Identification of a mutation in chloroplast DNA correlated with formation of defective chloroplasts in a variegated mutant of Nicotiana tabacum

Summary As in wild-type Nicotiana tabacum L., two satellite DNAs having densities of 1.700 and 1.705 g cm^–3 in CsCl were identified in the organelle fraction of homogenates made from variegated leaves of a cytoplasmic mutant of N. tabacum. As the proportion of white to green tissue increased a great reduction in the 1.700 chloroplast DNA occurred correlated with a concomitant reduction in the total number of defective and normal chloroplasts per cell. At the same time, there was an absolute increase in the 1.705 satellite DNA. Separation of the two satellite DNAs was achieved by one cycle of purification on NaI gradients. When the 1.700 chloroplast DNAs from white and from green tissue of variegated leaves were compared, identical properties were found by the conventional buoyant density, T _m and renaturation kinetics measurements. However, using a specially constructed difference melting system, the 1.700 DNA from defective chloroplasts was shown to have an approximately 1% higher GC composition than the DNA from normal chloroplasts. Also, by renaturation of a mixture of alkali denatured normal and defective chloroplast DNAs and subsequent spreading in formamide for electron microscopy, internal regions of mismatching were observed. The nonhomologous region corresponded to about 500–1000 base pairs. No differences in composition of the 1.705 satellite DNA derived from white or green tissues were detected either by difference melting or formation of heteroduplexes.     

Satellite DNA-correlated nucleosomal proteins in Drosophila virilis

Three major satellite DNAs comprise 40–45% of the genome of Drosophila virilis. Since these satellites are not substrates for most restriction enzymes, we were able to digest D. virilis nuclei with HaeIII and micrococcal nuclease and isolate chromatin fractions containing variable levels of satellite DNA. Electrophoretic analysis of these chromatin fractions revealed that the level of the acid-soluble chromosomal protein, cp17.3, was directly related to the percentage of satellite DNA in chromatin. The correlation between cp17.3 and satellite DNA abundance suggests that cp17.3 is involved in the heterochromatic condensation of satellite DNAs. cp17.3 occurs at a frequency of one molecule per 10–20 nucleosomes. It is detected in an electrophoretically distinguishable class of mononucleosomes, provisionally identified as MN1uH2A, which contains ubiquitinated histone H2A (uH2a) but lacks histone H1. It is not detected in MN1, a second class of mononucleosomes, which lacks uH2A and H1. Since cp17.3 is correlated with satellite DNAs and present in nucleosome cores, it might be a histone variant specifically associated with satellite DNAs.This work was supported by Grant GM22138 from the National Institutes of Health. G.A.V. was a predoctoral trainee supported by Grant GM07094 from the National Institutes of Health.     

Effects of tissue culture on a highly repetitive DNA sequence (E180 satellite) in Medicago sativa

Genomic DNA extracted from leaves of sixteen alfalfa genotypes, six-week-old callus cultures derived from them and from a suspension culture was used in Southern blots and slot blots probed with alfalfa E180 satellite DNA. The restriction patterns revealed by the E180 probe did not differ among alfalfa genotypes and no differences between the leaf and callus restriction patterns were seen. However, the number of copies of the E180 satellite was lower in the callus samples than in the corresponding leaf samples and significant differences in copy number among callus samples were detected. Genomic stress induced by tissue culture may have caused the reduction in copy number. This phenomenon may be important in the generation of somaclonal variation in alfalfa.     

Different methylation pattern of melon satellite DNA sequences in hypocotyl and callus tissues

Satellite DNA sequences from Cucumis melo have been examined with respect to modification at CCGG sequences in hypocotyls and in callus tissues. For this purpose, restriction fragments given by HpaII and MspI were compared (both enzymes recognize CCGG sequences but have different sensitivity to methylation at this site). Whereas the methylation level of satellite DNA sequences is on average higher in hypocotyls than in callus tissues, the comparison of partially methylated repeat units of satellite DNA reveals that in callus tissues, all methylated restriction sites are doubly methylated.     

Cytological Studies on Tissue Culture of Pinus cembra

Callus tissue of Swiss stone pine, Pinus cembra L. var. sibirica Loud., has been grown successfully for 9 months through 7 transfers. Excellent initial growth was obtained from hypocotyl segments of 7-day-old seedlings. A complex agar medium was used supplemented with 2 mg/l 2,4-D, 0.05 mg/l kinetin, 1 g/l Edamin and 10% v/v coconut milk. No deterioration of growth was observed on this medium after numerous transfers. The callus tissue did not produce shoots or roots, but showed an ability for cytodifferentiation. Tracheids or tracheid-like structures were formed in every passage, but the tracheids of the primary callus culture differed markedly from those of the subcultures. The tracheids of the primary culture probably already existed in the hypocotyl, whereas those of the subcultures were formed in vitro. The callus tissue was mainly diploid during the period studied, and more than 86% of the mitoses were diploid. A few mitoses with tetraploidy or a higher ploidy also occurred, but the tissue did not show any tendency to polyploidization.     

Analysis of eucaryotic DNAs with a restriction endonuclease from H.influenzae: isolation of “hidden” satellite DNAs

The restriction enzymes from H.influenzae have been used to study various eucaryotic DNAs. Fractions resistant to the action of these enzymes have been isolated from rat, mouse and calf DNAs. The method revealed the existence in rat of several components having the properties of satellite DNAs. Mouse DNA was shown to contain a new satellite of buoyant density 1. 704. Therefore, this appears to be a powerfull method for the isolation of "hidden" satellite DNAs.Calf satellite DNAs rho = 1.705 and rho = 1.723 were those resistant to the action of the restriction enzymes whilst satellite DNAs rho = 1.714 and rho = 1.710 gave fragments of discrete lengths, suggesting internal repeat units of 1 500 and 5 000 base pairs respectively.     

Denaturation of mouse satellite and ribosomal DNA during hydroxyapatite thermal chromatography of chromatin

Mouse DNA and chromatin were melted on hydroxyapatite and the denaturation profiles of ribosomal and satellite DNAs were followed by hybridization with their complementary RNAs. Neither ribosomal nor bulk DNA had significantly different melting profiles in chromatin as compared to DNA. However, most of satellite DNA eluted at higher temperature from chromatin than from purified DNA. One explanation for the higher melting temperature of mouse satellite DNA in chromatin suggests that the complex between this particular DNA component and at least some proteins in chromatin is more stable than the average DNA-protein interaction.     

影响四季桔器官发生的因素

对四季桔胚轴直接出芽、愈伤组织诱导及植株再生能力的研究表明：上、下胚轴在含有BA的MT培养基上,均能直接出芽,但上胚轴出芽能力明显高于下胚轴,最高出芽率为96．9％。外植体在培养基上的接种方式,对出芽也有一定影响,上胚轴切段以形态学下端垂直插入,出芽率高,且在培养前期表现尤为突出。胚轴愈伤诱导的适宜培养基为MT＋IBA0．5mg-1＋BAgmg-1。愈伤组织分化时,上、下胚轴愈伤组织所要求的BA浓度分别为4mgL-1及2mgL-1。在根的诱导中,附加的生长素种类,不仅影响生根率的高低,而且影响上部茎叶的生长,其中以加入lmgL-1IBA的效果最好,生根率达84．4％。     

Variations in the satellite DNA content of Cucumis melo in relation to dedifferentiation and hormone concentration.

Total DNA from Cucumis melo contains a 1.706 satellite DNA which can be resolved into two components; one of these components has a higher temperature of melting (component I) then the other component II). In this study, we have further investigated these components by thermal denaturation and by Eco R1 digestion. Component I reveals a homogeneous melting profile and is only partially cleaved by Eco R1, whereas component II reveals a heterogeneous melting profile and is entirely digested by Eco R1. A possible mitochondrial origin for component II is discussed. When an in vitro culture of root tissues from Cucumis melo was initiated or when the phytohormone (NAA) concentration of established cultures was modified, a new satellite DNA (1.719) appears transitorily and the satellite DNAs already present in seedlings undergo quantitative and possibly qualitative variations. Satellite DNAs therefore seem to be involved in the response to some physiological variations.     

Response to auxin changes during maturation-related loss of adventitious rooting competence in loblolly pine (Pinus taeda) stem cuttings

Hypocotyl cuttings (from 20- and 50-day-old Pinus taeda L. seedlings) rooted readily within 30 days in response to exogenous auxin, while epicotyl cuttings (from 50-day-old seedlings) rarely formed roots within 60 days. Responses to auxin during adventitious rooting included the induction of cell reorganization and cell division, followed by the organization of the root meristem. Explants from the bases of both epicotyl and hypocotyl cuttings readily formed callus tissue in response to a variety of auxins, but did not organize root meristems. Auxin-induced cell division was observed in the cambial region within 4 days, and later spread to the outer cortex at the same rate in both tissues. Cells at locations that would normally form roots in foliated hypocotyl cuttings did not produce callus any differently than those in other parts of the cortex. Therefore, auxin-induced root meristem organization appeared to occur independently of auxin-induced cell reorganization/division. The observation that N-(1-naphthyl)phthalamic acid (NPA) promoted cellular reorganization and callus formation but delayed rooting implies the existence of an auxin signal transduction pathway that is specific to root meristem organization. Attempts to induce root formation in callus or explants without foliage were unsuccessful. Both the cotyledon and epicotyl foliage provided a light-dependent product other than auxin that promoted root meristem formation in hypocotyl cuttings.     

Nuclear DNA content and phytohormone requirements of normal, crown gall and habituated tissues of Nicotiana tabacum var. White Burley

Determination of the nuclear DNA content of leaves and normal, habituated and Crown gall callus tissues of Nicotiana tabacum var. White Burley were performed using cytophotometry on Feulgen stained preparations. Several aspects concerning the reliability of the Feulgen technique for DNA determinations were investigated.Crown gall callus tissue used in this study had both a higher nuclear DNA content and chromosome number than normal callus (3.2C versus 2.5C). Both have a higher DNA content than the diploid tobacco leaf cells (2C).The normal callus tissue failed to grow on medium without indole acetic acid and kinetin when cultured in tubes. From this normal callus two habituated lines growing without both phytohormones were selected by culturing the normal callus first in the absence of either indole acetic acid or kinetin. Changing the culture conditions of the normal callus by using culture flasks instead of tubes resulted in a remarkably faster growth rate of the tissue. This was accompanied by an acquisition of the habituation characteristics since it was possible now to grow this tissue also directly on medium lacking both phytohormones. All habituated tissues showed a higher nuclear DNA content compared to the normal callus tissue from which they were derived. Interestingly, one of the tissues acquired a nuclear DNA content not different from that of Crown gall tissue. By changing the culture conditions of Crown gall callus tissue no concomitant change in nuclear DNA content occurred.The results suggest a correlation between the acquisition of a special chromosome complement and the loss of phytohormone requirement resulting in autonomous growth.     

Analysis of DNA from related and diverse species of Barley

DNAs of three closely related diploid species Hordeum vulgare, H. agriocrithon and H. spontaneum were compared among themselves and with a group of three species related to each other H. californicum (2x), H. jubatum (4x), and H. arizonicum (6x) having one genome in common.Buoyant densities of the DNAs from these species fall within a narrow range (1.700–1.701 g cm⁻³). Melting temperatures (T_m) of the DNAs are also similar (85.2–86.2°C). None of the DNAs showed any satellite band in neutral Cesium chloride gradients. In silver-cesium sulphate gradients, however, DNAs of all the species formed satellites on both the light and heavy sides of the main. band The diploid series have similar but not identical satellite patterns. The members of the polyploid series showed similar satellite patterns among themselves but distinct from those of the diploid series. In the polyploid group the amount of satellite showed a progressive decrease with the increase in the ploidy.The amount of repeated DNA (reassociating up to Cot 100) in H. vulgare was 69% and in H. arizonicum 65% of the total. The two species differed in their Cot curves. The low Cot fractions of H. arizonicum contained components of low buoyant densities which were absent in the corresponding Cot fractions of H. vulgare DNA.     

Transcriptome analysis of age-related gain of callus-forming capacity in Arabidopsis hypocotyls

Callus-forming capacity is enhanced with hypocotyl maturity in Arabidopsis. However, the genetic regulation of age-related gain in capacity for callus formation is unclear. We used a gene expression microarray assay to characterize the underlying mechanisms during callus formation in young and mature hypocotyl explants of Arabidopsis. As expected, genes involved in photosynthesis and cell wall thickening showed altered expression during hypocotyl maturation. In addition, genes involved in cytokinin perception were enriched in mature hypocotyl tissues. Phytohormone-induced callus formation in hypocotyl explants was accompanied by increased expression of genes mainly related to the cell cycle, histones and epigenetics. The induction level of these genes was higher in mature hypocotyl explants than young explants during callus formation. We identified a number of genes, including those with unknown function, potentially involved in age-related gain in callus formation. Our results provide insight into the effect of hypocotyl age on callus formation. Altered cytokinin signaling components, cell cycle regulation and epigenetics may work in concert to lead to gain of callus-forming capacity in hypocotyls with age.     

Methylation of satellite sequences in mouse spermatogenic and somatic DNAs.

The distribution of 5-methyl cytosine (5-MeC) residues in a highly repetitive sequence, mouse major satellite, was examined in germinal versus somatic DNAs by digestion with the methylation sensitive isoschizomers Msp I and Hpa II and Southern blot analysis, using a cloned satellite probe. DNA from liver, brain, and a mouse fibroblast cell line, C3H 10T1/2, yielded a multimeric hybridization pattern after digestion with Msp I (and control Eco RI) but were resistant to digestion with Hpa II, reflecting a high level of methylation of the satellite sequences. In contrast, DNA from mature sperm was undermethylated at these same sequences as indicated by the ability of Hpa II to generate a multimeric pattern. DNAs from purified populations of testis cells in different stages of spermatogenesis were examined to determine when during germ cell differentiation the undermethylation was established. As early as in primitive type A, type A, and type B spermatogonia, an undermethylation of satellite sequences was observed. This suggest that this highly specific undermethylation of germ cell satellite DNA occurs very early in the germ cell lineage, prior to entry into meiosis.     

Two AT-rich satellite DNAs in the chironomid Glyptotendipes barbipes (Staeger)

Two AT-rich satellite DNAs are present in the genome of Glyptotendipes barbipes. The two satellites have densities of 1.680 g/cm³ (=21% GC) and of 1.673 g/cm³ (=13% GC) in neutral CsCl-density gradients. The main band DNA has a density of 1.691 g/cm³ (=32% GC). This value is in agreement with the 33% GC-content of G. barbipes DNA calculated from thermal denaturation (T_M=83° C). — In brain DNA as well as in salivary gland DNA the two satellite sequences together comprise 12–15% of the total G. barbipes DNA. Comparisons of the density profiles of DNA extracted from polytene and non-polytene larval tissue gave no hints for underreplication of the satellite DNAs during polytenization. — The two satellite DNAs have been isolated from total DNA by Hoechst 33258-CsCl density centrifugation and then localized in the polytene salivary gland chromosomes by in situ hybridization. Both satellite sequences hybridize to all heterochromatic centromere bands of all four chromosomes of G. barbipes. Satellite I (1.673 g/cm³) hybridizes mainly with the middle of the heterochromatin, satellite II (1.680 g/cm³) hybridizes with two bands at the margin of the heterochromatin. In situ hybridization with polytene chromosomes of Chironomus thummi revealed the presence of G. barbipes satellite sequences also in the Ch. thummi genome at various locations, mainly the centromere regions.     

Epigenetic profiling of heterochromatic satellite DNA

Sugar beet (Beta vulgaris) chromosomes consist of large heterochromatic blocks in pericentromeric, centromeric, and intercalary regions comprised of two different highly abundant DNA satellite families. To investigate DNA methylation at single base resolution at heterochromatic regions, we applied a method for strand-specific bisulfite sequencing of more than 1,000 satellite monomers followed by statistical analyses. As a result, we uncovered diversity in the distribution of different methylation patterns in both satellite families. Heavily methylated CG and CHG (H=A, T, or C) sites occur more frequently in intercalary heterochromatin, while CHH sites, with the exception of CAA, are only sparsely methylated, in both intercalary and pericentromeric/centromeric heterochromatin. We show that the difference in DNA methylation intensity is correlated to unequal distribution of heterochromatic histone H3 methylation marks. While clusters of H3K9me2 were absent from pericentromeric heterochromatin and restricted only to intercalary heterochromatic regions, H3K9me1 and H3K27me1 were observed in all types of heterochromatin. By sequencing of a small RNA library consisting of 6.76 million small RNAs, we identified small interfering RNAs (siRNAs) of 24 nucleotides in size which originated from both strands of the satellite DNAs. We hypothesize an involvement of these siRNAs in the regulation of DNA and histone methylation for maintaining heterochromatin.     

Genetic transformation of green bean callus via Agrobacterium mediated DNA transfer

Summary Kanamycin resistant callus was produced from leaf disc or hypocotyl expiants of green bean (Phaseolus vulgaris L.) when cultured on a defined medium containing 50 mg/l kanamycin after 4 days of co-cultivation with Agrobacterium tumefaciens strain EHA101 containing the binary vector pKYLX71GUS. The presence of neomycin phosphotransferase II (NPT-II) in crude cellular extracts from the kanamycin resistant callus was confirmed by ELISA. The expression of the ß-glucuronidase (GUS) reporter gene was confirmed by histochemical and fluorimetric analyses. Southern blot border analysis confirmed the integration of the foreign DNA. In addition to the evidence obtained from Southern analysis, the absence of Agrobacterium in the transformed callus cultures was confirmed by microscopic observation and through test cultures. Using the above protocol, bean callus cultures were also transformed with a bean chalcone synthase promoter-GUS fusion. These cultures, when treated with the elicitor glutathione, showed higher levels of GUS expression than the unelicited callus clumps.     

H3K9 methylation and RNA interference regulate nucleolar organization and repeated DNA stability

Investigations aimed at identifying regulators of nuclear architecture in Drosophila demonstrated that cells lacking H3K9 methylation and RNA interference (RNAi) pathway components displayed disorganized nucleoli, ribosomal DNA (rDNA) and satellite DNAs. The levels of H3K9 dimethylation (H3K9me2) in chromatin associated with repeated DNAs decreased dramatically in Su(var)3-9 and dcr-2 (dicer-2) mutant tissues compared with wild type. We also observed a substantial increase in extrachromosomal circular (ecc) repeated DNAs in mutant tissues. The disorganized nucleolus phenotype depends on the presence of Ligase 4 and ecc DNA formation is not induced by removal of cohesin. We conclude that the structural integrity and organization of repeated DNAs and nucleoli are regulated by the H3K9 methylation and RNAi pathways, and other regulators of heterochromatin-mediated silencing. In addition, repeated DNA stability involves suppression of non-homologous end joining (NHEJ) or other recombination pathways. These results suggest a mechanism for how local chromatin structure can regulate genome stability, and the organization of chromosomal elements and nuclear organelles.     

Characterization of plant satellite DNA using restriction nucleases

The structural organization of satellite DNAs of mustard Brassica nigra and lemon Citrus limon has been studied by digestion with restriction nucleases. Analysis of DNA products produced by EcoRI and Bam I shows that two satellite DNAs contain long range periodicities belonging to several repeated sequences. The periodicities in two satellite DNAs differ characteristically, however, they have been found to contain common homologous sequences. Using the restriction nuclease Bsp I, a highly periodical fractions has been found in Citrus satellite DNA, composed of Bsp I fragments ranging from 80 to 1240 basepain. The major repeat units comprise five Bsp I fragments ranging from 80 to 200 bp. These fractions characterized by a high content of 5-methyl-cytosine.