Relations between the plastid gene dosage and the levels of 16S rRNA and rbcL gene transcripts during amyloplast to chloroplast change in mixotrophic spinach cell suspensions

Chloroplast nucleoids are highly dynamic in ploidy, number, and structure during angiosperm leaf development

Chloroplast nucleoids are large, compact nucleoprotein structures containing multiple copies of the plastid genome. Studies on structural and quantitative changes of plastid DNA (ptDNA) during leaf development are scarce and have produced controversial data. We have systematically investigated nucleoid dynamics and ptDNA quantities in the mesophyll of Arabidopsis, tobacco, sugar beet, and maize from the early post-meristematic stage until necrosis. DNA of individual nucleoids was quantified by DAPI-based supersensitive epifluorescence microscopy. Nucleoids occurred in scattered, stacked, or ring-shaped arrangements and in recurring patterns during leaf development that was remarkably similar between the species studied. Nucleoids per organelle varied from a few in meristematic plastids to >30 in mature chloroplasts (corresponding to about 20-750 nucleoids per cell). Nucleoid ploidies ranged from haploid to >20-fold even within individual organelles, with average values between 2.6-fold and 6.7-fold and little changes during leaf development. DNA quantities per organelle increased gradually from about a dozen plastome copies in tiny plastids of apex cells to 70-130 copies in chloroplasts of about 7 μm diameter in mature mesophyll tissue, and from about 80 plastome copies in meristematic cells to 2600-3300 copies in mature diploid mesophyll cells without conspicuous decline during leaf development. Pulsed-field electrophoresis, restriction of high-molecular-weight DNA from chloroplasts and gerontoplasts, and CsCl equilibrium centrifugation of single-stranded and double-stranded ptDNA revealed no noticeable fragmentation of the organelle DNA during leaf development, implying that plastid genomes in mesophyll tissues are remarkably stable until senescence.

Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing

Background

High throughput sequencing (HTS) technologies have revolutionized the field of genomics by drastically reducing the cost of sequencing, making it feasible for individual labs to sequence or resequence plant genomes. Obtaining high quality, high molecular weight DNA from plants poses significant challenges due to the high copy number of chloroplast and mitochondrial DNA, as well as high levels of phenolic compounds and polysaccharides. Multiple methods have been used to isolate DNA from plants; the CTAB method is commonly used to isolate total cellular DNA from plants that contain nuclear DNA, as well as chloroplast and mitochondrial DNA. Alternatively, DNA can be isolated from nuclei to minimize chloroplast and mitochondrial DNA contamination.

Results

We describe optimized protocols for isolation of nuclear DNA from eight different plant species encompassing both monocot and eudicot species. These protocols use nuclei isolation to minimize chloroplast and mitochondrial DNA contamination. We also developed a protocol to determine the number of chloroplast and mitochondrial DNA copies relative to the nuclear DNA using quantitative real time PCR (qPCR). We compared DNA isolated from nuclei to total cellular DNA isolated with the CTAB method. As expected, DNA isolated from nuclei consistently yielded nuclear DNA with fewer chloroplast and mitochondrial DNA copies, as compared to the total cellular DNA prepared with the CTAB method. This protocol will allow for analysis of the quality and quantity of nuclear DNA before starting a plant whole genome sequencing or resequencing experiment.

Conclusions

Extracting high quality, high molecular weight nuclear DNA in plants has the potential to be a bottleneck in the era of whole genome sequencing and resequencing. The methods that are described here provide a framework for researchers to extract and quantify nuclear DNA in multiple types of plants.

Genome-wide analysis of plastid gene expression in potato leaf chloroplasts and tuber amyloplasts: transcriptional and posttranscriptional control

Gene expression in nongreen plastids is largely uncharacterized. To compare gene expression in potato (Solanum tuberosum) tuber amyloplasts and leaf chloroplasts, amounts of transcripts of all plastid genes were determined by hybridization to plastome arrays. Except for a few genes, transcript accumulation was much lower in tubers compared with leaves. Transcripts of photosynthesis-related genes showed a greater reduction in tubers compared with leaves than transcripts of genes for the genetic system. Plastid genome copy number in tubers was 2- to 3-fold lower than in leaves and thus cannot account for the observed reduction of transcript accumulation in amyloplasts. Both the plastid-encoded and the nucleus-encoded RNA polymerases were active in potato amyloplasts. Transcription initiation sites were identical in chloroplasts and amyloplasts, although some differences in promoter utilization between the two organelles were evident. For some intron-containing genes, RNA splicing was less efficient in tubers than in leaves. Furthermore, tissue-specific differences in editing of ndh transcripts were detected. Hybridization of the plastome arrays with RNA extracted from polysomes indicated that, in tubers, ribosome association of transcripts was generally low. Nevertheless, some mRNAs, such as the transcript of the fatty acid biosynthesis gene accD, displayed relatively high ribosome association. Selected nuclear genes involved in plastid gene expression were generally significantly less expressed in tubers than in leaves. Hence, compared with leaf chloroplasts, gene expression in tuber amyloplasts is much lower, with control occurring at the transcriptional, posttranscriptional, and translational levels. Candidate regulatory sequences that potentially can improve plastid (trans)gene expression in amyloplasts have been identified.

From seedling to mature plant: arabidopsis plastidial genome copy number, RNA accumulation and transcription are differentially regulated during leaf development

Little is known about DNA and RNA metabolism during leaf development and aging in the model organism Arabidopsis. Therefore we examined the nuclear and plastidial DNA content of tissue ranging in age from 2-day-old cotyledons to 37-day-old senescent rosette leaves. Flow-cytometric analysis showed an increase in nuclear DNA ploidy levels of up to 128 genome copies per nucleus in older leaves. The copy numbers of nuclear 18S-rRNA genes were determined to be 700 +/- 60 per haploid genome. Adjusted to the average level of nuclear DNA polyploidism per cell, plastome copy numbers varied from about 1000 to 1700 per cell without significant variation during development from young to old rosette leaves. The transcription activity of all studied plastid genes was significantly reduced in older rosette leaves in comparison to that in young leaves. In contrast, levels of plastidial transcript accumulation showed different patterns. In the case of psbA, transcripts accumulated to even higher levels in older leaves, indicating that differential regulation of plastidial gene expression occurs during leaf development. Examination of promoter activity from clpP and rrn16 genes by primer extension analyses revealed that two RNA polymerases (NEP and PEP) transcribe these genes in cotyledons as well as in young and senescent leaves. However, PEP may have a more prominent role in older rosette leaves than in young cotyledons. We conclude that in cotyledons or leaves of different ages plastidial gene expression is regulated at the transcriptional and post-transcriptional levels, but not by plastome copy number.

Constancy of organellar genome copy numbers during leaf development and senescence in higher plants

In higher plants, plastid and mitochondrial genomes occur at high copy numbers per cell. Several recent publications have suggested that, in higher plants like Arabidopsis and maize, chloroplast DNA is virtually absent in mature and old leaves. This conclusion was mainly based on DAPI staining of isolated chloroplasts. If correct, the finding that chloroplasts in mature leaves lack DNA would change dramatically our understanding of gene expression, mRNA stability and protein stability in chloroplasts. In view of the wide implications that the disposal of chloroplast DNA during leaf development would have, we have reinvestigated the age dependency of genome copy numbers in chloroplasts and, in addition, tested for possible changes in mitochondrial genome copy number during plant development. Analyzing chloroplast and mitochondrial DNA amounts in Arabidopsis and tobacco plants, we find that organellar genome copy numbers remain remarkably constant during leaf development and are present in essentially unchanged numbers even in the senescing leaves. We conclude that, during leaf development, organellar gene expression in higher plants is not significantly regulated at the level of genome copy number and we discuss possible explanations for the failure to detect DNA in isolated chloroplasts stained with DAPI.

Tissue-specific expression of the large ATP synthase gene cluster in spinach plastids

Plastids present in different tissues may vary morphologically and functionally, despite the fact that all plastids within the same plant contain identical genomes. This is achieved by regulation of expression of the plastid genome by tissue-specific factors, the mechanisms of which are not fully understood. The proton translocating ATP synthase/ATPase is a multisubunit complex composed of nine subunits, six encoded in the plastid and three in the nucleus. We have investigated the tissue-specific expression of the large ATP synthase gene cluster in spinach (Spinacia oleracea). This gene cluster encodes four of the six plastid-encoded ATP synthase genes. Transcript abundance, transcriptional activity, and transcript stability were investigated relative to gene dosage in root plastids and in stem, leaf, and flower chloroplasts. All three of these factors display significant tissue-specific variation. It was intriguing to discover that, although transcript abundance normalized to gene dosage varies in each tissue, transcript abundance as a proportion of the entire plastid RNA population in each tissue is not significantly different. Thus it appears that in these tissues the variation in transcription and stability of transcripts derived from the large ATP synthase gene cluster balances to yield an equivalent proportion of these transcripts in the plastid RNA population. Expression of this gene cluster in photosynthetic as well as non-photosynthetic tissues may facilitate the plasticity of structure and function which is characteristic of plastids.

The first analysed archegoniate mitochondrial gene (COX3) exhibits extraordinary features

The first mitochondrial-encoded gene of an archegoniate has been identified, cloned and sequenced. The cytochrome oxidase III gene (cox3) of the moss Physcomitrella patens consists of a 618 bp open reading frame with high homology (around 72%) to known cox3 sequences of higher plants. Nevertheless, it is a quarter shorter than these. The cox3 gene of P. patens contains no introns and reveals a G + C-content of 41.3%. The region containing the cox3 gene exists as a single copy in the mitochondrial genome as shown by restriction mapping. In the 5' flanking sequence a putative ribosome binding site and a putative secondary structure were found. Two main transcripts of 2.4 kb and 2.6 kb were detected indicating a complex mitochondrial transcription pattern possibly due to co-transcription. Additional open reading frames were found downstream from, as well as upstream of, the cox3 gene. In Western blots a polyclonal cox3 antibody from yeast detected one single band with an apparent molecular weight of 22 kDa.

The components of the plastid ribosome are not accumulated synchronously during the early development of spinach plants

The expression of components of the 70S plastid ribosome has been determined during the first 13 days of spinach plant development. Total cellular RNA and proteins were used to determine the relative steady-state levels of mRNA for ribosomal proteins (r-proteins) by dot blot hybridization and the relative amounts of proteins by immunodetection with specific antibodies. The 16S rRNA as well as mRNAs for 9 out of 11 proteins studied, including those for the 32 kDa polypeptide of photosystem II and the large subunit (LSU) of ribulose-1,5-bisphosphate carboxylase (Rubisco) show a marked increase at the beginning of the germination (day 5). At this time the plastid DNA content increases from 4% to 6% of total DNA content and so the plastome copy number can only in part account for the important increase in mRNA steady-state levels. Interestingly the transcripts of the rpl23 and rps19 genes show a different accumulation pattern, indicating either a differential gene transcription and/or an increased stability of the transcripts. In the western blot analysis a group of r-proteins can be detected in dry seeds or after 24 hours of imbibition while a second group of proteins accumulates after 3 to 5 days of development. The differential accumulation pattern of r-proteins and mRNA for r-proteins indicates that post-transcriptional control plays an important role in plastid r-protein synthesis.

Transcription study of the genes encoded in the region of the junction between the large single copy and the inverted repeat A of spinach chloroplast DNA

The expression of the psbA, trnH-GUG and rps19' genes from spinach chloroplasts, coding respectively for the 32 kDa protein, the tRNA(His) (GUG), and the putative ribosomal protein CS19', has been studied by cloning, Northern hybridization and 3' and 5' S1 mapping experiments.It is demonstrated that the putative transcription termination signal of the psbA gene does not function as a rho-independent terminator of transcription in E. coli, whatever its orientation.Evidence is presented suggesting that, in spinach, the psbA and trnH-GUG genes are probably cotranscribed. The 3'-OH extremities of transcripts observed downstream from the putative psbA terminator are interpreted as resulting from processing of the psbA precursor.Using different approaches, it is shown that the rps19' gene, located on the other strand and overlapping the trnH-GUG gene, is not expressed.

Sequence organization of the chloroplast ribosomal spacer ofSpinacia oleracea including the 3' end of the 16S rRNA and the 5' end of the 23S rRNA

The 2201-bp spacer between the chloroplast ribosomal 16S and 23S genes ofSpinacia oleracea was sequenced. It contains the genes of the tRNA(Ile) (GAU) and tRNA(Ala) (UGC) which are both interrupted by introns of respectively 728 and 816 bp. These introns belong to the class II according to the classfication of Michel and Dujon [17]. Comparison of the rDNA spacer sequence of maize, tobacco and spinach indicates that no conserved polypeptide is encoded within the introns of the two tRNA genes and that the two main insertions/deletions between the three plants are located within two loops of the class II introns secondary structure, which is therefore conserved. Based on the sequence complementarity observed between the upstream and downstream parts, of the 16S and 23S rRNA genes, RNase III-like secondary structures involved in the processing of the rRNA precursor are proposed.