Changes in the structure of DNA molecules and the amount of DNA per plastid during chloroplast development in maize

We examined the DNA from chloroplasts obtained from different tissues of juvenile maize seedlings (from eight to 16 days old) and adult plants (50-58 days old). During plastid development, we found a striking progression from complex multigenomic DNA molecules to simple subgenomic molecules. The decrease in molecular size and complexity of the DNA paralleled a progressive decrease in DNA content per plastid. Most surprising, we were unable to detect DNA of any size in most chloroplasts from mature leaves, long before the onset of leaf senescence. Thus, the DNA content per plastid is not constant but varies during development from hundreds of genome copies in the proplastid to undetectable levels in the mature chloroplast. This loss of DNA from isolated, mature chloroplasts was monitored by three independent methods: staining intact chloroplasts with 4',6-diamidino-2-phenylindole (DAPI); staining at the single-molecule level with ethidium bromide after exhaustive deproteinization of lysed chloroplasts; and blot-hybridization after standard DNA isolation procedures. We propose a mechanism for the production of multigenomic chloroplast chromosomes that begins at paired DNA replication origins on linear molecules to generate a head-to-tail linear concatemer, followed by recombination-dependent replication.     

Localization and nucleotide sequence of the gene for the membrane polypeptide D2 from pea chloroplast DNA

Summary The gene for the membrane polypeptide D2 has been mapped on the pea (Pisum sativum) chloroplast genome. The nucleotide sequence of the gene and its flanking regions is presented. The only large open reading frame in the sequence codes for a protein of MW 39.5 kD. A potential ribosome binding site is located 6 nucleotides upstream from the initiation codon and there are two sets of putative promotor sequences in the 5 flanking region. The polypeptide has a high content of hydrophobic amino acids, predominatly grouped in clusters of 20 or more residues. The 3 end of the D2 gene is overlapped by 50 nucleotides of a second open reading frame (UORF I) which is at least 369 nucleotides long. Based on current data we suggest the D2 polypeptide to be a constituent of photosystem II (PSII).     

Most chloroplast DNA of maize seedlings in linear molecules with defined ends and branched forms

We used pulsed-field gel electrophoresis, restriction fragment mapping, and fluorescence microscopy of individual DNA molecules to analyze the structure of chloroplast DNA (cpDNA) from shoots of ten to 14 day old maize seedlings. We find that most of the cpDNA is in linear and complex branched forms, with only 3-4% as circles. We find the ends of linear genomic monomers and head-to-tail (h-t) concatemers within inverted repeat sequences (IRs) near probable origins of replication, not at random sites as expected from broken circles. Our results predict two major and three minor populations of linear molecules, each with different ends and putative origins of replication. Our mapping data predict equimolar populations of h-t linear concatemeric molecules differing only in the relative orientation (inversion) of the single copy regions. We show how recombination during replication can produce h-t linear concatemers containing an inversion of single copy sequences that has for 20 years been attributed to recombinational flipping between IRs in a circular chromosome. We propose that replication is initiated predominantly on linear, not circular, DNA, producing multi-genomic branched chromosomes and that most replication involves strand invasion of internal regions by the ends of linear molecules, rather than the generally accepted D-loop-to-theta mechanism. We speculate that if the minor amount of cpDNA in circular form is useful to the plant, its contribution to chloroplast function does not depend on the circularity of these cpDNA molecules.     

Universal primers for amplification of three non-coding regions of chloroplast DNA

Six primers for the amplification of three non-coding regions of chloroplast DNA via the polymerase chain reaction (PCR) have been designed. In order to find out whether these primers were universal, we used them in an attempt to amplify DNA from various plant species. The primers worked for most species tested including algae, bryophytes, pteridophytes, gymnosperms and angiosperms. The fact that they amplify chloroplast DNA non-coding regions over a wide taxonomic range means that these primers may be used to study the population biology (in supplying markers) and evolution (inter- and probably intraspecific phylogenies) of plants.     

Replication of chloroplast, mitochondrial and nuclear DNA during growth of unirradiated and UVB-irradiated Arabidopsis leaves

Replication of Arabidopsis nuclear, mitochondrial and chloroplast DNA (ncDNA, mtDNA, cpDNA) was assayed by measuring respective changes in copies per leaf, employing quantitative PCR (QPCR) analysis with genome-specific primer pairs. All three genomes showed parallel increases during growth of cotyledons and 5th leaves in planta, maintaining approximately 13 mtDNA copies and 280 cpDNA copies per haploid nuclear genome. Detached 5th leaves, which showed good growth and DNA replication on agar plates, were irradiated at (DNA-effective) UV-B fluences of 1.3-5.0 kJ m-2 and incubated under blue (photorepair-active) plus gold light or gold light only. Under blue light, replication of all genomes after all UV fluences was approximately as efficient as replication in unirradiated leaves. UV-irradiated leaves showed little growth under gold light only; 5 kJ m-2 stopped replication of all three genomes, 2.5 kJ m-2 stopped only cpDNA replication, and 1.3 kJ m-2 only delayed cpDNA replication. Immunoassays showed that 5 kJ m-2 induced about 1.2 cyclobutane pyrimidine dimers and 0.1 [6-4]photoproducts per kbp of bulk DNA, and that both photoproducts were completely removed during 2-3 days under blue light, suggesting efficient photorepair of at least ncDNA and cpDNA. The evidence for efficient photorepair of organellar DNA contrasts with previous studies of irradiated 5-day-old seedlings, and with the apparent absence of Arabidopsis photolyases bearing transit peptides.     

Inhibition of chloroplast protein synthesis by lincomycin and 2-(4-methyl-2,6- dinitroanilino)-N-methylpropionamide

Selective effects of lincomysin and cycloheximide in detached shoots of Pisum sativum on the synthesis of photosystem I and II proteins, and a chloroplast membrane protein of molecular weight 32000, confirm results obtained from studies of protein synthesis by isolated chloroplasts. A model is proposed in which one role of chloroplast ribosomes is to synthesize membrane proteins required for the immobilization of chloroplast components, such as photosystem I protein, which are synthesized by cytoplasmic ribosomes. 2-(4-Methyl-2,6-dinitroanilino)-N-methylpropionamide rapidly inhibits the synthesis of both the large and small subunits of Fraction I protein in greening detached pea shoots. This observation can be reconciled with the site of synthesis of the large subunit being in the chloroplast by a model which proposes that the small subunit is a positive initiation factor for the synthesis or translation of the messenger RNA for the large subunit.     

Heteroplasmy of chloroplast DNA in Medicago

Two chloroplast DNA (cpDNA) regions exhibiting a high frequency of intra- or inter-species variation were identified in 12 accessions of the genus Medicago. Restriction maps of both regions were prepared for alfalfa, and the probable nature of the events causing the DNA differences was identified. Specific DNA fragments were then cloned for use in identification of variants in each region. Two each of M. sativa ssp. varia and ssp. caerulea and one of six M. sativa ssp. sativa single plants examined possessed cpDNA heterogeneity as identified by screening extracts for fragments generated by the presence and absence of a specific Xba I restriction site. Three plants of M. sativa ssp. sativa, two of each of sspp. varia and caerulea, and three M. scutellata were also examined for single-plant cpDNA heterogeneity at a hypervariable region where differences resulted from small insertion-deletion events. A single M. scutellata plant with mixed cpDNAs was identified. Sorting out was seen when one spp. sativa plant with mixed plastid types identifiable by the Xba I restriction site difference was vegetatively propagated. This indicated that the initial stock plant was heteroplastidic. Controlled crosses will be required in order to test whether heteroplasmy results from chloroplast transmission in the pollen and to examine the dynamic of sorting out. However, heteroplasmy is apparently not a rare situation in Medicago.Contribution No 88-547-J from the Kansas Agricultural Experiment Station, Manhattan.     

Nucleotide sequence of the single ribosomal RNA operon of pea chloroplast DNA

The nucleotide sequence of an 8 kbp region of pea ( Pisum sativum L.) chloroplast DNA containing the rRNA operon and putative promoter sites has been determined and compared to the corresponding sequences from maize, tobacco and the liverwort Marchantia polymorpha . The chloroplast DNA species of all vascular plants investigated, with the exception of a few legumes including pea, and of Marchantia contain an inverted repeat with an rRNA operon. The pea rRNA operon is the first sequenced rRNA operon from a plant with only one copy of the rRNA genes per molecule of chloroplast DNA. The organization of the operon is the same as for maize, tobacco and Marchantia . i.e. tRNA-Val gene/16S rRNA gene/spacer with intron-containing genes for tRNA-Ile and tRNA-Ala/23S rRNA gene/4.5S rRNA gene/5S rRNA gene. Current evidence suggests that the tRNA-Val gene may not be contranscribed with the other genes. For pea 16S, 23S, 4.5S and 5S rRNA have 1488, 2813, 105 and 121 nucleotides, respectively. The homologies of the entire operon (the tRNA-Val gene - 5S rRNA region) to those from tobacco, maize and Marchantia are 88, 82 and 79%, respectively. The corresponding homologies for tobacco/maize, tobacco/ Marchantia and maize/ Marchantia have similar values. The 16S and 23S rRNA genes from pea are more than 90% homologous to those from the 3 other species. We conclude that the fact that pea only has one set of rRNA genes per molecule of chloroplast DNA is apparently not correlated with any significant difference between the pea operon and the rRNA operons from tobacco, maize and Marchantia .     

Isolation and preliminary characterization of cryptic satellite DNA in pea

Optimum conditions have been established for isolation of ‘cryptic’ satellite DNA from the genome of pea (Pisum sativum), using gradients of CS₂SO₄ containing silver ions. At an Ag⁺ :DNA-P ratio (R) of 0.1, and at alkaline pH, four fractions are obtained: mainband (buoyant density 1.437 g cm³; 67% of total DNA), satellite I (buoyant density 1.582 g/cm³; 7% of total DNA), satellite II (buoyant density 1.520 g/cm³, 11% of total) and satellite III (buoyant density variable between 1.45 and 1.51 g/cm³; 15% of total). The reiterated DNA content of these four fractions has been investigated by reassociation experiments conducted over a Cot range of 1 × 10^?5 to 2.0. All four fractions contain at least two kinetic components; each fraction, including the mainband, consists at least partly of highly reiterated DNA. Ribosomal RNA hybridizes only to the mainband.     

Discrete character of the development of the photosynthetic apparatus in greening barley leaves

Biogenesis of the photosynthetic apparatus in greening etiolated leaves of barley (Hordeum vulgare L) was investigated by an approach permitting investigation of this process under conditions that minimize differences in plastid development. Distributions of barley leaves greening for 24 h as to chlorophyll content and of chloroplast grana as to number of thylakoids were shown to be of a multimodal character. The shape of time-course curves of chlorophyll accumulation in local sites of greening etiolated leaves was of a stepped or (at the end of greening) undulated character. The stepwise accumulation of chlorophyll was accompanied by wave-like changes in chlorophyll b/a ratio, intensity of low-temperature chlorophyll fluorescence and photosynthetic activity with minima at the time points of transition to accelerated chlorophyll accumulation. It is assumed that (1) development of the photosynthetic apparatus in local sites of greening etiolated leaves occurs stepwise, from one steady level to another, but not as gradually as is generally accepted, and (2) every separate step in development of the photosynthetic apparatus seems to begin with formation of photosystem cores and to end with the synthesis of light-harvesting complexes. This revised version was published online in June 2006 with corrections to the Cover Date.     

DNA polymerase activity and DNA synthesis in roots of pea (Pisum sativum) seedlings

Soluble DNA polymerase (DNA polymerase-α) and chromatin-bound DNA polymerase (DNA polymerase-β) have been assayed in serial sections cut from the roots of 5-day-old pea seedlings. The activity of DNA polymerase-α is high in regions of the root which exhibit high rates of DNA replication, and declines during cell differentiation and maturation. The activity of DNA polyrnerase-β is low in cells which show high rates of DNA replication, and increases during differentiation and maturation.     

Reduction of nuclear DNA contamination in the analysis of chloroplast DNA with restriction endonucleases

If chloroplasts purified on sucrose step gradients are treated for 10 min at 4°C with 2 M NaCl, followed by a 1000-g centrifugation, nuclear DNA contamination is reduced 1.5 to 3 fold as estimated by densitometry.     

乙草胺对葡萄叶片光合和叶绿素荧光特性及叶绿体结构的影响

以沙培1年生巨峰葡萄为材料,研究土施乙草胺对葡萄叶片光合、叶绿素荧光特性和叶绿体结构的影响.结果表明：喷施初期(处理后第13天),上部叶片净光合速率和气孔导度显著下降,PSII最大光化学效率和实际光化学效率显著低于对照,快速叶绿素荧光诱导动力学曲线中J点和K点荧光显著上升,性能指数PI_ABS显著下降,其PSII反应中心和放氧复合体受损伤程度显著高于中部叶片,但随着处理时间的延长,受损伤的程度减轻.在喷施后期(处理后第60天),上部叶片与中部叶片各指标之间的差距变小;下部叶片对除草剂的响应滞后,PSII反应中心和放氧复合体受到较大损伤,J点和K点荧光上升及PI_ABS下降的幅度高于中、上部叶片.乙草胺处理后第60天,葡萄叶片可溶性糖和淀粉含量增加,中、上部叶片色素含量显著下降,叶绿体膜受损,叶绿体变小,片层结构模糊或间隙增大.表明土施乙草胺可传导至葡萄地上部,导致叶片光合机构损伤、PSII活性下降和光合速率降低.     

Changes in chloroplast DNA during development in tobacco, Medicago truncatula, pea, and maize

We examined the DNA from chloroplasts obtained from young and fully expanded leaves of tobacco (Nicotiana tabacum L.), Medicago truncatula, pea (Pisum sativum L.), and maize (Zea mays L.). The changes in plastid DNA content and structure were monitored by four independent methods: 4′,6-diamidino-2-phenylindole (DAPI) staining with intact chloroplasts, in situ DAPI staining of cytological sections, ethidium bromide staining at the single-molecule level after exhaustive deproteinization of lysed chloroplasts, and pulsed-field gel electrophoresis. During leaf development, we found a decline of chloroplast DNA (cpDNA) in all four plants. For tobacco, for which plants can readily be regenerated from somatic cells, cpDNA persisted longer than in the other three plants. We also found a striking progression from complex multigenomic DNA molecules to simple subgenomic molecules during plastid development. Although the decrease in molecular size and complexity paralleled the decrease in DNA content per plastid, 6% of the chloroplasts in a fully expanded tobacco leaf still contained DNA in complex branched structure, whereas no such complex structures were found in mature leaves for the hard-to-regenerate maize.     

Iron-deficiency in pea leaves: Effect on lipid composition and synthesis

The lipid composition of chlorotic leaves of Pisum sativum L. cv. Kelvedon Wonder, developed under iron-deficiency was determined and compared to similar material developed under normal nutrient conditions. All lipid classes were affected by iron-deficiency but to different extents, and thylakoid lipids were more affected than non-thylakoid lipids. The most striking results concerned changes in the fatty acid content of the main polar lipids. The linolenic acid of the galactolipids decreased to the benefit of more saturated fatty acids, mainly linoleic acid. In phosphatidylglycerol, the proportion of Δ³- trans -hexadecenoic acid decreased. Using radioactive acetate, lipid synthesis was investigated. Desaturation leading to linoleic acid was less affected by iron-deficiency than desaturation leading to Δ³- trans -hexadecenoic and linolenic acids.     

Inclination of sun and shade leaves influences chloroplast light harvesting and utilization

Light harvesting and utilization by chloroplasts located near the adaxial vs the abaxial surface of sun and shade leaves were examined by fluorometry in two herbaceous perennials that differed in their anatomy and leaf inclination. Leaves of Thermopsis montana had well-developed palisade and spongy mesophyll whereas the photosynthetic tissue of Smilacina stellata consisted of spongy mesophyll only. Leaf orientation depended upon the irradiance during leaf development. When grown under low-light levels, leaves of S. stellata and T. montana were nearly horizontal, whereas under high-light levels, S. stellata leaves and T. montana leaves were inclined 60⁰ and 30⁰, respectively. Leaf inclination increased the amount of light that was intercepted by the lower leaf surfaces and affected the photosynthetic properties of the chloroplasts located near the abaxial leaf surface. The slowest rates of quinone pool reduction and reoxidation were found in chloroplasts located near the adaxial leaf surface of T. montana plants grown under high light, indicating large quinone pools in these chloroplasts. Chloroplasts near the abaxial surface of low-light leaves had lower light utilization capacities as shown by photochemical quenching measurements. The amount of photosystem II (PSII) down regulation, measured from each leaf surface, was also found to be influenced by irradiance and leaf inclination. The greatest difference between down regulation monitored from the adaxial vs abaxial surfaces was found in plants with horizontal leaves. Different energy dissipation mechanisms may be employed by the two species. Values for down regulation in S. stellata were 2–3 times higher than those in T. montana, while the portion of the PSII population which was found to be Q_B nonreducing was 4–6 times lower in high light S. stellata leaves than in T. montana. All values of Stern-Volmer type nonphotochemical quenching (NPQ) from S. stellata leaves were similar when quenching analysis was performed at actinic irradiances that were higher than the irradiance to which the leaf surface was exposed during growth. In contrast, with T. montana, NPQ values from the abaxial leaf surface were up to 45% higher than those from the adaxial leaf surface regardless of growth conditions. The observed differences in chloroplast properties between species and between the adaxial and abaxial leaf surfaces may depend upon a complex interaction among light, leaf anatomy and leaf inclination.     

Temperature treatments of dark-grown pea seedlings cause an accelerated greening in the light at different levels of gene expression

We have previously shown that heat-shock in the dark evokes photomorphogenesis-like effects and circadian rhythmicity at the level of mRNAs when applied to emerging pea plantlets during several consecutive days [15]. Here we extend these findings by showing that a temperature shift to 10 °C above average and a single heat-shock are sufficient for induction of circadian rhythmicity and changes in morphogenesis. The maximum response to a single heat-shock occurs at days 2 to 3 after sowintreatments intensifies the morphogenetic effect. The heat-shocked plantlets have an elevated level of the xanthophyll lutein in the dark. Upon illumination of heat-shocked plantlets accumulation of chloroplast pigments as well as that of individual thylakoid membrane proteins and their corresponding mRNAs occur much faster than in the etiolated controls. This is reflected in an accelerated formation of grana stacks. Therefore, heat-shock seems to evoke a responsiveness of plantlets similar to that obtained earlier by other authors using pre-illumination. The working hypothesis is put forward that induction or synchronization of circadian rhythmicity by either light or heat-shock might be sufficient to explain the observed morphogenetic changes.Abbreviations CCI reaction center I core - CHS cyclic heat-shock - D1 protein 32 kDa psbA gene product - ELIP early light-inducible protein - LHCP light-harvesting chlorophyll a/b protein - PCOR protochlorophyllide oxidoreductase - SSU small subunit of ribulose-1,5-bisphosphate carboxylase - WSP proteins of the oxygen-evolving (water-splitting) complex     

木根麦冬（Ophiopogon xylorrhizus）干叶提取DNA用于RAPD分析

木根麦冬（Ｏｐｈｉｏｐｏｇｏｎｘｙｌｏｒｒｈｉｚｕｓ）是我国珍稀濒危植物,分布仅限于云南西双版纳雨林,在植物系统学和保护生物学研究中具有独特的意义。随机扩增多态ＤＮＡ（ＲＡＰＤ）方法是揭示群体遗传多样性的高效、简便方法,但一般均以新鲜材料提取总ＤＮＡ,对一些分布边远地区物种难以采用此法。本文研究从木根麦冬干叶片中提取总ＤＮＡ,进行ＲＡＰＤ分析。样品取自４个居群、４９个个体。选取生长旺盛的叶片,在野外用硅胶快速干燥保存样品。采用高盐低ｐＨ值法提取总ＤＮＡ,每克鲜重所得的干叶可得８０～１６０μｇ。通过对模板ＤＮＡ的各种处理和ＰＣＲ扩增程序的调整,解决了扩增片段边缘弥散、界线模糊、产率低等问题,获得了理想的扩增带型。这一成果对其它从野外直接采样的干叶提取ＤＮＡ进行ＲＡＰＤ研究具有指导意义     

Studies on light absorption and photochemical activity changes in chloroplast suspensions and leaves due to light scattering and light filtration across chloroplast and vegetation layers

An experimental analysis is presented concerning the effect on relative light absorption by the two photosystems caused by (a) a highly light scattering environment (the detour effect) and (b) light filtration across successive chloroplast layers (the light attenuation effect). Both suspensions of isolated chloroplasts and leaves were employed.It is concluded that within a single spinach leaf these phenomena are likely to lead to only rather small increases in relative photosystem I absorption and activity with respect to photosystem II and will thus not exert a significant effect on non cyclic electron transport. On the contrary when light is filtrated across successive vegetation layers (shade light) significant increases in the relative PSI absorption and activity may be encountered.It is determined that the detour effect in mature leaves from a variety of plants increases overall photosynthetically useful light absorption by 35–40%.Abbreviations F_M maximal fluorescence - LHCP₂ light-harvesting chlorophyl a/b protein complex II - Q_A-primary quinone acceptor of photosystem II