Expression of Amyloplast and Chloroplast DNA in Suspension-Cultured Cells of Sycamore (Acer pseudoplatanus L.)

Integrative analysis of chloroplast DNA methylation in a marine alga-Saccharina japonica

KEY MESSAGE

We applied an integrative approach using multiple methods to verify cytosine methylation in the chloroplast DNA of the multicellular brown alga Saccharina japonica. Cytosine DNA methylation is a heritable process which plays important roles in regulating development throughout the life cycle of an organism. Although methylation of nuclear DNA has been studied extensively, little is known about the state and role of DNA methylation in chloroplast genomes, especially in marine algae. Here, we have applied an integrated approach encompassing whole-genome bisulfite sequencing, methylated DNA immunoprecipitation, gene co-expression networks and photophysiological analyses to provide evidence for the role of chloroplast DNA methylation in a marine alga, the multicellular brown alga Saccharina japonica. Although the overall methylation level was relatively low in the chloroplast genome of S. japonica, gametophytes exhibited higher methylation levels than sporophytes. Gene-specific bisulfite-cloning sequencing provided additional evidence for the methylation of key photosynthetic genes. Many of them were highly expressed in sporophytes whereas genes involved in transcription, translation and biosynthesis were strongly expressed in gametophytes. Nucleus-encoded photosynthesis genes were co-expressed with their chloroplast-encoded counterparts potentially contributing to the higher photosynthetic performance in sporophytes compared to gametophytes where these co-expression networks were less pronounced. A nucleus-encoded DNA methyltransferase of the DNMT2 family is assumed to be responsible for the methylation of the chloroplast genome because it is predicted to possess a plastid transit peptide.

Comparative sequence and methylation analysis of chloroplast and amyloplast genomes from rice

Grain amyloplast and leaf chloroplast DNA sequences are identical in rice plants but are differentially methylated. The leaf chloroplast DNA becomes more methylated as the rice plant ages. Rice is an important crop worldwide. Chloroplasts and amyloplasts are critical organelles but the amyloplast genome is poorly studied. We have characterised the sequence and methylation of grain amyloplast DNA and leaf chloroplast DNA in rice. We have also analysed the changes in methylation patterns in the chloroplast DNA as the rice plant ages. Total genomic DNA from grain, old leaf and young leaf tissues were extracted from the Oryza sativa ssp. indica cv. MR219 and sequenced using Illumina Miseq. Sequence variant analysis revealed that the amyloplast and chloroplast DNA of MR219 were identical to each other. However, comparison of CpG and CHG methylation between the identical amyloplast and chloroplast DNA sequences indicated that the chloroplast DNA from rice leaves collected at early ripening stage was more methylated than the amyloplast DNA from the grains of the same plant. The chloroplast DNA became more methylated as the plant ages so that chloroplast DNA from young leaves was less methylated overall than amyloplast DNA. These differential methylation patterns were primarily observed in organelle-encoded genes related to photosynthesis followed by those involved in transcription and translation.

Arabidopsis Mutants by Activation Tagging in which Photosynthesis Genes are Expressed in Dedifferentiated Calli

In an effort to delineate the precise mechanisms underlying the organ-specific expression of photosynthesis genes, Arabidopsis lines homozygous for each transgene construct made with the gene for hygromycin B phosphotransferase or beta-glucuronidase (GUS) placed under control of the promoter of the nuclear gene for the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RBCS-3B) were constructed. Furthermore, activation tagging with T-DNA possessing quadruply repeated enhancers derived from the cauliflower mosaic virus 35S promoter was applied to a transgenic line of Arabidopsis. Mutants resistant to hygromycin B during the growth of calli generated from non-green roots on callus-inducing medium resulted from the expression of hygromycin B phosphotransferase driven by the RBCS-3B promoter. Three mutant lines, ces101 to ces103 (callus expression of RBCS), were obtained from approximately 4,000 calli resistant to a selectable marker for transformation. The active transcription driven by the RBCS-3B promoter in all the calli of ces mutants was confirmed by expression of both the GUS reporter gene and endogenous RBCS-3B. Chlorophyll and carotenoids, as well as light-dependent O(2) evolution, have been detected in the calli of all ces mutants. The loci where T-DNA was integrated in the ces101 line were determined by thermal asymmetric interlaced (TAIL)-PCR. The introduction of a DNA fragment harboring the gene for receptor-like kinase placed under the influence of enhancers into the parental line reproduced the phenotype of ces mutants. We have thus concluded that CES101 is a receptor-like kinase. The strategy presented in this investigation may promise to select a greater number of ces mutants.

Conversion of proplastids to amyloplasts in tobacco cultured cells is accompanied by changes in the transcriptional activities of plastid genes

When tobacco (Nicotiana tabacum L.) cultured cells (line BY-2) at the stationary phase were transferred to culture medium that contained cytokinin (benzyladenine) instead of auxin (2,4-dichlorophenoxyacetic acid), proplastids in the BY-2 cells were converted to amyloplasts within 48 h. The data obtained from in vitro transcription assays using isolated plastid-nucleoids (nuclei) strongly suggested that amyloplast formation in BY-2 cells was accompanied by changes in the transcriptional activities of plastid genes.

Plastid DNA in developing maize endosperm : genome structure, methylation, and transcript accumulation patterns

Amyloplasts in storage organs such as maize (Zea mays L.) endosperm are plastid-derived, nonphotosynthetic, starch-accumulating organelles. This study was initiated to characterize the plastid genome in maize endosperm cells containing differentiated amyloplasts and to determine whether plastid genes are transcribed during the period of amyloplast biogenesis in endosperm development. Four cosmid clones representing the total sequence diversity of the maize plastid genome were hybridized to restriction digests of total cellular DNA from isolated 16-day-old endosperms. The hybridization patterns indicated that the plastid DNA present in endosperm tissue was indistinguishable from that in leaf total DNA. Methylation of maize endosperm amyloplast DNA or leaf chloroplast DNA was not detected with the methylation-sensitive enzymes HpaII and EcoRII. Transcripts homologous to the 17 specific plastid DNA BamHI fragments tested were detectable in total RNA prepared from 16-day-old endosperm tissue. Compared with leaf transcripts, the abundance of endosperm transcripts was substantially lower for transcripts detected by 12 different BamHI fragments and was similar or relatively higher for some transcripts homologous to five BamHi fragments. Transcripts homologous to genes for plastid ribosomal small subunit proteins 7 and 12 on fragments 10 and 23 and to an open reading frame on fragment 14 accumulated primarily as unprocessed or partially processed species in endosperm RNA. The demonstration that maize endosperm cells contain an intact, transcriptionally active plastid genome indicates that plastid genes could contribute to amyloplast biogenesis, although no transcripts unique to endosperm were identified.

Characterization and Intraorganellar Distribution of Protein Kinases in Amyloplasts Isolated from Cultured Cells of Sycamore (Acer pseudoplatanus L.)

Incubation of amyloplasts isolated from cultured cells of sycamore (Acer pseudoplatanus L.) with [gamma-(32)P]ATP resulted in the rapid phosphorylation (half-time of 40 seconds at 25 degrees Celcius) of organellar polypeptides. The preferred substrate for amyloplast protein kinases was Mg(2+). ATP, and recovery of only [(32)P]serine after partial acid hydrolysis indicated the predominance of protein serine kinases in the organelle. These activities were located in the envelope and stromal fractions of the plastid, which showed different specificities toward exogenous protein substrates and distinct patterns of phosphorylation of endogenous polypeptides. A 66-kilodalton polypeptide, inaccessible to an exogenously added protease, was one of the major phosphorylated products found in intact amyloplasts at low [gamma-(32)P] adenosine triphosphate concentrations. This polypeptide represented the major phosphoprotein observed with the isolated envelope fraction. The patterns of polypeptide phosphorylation found in intact amyloplasts and chloroplasts from cultured cell lines of sycamore were clearly distinguishable. The overall results indicate the presence of protein phosphorylation systems unique to this reserve plastid present in nonphotosynthetic tissues.

Application of an efficient strategy with a phage lambda vector for constructing a physical map of the amyloplast genome of sycamore (Acer pseudoplatanus)

Amyloplasts were isolated from a heterotrophic culture cell line of a woody plant, sycamore (Acer pseudoplatanus), and their DNA was purified. Conventional procedures for making a physical map were not easily applicable to the amyloplast DNA, since the yield of DNA was too low and the presence of repeated sequences interfered with the analysis. Therefore, the pieces of amyloplast DNA starting with a few micrograms of DNA were cloned in the lambda Fix vector, which is a derivative of lambda EMBL vectors improved for efficient cloning and gene walking. Cloned DNA fragments were randomly picked, mapped for restriction endonuclease sites by a refined procedure, and combined by overlapping their physical maps. The DNA library was also subjected to screening by gene walking using promoters recognized by T3 and T7 RNA polymerases in the vector to fill the gaps between sequences determined by overlapping the physical maps. In this way, we constructed the entire DNA library and the complete physical map of the amyloplast DNA. The sycamore amyloplast genome was composed of 141.7-kbp nucleotides with the same gene arrangement as that of tobacco chloroplasts.

Transcriptional regulation and DNA methylation of nuclear genes for photosynthesis in nongreen plant cells

The transcripts of nuclear genes for the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcS), chlorophyll a/b-binding protein (cab), and extrinsic 33-kDa protein involved in photosystem II water oxidation (woxA) were not detectable in the white wild cultured cells of sycamore (Acer pseudoplatanus), in contrast to their high levels in the sibling green mutant cells and the constitutive expression of actin genes (act) in both cell types. We have examined the template activities of nuclear DNAs using the HeLa cell in vitro transcription system. All of the three photosynthesis genes from the green cell line and act from both cell types were well transcribed in vitro, but these photosynthesis genes from the white cell line were not, indicating that the transcriptional regulation is ascribable to DNA templates. Digestion of nuclear DNA with methyl-sensitive and -insensitive isoschizomeric endonucleases and the subsequent Southern hybridization showed that each gene has the identical recognition sites of restriction enzymes in the green and white cell lines, but some of the sites were methylated only in the photosynthesis genes in the white cells. There was observed a clear inverse relationship between the level of expressed transcripts and the extent of DNA methylation. Thus, it is inferred that the selective methylation of DNA is a likely mechanism for suppressing transcription of nuclear genes for photosynthesis in the nonphotosynthetic plant cells.

Immunochemical Analysis Shows That an ATP/ADP-Translocator Is Associated with the Inner-Envelope Membranes of Amyloplasts from Acer pseudoplatanus L

Pure preparations of intact amyloplasts and chloroplasts, free from mitochondrial contamination, were isolated from cultured cells of the white-wild and green-mutant lines of sycamore (Acer pseudoplatanus L.), respectively. A specific rabbit antiserum against yeast mitochondrial cytochrome c(1) only cross-reacted with mitochondrial membranes from the white-wild sycamore cells. The outer and inner envelope-membranes of the two plastid-types were isolated and subsequently analyzed by sodium dodecylsulfate-polyacrylamide gel electrophoresis to characterize polypeptide patterns in each fraction. Analysis by immunoblotting clearly showed that antiserum against the 29-kilodalton inorganic orthophosphate translocator isolated from pea chloroplasts cross-reacted with a 31-kilodalton polypeptide residing in the inner-envelope membranes from both sycamore chloroplasts and amyloplasts. In contrast, antiserum against the ADP/ATP-translocator isolated from mitochondria of Neurospora crassa yielded a positive signal with a 32-kilodalton polypeptide in the inner-membranes isolated from amyloplasts, but not green-mutant chloroplasts. We propose that this 32-kilodalton polypeptide in the amyloplast envelope is a putative ATP/ADP-translocator and its possible functional significance is discussed.

Characterization of an ATPase Associated with the Inner Envelope Membrane of Amyloplasts from Suspension-Cultured Cells of Sycamore (Acer pseudoplatanus L.)

Amyloplast envelope membranes isolated from cultured, white-wild cells of sycamore (Acer pseudoplatanus L.) have been found to contain a Mg(2+)-ATPase, ranging in specific activity from 5 to 30 nanomoles per minute per milligram protein. This ATPase hydrolyzes a broad range of nucleoside triphosphates, whereas it hydrolyzes nucleoside mono- and diphosphates poorly, if at all. The ATPase activity was stimulated by several divalent cations, including Mg(2+), Mn(2+) and Ca(2+), whereas it was not affected by Sr(2+), K(+), or Na(+). The K(m) for total ATP was 0.6 millimolar, and the activity showed a broad pH optimum between 7.5 and 8.0. The ATPase was insensitive to N,N'-dicyclohexylcarbodiimide and oligomycin, but it was inhibited by vanadate. All these characteristics are basically similar to those reported previously for the Mg(2+)-ATPase of the chloroplast inner-envelope membrane. Likewise, the amyloplast envelope enzyme was shown to be located specifically on the inner envelope membrane. The amyloplast envelope membranes were chemically modified with a series of unique affinity labeling reagents, the adenosine polyphosphopyridoxals (M Tagaya, T Fukui 1986 Biochemistry 25: 2958-2964). About 90% of the ATPase activity was lost when the envelope membranes were preincubated with 0.1 millimolar adenosine triphosphopyridoxal. Notably, the enzyme was protected completely from inactivation in the presence of its substrate, ATP. In contrast, both adenosine diphosphopyridoxal and pyridoxal phosphate caused much less of an inhibitory effect. This greater relative reactivity of the triphosphopyridoxal analog is similar to that reported previously with Escherichia coli F(1) ATPase (T Noumi et al. 1987 J Biol Chem 262: 7686-7692).

DNA Methylation Occurred around Lowly Expressed Genes of Plastid DNA during Tomato Fruit Development

We have analyzed DNA methylation of plastid DNA from fully ripened red fruits, green mature fruits, and green leaves of tomato (Lycopersicon esculentum var. Firstmore). Essentially identical restriction profiles were obtained between chromoplast and chloroplast DNAs by EcoRI digestion. BstNI/EcoRII and HpaII/MspI are pairs of isoschizomers that can discriminate between methylated and unmethylated DNAs. These endonucleases produced different restriction patterns of plastid DNAs from tomato fruits compared to tomato leaves. Moreover, we have found from Southern blots that methylation was not detected in DNA fragments containing certain genes that are actively expressed in chromoplasts, whereas DNA fragments bearing genes that are barely transcribed in chromoplasts are methylated.

DNA methylation as a mechanism of transcriptional regulation in nonphotosynthetic plastids in plant cells

Transcription of amyloplast DNA in a heterotrophic line of cultured cells of sycamore (Acer pseudoplatanus L.) appeared to be greatly suppressed. A mutant cell line obtained from the heterotrophic line is green and autotrophic. Heavy modification of amyloplast DNA with a variety of methylated bases was demonstrated by analysis of the acid hydrolysate of DNA by high-performance liquid chromatography, but little modification of chloroplast DNA from the green line was detected. When plastid DNAs from the original and green cell lines were digested with methyl-sensitive restriction enzymes, DNA methylation was detected in regions containing the genes for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL), subunits of chloroplast coupling factor 1 (atpA, -B, and -E), the apoprotein of P700 (psaA), and ribosomal protein S4 (rps4) but not the genes for 16S rRNA and the 32-kDa QB protein (psbA) in the original line, whereas no methylation was observed in the green line. The genes for which methylation was not detectable were found to be active as templates for in vitro transcription by Escherichia coli RNA polymerase, but the methylated genes were apparently inactive. Methylation of DNA is a likely mechanism for the regulation of expression of amyloplast DNA in sycamore cells.

Isolation and Characterization of the Amyloplast Envelope-Membrane from Cultured White-Wild Cells of Sycamore (Acer pseudoplatanus L.)

To study the characteristic features of the amyloplast, a uniquely differentiated plastid-type which synthesizes and accumulates reserve starch, in comparison with those of the chloroplast, these two types of plastids were isolated from white-wild and green-mutant protoplasts of cultured sycamore (Acer pseudoplatanus L.) cells, respectively. The intactness of the isolated amyloplast preparations was 70%. Electron microscopic ultrastructural analysis of both plastid types revealed unique structural features of the green-mutant chloroplasts, including well developed grana membranes and abundant ribosomal particles and plastoglobuli. After osmotic rupture of the isolated amyloplasts and chloroplasts, a clear separation of the envelope-membranes was achieved by discontinuous sucrose density gradient centrifugation. Although the visible absorption spectra of the envelope lipid components were indistinguishable between the amyloplasts and chloroplasts, the envelope-membrane polypeptide patterns were clearly distinct as judged by denaturing electrophoresis. By immunoblotting analysis using the specific antiserum raised against the pea chloroplast 29-kilodalton Pi-translocator, the amount of this carrier-protein (31-kilodalton) in the white-wild amyloplast envelope-membranes was estimated to be at least 10-fold less than in the green-mutant envelopes.