Negative phototropic response of rhizoid cells in the fern Adiantum capillus-veneris

In general, phototropic responses in land plants are induced by blue light and mediated by blue light receptor phototropins. In many cryptogam plants including the fern Adiantum capillus-veneris, however, red as well as blue light effectively induces a positive phototropic response in protonemal cells. In A. capillus-veneris, the red light effect on the tropistic response is mediated by phytochrome 3 (phy3), a chimeric photoreceptor of phytochrome and full-length phototropin. Here, we report red and blue light-induced negative phototropism in A. capillus-veneris rhizoid cells. Mutants deficient for phy3 lacked red light-induced negative phototropism, indicating that under red light, phy3 mediates negative phototropism in rhizoid cells, contrasting with its role in regulating positive phototropism in protonemal cells. Mutants for phy3 were also partially deficient in rhizoid blue light-induced negative phototropism, suggesting that phy3, in conjunction with phototropins, redundantly mediates the blue light response.     

Achlya mitochondrial DNA: gene localization and analysis of inverted repeats

Summary Mitochondrial DNA from four strains of the oomycete Achlya has been compared and nine gene loci mapped, including that of the ribosomal protein gene, var1. Examination of the restriction enzyme site maps showed the presence of four insertions relative to a map common to all four strains. All the insertions were found in close proximity to genic regions. The four strains also cotained the inverted repeat first observed in A. ambisexualis (Hudspeth et al. 1983), allowing an examination by analysis of retained restriction sites of the evolutionary stability of repeated DNA sequences relative to single copy sequences. Although the inverted repeat is significantly more stable than single copy sequences, more detailed analysis indicated that this stability is limited to the portion encoding the ribosomal RNA genes. Thus, the apparent evolutionary stability of the repeat does not appear to derive from the inverted repeat structure per se.Abbreviations ATPase 6, 9 genes for ATPase subunits 6 and 9 - COI, II, III genes for cytochrome oxidase subunits 1, 2, and 3 - COB gene for apocytochrome b - L-, S-RNA genes for the mitochondrial large and small ribosomal RNAs - mtDNA mitochondrial DNA - var1 gene for the S. cerevisiae mitochondrially, encoded ribosomal protein - m.u. map units - bp base pairs - kb kilobase pairs     

Ebb and flow of the chloroplast inverted repeat

The endpoints of the large inverted repeat (IR) of chloroplast DNA in flowering plants differ by small amounts between species. To quantify the extent of this movement and define a possible mechanism for IR expansion, DNA sequences across the IR—large single-copy (IR-LSC) junctions were compared among 13Nicotiana species and other dicots. In mostNicotiana species the IR terminates just upstream of, or somewhere within, the 5 portion of therps19 gene. The truncated copy of this gene,rps19, varies in length even between closely related species but is of constant size within a single species. InNicotiana, six differentrps19 structures were found. A phylogenetic tree ofNicotiana species based on restriction site data shows that the IR has both expanded and contracted during the evolution of this genus. Gene conversion is proposed to account for these small and apparently random IR expansions. A large IR expansion of over 12 kb has occurred inNicotiana acuminata. The new IR-LSC junction in this species lies within intron 1 of theclpP gene. This rearrangement occurred via a double-strand DNA break and recombination between poly (A) tracts inclpP intron 1 and upstream ofrps19. Nicotiana acuminata chloroplast DNA contains a molecular fossil of the IR-LSC junction that existed prior to this dramatic rearrangement.     

The occurrence and morphology of Adiantum X variopinnatum (Pteridaceae)

Two populations ofAdiantum Xvariopinnatum were found at the La Selva Biological Field Station in Costa Rica. The plants were morphologically intermediate between their parents, showed additive isozyme banding patterns, and had aborted spores. Herbarium searches for the hybrid turned up specimens from Nicaragua, Costa Rica, Panama, Venezuela, and Colombia. These are the first reports of the hybrid outside of Trinidad.     

A chloroplast DNA hypervariable region in eucalypts

Eucalypt chloroplast DNA (cpDNA) provides useful markers for phylogenetic and population research including gene flow and maternity studies. All cpDNA studies in Eucalyptus to date have been based on the RFLP technique, which requires relatively large amounts of clean DNA. The objective of this study was to develop PCR-based cpDNA markers for Eucalyptus. The chloroplast genome of Eucalyptus, like that of most angiosperms, possesses inverted repeats (IR). The two junctions between the IRs and the large single copy (LSC) regions are defined as J_LA andJ_LB. The region surrounding the J_LA junction was sequenced from 26 Eucalyptus DNA samples (21 of E. globulus, plus 5 other species), andtheJ_LB region was sequenced using 5 of these samples. The samples were chosen to represent all major haplotypes identified in previous cpDNA RFLP studies. The J_LA products were 150–210 bp in size, while those fromJ_LB were approximately 500 bp in size. Eighteen mutations were scored in total. Extensive variation was found in the IR within the intergenic spacer between rpl2 and the IR/LSC junctions. Many of these characters were complex indels. One sample of E. globulus possessed a relatively large (38 bp) insertion which caused displacement of the IR/LSC junctions. This is the first report of intraspecific variation in the position of IR/LSC junctions; interspecific variation was also found. The LSC region near J_LB had a low rate of mutation and none were informative. The LSC region near J_LA possessed 2 informative mutations. The variation revealed from these sequences reflects the differentiation previously uncovered in an extensive RLFP analysis on the same samples. These results suggest that the J_LA region will provide very useful cpDNA polymorphisms for future studies in Eucalyptus. Received: 20 March 1999 / Accepted: 16 December 1999     

Isolation and phenotypic characterization ofChlamydomonas reinhardtii mutants defective in chloroplast DNA segregation

Summary Each wild-typeChlamydomonas reinhardtii cell has one large chloroplast containing several nuclei (nucleoids). We used DNA insertional mutagenesis to isolate Chlamydomonas mutants which contain a single, large chloroplast (cp) nucleus and which we namedmoc (monokaryotic chloroplast). DAPI-fluorescence microscopy and microphotometry observations revealed thatmoc mutant cells only contain one cp-nucleus throughout the cell division cycle, and that unequal segregation of cpDNA occurred during cell division in themoc mutant. One cell with a large amount of cpDNA and another with a small amount of cpDNA were produced after the first cell division. Unequal segregation also occurred in the second cell division, producing one cell with a large amount (about 70 copies) of cpDNA and three other cells with a small amount (only 2–8 copies) of cpDNA. However, most individualmoc cells contained several dozen cpDNA copies 12 h after the completion of cell division, suggesting that cpDNA synthesis was activated immediately after chloroplast division. In contrast to the cpDNA, the mitochondrial (mt) DNA of themoc mutants was observed as tiny granules scattered throughout the entire cell. These segregated to each daughter cell equally during cell division. Electron-microscopic observation of the ultrastructure ofmoc mutants showed that a low-electron-density area, which was identified as the cp-nucleus by immunoelectron microscopy with anti-DNA antibody, existed near the pyrenoid. However, there were no other structural differences between the chloroplasts of wild-type cells andmoc mutants. The thylakoid membranes and pyrenoid were identical. Therefore, we propose that the novelmoc mutants are only defective in the dispersion and segregation of cpDNA. This strain should be useful to elucidate the mechanism for the segregation of cpDNA.Abbreviations DAPI 4,6-diamidino-2-phenylindole - VIMPCS video-intensified microscope photon-counting system     

An update on chloroplast genomes

Plant cells possess two more genomes besides the central nuclear genome: the mitochondrial genome and the chloroplast genome (or plastome). Compared to the gigantic nuclear genome, these organelle genomes are tiny and are present in high copy number. These genomes are less prone to recombination and, therefore, retain signatures of their age to a much better extent than their nuclear counterparts. Thus, they are valuable phylogenetic tools, giving useful information about the relative age and relatedness of the organisms possessing them. Unlike animal cells, mitochondrial genomes of plant cells are characterized by large size, extensive intramolecular recombination and low nucleotide substitution rates and are of limited phylogenetic utility. Chloroplast genomes, on the other hand, show resemblance to animal mitochondrial genomes in terms of phylogenetic utility and are more relevant and useful in case of plants. Conservation in gene order, content and lack of recombination make the plastome an attractive tool for plant phylogenetic studies. Their importance is reflected in the rapid increase in the availability of complete chloroplast genomes in the public databases. This review aims to summarize the progress in chloroplast genome research since its inception and tries to encompass all related aspects. Starting with a brief historical account, it gives a detailed account of the current status of chloroplast genome sequencing and touches upon RNA editing, ycfs, molecular phylogeny, DNA barcoding as well as gene transfer to the nucleus.     

Freeze-fracture observations on the plasma membrane,the cell wall and the cuticle of growing protonemata of Adiantum capillus-veneris L.

Using freeze-fracture electron microscopy we have examined the morphology of the plasma membrane and the cell wall of single-celled protonemal filaments of the fern Adiantum capillus-veneris grown under continuous red light. The surface of the protonemal cell wall is completely covered by a multilayered, lipid-like coat, probably consisting of cuticular waxes. The rhizoid seems to lack this type of coat. The cell walls of the protonemata contain 8-nm thick, randomly oriented fibrils. In rapidly growing protonemata the P-face of the plasma membrane contains both randomly distributed particles and distinct particle rosettes. The rosettes consist of six 8–9-nm-wide particles in a ring-like configaration and have an outer diameter of 24 nm. They closely resemble the particle rosettes seen on the P-face of the plasma membrane of green algae and of higher plants, which recently have been implicated in the synthesis of cellulose fibrils. Within 20 m from the tip of the protonemata, and coinciding with the region of maximal cell-wall growth and expansion and thus cellulose-fibril synthesis, the greatest density of rosettes (20/m²) is observed. Beyond 20 m from the tip this number drops rapidly to near zero at 50 m. The rosettes have a tendency to form small, irregular clusters, but only very rarely are three or more rosettes found in a row or in a geometrical pattern. Our measurements of the size and the density of the randomly distributed plasma membrane particles indicate that the tip region must be specialized with respect to other plasma-membrane activities as well. Thus the tip region contains not only the highest density of randomly destributed intramembrane particles, but also particles of different sizes than those found elsewhere in the plasma membrane.     

Characterization and phylogenetic distribution of a chloroplast DNA rearrangement in theBerberidaceae

Restriction site maps and a clone bank of chloroplast DNA (cpDNA) ofMahonia higginsae (Munz)Ahrendt (Berberidaceae) were constructed. The size ofMahonia cpDNA was about 167 kb. Precise mapping using gene probes revealed that cpDNA ofM. higginsae has an inverted repeat (IR) 11.5 kb larger than the tobacco IR. The expansion of the IR into the large single copy region has resulted in the duplication of at least ten genes includingpsbB. The phylogenetic distribution of the expanded IR was examined in twenty-five species ofBerberis andMahonia, twenty species representing the fifteen remaining genera of theBerberidaceae, and four species from four allied families. Our survey indicates that only the species of the closely related generaBerberis andMahonia share the 11.5kb expansion of IR. This result supports their close phylogenetic relationship, which has been suggested previously by chromosomal, morphological, and serological data.     

Phytochrome-mediated polarotropism of Adiantum capillus-veneris L. protonemata as analyzed by microbeam irradiation with polarized light

Summary Perception of polarized light inducing phytochrome-mediated polarotropism in protonemata of the fern Adiantum capillus-veneris L. was analyzed using brief microbeam irradiation with polarized red (R) or far-red light (FR). The polarotropic response inducible by irradiation of the subapical 10–30-m part with polarized R vibrating parallel to the cell axis was nullified by subsequently giving R at the apical 0–2.5-m region. This inhibitory effect of R showed an action dichroism, that is, polarized R vibrating normal to the cell axis was effective but the parallel-vibrating R was not. On the other hand, FR irradiation of the extreme tip after irradiation of the whole cell with depolarized R effectively induced a tropic response. This FR effect also showed action dichroism, with parallel-vibrating polarized FR being more effective than FR vibrating normal to the cell axis. When the apical-dome region and the adjacent subapical 10–20-m region were sequentially irradiated with polarized R vibrating obliquely in different directions, polarotropism took place depending on the vibrating direction of the light given to the apical-dome region. Obliquely vibrating polarized FR given to the apical dome after irradiation of the whole cell with depolarized R also induced polarotropism. Thus, the difference in amount (or percent) of the far-redabsorbing form of phytochrome (Pfr) between the extreme tip and the subapical region appears to be crucial in regulating the direction of apical growth; the difference in Pfr level between the two sides of the protonemal apex may occur mainly at the apical dome. Furthermore, the transition moments of the red-absorbing form of phytochrome (Pr) and Pfr seem to be aligned parallel and normal, respectively, to the cell surface at the periphery of the apical hemisphere.Abbreviations FR far-red light - Pfr far-red-absorbing form of phytochrome - Pr red-absorbing form of phytochrome - R red light     

Insertion polymorphism in pea chloroplast DNA

Summary The chloroplast DNA of higher plants is suitable for restriction endonuclease analysis due to its size and homogeneity. We have analysed 48 different cultivars of pea (Pisum sativum) with EcoRI and HindIII. Of these, only 24 show the standard genotype, the remaining 24 comprise four different classes of short insertions, three of which are found at the same site. Even though this kind of insertion polymorphism has not been detected elsewhere in the plant kingdom, it is consistent with the discovery that the chloroplast DNA of pea is destabilised through the loss of an inverted repeat.     

Nicotiana chloroplast genome

Summary A physical map containing six restriction sites of the Nicotiana tabacum chloroplast genome, together with the BamHI maps of N. tabacum, N. otophora and N. knightiana, and the SmaI maps of N. acuminata, N. plumbaginifolia, N. langsdorffii, N. otophora, N. tabacum, N. tomentosiformis and N. knightiana was constructed. In Nicotiana chloroplast genomes, the most frequently observed variations are point mutations. Deletions are also detected. Most of the observed changes are confined to one area of the large single copy region, which is designated as the hot spot. Based on the evidence obtained from Nicotiana chloroplast genomes, an origin of the inverted repeats in this genus is proposed. We suggest that the inverted repeats represent a vestige of what were once two identical, complete chloroplast genomes joined together in a head-to-head and tail-to-tail fashion, and that deletions generated the current chloroplast genome organization.     

Extensive homologous chloroplast DNA recombination in the pt14 Nicotiana somatic hybrid

Summary In a previous study, six recombination sites have been confirmed in the chloroplast DNA (cpDNA) of pt14, a somatic hybrid of Nicotiana tabacum and Nicotiana plumbaginifolia. In the present study, physical mapping revealed six recombination sites in the 11.4-kb SalI fragment alone, only one of which has been previously identified. This fragment is located in the large unique region. We assume, therefore, that the pt14 cpDNA is a fine mosaic of the parental genomes with a recombination site about every 2 kb. A 748-bp region that comprised the intergenic region between ORF73 and ORF74B, and 460 bp of the petD intron have been sequenced. Parent-specific sequences in the pt14 DNA defined the regions within which recombination took place. The exact site of recombination events could not be determined because the parental sequences were identical between the polymorphic markers, and these sequences have been preserved in the pt14 line.     

Complete nucleotide sequence of the chloroplast genome from a leptosporangiate fern, Adiantum capillus-veneris L.

We determined the complete nucleotide sequence of the chloroplast genome of the leptosporangiate fern, Adiantum capillus-veneris L. (Pteridaceae). The circular genome is 150,568 bp, with a large single-copy region (LSC) of 82,282 bp, a small-single copy region (SSC) of 21,392 bp and inverted repeats (IR) of 23,447 bp each. We compared the sequence to other published chloroplast genomes to infer the location of putative genes. When the IR is considered only once, we assigned 118 genes, of which 85 encode proteins, 29 encode tRNAs and 4 encode rRNAs. Four protein-coding genes, all four rRNA genes and six tRNA genes occur in the IR. Most (57) putative protein-coding genes appear to start with an ATG codon, but we also detected five other possible start codons, some of which suggest tRNA editing. We also found 26 apparent stop codons in 18 putative genes, also suggestive of RNA editing. We found all but one of the tRNA genes necessary to encode the complete repertoire required for translation. The missing trnK gene appears to have been disrupted by a large inversion, relative to other published chloroplast genomes. We detected several structural rearrangements that may provide useful information for phylogenetic studies.     

The origin of the cultivated tetraploid potato based on chloroplast DNA

Summary By using restriction enzyme analysis of chloroplast DNA, a geographical cline from the Andean region to coastal Chile was found for the tetraploid potato (Solanum tuberosum). This supports the Andean origin of Chilean ssp. tuberosum. One of the relic cultivars of the early introduction of potato to Europe had ssp. andigena type chloroplast DNA. Its derivatives were largely lost in the mid-19th century due to the late blight epidemic and were replaced by ssp. tuberosum originally introduced from Chile. Therefore, the present common potato has the same type chloroplast DNA as Chilean ssp. tuberosum.     

The course of chloroplast DNA replication and its relationship to other reproductive processes in the chloroplast and nucleocytoplasmic compartment during the cell cycle of the algaScenedesmus quadricauda

Summary DNA containing structures (cellular, chloroplast and mitochondrial nuclei) were stained with the fluorochrome DAPI. Fluorescence intensity, as a measure of DNA content, was estimated during the mitotic cycle in synchronized populations of the chlorococcal alga,Scenedesmus quadricauda. In cells yielding eight daughter cells, three consecutive steps in chloroplast DNA increase occurred over one mitotic cycle. The first step was performed shortly after releasing the daughter cells, the second and third steps occurred consecutively during the first half of the mitotic cycle. Commitment to chloroplast DNA replication was chronologically separated from commitment to division of chloroplast nuclei, revealing that these two chloroplast reproductive steps were under different control mechanisms. The replication of chloroplast DNA occurred at a different time to that of cell-nuclear DNA. The coordination of chloroplast reproductive processes and those in the nucleocytoplasmic compartment were governed by the mutual trophic and metabolic dependency of these compartments rather than by any direct or feedback control controlled by either of them.Abbreviations DAPI 46-diamidino-2-phenylindole - ptDNA DNA in chloroplast nuclei - nucDNA DNA in cell nuclei     

The chloroplast genomes of conifers lack one of the rRNA-encoding inverted repeats

Summary Chloroplast DNA from species of five different conifer genera was extracted and studied by Southern blot analysis. For all these species, hybridization with heterologous probes specific for 16 S and 23 S rDNA detected only one chloroplast DNA fragment per enzyme digest. This observation suggests that the 16 S and 23 S rRNA genes are not duplicated in these genomes. The unique 16 S rDNA-containing BamHI fragment from Pinus contorta Dougl. was cloned and restriction mapped. Apart from the 16 S rRNA gene, this fragment also contained the psbC and psbD genes. It is concluded that the chloroplast genomes of a wide taxonomic range of conifers lack one of the inverted repeat elements and that a dislocation of the psbDC gene cluster has occurred in P. contorta.     

Variations in chloroplast DNA from rice (Oryza sativa): differences between deletions mediated by short direct-repeat sequences within a single species

In a previous study, we compared chloroplast DNAs (ctDNAs) from four species ofOryza and detected two independent deletions of DNA fragments in the ctDNAs (Kanno and Hirai 1992a). These deletions were genotype-specific variations. Since short direct-repeat sequences were detected at the borders of both deletions, the deletions were apparently the result of intramolecular recombination mediated by these direct-repeat sequences. In the present study, we examined whether or not this type of variation exists within a single species. Ishii et al. demonstrated three types of ctDNA inO. Sativa (1988), and the source of the variations that they identified seemed to be deletions. We determined the precise locations of the deletions and the sequences around them. As expected, our results showed that these variations were the results of deletions that were mediated by short direct-repeat sequences. While the deletions that had been found previously were located on spacer regions, those found in this study were located within open reading frames (ORFs). Northern hybridization analysis showed that one of the ORFs was-transcribed. In the case of this deletion, the amino acid sequence encoded by the C-terminal region of the ORF was altered and the short inverted-repeat sequences downstream of the ORF were deleted. In addition, there were other short inverted-repeat sequences downstream of the altered ORF.     

Oenothera chloroplast DNA polymorphisms associated with plastome mutator activity

Summary Oenothera plants homozygous for a recessive allele at the plastome mutator (pm) locus show non-Mendelian mutation frequencies that are 1000-fold higher than spontaneous levels. Chloroplast DNA (cpDNA) was isolated from nine mutants and two green isolates of the plastome mutator line. cpDNA restriction patterns were compared to cpDNA from a representative of the progenitor Johansen strain, and cpDNAs from all eleven plastome mutator lines show changes of fragment mobility due to deletion events at five discrete regions of the plastome. Most of the mutants have cpDNA restriction patterns identical to that of one of the green isolates from the plastome mutator line, and therefore, most of the differences in fragment length are probably not responsible for the mutant phenotypes. In contrast to the plastome mutator line, cpDNA from several populations of a closely related wild-type Oenothera species have few restriction fragment length polymorphisms. This suggests that both mutation frequencies and site-specific cpDNA deletions are elevated in the plastome mutator line, and implicates a defect in the cpDNA repair or replication machinery.