AtNSP2). Recombinant AtNSP2 expressed in Escherichia coli was used to test its impact on the outcome of glucosinolate hydrolysis using a gas chromatography-mass spectrometry approach. AtNSP proteins share 30–45% sequence homology with A. thaliana ESP. Although AtESP and AtNSP proteins can switch myrosinase-catalyzed degradation of 2-propenylglucosinolate from isothiocyanate to nitrile, only AtESP generates the corresponding epithionitrile. Using the aromatic benzylglucosinolate, recombinant AtNSP2 is also able to direct product formation to the nitrile. Analysis of glucosinolate hydrolysis profiles of transgenic A. thaliana plants overexpressing AtNSP2 confirms its nitrile-specifier activity in planta. In silico expression analysis reveals distinctive expression patterns of AtNSPs, which supports a biological role for these proteins. In conclusion, we show that AtNSPs belonging to a new family of A. thaliana proteins structurally related to AtESP divert product formation from myrosinase-catalyzed glucosinolate hydrolysis and, thereby, likely affect the biological consequences of glucosinolate degradation. We discuss similarities and properties of AtNSPs and related proteins and the biological implications.Brassicaceae plants such as oilseed rape (Brassica napus), turnip (Brassica rapa), and white mustard (Sinapis alba) as well as the model plant Arabidopsis thaliana contain a group of secondary metabolites known as glucosinolates (GSLs)² (1, 2). These are β-thioglucoside N-hydroxysulfates with a sulfur-linked β-d-glucopyranose moiety and a variable side chain that is derived from one of eight amino acids or their methylene group-elongated derivatives. Aliphatic GSLs are derived from alanine, leucine, isoleucine, valine, or predominantly methionine. Tyrosine or phenylalanine give aromatic GSLs, and tryptophan-derived GSLs are called indolic GSLs (for review, see Ref. 3). Although more than 120 different GSLs have been identified in total so far, individual plant species usually contain only a few GSLs (2). Quantitative and qualitative differences of GSL profiles are also observed within a species, such as, for example, for different A. thaliana ecotypes (4–6). In addition, GSL composition varies among organs and during the life cycle of plants (7, 8) and is affected by external factors (9).Intact GSLs are mostly considered to be biologically inactive. Most GSL degradation products have toxic effects on insect, fungal, and bacterial pests, serve as attractants for specialist insects, or may have beneficial health effects for humans (10–15). The enzymatic degradation of GSLs (Fig. 1A), which occurs massively upon tissue damage, is catalyzed by plant thioglucosidases called myrosinases (EC 3.2.1.147; glycoside hydrolase family 1). Depending on several factors (e.g. GSL structure, proteins, cofactors, pH) myrosinase-catalyzed hydrolysis of GSLs can lead to a variety of products (Fig. 1B; for review, see Refs. 16 and 17). Of these, isothiocyanates are the most common as their formation only requires myrosinase activity. Thiocyanates on the other hand are only produced from a very limited number of GSLs, and their formation necessitates the presence of a thiocyanate-forming factor in addition to myrosinase (18). A thiocyanate-forming protein (TFP) has recently been identified in Lepidium sativum (19). Alkenyl GSLs, a subgroup of aliphatic GSLs containing a terminal unsaturation in their side chain, can lead to the production of epithionitriles through the cooperative action of myrosinase and a protein called epithiospecifier protein (ESP (20)) in a ferrous ion-dependent way (21–23). Both TFP and ESP contain a series of Kelch repeats (19). Kelch repeats are involved in protein-protein interactions, and Kelch repeat-containing proteins are involved in a number of diverse biological processes (24). In addition to isothiocyanates, nitriles are the major group of GSL hydrolysis products. Although ESP and TFP activities can generate nitriles (19, 21, 25, 26), indications for an ESP-independent nitrile-specifier activity exist. The GSL hydrolysis profile of A. thaliana roots, an organ that does not show ESP expression or activity (27), reveals predominantly the presence of nitriles (28). In addition, leaf tissue of A. thaliana ecotypes supposedly devoid of ESP activity produces a certain amount of nitriles upon autolysis (21). Under acidic buffer conditions, a non-enzymatic production of nitriles from GSLs is observed (Ref. 29 and references therein). Increasing Fe²⁺ concentrations have also been shown to favor nitrile formation over isothiocyanate formation from a number of GSLs in the presence of myrosinase and absence of ESP (21, 22). Therefore, a non-enzymatic origin of this nitrile production cannot be excluded, although the presence of a nitrile-specifier protein is a tempting alternative. Although ESP is able to generate nitriles, it has also been shown that the conversion rates of GSLs to nitriles are lower than those of GSLs to epithionitriles for ESP (21, 22).Open in a separate windowFIGURE 1.Simplified scheme of enzymatic GSL hydrolysis (A) and structures and names of GSLs and their hydrolysis products that are mentioned in the article. (B). A, myrosinase acts on GSLs to form an unstable aglycone intermediate that can rearrange spontaneously to form an isothiocyanate. Hydrolysis can be diverted from this default route under certain conditions (e.g. the presence of NSPs, ferrous ions, or at pH < 5) to give the corresponding nitrile. ESP is responsible for the formation of epithionitriles from alkenyl GSLs in a ferrous ion-dependent mechanism. B, the general structure of GSLs, indicating the variable side chain as R, is given as well as the three major classes of hydrolysis products (i.e. isothiocyanates, nitriles, and epithionitriles). The listed GSLs are the ones mentioned in this article and are arranged according to the class of GSLs they belong to and with an increase in chain length or complexity. The names of the respective hydrolysis products are given for a better understanding of the present article, and not all were encountered during our studies.A nitrile-specifier protein (NSP) that is able to redirect the hydrolysis of GSLs toward nitriles has been cloned from the larvae of the butterfly Pieris rapae (30). This protein does not, however, exhibit sequence similarity to plant ESP, and a corresponding plant nitrile-specifier protein has not yet been identified. We report here the identification of a group of six A. thaliana genes with some sequence similarity to A. thaliana ESP, providing evidence for a new family of nitrile-specifier proteins and a more detailed characterization of one member that possesses nitrile-specifier activity in vitro, when applied exogenously to plant tissue and after ectopic expression in the two A. thaliana ecotypes Col-0 and C24. Despite its sequence homology to A. thaliana epithiospecifier protein (AtESP), it does not possess epithiospecifier activity under similar conditions. Therefore, we propose to designate this protein as A. thaliana nitrile-specifier protein 2 (AtNSP2). Although the biological roles of AtNSP2 and related proteins are not yet known, their specificities and distinctive expression patterns indicate the presence of a fine-tuned mechanism for GSL degradation controlling the outcome of an array of biologically active molecules.     

Polygalacturonase-Mediated Solubilization and Depolymerization of Pectic Polymers in Tomato Fruit Cell Walls : Regulation by pH and Ionic Conditions

The hydrolysis of cell wall pectins by tomato (Lycopersicon esculentum) polygalacturonase (PG) in vitro is more extensive than the degradation affecting these polymers during ripening. We examined the hydrolysis of polygalacturonic acid and cell walls by PG isozyme 2 (PG2) under conditions widely adopted in the literature (pH 4.5 and containing Na⁺) and under conditions approximating the apoplastic environment of tomato fruit (pH 6.0 and K⁺ as the predominate cation). The pH optima for PG2 in the presence of K⁺ were 1.5 and 0.5 units higher for the hydrolysis of polygalacturonic acid and cell walls, respectively, compared with activity in the presence of Na⁺. Increasing K⁺ concentration stimulated pectin solubilization at pH 4.5 but had little influence at pH 6.0. Pectin depolymerization by PG2 was extensive at pH values from 4.0 to 5.0 and was further enhanced at high K⁺ levels. Oligomers were abundant products in in vitro reactions at pH 4.0 to 5.0, decreased sharply at pH 5.5, and were negligible at pH 6.0. EDTA stimulated PG-mediated pectin solubilization at pH 6.0 but did not promote oligomer production. Ca²⁺ suppressed PG-mediated pectin release at pH 4.5 yet had minimal influence on the proportional recovery of oligomers. Extensive pectin breakdown in processed tomato might be explained in part by cation- and low-pH-induced stimulation of PG and other wall-associated enzymes.