The complete structure of the cucumber (<Emphasis Type="Italic">Cucumis sativus</Emphasis> L.) chloroplast genome: Its composition and comparative analysis

The complete nucleotide sequence of the cucumber (C. sativus L. var. Borszczagowski) chloroplast genome has been determined. The genome is composed of 155,293 bp containing a pair of inverted repeats of 25,191 bp, which are separated by two single-copy regions, a small 18,222-bp one and a large 86,688-bp one. The chloroplast genome of cucumber contains 130 known genes, including 89 protein-coding genes, 8 ribosomal RNA genes (4 rRNA species), and 37 tRNA genes (30 tRNA species), with 18 of them located in the inverted repeat region. Of these genes, 16 contain one intron, and two genes and one ycf contain 2 introns. Twenty-one small inversions that form stem-loop structures, ranging from 18 to 49 bp, have been identified. Eight of them show similarity to those of other species, while eight seem to be cucumber specific. Detailed comparisons of ycf2 and ycf15, and the overall structure to other chloroplast genomes were performed.     

Chemical biology tools for imaging-based analysis of organelle membranes and lipids

Membrane biology studies have revealed that in addition to providing structural support for compartment formation and membrane protein function, subcellular biomembranes are also critically involved in many biological events. To facilitate our understanding of the functions, biophysical properties and structural dynamics of organelle membranes, various exciting chemical biology tools have recently emerged. This short review aims to describe the latest molecular probes for organelle membrane studies. In particular, we will feature chemical strategies to visualize and quantitatively analyze the dynamic propeties of organelle membranes and lipids and discuss current limitations and potential future directions of this challenging research area.     

Cytoplasmic motors and pollen tube growth

The growth of pollen tubes is characterized by an intense cytoplasmic streaming, during which the movements of smaller organelles (like secretory vesicles) and larger ones (including the generative cell and vegetative nucleus) are precisely coordinated. A well-characterized cytoskeletal apparatus is likely responsible for these intracellular movements. In recent years both microfilament and microtubule-based motor proteins have been identified and assumed to be the translocators of the several organelle categories. Their precise function during pollen tube growth is not yet clear, but apparently an actomyosin-based system is mainly responsible for pollen tube elongation. On the other hand, microtubules and microtubule-based motors have been thought to play a role in the maintenance of cell polarity. Both cytoskeletal systems (and their respective motor activities) could cooperate to ensure a precise regulation of pollen tube growth.     

Cloning and characterization of a linear 2.3 kb mitochondrial plasmid of maize

Summary A linear 2.3 kb DNA molecule found in maize mitochondria was cloned into pUC8. A natural deletion of this plasmid, found in cmsT and some N (fertile) types of maize plants, was mapped to one end of the plasmid. A minor sequence homology to S-2, another linear mitochondrial plasmid, was detected, as well as more significant sequence homology with chloroplast and maize nuclear DNA. Hybridization to teosinte mitochondrial DNA (mtDNA) revealed the presence of part of the maize plasmid in the high molecular weight mtDNA of the maize relatives. RNA dot hybridization indicates that the plasmid is transcribed in mitochondria. The termini of the 2.3 kb linear plasmid contain inverted repeated sequences; of the first 17 nucleotides of the termini, 16 are identical to the terminal inverted repeats of the linear S plasmids found in the mitochondria of cmsS maize plants.     

叶绿体蛋白质组学研究进展

蛋白质组分析是鉴定蛋白质种类和功能的有力工具之一。叶绿体作为光合作用的重要细胞器,叶绿体蛋白质组学成为了研究的热点,涉及的领域包括叶绿体的总蛋白质组学、亚细胞蛋白质组学、差异蛋白质组学和蛋白质的功能等。现主要介绍蛋白质组学的常用技术以及叶绿体蛋白质组学的最新研究进展。     

Organelle Movement in the Germinated Plooen Grains and Pollen Tubes of Oenothera odorata

The movement of organelles in the germinated pollen of Oenothera odorata was studied in detail by video microscopy. The image of the organelle movement was processed by computergation. The pollen grain of Oenothera odorata is large and easy to germinate in vitro and is suitable for the study of organelle movement . The motion of organelles in the germinated pollen grains and pollen tubes is very vigorous. But the movement of organelles in the pollen tubes is more vigorous than that in the germinating pollen grains. Some of their motion is saltatory. A kind of fibrils was observed in the germinated pollen grains. They are supposed to be made up of actin filaments. Some of the fibrils have one end connected to the plasma membrane and others have both ends linked to the plasma membrane , forming a network. Organelles move along the fibrils continuosely and the speed changes constantly . The speed of movement of organelles is not related to their dimensions. Cytochalasin B can inhibit the movement of organelles. Our results suggest that the movement of organelles is independent of the cytoplasmic streaming in the germinated pollen grains and pollen tubes.     

Variation in generative cell plastid nucleoids and male fertility in Medicago sativa

Biparental inheritance of plastids has been documented in numerous angiosperm species. The adaptive significance of the mode of plastid inheritance (unior biparental) is poorly understood. In plants exhibiting paternal inheritance of plastids, DNA-containing plastids in the microgametophyte may affect survival or growth of the gametophyte or the embryo. In this study the number of plastids containing DNA (nucleoids) in generative cells and generative cell and pollen volumes were evaluated in a range of genotypes of Medicago sativa (alfalfa). M. sativa exhibits biparental inheritance of plastids with strong paternal bias. The M. sativa genotypes used were crossed as male parents to a common genotype and the relationships between the gametophytic traits measured and male reproductive success were assessed. Generative cell plastid number and pollen grain size exhibited opposing associations with male fertility. Path analysis showed that generative cell plastid number was negatively associated with male fertility. This study provides evidence that there may be a competitive advantage at fertilization afforded sperm that have minimized their organelle content. The apparent lack of strong selection for reduced plastid number in generative cells of M. sativa may be a reflection of the diminished importance of reproductive success due to its perenniality or its long use in cultivation.     

Cytological Basis of Plastid Inheritance in Phaseolus vulgaris-Investigations of Plastids,Mitochondria and Their DNA Nucleoids During Pollen Development

Electron microscopic and DNA fluorescence microscopic observations of the plastids, mitochondria and their DNA in the developing pollen of Phaseolus vulgaris L. have demonstrated that the male plastids were excluded during microspore mitosis. The formed generative cell was free of plastids because of regional localization of plastids in early developing microspore and the extremely unequal distribution during division. The fluorescence observations of DNA showed that cytoplasmic (plastid and mitochondria) nucleoids degenerated and disappeared during the development of microspore/pollen, and were never presented in the generative cell at different development stages. These results provided precise cytological evidence of maternal plastid inheritance in Phaseolus vulgaris, which was not in accord with the biparental plastid inheritance identified from early genetic analysis. Based on authors' previous observations in a variety of common bean that the organelle DNA of male gamete was completely degenerated, the early genetic finding of the biparental plastid inheritance was unlikely to be effected by genotypic difference. Thus those biparental plastid inheritance might be caused by occational male plastid transmission, and plastid uniparental maternal inheritance was the species character of Phaseolus vulgaris.     

菜豆花粉发育中质体和线粒体及其DNA存在的状况——着重阐明质体遗传的细胞学基础

应用电镜和DNA的DAPI荧光检测技术研究了菜豆(Phaseolus vulgaris L.)小孢子/花粉发育中质体和线粒体及其DNA存在的状况。观察表明:在小孢子分裂时质体全部分配到营养细胞中,初形成的生殖细胞已不含质体。线粒体和质体的DNA在花粉发育中也先后降解,生殖细胞从刚形成时发育至成熟花粉时期这两种细胞器DNA均不存在。研究结果为菜豆质体母系遗传提供了确切的细胞学证据。遗传分析的研究曾确定菜豆质体为双亲遗传,对与本研究结论不同的原因进行了讨论。     

Microbody proliferation and segregation cycle in the single-microbody alga Cyanidioschyzon merolae

The proliferation cycle of the microbody was studied in the primitive red alga Cyanidioschyzon merolae, which contains one microbody per cell. Cells were synchronized with a dark/light cycle, and the morphology of the microbody and its interaction with other organelles were observed three-dimensionally by fluorescence microscopy, transmission electron microscopy, and computer-assisted three-dimensional reconstruction of serial thin sections. The microbody in interphase cells is a sphere of 0.3 μm in diameter without a core. In M-phase, the microbody passes through a series of irregular shapes, in the order rod, worm, branched, H-shaped and dumbbell, and symmetric fission occurs just before cytokinesis. The microbody duplicates its volume in M-phase and three-dimensional quantitative analysis revealed that its surface area increases before its volume does. The microbody touches the mitochondrion and the chloroplast throughout its proliferation cycle, except briefly in interphase cells, winding around the divisional plane of the mitochondrion at one phase. Immunocytochemical labeling of catalase as a marker of matrix proteins of the microbody revealed that the duplication of catalase occurs in tandem with the volume increase. While no specific apparatus was identified in the microbody divisional areas, we identified an electron-dense apparatus about 30–50 nm in diameter between the microbody and the mitochondrion that may play a role in segregating the daughter microbodies. These results are the first characterization to show the morphological changes of one microbody in a one-microbody alga without proliferation-inducing substrates, which have been used in many studies, and clearly show that two daughter microbodies arise by binary fission of the pre-existing microbody. Received: 11 November 1998 / Accepted: 22 December 1998     

The peroxisome: still a mysterious organelle

More than half a century of research on peroxisomes has revealed unique features of this ubiquitous subcellular organelle, which have often been in disagreement with existing dogmas in cell biology. About 50 peroxisomal enzymes have so far been identified, which contribute to several crucial metabolic processes such as β-oxidation of fatty acids, biosynthesis of ether phospholipids and metabolism of reactive oxygen species, and render peroxisomes indispensable for human health and development. It became obvious that peroxisomes are highly dynamic organelles that rapidly assemble, multiply and degrade in response to metabolic needs. However, many aspects of peroxisome biology are still mysterious. This review addresses recent exciting discoveries on the biogenesis, formation and degradation of peroxisomes, on peroxisomal dynamics and division, as well as on the interaction and cross talk of peroxisomes with other subcellular compartments. Furthermore, recent advances on the role of peroxisomes in medicine and in the identification of novel peroxisomal proteins are discussed.     

Genome analysis and its significance in four unicellular algae, Cyanidioshyzon merolae, Ostreococcus tauri, Chlamydomonas reinhardtii, and Thalassiosira pseudonana

Algae play a more important role than land plants in the maintenance of the global environment and productivity. Progress in genome analyses of these organisms means that we can now obtain information on algal genomes, global annotation and gene expression. The full genome information for several algae has already been analyzed. Whole genomes of the red alga Cyanidioshyzon merolae, the green algae Ostreococcus tauri and Chlamydomonas reinhardtii, and the diatom Thalassiosira pseudonana have been sequenced. Genome composition and the features of cells among the four algae were compared. Each alga maintains basic genes as photosynthetic eukaryotes and possesses additional gene groups to represent their particular characteristics. This review discusses and introduces the latest research that makes the best use of the particular features of each organism and the significance of genome analysis to study biological phenomena. In particular, examples of post-genome studies of organelle multiplication in C. merolae based on analyzed genome information are presented.     

Regular arrangements of mitochondria and plastids during sporogenesis inEquisetum

Summary Plastids and mitochondria in premeiotic cells ofEquisetum were situated at random. By early prophase I all these organelles aggregated for a short period into one group at the nuclear envelope, but subsequently the organelles became again scattered. By late prophase I they aggregated into two groups at opposite sides of the nucleus, then moved towards the equator of the cell. By interphase plastids and mitochondria aggregated into a layer which divided each dyad into two parts. After telophase II the reorganized layer divided the tetrad into four parts. The organelle layer underwent differentiation into three strata. The cell plate was formed in the middle one which was constituted of mitochondria.     

脂滴——细胞脂类代谢的细胞器

脂滴是细胞内中性脂贮存的主要场所,由极性单磷脂层包裹疏水核心组成。近年来的蛋白质组学研究表明,脂滴表面还存在着许多功能蛋白,进一步揭示了脂滴可能参与细胞内物质的代谢和转运,以及细胞信号传导等过程,是一个活动旺盛的多功能细胞器。实验结果还证明,脂滴不但是甘油三酯贮存和分解、花生四烯酸代谢和前列腺素合成的主要场所,脂滴还具有合成甘油三酯和磷酯的功能。由此可见,脂滴可能是细胞内参与脂类合成代谢的细胞器。     

The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae)

We used a unique combination of techniques to sequence the first complete chloroplast genome of a lycophyte, Huperzia lucidula. This plant belongs to a significant clade hypothesized to represent the sister group to all other vascular plants. We used fluorescence-activated cell sorting (FACS) to isolate the organelles, rolling circle amplification (RCA) to amplify the genome, and shotgun sequencing to 8× depth coverage to obtain the complete chloroplast genome sequence. The genome is 154,373 bp, containing inverted repeats of 15,314 bp each, a large single-copy region of 104,088 bp, and a small single-copy region of 19,657 bp. Gene order is more similar to those of mosses, liverworts, and hornworts than to gene order for other vascular plants. For example, the Huperzia chloroplast genome possesses the bryophyte gene order for a previously characterized 30 kb inversion, thus supporting the hypothesis that lycophytes are sister to all other extant vascular plants. The lycophyte chloroplast genome data also enable a better reconstruction of the basal tracheophyte genome, which is useful for inferring relationships among bryophyte lineages. Several unique characters are observed in Huperzia, such as movement of the gene ndhF from the small single copy region into the inverted repeat. We present several analyses of evolutionary relationships among land plants by using nucleotide data, inferred amino acid sequences, and by comparing gene arrangements from chloroplast genomes. The results, while still tentative pending the large number of chloroplast genomes from other key lineages that are soon to be sequenced, are intriguing in themselves, and contribute to a growing comparative database of genomic and morphological data across the green plants.     

Zooming in: fractionation strategies in proteomics

The recent development of mass spectrometry, i.e., high sensitivity, automation of protein identification and some post-translational modifications (PTMs) significantly increased the number of large-scale proteomics projects. However, there are still considerable limitations as none of the currently available proteomics techniques allows the analysis of an entire proteome in a single step procedure. On the other hand, there are several successful studies analyzing well defined groups of proteins, e.g., proteins of purified organelles, membrane microdomains or isolated proteins with certain PTMs. Coupling of advanced separation methodologies (different prefractionation strategies, such as subcellular fractionation, affinity purification, fractionation of proteins and peptides according to their physicochemical properties) to highly sensitive mass spectrometers provides powerful means to detect and analyze dynamic changes of low abundant regulatory proteins in eukaryotic cells on the subcellular level. This review summarizes and discusses recent strategies in proteomics approaches where different fractionation strategies were successfully applied.     

Effects of the Actin‐Stabilizing Drug,Jasplakinolide, on Pigment Granule Motility in Isolated Retinal Pigment Epithelial (RPE) Cells of Green Sunfish,Lepomis cyanellus

The retinal pigment epithelium (RPE) of teleosts contains pigment granules that migrate in response to changes in light condition. Dissociated, cultured RPE cells in vitro can be triggered to aggregate or disperse pigment granules by the application of cAMP or dopamine, respectively. Previous research using the actin‐disrupting drug, cytochalasin D, suggested that pigment granule motility is actin dependent. To further examine the role of actin in pigment granule motility, we tested the effects of the actin‐stabilizing drug, jasplakinolide, on pigment granule motility. Pigment granules in previously dispersed RPE cells remained dispersed after jasplakinolide exposure (0.1–1 μM), but the drug halted movement of most pigment granules and stimulated rapid bi‐directional movements in a small subset of granules. Jasplakinolide also blocked net pigment granule aggregation and interfered with the maintenance of full aggregation. Although jasplakinolide did not block pigment granule dispersion, it did alter the motility of dispersing granules compared to control cells; rather than the normal saltatory, primarily centrifugal movements, granules of jasplakinolide‐treated cells demonstrated slow, creeping centrifugal movements and more rapid bi‐directional movements. Jasplakinolide also altered cell morphology; the length and thickness of apical projections increased, and enlarged, paddle‐like structures, which contained F‐actin appeared at the tips of projections. Actin antibody labeling of jasplakinolide‐treated cells revealed a more reticulated network of actin compared to antibody‐labeled control cells. These results indicate that jasplakinolide‐induced disruption of the actin network compromises normal pigment granule dispersion and aggregation in isolated RPE cells, thus providing further evidence that these movements are actin dependent.     

脂滴:与肿瘤发展密切相关的特殊细胞器

脂滴(Lipid droplet,LD)存在于从酵母菌到人类的大多数细胞中,是储存中性脂的主要场所。近年来提出脂滴是一种高度活跃的细胞脂类代谢细胞器,是脂质代谢、转运以及信号传递的主要调控因子。脂滴作为脂质中心,可以参与细胞内的脂质合成与代谢,其代谢与肿瘤密切联系在一起,并在各种肿瘤细胞中大量积累。本文从脂滴的生物发生、结构和功能等方面进行了详细的描述,进一步探讨了脂滴在不同类型肿瘤发展过程中的作用,以期为肿瘤的临床诊疗提供参考依据。     

From observing to controlling: Inducible control of organelle dynamics and interactions

The dynamics and interactions of cellular organelles underlie many aspects of cellular functioning. Until recently, assessment of organelle dynamics has been primarily observational or required whole-cell perturbations to assess the implications of altered organelle motility and positioning. However, thanks to recently developed and optimized intervention strategies, we now have the ability to control organelles in their unperturbed state, altering organelle positioning, membrane trafficking pathways, as well as organelle interactions. This can be performed both globally and locally, giving fine control over the range, reversibility, and extent of organelle dynamics. Here, we describe how these tools are currently used for controlling organelles and give insight into the exciting future of this emerging field.     

Podosomes: Multipurpose organelles?

Thirty years of research have accumulated ample evidence that podosome clusters qualify as genuine cellular organelles that are being found in more and more cell types. A podosome is a dynamic actin-based and membrane-bound microdomain and the organelle consists in an interconnected network of such basic units, forming a cytoskeletal superstructure linked to the plasma membrane. At this strategic location, podosomes are privileged sites of interactions with the pericellular environment that regulates their formation, density, lifetime, distribution, architecture and functioning. Actin polymerization is the driving force behind most podosome characteristics. In contrast to classical organelles, podosomes are not vital at the cell level but rather serve diverse and often intricate functions of which adhesion, matrix degradation and substrate sensing are the most established. These capabilities involve specific molecules, depend on podosome organization and may vary according to the cell type in which they form. Podosome-associated diseases manifest by loss or gain of podosome functions and include genetic diseases affecting podosome components and various cancers where tumor cells ectopically express podosome equivalents (invadopodia).