A Possible Role for Short Introns in the Acquisition of Stroma-Targeting Peptides in the Flagellate Euglena gracilis

The chloroplasts of Euglena gracilis bounded by three membranes arose via secondary endosymbiosis of a green alga in a heterotrophic euglenozoan host. Many genes were transferred from symbiont to the host nucleus. A subset of Euglena nuclear genes of predominately symbiont, but also host, or other origin have obtained complex presequences required for chloroplast targeting. This study has revealed the presence of short introns (41–93 bp) either in the second half of presequence-encoding regions or shortly downstream of them in nine nucleus-encoded E. gracilis genes for chloroplast proteins (Eno29, GapA, PetA, PetF, PetJ, PsaF, PsbM, PsbO, and PsbW). In addition, the E. gracilis Pbgd gene contains two introns in the second half of presequence-encoding region and one at the border of presequence-mature peptide-encoding region. Ten of 12 introns present within presequence-encoding regions or shortly downstream of them identified in this study have typical eukaryotic GT/AG borders, are T-rich, 45–50 bp long, and pairwise sequence identities range from 27 to 61%. Thus single recombination events might have been mediated via these cis-spliced introns. A double crossing over between these cis-spliced introns and trans-spliced introns present in 5′-UTRs of Euglena nuclear genes is also likely to have occurred. Thus introns and exon-shuffling could have had an important role in the acquisition of chloroplast targeting signals in E. gracilis. The results are consistent with a late origin of photosynthetic euglenids.     

Evolution of the Chloroplast Genome in Photosynthetic Euglenoids: A Comparison of Eutreptia viridis and Euglena gracilis (Euglenophyta)

The chloroplast genome of Eutreptia viridis Perty, a basal taxon in the photosynthetic euglenoid lineage, was sequenced and compared with that of Euglena gracilis Ehrenberg, a crown species. Several common gene clusters were identified and gene order, conservation, and sequence similarity was assessed through comparisons with Euglena gracilis. Significant gene rearrangements were present between Eutreptia viridis and Euglena gracilis chloroplast genomes. In addition, major expansion has occurred in the Euglena gracilis chloroplast accounting for its larger size. However, the key chloroplast genes are present and differ only in the absence of psaM and roaA in Eutreptia viridis, and psaI in Euglena gracilis, suggesting a high level of gene conservation within the euglenoid lineage. Further comparisons with the plastid genomes of closely related green algal taxa have provided additional support for the hypothesis that a Pyramimonas-like alga was the euglenoid chloroplast donor via secondary endosymbiosis.     

Indications for acceleration-dependent changes of membrane potential in the flagellate Euglena gracilis

Summary. The effects of the calcium sequester EGTA on gravitactic orientation and membrane potential changes in the unicellular flagellate Euglena gracilis were investigated during a recent parabolic-flight experiment aboard of an Airbus A300. In the course of a flight parabola, an acceleration profile is achieved which yields subsequently about 20 s of hypergravity (1.8 g _n), about 20 s of microgravity, and another 20 s of hypergravity phases. The movement behavior of the cells was investigated with real-time, computer-based image analysis. Membrane potential changes were detected with a newly developed photometer which measures absorption changes of the membrane potential-sensitive probe oxonol VI. To test whether the data obtained by the oxonol device were reliable, the signal of non-oxonol-labelled cells was recorded. In these samples, no absorption shift was detected. Changes of the oxonol VI signals indicate that the cells depolarize during acceleration (very obvious in the step from microgravity to hypergravity) and slightly hyperpolarize in microgravity, which can possibly be explained with the action of Ca-ATPases. These signals (mainly the depolarization) were significantly suppressed in the presence of EGTA (5 mM). Gravitaxis in parallel was also inhibited after addition of EGTA. Initially, negative gravitaxis was inverted into a positive one. Later, gravitaxis was almost undetectable. Correspondence and reprints: Department of Plant Ecophysiology, University of Erlangen-Nürnberg, Staudtstrasse 5, 91058 Erlangen, Federal Republic of Germany.     

植物早期光诱导蛋白基因研究进展

植物早期光诱导蛋白（ELIP）是核编码的叶绿体蛋白,它属于叶绿素结合蛋白超家族的成员。皿伊基因是一古老的基因,在原核细胞中即已存在。真核生物细胞核中的皿,尸基因最初可能来源于其质体基因组。目前,已从30多种不同植物中克隆到该基因,研究发现它们多属于胁迫诱导基因,其功能可能涉及光保护作用。本文介绍了20多年来皿,尸基因的克隆、生物发生、表达调控和功能方面的研究进展,以期为今后的进一步研究奠定基础。     

The Effects of Regulatory Proteins RcsA and RcsB on the Expression of the Vibrio fischeri lux Operon in Escherichia coli

A study was made of the effect of RcsA and RcsB on the Vibrio fischeri lux expression in Escherichia coli. RcsA suppressed the LuxR activity and thereby inhibited expression of the lux genes coding for luciferase and reductase. In osmotic shock, RcsA–RcsB activated lux expression and, consequently, the bioluminescence of E. coli cells in the early log phase.     

Biphasic and Dually Coordinated Expression of the Genes Encoding Major Shell Matrix Proteins in the Pearl Oyster Pinctada fucata

Regional expression patterns of shell matrix protein genes of Pinctada fucata were investigated using real-time quantitative polymerase chain reaction (PCR) and in situ hybridization. Six shell matrix proteins examined in this study indicated a distinct biphasic pattern of expression, falling into one of the following three groups: (1) expressed only in the more dorsal region of the mantle (MSI60 and N16); (2) expressed only in the more ventral region (MSI31, Prismalin-14, and Aspein); and (3) expressed in both regions (nacrein). The ubiquity of the last protein probably reflects its general role as a carbonate-producing enzyme, while the other groups are interpreted as corresponding to the distinction between the two varieties of shell layers, the aragonitic nacreous layer and the calcitic prismatic layer. In addition, the constituent genes of each of these two groups indicated similar levels of relative expression among different sites even among different individuals, suggesting that the genes of each group share a single upstream regulatory factor, respectively, and that these genes are expressed in a dually coordinated fashion.     

在发育性变化相关基因表达特性检测中内参基因的有效性和实时定量PCR解析方法的适用性

实时定量PCR技术(quantitative real-time PCR assay, rtQ-PCR)是一种快速检测核酸水平的方法.在多数相对定量法的运用过程中,会同时引入内参基因用以校正由于采样和操作误差所带来的样本之间核酸总量的差别.一个理想的内参基因的表达水平必须维持恒定或至少不受实际试验条件和机体发育变化的影响.由于作为候选内参基因的看家基因也可能会随着试验条件改变呈现出发育性变化和/或差异表达,故在相关研究中,内参基因的选择就成为试验的关键和难点.本研究采用rtQ-PCR技术,以鸭胚胎期和出雏早期肝脏中IGF-玉mRNA表达的发育性变化检测为例,探讨涉及发育性变化的基因表达解析过程中内参基因的选择,并评估绝对和相对定量两种解析方法的适用性.我们认为涉及发育性变化的基因表达解析过程中内参基因的选择时,采用2-△Ct法对内参基因的有效性进行的组间评价,比Genorm等方法对内参基因的有效性进行的整体评价更为科学;涉及发育性变化的基因表达解析过程中,如果难以找到一个理想的内参基因时,绝对rtQ-PCR解析方法将比随意选取一种内参基因作为内标的相对rtQ-PCR解析方法更为简单和适用,结果的解析也更为直观和可靠.     

Powers of Multiple-Testing Procedures for Identification of Genes Significantly Differentially Expressed in Microarray Experiments

Because of the high operation costs involved in microarray experiments, the determination of the number of replicates required to detect a gene significantly differentially expressed in a given multiple-testing procedure is of considerable significance. Calculation of power/replicate numbers required in multiple-testing procedures provides design guidance for microarray experiments. Based on this model and by choice of a multiple-testing procedure, expression noises based on permutation resampling can be considerably minimized. The method for mixture distribution model is suitable to various microarray data types obtained from single noise sources, or from multiple noise sources. By using the biological replicate number required in microarray experiments for a given power or by determining the power required to detect a gene significantly differentially expressed, given the sample size, or the best multiple-testing method can be chosen. As an example, a single-distribution model of t-statistic was fitted to an observed microarray dataset of 3 000 genes responsive to stroke in rat, and then used to calculate powers of four popular multiple-testing procedures to detect a gene of an expression change D. The results show that the B-procedure had the lowest power to detect a gene of small change among the multiple-testing procedures, whereas the BH-procedure had the highest power. However, all multiple-testing procedures had the same power to identify a gene having the largest change. Similar to a single test, the power of the BH-procedure to detect a small change does not vary as the number of genes increases, but powers of the other three multiple-testing procedures decline as the number of genes increases.     

An Integrated Computer System for Studying the Regulation of Eukaryotic Gene Expression

The review describes several modules of the GeneExpress integrated computer system concerning the regulation of gene expression in eukaryotes. Approaches to the presentation of experimental data in databases are considered. The employment of GeneExpress in computer analysis and modeling of the organization and function of genetic systems is illustrated with examples. GeneExpress is available at http://wwwmgs.bionet.nsc.ru/mgs/gnw/.     

Shift in Expression of the Genes of Primary Metabolism and Chloroplast Transporters in Chlamydomonas reinhardtii under Different Trophic Conditions

Russian Journal of Plant Physiology - Chlamydomonas reinhardtii P.A. Dangeard is a unicellular green alga capable to assimilate acetate. C. reinhardtii growth and metabolism distinctly depend on...