Evidence for transcriptional regulation of plastid photosynthesis genes in Arabidopsis thaliana roots

Removal of the large inverted repeat from the plastid genome reveals gene dosage effects and leads to increased genome copy number

The chloroplast genomes of most plants and algae contain a large inverted repeat (IR) region that separates two single-copy regions and harbours the ribosomal RNA operon. We have addressed the functional importance of the IR region by removing an entire copy of the 25.3-kb IR from the tobacco plastid genome. Using plastid transformation and subsequent selectable marker gene elimination, we precisely excised the IR, thus generating plants with a substantially reduced plastid genome size. We show that the lack of the IR results in a mildly reduced plastid ribosome number, suggesting a gene dosage benefit from the duplicated presence of the ribosomal RNA operon. Moreover, the IR deletion plants contain an increased number of plastid genomes, suggesting that genome copy number is regulated by measuring total plastid DNA content rather than by counting genomes. Together, our findings (1) demonstrate that the IR can enhance the translation capacity of the plastid, (2) reveal the relationship between genome size and genome copy number, and (3) provide a simplified plastid genome structure that will facilitate future synthetic biology applications.

High-resolution map of plastid-encoded RNA polymerase binding patterns demonstrates a major role of transcription in chloroplast gene expression

Plastids contain their own genomes, which are transcribed by two types of RNA polymerases. One of those enzymes is a bacterial-type, multi-subunit polymerase encoded by the plastid genome. The plastid-encoded RNA polymerase (PEP) is required for efficient expression of genes encoding proteins involved in photosynthesis. Despite the importance of PEP, its DNA binding locations have not been studied on the genome-wide scale at high resolution. We established a highly specific approach to detect the genome-wide pattern of PEP binding to chloroplast DNA using plastid chromatin immunoprecipitation-sequencing (ptChIP-seq). We found that in mature Arabidopsis thaliana chloroplasts, PEP has a complex DNA binding pattern with preferential association at genes encoding rRNA, tRNA, and a subset of photosynthetic proteins. Sigma factors SIG2 and SIG6 strongly impact PEP binding to a subset of tRNA genes and have more moderate effects on PEP binding throughout the rest of the genome. PEP binding is commonly enriched on gene promoters, around transcription start sites. Finally, the levels of PEP binding to DNA are correlated with levels of RNA accumulation, which demonstrates the impact of PEP on chloroplast gene expression. Presented data are available through a publicly available Plastid Genome Visualization Tool (Plavisto) at https://plavisto.mcdb.lsa.umich.edu/.

Plastid Gene Transcription: An Update on Promoters and RNA Polymerases

Chloroplasts, the sites of photosynthesis and sources of reducing power, are at the core of the success story that sets apart autotrophic plants from most other living organisms. Along with their fellow organelles (e.g., amylo-, chromo-, etio-, and leucoplasts), they form a group of intracellular biosynthetic machines collectively known as plastids. These plant cell constituents have their own genome (plastome), their own (70S) ribosomes, and complete enzymatic equipment covering the full range from DNA replication via transcription and RNA processive modification to translation. Plastid RNA synthesis (gene transcription) involves the collaborative activity of two distinct types of RNA polymerases that differ in their phylogenetic origin as well as their architecture and mode of function. The existence of multiple plastid RNA polymerases is reflected by distinctive sets of regulatory DNA elements and protein factors. This complexity of the plastid transcription apparatus thus provides ample room for regulatory effects at many levels within and beyond transcription. Research in this field offers insight into the various ways in which plastid genes, both singly and groupwise, can be regulated according to the needs of the entire cell. Furthermore, it opens up strategies that allow to alter these processes in order to optimize the expression of desired gene products.

Changes in plastid biogenesis leading to the formation of albino regenerants in barley microspore culture

BACKGROUND

Microspore embryogenesis is potentially the most effective method of obtaining doubled haploids (DH) which are utilized in breeding programs to accelerate production of new cultivars. However, the regeneration of albino plants significantly limits the exploitation of androgenesis for DH production in cereals. Despite many efforts, the precise mechanisms leading to development of albino regenerants have not yet been elucidated. The objective of this study was to reveal the genotype-dependent molecular differences in chloroplast differentiation that lead to the formation of green and albino regenerants in microspore culture of barley.

RESULTS

We performed a detailed analysis of plastid differentiation at successive stages of androgenesis in two barley cultivars, 'Jersey' and 'Mercada' that differed in their ability to produce green regenerants. We demonstrated the lack of transition from the NEP-dependent to PEP-dependent transcription in plastids of cv. 'Mercada' that produced mostly albino regenerants in microspore culture. The failed NEP-to-PEP transition was associated with the lack of activity of Sig2 gene encoding a sigma factor necessary for transcription of plastid rRNA genes. A very low level of 16S and 23S rRNA transcripts and impaired plastid translation machinery resulted in the inhibition of photomorphogenesis in regenerating embryos and albino regenerants. Furthermore, the plastids present in differentiating 'Mercada' embryos contained a low number of plastome copies whose replication was not always completed. Contrary to 'Mercada', cv. 'Jersey' that produced 90% green regenerants, showed the high activity of PEP polymerase, the highly increased expression of Sig2, plastid rRNAs and tRNAGlu, which indicated the NEP inhibition. The increased expression of GLKs genes encoding transcription factors required for induction of photomorphogenesis was also observed in 'Jersey' regenerants.

CONCLUSIONS

Proplastids present in microspore-derived embryos of albino-producing genotypes did not pass the early checkpoints of their development that are required for induction of further light-dependent differentiation of chloroplasts. The failed activation of plastid-encoded RNA polymerase during differentiation of embryos was associated with the genotype-dependent inability to regenerate green plants in barley microspore culture. The better understanding of molecular mechanisms underlying formation of albino regenerants may be helpful in overcoming the problem of albinism in cereal androgenesis.

Opposite roles of the Arabidopsis cytokinin receptors AHK2 and AHK3 in the expression of plastid genes and genes for the plastid transcriptional machinery during senescence

Cytokinin membrane receptors of the Arabidopsis thaliana AHK2 and AHK3 play opposite roles in the expression of plastid genes and genes for the plastid transcriptional machinery during leaf senescence Loss-of-function mutants of Arabidopsis thaliana were used to study the role of cytokinin receptors in the expression of chloroplast genes during leaf senescence. Accumulation of transcripts of several plastid-encoded genes is dependent on the АНК2/АНК3 receptor combination. АНК2 is particularly important at the final stage of plant development and, unlike АНК3, a positive regulator of leaf senescence. Cytokinin-dependent up-regulation of the nuclear encoded genes for chloroplast RNA polymerases RPOTp and RPOTmp suggests that the hormone controls plastid gene expression, at least in part, via the expression of nuclear genes for the plastid transcription machinery. This is further supported by cytokinin dependent regulation of genes for the nuclear encoded plastid σ-factors, SIG1-6, which code for components of the transcriptional apparatus in chloroplasts.

The Plastomes of Two Species in the Endoparasite Genus Pilostyles (Apodanthaceae) Each Retain Just Five or Six Possibly Functional Genes

The 23 species of mycoheterotrophic or exoparasitic land plants (from 15 genera and 6 families) studied so far all retain a minimal set of 17 of the normally 116 plastome genes. Only Rafflesia lagascae, an endoparasite concealed in its host except when flowering, has been reported as perhaps lacking a plastome, although it still possesses plastid-like compartments. We analyzed two other endoparasites, the African Apodanthaceae Pilostyles aethiopica and the Australian Pilostyles hamiltonii, both living inside Fabaceae. Illumina and 454 data and Sanger resequencing yielded circularized plastomes of 11,348 and 15,167 bp length, with both species containing five possibly functional genes (accD, rps3, rps4, rrn16, rrn23) and two/three pseudogenes (rpoC2 in P. aethiopica and rpl2 and rps12 in both species; rps12 may be functional in P. hamiltonii). Previously known smallest land plant plastomes contain 27–29 genes, making these Apodanthaceae plastomes the most reduced in size and gene content. A similar extent of divergence might have caused the plastome of Rafflesia to escape detection. The higher plastome degeneration in both these families of endoparasites, Rafflesiaceae and Apodanthaceae, of similar high age, compared with exoparasites points to a difference of plastome function between those two modes of parasitic life.

SENESCENCE-SUPPRESSED PROTEIN PHOSPHATASE Directly Interacts with the Cytoplasmic Domain of SENESCENCE-ASSOCIATED RECEPTOR-LIKE KINASE and Negatively Regulates Leaf Senescence in Arabidopsis

Reversible protein phosphorylation mediated by protein kinases and phosphatases plays an important role in the regulation of leaf senescence. We previously reported that the leucine-rich repeat receptor-like kinase SENESCENCE-ASSOCIATED RECEPTOR-LIKE KINASE (AtSARK) positively regulates leaf senescence in Arabidopsis (Arabidopsis thaliana). Here, we report the involvement of a protein serine/threonine phosphatase 2C-type protein phosphatase, SENESCENCE-SUPPRESSED PROTEIN PHOSPHATASE (SSPP), in the negative regulation of Arabidopsis leaf senescence. SSPP transcript levels decreased greatly during both natural senescence and SARK-induced precocious senescence. Overexpression of SSPP significantly delayed leaf senescence in Arabidopsis. Protein pull-down and bimolecular fluorescence complementation assays demonstrated that the cytosol-localized SSPP could interact with the cytoplasmic domain of the plasma membrane-localized AtSARK. In vitro assays showed that SSPP has protein phosphatase function and can dephosphorylate the cytosolic domain of AtSARK. Consistent with these observations, overexpression of SSPP effectively rescued AtSARK-induced precocious leaf senescence and changes in hormonal responses. All our results suggested that SSPP functions in sustaining proper leaf longevity and preventing early senescence by suppressing or perturbing SARK-mediated senescence signal transduction.

Rubisco accumulation is important for the greening of the fln2-4 mutant in Arabidopsis

The fructokinase-like protein2 (FLN2) is a component of the PEP complex. FLN2 knockout mutants displayed a delayed greening phenotype on sucrose-containing medium. Our previous work indicated that partial PEP activity is essential for its greening phenotype. In this study, we further report that sufficient Rubisco accumulation is critical for fln2-4 greening. Sugar serves many important functions, such as an energy source and signaling molecule. Through pharmacological experiments using a sugar analog and sugar signaling inhibitor, we demonstrate that sugar serves as energy to support the fln2-4 greening. Seed-reserve and photosynthetic CO2-fixation are the primary energy sources for early seedling growth. No obvious differences were observed in the seed-reserve of the wild-type and fln2-4 by comparing their seed size and dark-germination, indicating that the defective carbon fixation may account for the energy deficit in fln2-4 during its early seedling growth. The Rubisco content was low in fln2-4, but it rapidly accumulated during the greening of fln2-4. Expression of a nuclear-encoded rbcL gene facilitates Rubisco accumulation and partially complements the mutant defects. These results suggest that the Rubisco accumulation is critical for fln2-4 greening. In summary, the rapid Rubisco accumulation that depends on sufficient PEP activity is important for normal seedling growth.

Profiling gene expression in citrus fruit calyx abscission zone (AZ-C) treated with ethylene

On-tree storage and harvesting of mature fruit account for a large proportion of cost in the production of citrus, and a reduction of the cost would not be achieved without a thorough understanding of the mechani sm of the mature fruit abscission. Genome-wide gene expression changes in ethylene-treated fruit calyx abscission zone (AZ-C) of Citrus sinensis cv. Olinda were therefore investigated using a citrus genome array representing up to 33,879 citrus transcripts. In total, 1313 and 1044 differentially regulated genes were identified in AZ-C treated with ethylene for 4 and 24 h, respectively. The results showed that mature citrus fruit abscission commenced with the activation of ethylene signal transduction pathway that led to the activation of ethylene responsive transcription factors and the subsequent transcriptional regulation of a large set of ethylene responsive genes. Significantly down-regulated genes included those of starch/sugar biosynthesis, transportation of water and growth promoting hormone synthesis and signaling, whereas significantly up-regulated genes were those involved in defense, cell wall degradation, and secondary metabolism. Our data unraveled the underlying mechanisms of some known important biochemical events occurring at AZ-C and should provide informative suggestions for future manipulation of the events to achieve a controllable abscission for mature citrus fruit.

The CLE40 and CRN/CLV2 signaling pathways antagonistically control root meristem growth in Arabidopsis

Differentiation processes in the primary root meristem are controlled by several signaling pathways that are regulated by phytohormones or by secreted peptides. Long-term maintenance of an active root meristem requires that the generation of new stem cells and the loss of these from the meristem due to differentiation are precisely coordinated. Via phenotypic and large-scale transcriptome analyses of mutants, we show that the signaling peptide CLE40 and the receptor proteins CLV2 and CRN act in two genetically separable pathways that antagonistically regulate cell differentiation in the proximal root meristem. CLE40 inhibits cell differentiation throughout the primary root meristem by controlling genes with roles in abscisic acid, auxin, and cytokinin signaling. CRN and CLV2 jointly control target genes that promote cell differentiation specifically in the transition zone of the proximal root meristem. While CRN and CLV2 are not acting in the CLE40 signaling pathway under normal growth conditions, both proteins are required when the levels of CLE40 or related CLE peptides increase. We show here that two antagonistically acting pathways controlling root meristem differentiation can be activated by the same peptide in a dosage-dependent manner.

Possible loss of the chloroplast genome in the parasitic flowering plant Rafflesia lagascae (Rafflesiaceae)

Rafflesia is a genus of holoparasitic plants endemic to Southeast Asia that has lost the ability to undertake photosynthesis. With short-read sequencing technology, we assembled a draft sequence of the mitochondrial genome of Rafflesia lagascae Blanco, a species endemic to the Philippine island of Luzon, with ∼350× sequencing depth coverage. Using multiple approaches, however, we were only able to identify small fragments of plastid sequences at low coverage depth (<2×) and could not recover any substantial portion of a chloroplast genome. The gene fragments we identified included photosynthesis and energy production genes (atp, ndh, pet, psa, psb, rbcL), ribosomal RNA genes (rrn16, rrn23), ribosomal protein genes (rps7, rps11, rps16), transfer RNA genes, as well as matK, accD, ycf2, and multiple nongenic regions from the inverted repeats. None of the identified plastid gene sequences had intact reading frames. Phylogenetic analysis suggests that ∼33% of these remnant plastid genes may have been horizontally transferred from the host plant genus Tetrastigma with the rest having ambiguous phylogenetic positions (<50% bootstrap support), except for psaB that was strongly allied with the plastid homolog in Nicotiana. Our inability to identify substantial plastid genome sequences from R. lagascae using multiple approaches—despite success in identifying and developing a draft assembly of the much larger mitochondrial genome—suggests that the parasitic plant genus Rafflesia may be the first plant group for which there is no recognizable plastid genome, or if present is found in cryptic form at very low levels.

Plastid gene transcription: promoters and RNA polymerases

Chloroplasts, the sites of photosynthesis and sources of reducing power, are at the core of the success story that sets apart autotrophic plants from most other living organisms. Along with their fellow organelles (e.g., amylo-, chromo-, etio-, and leucoplasts), they form a group of intracellular biosynthetic machines collectively known as plastids. These plant cell constituents have their own genome (plastome), their own (70S) ribosomes, and complete enzymatic equipment covering the full range from DNA replication via transcription and RNA processive modification to translation. Plastid RNA synthesis (gene transcription) involves the collaborative activity of two distinct types of RNA polymerases that differ in their phylogenetic origin as well as their architecture and mode of function. The existence of multiple plastid RNA polymerases is reflected by distinctive sets of regulatory DNA elements and protein factors. This complexity of the plastid transcription apparatus thus provides ample room for regulatory effects at many levels within and beyond transcription. Research in this field offers insight into the various ways in which plastid genes, both singly and groupwise, can be regulated according to the needs of the entire cell. Furthermore, it opens up strategies that allow to alter these processes in order to optimize the expression of desired gene products.

Photosynthetic gene expression in higher plants

Within the chloroplasts of higher plants and algae, photosynthesis converts light into biological energy, fueling the assimilation of atmospheric carbon dioxide into biologically useful molecules. Two major steps, photosynthetic electron transport and the Calvin-Benson cycle, require many gene products encoded from chloroplast as well as nuclear genomes. The expression of genes in both cellular compartments is highly dynamic and influenced by a diverse range of factors. Light is the primary environmental determinant of photosynthetic gene expression. Working through photoreceptors such as phytochrome, light regulates photosynthetic genes at transcriptional and posttranscriptional levels. Other processes that affect photosynthetic gene expression include photosynthetic activity, development, and biotic and abiotic stress. Anterograde (from nucleus to chloroplast) and retrograde (from chloroplast to nucleus) signaling insures the highly coordinated expression of the many photosynthetic genes between these different compartments. Anterograde signaling incorporates nuclear-encoded transcriptional and posttranscriptional regulators, such as sigma factors and RNA-binding proteins, respectively. Retrograde signaling utilizes photosynthetic processes such as photosynthetic electron transport and redox signaling to influence the expression of photosynthetic genes in the nucleus. The basic C3 photosynthetic pathway serves as the default form used by most of the plant species on earth. High temperature and water stress associated with arid environments have led to the development of specialized C4 and CAM photosynthesis, which evolved as modifications of the basic default expression program. The goal of this article is to explain and summarize the many gene expression and regulatory processes that work together to support photosynthetic function in plants.

A comprehensive expression profile of microRNAs and other classes of non-coding small RNAs in barley under phosphorous-deficient and -sufficient conditions

Phosphorus (P) is essential for plant growth. MicroRNAs (miRNAs) play a key role in phosphate homeostasis. However, little is known about P effect on miRNA expression in barley (Hordeum vulgare L.). In this study, we used Illumina's next-generation sequencing technology to sequence small RNAs (sRNAs) in barley grown under P-deficient and P-sufficient conditions. We identified 221 conserved miRNAs and 12 novel miRNAs, of which 55 were only present in P-deficient treatment while 32 only existed in P-sufficient treatment. Total 47 miRNAs were significantly differentially expressed between the two P treatments (|log₂| > 1). We also identified many other classes of sRNAs, including sense and antisense sRNAs, repeat-associated sRNAs, transfer RNA (tRNA)-derived sRNAs and chloroplast-derived sRNAs, and some of which were also significantly differentially expressed between the two P treatments. Of all the sRNAs identified, antisense sRNAs were the most abundant sRNA class in both P treatments. Surprisingly, about one-fourth of sRNAs were derived from the chloroplast genome, and a chloroplast-encoded tRNA-derived sRNA was the most abundant sRNA of all the sRNAs sequenced. Our data provide valuable clues for understanding the properties of sRNAs and new insights into the potential roles of miRNAs and other classes of sRNAs in the control of phosphate homeostasis.

Identification of cis-elements conferring high levels of gene expression in non-green plastids

Although our knowledge about the mechanisms of gene expression in chloroplasts has increased substantially over the past decades, next to nothing is known about the signals and factors that govern expression of the plastid genome in non-green tissues. Here we report the development of a quantitative method suitable for determining the activity of cis-acting elements for gene expression in non-green plastids. The in vivo assay is based on stable transformation of the plastid genome and the discovery that root length upon seedling growth in the presence of the plastid translational inhibitor kanamycin is directly proportional to the expression strength of the resistance gene nptII in transgenic tobacco plastids. By testing various combinations of promoters and translation initiation signals, we have used this experimental system to identify cis-elements that are highly active in non-green plastids. Surprisingly, heterologous expression elements from maize plastids were significantly more efficient in conferring high expression levels in root plastids than homologous expression elements from tobacco. Our work has established a quantitative method for characterization of gene expression in non-green plastid types, and has led to identification of cis-elements for efficient plastid transgene expression in non-green tissues, which are valuable tools for future transplastomic studies in basic and applied research.

The transcription machineries of plant mitochondria and chloroplasts: Composition, function, and regulation

Although genomes of mitochondria and plastids are very small compared to those of their bacterial ancestors, the transcription machineries of these organelles are of surprising complexity. With respect to the number of different RNA polymerases per organelle, the extremes are represented on one hand by chloroplasts of eudicots which use one bacterial-type RNA polymerase and two phage-type RNA polymerases to transcribe their genes, and on the other hand by Physcomitrella possessing three mitochondrial RNA polymerases of the phage type. Transcription of genes/operons is often driven by multiple promoters in both organelles. This review describes the principle components of the transcription machineries (RNA polymerases, transcription factors, promoters) and the division of labor between the different RNA polymerases. While regulation of transcription in mitochondria seems to be only of limited importance, the plastid genes of higher plants respond to exogenous and endogenous cues rather individually by altering their transcriptional activities.

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.

Unique and overlapping expression patterns among members of photosynthesis-associated nuclear gene families in Arabidopsis

Light provides crucial positional information in plant development, and the morphogenetic processes that are orchestrated by light signals are triggered by changes of gene expression in response to variations in light parameters. Control of expression of members of the RbcS and Lhc families of photosynthesis-associated nuclear genes by light cues is a paradigm for light-regulated gene transcription, but high-resolution expression profiles for these gene families are lacking. In this study, we have investigated expression patterns of members of the RbcS and Lhc gene families in Arabidopsis (Arabidopsis thaliana) at the cellular level during undisturbed development and upon controlled interference of the light environment. Members of the RbcS and Lhc gene families are expressed in specialized territories, including root tip, leaf adaxial, abaxial, and epidermal domains, and with distinct chronologies, identifying successive stages of leaf mesophyll ontogeny. Defined spatial and temporal overlap of gene expression fields suggest that the light-harvesting and photosynthetic apparatus may have a different polypeptide composition in different cells and that such composition could change over time even within the same cell.

Rice peptide deformylase PDF1B is crucial for development of chloroplasts

Because protein synthesis begins with N-formylmethionine in plant endosymbiotic organelles, removal of the formyl group by peptide deformylase (PDF) is essential to allowing the excision of the first methionine. Rice contains three copies (OsPDF1A, OsPDF1B and OsPDF1B2) of the PDF genes. Unlike OsPDF1A and OsPDF1B, OsPDF1B2 is apparently non-functional, with several deleterious substitutions and deletions. OsPDF1A is more strongly expressed in the roots, while OsPDF1B is expressed at higher levels in mature leaves. Transient expression of PDF-green fluorescent protein (GFP) fusion proteins in the protoplasts demonstrates that, unlike OsPDF1A, OsPDF1B is localized in both the chloroplasts and the mitochondria. We used T-DNA insertional alleles to elucidate functional roles associated with OsPDF1B. Homozygous plants of pdf1b/pdf1b exhibited the phenotypes of chlorina and growth retardation. Histochemical analysis showed that the length of their mesophyll cells was increased 4- to 5-fold, resulting in a reduction in the total number of cells. Transmission electron microscopy analyses revealed that chloroplasts were severely damaged and mitochondria appeared to be mildly altered in the pdf1b mutants. Expression of genes encoded in the chloroplasts and mitochondria was altered in the mutants. Based on these results, we conclude that OsPDF1B is essential for the development of chloroplast and perhaps mitochondria.

Functional analysis of the plastid and nuclear encoded CbbX proteins of Cyanidioschyzon merolae

CbbX is believed to be a transcriptional regulator of the subunit genes (rbcL and rbcS) of RuBisCO (Ribulose 1,5-bisphosphate carboxylase/oxygenase) as well as possibly a molecular chaperon of RuBisCO subunit assembly. The unicellular red alga Cyanidioschyzon merolae strain 10D possesses two distinct cbbX genes; one is part of the plastid genome and the other is found in the cell nucleus, whereas the RuBisCO operon (rbcL-rbcS-cbbX) is located only on the plastid genome. We examined the role of CbbX proteins of C. merolae in the expression of the RuBisCO operon. First, His-tagged nuclear and plastid CbbX proteins were produced in Escherichia coli and purified by affinity column chromatography. Both proteins showed binding activity to upstream of the coding region of rbcL. Yeast two hybrid analysis showed direct interaction between nuclear and plastid CbbX proteins but no interaction were found among CbbX, RbcL and RbcS. Then the transcription initiation site of the RuBisCO operon of C. merolae was determined. Next, in order to examine the role of CbbX in vivo, we constructed a plasmid carrying the promoter region of the RuBisCO operon fused to Escherichia coli lacZ, and introduced it into E. coli cells into which a cloned nuclear or plastid cbbX gene under IPTG inducible promoter control was also introduced. Expression of LacZ in the transformed E.coli was observed. Enforced expression of either one of the cbbX genes resulted in a remarkable reduction of lacZ expression suggesting that CbbXs are rather transcriptional regulators than the molecular chaperon of RuBisCO. We discuss the mechanism by which the nuclear and plastid CbbX proteins regulate the RuBisCO operon of C. merolae.

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.

“Multicolor” Electrochemical Labeling of DNA Hybridization Probes with Osmium Tetroxide Complexes

Labeling of oligonucleotide reporter probes (RP) with electroactive markers has frequently been utilized in electrochemical detection of DNA hybridization. Osmium tetroxide complexes with tertiary amines (Os,L) bind covalently to pyrimidine (predominantly thymine) bases in DNA, forming stable, electrochemically active adducts. We propose a technique of electrochemical "multicolor" DNA coding based on RP labeling with Os,L markers involving different nitrogenous ligands (such as 2,2' -bipyridine, 1,10-phenanthroline derivatives or N,N,N',N'-tetramethylethylenediamine). At carbon electrodes the Os,L-labeled RPs produce specific signals, with the potentials of these differing depending on the ligand type. When using Os,L markers providing sufficiently large differences in their peak potentials, parallel analysis of multiple target DNA sequences can easily be performed via DNA hybridization at magnetic beads followed by voltammetric detection at carbon electrodes. Os,L labeling of oligonucleotide probes comprising a segment complementary to target DNA and an oligo(T) tail (to be modified with the osmium complex) does not require any organic chemistry facilities and can be achieved in any molecular biological laboratory. We also for the first time show that this technology can be used for labeling of oligonucleotide probes hybridizing with target DNAs that contain both purine and pyrimidine bases.

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.

Plastid RNA polymerases, promoters, and transcription regulators in higher plants

Plastids are semiautonomous plant organelles exhibiting their own transcription-translation systems that originated from a cyanobacteria-related endosymbiotic prokaryote. As a consequence of massive gene transfer to nuclei and gene disappearance during evolution, the extant plastid genome is a small circular DNA encoding only ca. 120 genes (less than 5% of cyanobacterial genes). Therefore, it was assumed that plastids have a simple transcription-regulatory system. Later, however, it was revealed that plastid transcription is a multistep gene regulation system and plays a crucial role in developmental and environmental regulation of plastid gene expression. Recent molecular and genetic approaches have identified several new players involved in transcriptional regulation in plastids, such as multiple RNA polymerases, plastid sigma factors, transcription regulators, nucleoid proteins, and various signaling factors. They have provided novel insights into the molecular basis of plastid transcription in higher plants. This review summarizes state-of-the-art knowledge of molecular mechanisms that regulate plastid transcription in higher plants.

cDNA microarray analysis of developing grape (Vitis vinifera cv. Shiraz) berry skin

Microarray analysis of Vitis vinifera cv. Shiraz developing berries has revealed the expression patterns of several categories of genes. Microarray slides were constructed from 4,608 PCR-amplified cDNA clones derived from a ripening grape berry cDNA library. The mRNA expression levels of the genes represented by these cDNAs were measured in flowers, week 2 post-flowering whole berries, week 5, week 8, week 10 (véraison, green berries), week 12 and week 13 berry skin. In addition, a comparison of RNA expression in pigmented and unpigmented berry skin at véraison (week 10) was undertaken. Image and statistical analysis revealed four sets of genes with distinctive and similar expression profiles over the course of berry development. The first set was composed of genes which had maximum RNA expression in flowers, followed by a steady decrease in expression. The most prominent group within this set were genes which have a role in photosynthesis. The second set of cDNAs was dominated by genes involved in flavonoid biosynthesis and had a peak of expression week 2 post-flowering. The data indicate co-ordinate regulation of flavonoid biosynthetic genes which code for the enzymes 4-coumarate-CoA ligase, chalcone synthase, chalcone isomerase, flavonone hydroxylase, anthocyanidin reductase and cytochrome b5. The third set of cDNAs exhibited maximum expression week 5 post-flowering, midway between flowering and véraison, a period of rapid berry growth. This set of cDNAs is dominated by genes which code for structural cell wall proteins. The fourth set of genes was dramatically up-regulated at véraison and remained up-regulated until 13 weeks post-flowering. This set of genes was composed of a diverse range of genes, a reflection of the complexity of ripening, most with no known function.

Mechanism and importance of post-translational regulation of nitrate reductase

In higher plants, nitrate reductase (NR) is inactivated by the phosphorylation of a conserved Ser residue and binding of 14-3-3 proteins in the presence of divalent cations or polyamines. A transgenic Nicotiana plumbaginifolia line (S521) has been constructed where the regulatory, conserved Ser 521 of tobacco NR (corresponding to Ser 534 in Arabidopsis) was mutated into Asp. This mutation resulted in the complete abolition of activation/inactivation in response to light/dark transitions or other treatments known to regulate the activation state of NR. Analysis of the transgenic plants showed that, under certain conditions, when whole plants or cut tissues are exposed to high nitrate supply, post-translational regulation is necessary to avoid nitrite accumulation. Abolition of the post-translational regulation of NR also results in an increased flux of nitric oxide from the leaves and roots. In view of the results obtained from examining the different transgenic N. plumbaginifolia lines, compartmentation of nitrate into an active metabolic pool and a large storage pool appears to be an important factor for regulating nitrate reduction. The complex regulation of nitrate reduction is likely to have evolved not only to optimize nitrogen assimilation, but also to prevent and control the formation of toxic, and possibly regulatory, products of NR activities. Phos phorylation of NR has previously been found to influence the degradation of NR in spinach leaves and Arabidopsis cell cultures. However, experiments with whole plants of N. plumbaginifolia, Arabidopsis, or squash are in favour of NR degradation being the same in light and darkness and independent of phosphorylation at the regulatory Ser.

DNA-binding and transcription characteristics of three cloned sigma factors from mustard (Sinapis alba L.) suggest overlapping and distinct roles in plastid gene expression

We have isolated and studied the cloned sigma factors SASIG1-3 from mustard (Sinapis alba). In functional analyses using both promoter and factor mutants, the three recombinant proteins all had similar basic properties but also revealed differences in promoter preference and requirements for single nucleotide positions. Directed muta- genesis of SASIG1 identified critical residues within the conserved regions 2.4 and 4.2 necessary for binding of the -10 and -35 promoter elements, respectively. SASIG1 and 2, but not SASIG3, each have a typical region 2.5 for binding of the extended -10 promoter element. SASIG3 has a pro-sequence reminiscent of sigma K from Bacillus subtilis, suggesting that proteolytic cleavage from an inactive precursor is involved in the regulation of plastid transcription. In addition, SASIG2 was found to be more abundant in light-grown as compared to dark-grown mustard seedlings, while the converse was true for SASIG3.

The chloroplast clpP gene, encoding a proteolytic subunit of ATP-dependent protease, is indispensable for chloroplast development in tobacco

ClpP is a proteolytic subunit of the ATP-dependent Clp protease, which is found in chloroplasts in higher plants. Proteolytic subunits are encoded both by the chloroplast gene, clpP, and a nuclear multi gene family. We insertionally disrupted clpP by chloroplast transformation in tobacco. However, complete segregation was impossible, indicating that the chloroplast-encoded clpP gene has an indispensable function for cell survival. In the heteroplasmic clpP disruptant, the leaf surface was rough by clumping, and the lateral leaf expansion was irregularly arrested, which led to an asymmetric, slender leaf shape. Chloroplasts consisted of two populations: chloroplasts that were similar to the wild type, and small chloroplasts that emitted high chl fluorescence. Ultrastructural analysis of chloroplast development suggested that clpP disruption also induced swelling of the thylakoid lumen in the meristem plastids and inhibition of etioplast development in the dark. In mature leaves, thylakoid membranes of the smaller chloroplast population consisted exclusively of large stacks of tightly appressed membranes. These results indicate that chloroplast-encoded ClpP is involved in multiple processes of chloroplast development, including a housekeeping function that is indispensable for cell survival.

The role of sigma factors in plastid transcription

Expression of plastid genes is controlled at both transcriptional and post-transcriptional levels in response to developmental and environmental signals. In many cases this regulation is mediated by nuclear-encoded proteins acting in concert with the endogenous plastid gene expression machinery. Transcription in plastids is accomplished by two distinct RNA polymerase enzymes, one of which resembles eubacterial RNA polymerases in both subunit structure and promoter recognition properties. The holoenzyme contains a catalytic core composed of plastid-encoded subunits, assembled with a nuclear-encoded promoter-specificity factor, sigma. Based on examples of transcriptional regulation in bacteria, it is proposed that differential activation of sigma factors may provide the nucleus with a mechanism to control expression of groups of plastid genes. Hence, much effort has focused on identifying and characterizing sigma-like factors in plants. While fractionation studies had identified several candidate sigma factors in purified RNA polymerase preparations, it was only 4 years ago that the first sigma factor genes were cloned from two photosynthetic eukaryotes, both of which were red algae. More recently this achievement has extended to the identification of families of sigma-like factor genes from several species of vascular plants. Now, efforts in the field are directed at understanding the roles in plastid transcription of each member of the rapidly expanding plant sigma factor gene family. Recent results suggest that accumulation of individual sigma-like factors is controlled by light, by plastid type and/or by a particular stage of chloroplast development. These data mesh nicely with accumulating evidence that the core sigma-binding regions of plastid promoters mediate regulated transcription in response to light-regime and plastid type or developmental state. In this review I will outline progress made to date in identifying and characterizing the sigma-like factors of plants, and in dissecting their potential roles in chloroplast gene expression.

Molecular cloning of a cDNA encoding a novel Ca(2+)-dependent nuclease of Arabidopsis that is similar to staphylococcal nuclease

We have isolated a cDNA from Arabidopsis thaliana for a protein consisting of 323 amino acids with similarity to an extracellular nuclease from Staphylococcus. Nuclease assay using toluidine blue-DNA plates has demonstrated that the gene product has nuclease activity dependent on Ca(2+) and inhibited by Zn(2+), designated CAN (Ca(2+)-dependent nuclease). Differing from the staphylococcal nuclease, CAN has neither a signal peptide nor any long hydrophobic regions, suggesting that it is not a secreted protein.

An Arabidopsis cDNA encoding a DNA-binding protein that is highly similar to the DEAH family of RNA/DNA helicase genes

A cDNA encoding a putative RNA and/or DNA helicase has been isolated from Arabidopsis thaliana cDNA libraries. The cloned cDNA is 5166 bases long, and its largest open reading frame encodes 1538 amino acids. The central region of the predicted protein is homologous to a group of nucleic acid helicases from the DEAD/H family. However, the N- and C-terminal regions of the Arabidopsis cDNA product are distinct from these animal DEIH proteins. We have found that the C-terminal region contains three characteristic sequences: (i) two DNA-binding segments that form a probe helix (PH) involved in DNA recognition; (ii) an SV40-type nuclear localization signal; and (iii) 11 novel tandem-repeat sequences each consisting of about 28 amino acids. We have designated this cDNA as NIH (nuclear DEIH-boxhelicase). Functional character-ization of a recombinant fusion product containing the repeated region indicates that NIH may form homodimers, and that this is the active form in solution. Based on this information and the observation that the sequence homology is limited to the DEAH regions, we conclude that the biological roles of the plant helicase NIH differ from those of the animal DEIH family.

Light-dependent and rhythmic psbA transcripts in homologous/heterologous cyanobacterial cells

The psbA2 gene exhibits light-dependent and rhythmic expression in a unicellular cyanobacterium, Microcystis aeruginosa (Synechocystis) K-81. To further understand the psbA2 expression, biological analyses were performed in homologous and heterologous cyanobacterial cells. The results of the experiments using the K-81 cells revealed that (i) the light-dependent expression appeared on transcriptional and/or post-transcriptional level(s) under light/dark cycles, (ii) circadian-rhythmic transcripts were also observed under the control of an endogenous clock. To assess whether light-dependent and rhythmic psbA2 expression occurs in heterologous cyanobacterium, Synechococcus sp. strain PCC 7942, the K-81 psbA2 5'-upstream region of which the promoter and its around sequences share with those of PCC 7942 psbAII, was fused to the bacterial lacZ reporter gene, introduced into the genome of PCC 7942 and the psbA2 transcripts were directly investigated by primer extension. The K-81 psbA2 specific transcripts were also light-dependent and rhythmic in PCC 7942, strongly demonstrating that a common regulatory mechanism exists per se for the psbA2 expression in both strains. Furthermore, psbA2 expression in the recombinant PCC 7942 strain, AG400 in which the region from -404 to +111 of psbA2 is fused to lacZ, exhibited clear rhythmicity, while very little or no rhythmicity was observed in AG429 (-38 to +14, the only promoter region), suggesting that the region(s) around the promoter was essentially required for clear rhythmic expression.

In vitro characterization of the tobacco rpoB promoter reveals a core sequence motif conserved between phage-type plastid and plant mitochondrial promoters

We report here the in vitro characterization of PrpoB-345, the tobacco rpoB promoter recognized by NEP, the phage-type plastid RNA polymerase. Transcription extracts were prepared from mutant tobacco plants lacking PEP, the Escherichia coli-like plastid-encoded RNA polymerase. Systematic dissection of a approximately 1 kb fragment determined that the rpoB promoter is contained in a 15-nucleotide segment (-14 to +1) upstream of the transcription initiation site (+1). Point mutations at every nucleotide reduced transcription, except at the -5 position which was neutral. Critical for rpoB promoter function was a CRT-motif (CAT or CGT) at -8 to -6 (transcription <30%), defining it as the promoter core. The core CAT sequence is also present in the maize rpoB promoter, which is faithfully recognized by tobacco extracts. Alignment of NEP promoters identified a CATA or TATA (=YATA) sequence at the rpoB core position, also present in plant mitochondrial promoters. Furthermore, NEP and the phage T7 RNA polymerase exhibit similar sensitivity to inhibitors of transcription. These data indicate that the nuclear RpoZ gene, identified by sequence conservation with mitochondrial RNA polymerases, encodes the NEP catalytic subunit.

EIN4 and ERS2 are members of the putative ethylene receptor gene family in Arabidopsis

The Arabidopsis ethylene receptor gene ETR1 and two related genes, ERS1 and ETR2, were identified previously. These three genes encode proteins homologous to the two-component regulators that are widely used for environment sensing in bacteria. Mutations in these genes confer ethylene insensitivity to wild-type plants. Here, we identified two Arabidopsis genes, EIN4 and ERS2, by cross-hybridizing them with ETR2. Sequence analysis showed that they are more closely related to ETR2 than they are to ETR1 or ERS1. EIN4 previously was isolated as a dominant ethylene-insensitive mutant. ERS2 also conferred dominant ethylene insensitivity when certain mutations were introduced into it. Double mutant analysis indicated that ERS2, similar to ETR1, ETR2, ERS1, and EIN4, acts upstream of CTR1. Therefore, EIN4 and ERS2, along with ETR1, ETR2, and ERS1, are members of the ethylene receptor-related gene family of Arabidopsis. RNA expression patterns of members of this gene family suggest that they might have distinct as well as redundant functions in ethylene perception.

NUCLEAR CONTROL OF PLASTID AND MITOCHONDRIAL DEVELOPMENT IN HIGHER PLANTS

The nucleus must coordinate organelle biogenesis and function on a cell and tissue-specific basis throughout plant development. The vast majority of plastid and mitochondrial proteins and components involved in organelle biogenesis are encoded by nuclear genes. Molecular characterization of nuclear mutants has illuminated chloroplast development and function. Fewer mutants exist that affect mitochondria, but molecular and biochemical approaches have contributed to a greater understanding of this organelle. Similarities between organelles and prokaryotic regulatory molecules have been found, supporting the prokaryotic origin of chloroplasts and mitochondria. A striking characteristic for both mitochondria and chloroplast is that most regulation is posttranscriptional.

Leaf-specifically expressed genes for polypeptides destined for chloroplasts with domains of sigma70 factors of bacterial RNA polymerases in Arabidopsis thaliana

Genes for sigma-like factors of bacterial-type RNA polymerase have not been characterized from any multicellular eukaryotes, although they probably play a crucial role in the expression of plastid photosynthesis genes. We have cloned three distinct cDNAs, designated SIG1, SIG2, and SIG3, for polypeptides possessing amino acid sequences for domains conserved in sigma70 factors of bacterial RNA polymerases from the higher plant Arabidopsis thaliana. Each gene is present as one copy per haploid genome without any additional sequences hybridized in the genome. Transient expression assays using green fluorescent protein demonstrated that N-terminal regions of the SIG2 and SIG3 ORFs could function as transit peptides for import into chloroplasts. Transcripts for all three SIG genes were detected in leaves but not in roots, and were induced in leaves of dark-adapted plants in rapid response to light illumination. Together with results of our previous analysis of tissue-specific regulation of transcription of plastid photosynthesis genes, these results indicate that expressed levels of the genes may influence transcription by regulating RNA polymerase activity in a green tissue-specific manner.