Plastid-encoded Genes Research Articles

Description of the new species Mallomonas okhapkinii (Synurales, Chrysophyceae) based on morphological and molecular data

This paper describes a new species of Mallomonas discovered in a swamp area in Russia. The species was identified based on scale morphology, examined using scanning and transmission electron microscopy, and subjected to molecular analysis. The new species, Mallomonas okhapkinii sp. nov., belongs to the section Planae and is most similar in scale and bristle ultrastructure to M. matvienkoae sensu stricto. Phylogenetic analysis, performed using a concatenated dataset of nuclear-encoded small subunit rRNA and plastid-encoded rbcL genes, revealed that the strains of the new species form a distinct clade with high statistical support, closely related to the clade of M. paragrandis and M. sorohexareticulata. This species was found in only one habitat.

Interpreting the complexities of the plastid genome in dinoflagellates: a mini-review of recent advances.

Photosynthetic dinoflagellates play crucial roles in global primary production and carbon fixation. Despite their success in filling various ecological niches, numerous mysteries about their plastid evolution and plastid genomes remain unsolved. The plastid genome of dinoflagellates presents one of the most complex lineages in the biological realm, mainly due to multiple endosymbiotic plastid events in their evolutionary history. Peridinin-containing dinoflagellates possess the most reduced and fragmented genome, with only a few genes located on multiple "minicircles", whereas replacement plastids in dinoflagellate lineages have undergone different degrees of endosymbiotic gene transfer. Recent advancements in high-throughput sequencing have improved our understanding of plastid genomes and plastid-encoded gene expression in many dinoflagellate species. Plastid transcripts of dinoflagellates exhibit two unconventional processing pathways: the addition of a 3' poly(U) tail and substitutional RNA editing. These pathways are widely employed across dinoflagellate lineages, which are possibly retained from the ancestral peridinin plastid. This mini-review summarizes the developments in the plastid genomes of dinoflagellates and pinpoints the research areas that necessitate further exploration, aiming to provide valuable insights into plastid evolution in these fascinating and important organisms.

Orchestration of Photosynthesis-Associated Gene Expression and Galactolipid Biosynthesis during Chloroplast Differentiation in Plants.

The chloroplast thylakoid membrane is composed of membrane lipids and photosynthetic protein complexes, and the orchestration of thylakoid lipid biosynthesis and photosynthesis-associated protein accumulation is considered important for thylakoid development. Galactolipids consist of ∼80% of the thylakoid lipids, and their biosynthesis is fundamental for chloroplast development. We previously reported that the suppression of galactolipid biosynthesis decreased the expression of photosynthesis-associated nuclear-encoded genes (PhAPGs) and photosynthesis-associated plastid-encoded genes (PhAPGs). However, the mechanism for coordinative regulation between galactolipid biosynthesis in plastids and the expression of PhANGs and PhAPGs remains largely unknown. To elucidate this mechanism, we investigated the gene expression patterns in galactolipid-deficient Arabidopsis seedlings during the de-etiolation process. We found that galactolipids are crucial for inducing both the transcript accumulation of PhANGs and PhAPGs and the accumulation of plastid-encoded photosynthesis-associated proteins in developing chloroplasts. Genetic analysis indicates the contribution of the GENOMES UNCOUPLED1 (GUN1)-mediated plastid-to-nucleus signaling pathway to PhANG regulation in response to galactolipid levels. Previous studies suggested that the accumulation of GUN1 reflects the state of protein homeostasis in plastids and alters the PhANG expression level. Thus, we propose a model that galactolipid biosynthesis determines the protein homeostasis in plastids in the initial phase of de-etiolation and optimizes GUN1-dependent signaling to regulate the PhANG expression. This mechanism might contribute to orchestrating the biosynthesis of lipids and proteins for the biogenesis of functional chloroplasts in plants.

Characterisation of a Spontaneous Mutant of Lemna gibba G3 (Lemnaceae).

A spontaneous mutant of the duckweed Lemna gibba clone no. 7796 (known as strain G3, WT) was discovered. In this mutant clone, L. gibba clone no. 9602 (mt), the morphological parameters (frond length, frond width, root length, root diameter) indicated an enlarged size. A change in the frond shape was indicated by the decreased frond length/width ratio, which could have taxonomic consequences. Several different cell types in both the frond and the root were also enlarged. Flow cytometric measurements disclosed the genome size of the WT as 557 Mbp/1C and that of the mt strain as 1153 Mbp/1C. This represents the results of polyploidisation of a diploid clone to a tetraploid one. The mutant clone flowered under the influence of long day-treatment in half-strength Hutner's medium in striking contrast to the diploid WT. Low concentration of salicylic acid (<1 µM) induced flowering in the tetraploid mutant but not in the diploid plants. The transcript levels of nuclear-encoded genes of the photosynthetic apparatus (CAB, RBCS) showed higher abundance in light and less dramatic decline in darkness in the mt than in WT, while this was not the case with plastid-encoded genes (RBCL, PSAA, PSBA, PSBC).

PtrDJ1C, an atypical member of the DJ-1 superfamily, is essential for early chloroplast development and lignin deposition in poplar

The nuclear-encoded factors and the photosynthetic apparatus have been studied extensively during chloroplast biogenesis. However, many questions regarding these processes remain unanswered, particularly in perennial woody plants. As a model material of woody plants, poplar not only has very significant value of research, but also possesses economic and ecological properties. This study reports the Populus trichocarpa DJ-1C (PtrDJ1C) factor, encoded by a nuclear gene, and a member of the DJ-1 superfamily. PtrDJ1C knock-out with the CRISPR/Cas9 system resulted in different albino phenotypes. Chlorophyll fluorescence and immunoblot analyses showed that the levels of photosynthetic complex proteins decreased significantly. Moreover, the transcript level of plastid-encoded RNA polymerase-dependent genes and the splicing efficiency of several introns were affected in the mutant line. Furthermore, rRNA accumulation was abnormal, leading to developmental defects in chloroplasts and affecting lignin accumulation. We concluded that the PtrDJ1C protein is essential for early chloroplast development and lignin deposition in poplar.

Habitat-related plastome evolution in the mycoheterotrophic Neottia listeroides complex (Orchidaceae, Neottieae)

BackgroundMycoheterotrophs, acquiring organic carbon and other nutrients from mycorrhizal fungi, have evolved repeatedly with substantial plastid genome (plastome) variations. To date, the fine-scale evolution of mycoheterotrophic plastomes at the intraspecific level is not well-characterized. A few studies have revealed unexpected plastome divergence among species complex members, possibly driven by various biotic/abiotic factors. To illustrate evolutionary mechanisms underlying such divergence, we analyzed plastome features and molecular evolution of 15 plastomes of Neottia listeroides complex from different forest habitats.ResultsThese 15 samples of Neottia listeroides complex split into three clades according to their habitats approximately 6 million years ago: Pine Clade, including ten samples from pine-broadleaf mixed forests, Fir Clade, including four samples from alpine fir forests and Fir-willow Clade with one sample. Compared with those of Pine Clade members, plastomes of Fir Clade members show smaller size and higher substitution rates. Plastome size, substitution rates, loss and retention of plastid-encoded genes are clade-specific. We propose to recognized six species in N. listeroides complex and slightly modify the path of plastome degradation.ConclusionsOur results provide insight into the evolutionary dynamics and discrepancy of closely related mycoheterotrophic orchid lineages at a high phylogenetic resolution.

Young Leaf White Stripe encodes a P-type PPR protein required for chloroplast development.

Pentatricopeptide repeat (PPR) proteins function in post-transcriptional regulation of organellar gene expression. Although several PPR proteins are known to function in chloroplast development in rice (Oryza sativa), the detailed molecular functions of many PPR proteins remain unclear. Here, we characterized a rice young leaf white stripe (ylws) mutant, which has defective chloroplast development during early seedling growth. Map-based cloning revealed that YLWS encodes a novel P-type chloroplast-targeted PPR protein with 11 PPR motifs. Further expression analyses showed that many nuclear- and plastid-encoded genes in the ylws mutant were significantly changed at the RNA and protein levels. The ylws mutant was impaired in chloroplast ribosome biogenesis and chloroplast development under low-temperature conditions. The ylws mutation causes defects in the splicing of atpF, ndhA, rpl2, and rps12, and editing of ndhA, ndhB, and rps14 transcripts. YLWS directly binds to specific sites in the atpF, ndhA, and rpl2 pre-mRNAs. Our results suggest that YLWS participates in chloroplast RNA group II intron splicing and plays an important role in chloroplast development during early leaf development.

ABSCISIC ACID INSENSITIVE4 coordinates eoplast formation to ensure acquisition of seed longevity during maturation in Medicago truncatula.

Seed longevity, the capacity to remain alive during dry storage, is pivotal to germination performance and is essential for preserving genetic diversity. It is acquired during late maturation concomitantly with seed degreening and the de-differentiation of chloroplasts into colorless, non-photosynthetic plastids, called eoplasts. As chlorophyll retention leads to poor seed performance upon sowing, these processes are important for seed vigor. However, how these processes are regulated and connected to the acquisition of seed longevity remains poorly understood. Here, we show that such a role is at least provided by ABSCISIC ACID INSENSITIVE4 (ABI4) in the legume Medicago truncatula. Mature seeds of Mtabi4 mutants contained more chlorophyll than wild-type seeds and exhibited a 75% reduction in longevity and reduced dormancy. MtABI4 was necessary to stimulate eoplast formation, as evidenced by the significant delay in the dismantlement of photosystemII during the maturation of mutant seeds. Mtabi4 seeds also exhibited transcriptional deregulation of genes associated with retrograde signaling and transcriptional control of plastid-encoded genes. Longevity was restored when Mtabi4 seeds developed in darkness, suggesting that the shutdown of photosynthesis during maturation, rather than chlorophyll degradation perse, is a requisite for the acquisition of longevity. Indeed, the shelf life of staygreen mutant seeds that retained chlorophyll was not affected. Thus, ABI4 plays a role in coordinating the dismantlement of chloroplasts during seed development to avoid damage that compromises the acquisition of seed longevity. Analysis of Mtabi4Mtabi5 double mutants showed synergistic effects on chlorophyll retention and longevity, suggesting that they act via parallel pathways.

Diagnostic KASP markers differentiate Vanilla planifolia, V. odorata, V. pompona, and their hybrids using leaf or cured pod tissues.

Vanilla is a globally important spice crop used in a variety of food, cosmetic, and pharmaceutical products. V. planifolia is the primary commercial species with V. x tahitensis also permissible for food use. Other aromatic species, including V. pompona, are used for food throughout Central and South America. Supply chain complexity hinders the vanilla bean industry and can lead to false claims of genetic and geographical origins to obtain higher prices. Beans of some species can be differentiated by experienced buyers, but hybrids and morphological differences caused by environmental variability or disease would best be resolved by diagnostic tests. METHODS ANDRESULTS: Kompetitive Allele Specific Polymerase Chain Reaction is a widely used molecular marker that can genotype single nucleotide polymorphisms efficiently and inexpensively. Assays were designed to differentiate V. planifolia, V. x tahitensis, and V. pompona using publicly available vanilla genomics data. Ten KASP assays on chromosomes 1 through 7, the ITS region, and plastid-encoded rbcL gene successfully differentiated V. planifolia, V. odorata, and V. x tahitensis. Additional KASP assays on chromosomes 1 through 4, the ITS region, and rbcL gene successfully differentiated V. planifolia and V. pompona. Further, a method for extracting KASP-quality DNA from cured vanilla bean seeds was developed and successfully differentiated V. planifolia, V. odorata, V. x tahitensis, V. pompona, and their hybrids. The methods and results from this study can be used to identify interspecific hybrids, ensure the authenticity of cured vanilla beans, and reduce abuse within the vanilla supply chain.

Phylogenomics, plastome degradation and mycoheterotrophy evolution of Neottieae (Orchidaceae), with emphasis on the systematic position and Loess Plateau-Changbai Mountains disjunction of Diplandrorchis

BackgroundMycoheterotrophy is a unique survival strategy adapted to dense forests and has attracted biologists’ attention for centuries. However, its evolutionary origin and related plastome degradation are poorly understood. The tribe Neottieae contains various nutrition types, i.e., autotrophy, mixotrophy, and mycoheterotrophy. Here, we present a comprehensive phylogenetic analysis of the tribe based on plastome and nuclear ITS data. We inferred the evolutionary shift of nutrition types, constructed the patterns of plastome degradation, and estimated divergence times and ancestral ranges. We also used an integration of molecular dating and ecological niche modeling methods to investigate the disjunction between the Loess Plateau and Changbai Mountains in Diplandrorchis, a mycoheterotrophic genus endemic to China that was included in a molecular phylogenetic study for the first time.ResultsDiplandrorchis was imbedded within Neottia and formed a clade with four mycoheterotrophic species. Autotrophy is the ancestral state in Neottieae, mixotrophy independently originated at least five times, and three shifts from mixotrophy to mycoheterotrophy independently occurred. The five mixotrophic lineages possess all plastid genes or lost partial/all ndh genes, whereas each of the three mycoheterotroph lineages has a highly reduced plastome: one lost part of its ndh genes and a few photosynthesis-related genes, and the other two lost almost all ndh, photosynthesis-related, rpo, and atp genes. These three mycoheterotrophic lineages originated at about 26.40 Ma, 25.84 Ma, and 9.22 Ma, respectively. Diplandrorchis had presumably a wide range in the Pliocene and migrated southward in the Pleistocene.ConclusionsThe Pleistocene climatic fluctuations and the resultant migration resulted in the Loess Plateau-Changbai Mountains disjunction of Diplandrorchis. In the evolution of mycoheterotrophic lineages, the loss of plastid-encoded genes and plastome degradation are staged and irreversible, constraining mycoheterotrophs to inhabit understories with low light levels. Accordingly, the rise of local forests might have promoted the origin of conditions in which mycoheterotrophy is advantageous.

The role of PAP4/FSD3 and PAP9/FSD2 in heat stress responses of chloroplast genes

Chloroplasts’ mechanisms of adaptation to elevated temperatures are largely determined by the gene expression of the plastid transcription apparatus. Gene disruption of iron-containing superoxide dismutase PAP4/FSD3 and PAP9/FSD2, which are parts of the DNA–RNA polymerase complex of plastids, contributed to a decrease in resistance to oxidative stress caused by the prolonged action of elevated temperatures (5 days, 30 °C). Under heat stress conditions, pap4/fsd3 and pap9/fsd2 mutants showed a decline in chlorophyll content and photosynthesis level, as measured by photosynthetic parameters, and a different amplitude of HSP gene response to heat stress. The expression of nuclear- and plastid-encoded photosynthesis genes and corresponding proteins was strongly inhibited in the mutants as compared with wild-type plants and was further suppressed or displayed no additional changes at 30 °C. NEP-dependent plastid genes, as well as NEP genes RPOTp and RPOTmp, were also downregulated in the mutants by high temperature or remained stable, unlike in wild-type seedlings where these genes were strongly upregulated. The results obtained correspond to the concept of the complex effect of various forms of reactive oxygen species under all types of stresses, including heat stress, and confirm the hypothesis of a new regulatory function in plastid transcription acquired by enzymatic proteins during evolution.

DNA Barcoding and ITS-tufA multi-local molecular phylogeny of nitrophilic alga Prasiola crispa growing on penguin guano at Larsemann Hills, Eastern Antarctica

Antarctica is the coldest and driest continent globally and has always been an exciting habitat to study extremophiles. The study reveals a monostromatic nitrophilic green alga Prasiola crispa (Trebouxiophyceae) growing on Adelie penguin guano at a penguin rockery, Larsemann Hills, Eastern Antarctica. This study is the first report of the barcode of this algal genus from Eastern Antarctica in general and the Larsemann Hills in particular. There are 35 species currently accepted in this genus, while four were reported from Antarctica. The present study relied on morphological diagnoses as well as the phylogenetic inference based on nuclear-encoded ITS gene and plastid-encoded tufA gene for species identification. The study generated phylogenetic reconstruction at the two selected loci for the first time for this species from Antarctica.

Impacts of phosphatidylglycerol on plastid gene expression and light induction of nuclear photosynthetic genes.

Phosphatidylglycerol (PG) is the only major phospholipid in the thylakoid membrane of chloroplasts. PG is essential for photosynthesis, and loss of PG in Arabidopsis thaliana results in severe defects of growth and chloroplast development, with decreased chlorophyll accumulation, impaired thylakoid formation, and down-regulation of photosynthesis-associated genes encoded in nuclear and plastid genomes. However, how the absence of PG affects gene expression and plant growth remains unclear. To elucidate this mechanism, we investigated transcriptional profiles of a PG-deficient Arabidopsis mutant pgp1-2 under various light conditions. Microarray analysis demonstrated that reactive oxygen species (ROS)-responsive genes were up-regulated in pgp1-2. However, ROS production was not enhanced in the mutant even under strong light, indicating limited impacts of photooxidative stress on the defects of pgp1-2. Illumination to dark-adapted pgp1-2 triggered down-regulation of photosynthesis-associated nuclear-encoded genes (PhANGs), while plastid-encoded genes were constantly suppressed. Overexpression of GOLDEN2-LIKE1 (GLK1), a transcription factor gene regulating chloroplast development, in pgp1-2 up-regulated PhANGs but not plastid-encoded genes along with chlorophyll accumulation. Our data suggest a broad impact of PG biosynthesis on nuclear-encoded genes partially via GLK1 and a specific involvement of this lipid in plastid gene expression and plant development.

Systematics of Hypnea (Cystocloniaceae, Rhodophyta) from coastal North Carolina, with a first report of Calliblepharis saidana from the United States Atlantic Coast

Abstract Complete and/or partial DNA sequences for the plastid-encoded rbcL gene and the 5′ end of the mitochondrial cytochrome oxidase I (COI-5P) gene were used to re-examine the systematics of Hypnea species (Cystocloniaceae, Rhodophyta) from North Carolina, USA. These data, combined with light microscopic observations, indicate that two species (Hypnea cryptica and H. musciformis sensu stricto) are present in nearshore waters of coastal North Carolina. Molecular and morphological analyses with topotype material of Hypnea volubilis from North Carolina offshore waters revealed that it and Calliblepharis saidana are conspecific. Hypnea volubilis is proposed as a heterotypic synonym of C. saidana. This is the first report of Calliblepharis from the United States Atlantic coast and only the second report from the western hemisphere.

A new cryptic species of the unicellular red algal genus Dixoniella (Rhodellophyceae, Proteorhodophytina): Dixoniella giordanoi

ABSTRACT During samplings aimed at isolating microalgal strains, a coccoid greyish-green alga was collected along the North Adriatic coasts (Mediterranean Sea, Italy) and grown in culture. The microalgal strain (named strain B1A) was then subjected to an integrative taxonomy approach in order to correctly identify it. Morphological and ultrastructural observations and phycobiliprotein content analysis were carried out, as well as molecular analyses based on the 18S rRNA, rbcL, psbA and plastid-encoded 23S rRNA genes. Phylogenetic placement and ultrastructural observations clearly indicated that strain B1A is a member of the red microalgal genus Dixoniella (Rhodellophyceae, Proteorhodophytina) and is distinct from the only species so far described for this taxon. Therefore, a new species was described to encompass the isolate from the North Adriatic Sea and another isolate from Japan (MF-G2), which was phylogenetically related to strain B1A: Dixoniella giordanoi sp. nov.

Characterization and Dynamics of Intracellular Gene Transfer in Plastid Genomes of Viola (Violaceae) and Order Malpighiales.

Functional gene transfer from organelles to the nucleus, known as intracellular gene transfer (IGT), is an ongoing process in flowering plants. The complete plastid genomes (plastomes) of two Ulleung island endemic violets, Viola ulleungdoensis and V. woosanensis, were characterized, revealing a lack of the plastid-encoded infA, rpl32, and rps16 genes. In addition, functional replacement of the three plastid-encoded genes in the nucleus was confirmed within the genus Viola and the order Malpighiales. Three strategies for the acquisition of a novel transit peptide for successful IGT were identified in the genus Viola. Nuclear INFA acquired a novel transit peptide with very low identity between these proteins, whereas the nuclear RPL32 gene acquired an existing transit peptide via fusion with the nuclear-encoded plastid-targeted SOD gene (Cu-Zn superoxide dismutase superfamily) as one exon, and translated both proteins in the cytosol using alternative mRNA splicing. Nuclear RPS16 contains an internal transit peptide without an N-terminal extension. Gene loss or pseudogenization of the plastid-borne rpl32 and rps16 loci was inferred to occur in the common ancestor of the genus Viola based on an infrageneric phylogenetic framework in Korea. Although infA was lost in the common ancestor of the order Malpighiales, the rpl32 and rps16 genes were lost multiple times independently within the order. Our current study sheds additional light on plastid genome composition and IGT mechanisms in the violet genus and in the order Malpighiales.

A rice geranylgeranyl reductase is essential for chloroplast development

Chloroplasts are essential for plant photosynthesis and growth. Many genes have been identified that regulate plant chloroplast development. However, it is not known at a molecular level how these genes regulate chloroplast biogenesis. In this study, we isolated a mutant ygl2 (yellow-green leaf2) that exhibited a pigment-defective phenotype. YGL2 encodes a geranylgeranyl reductase, and in mutant ygl2, there was a single base change (T1361G) located in the third exon of YGL2 that resulted in a missense mutation (L454R) in the encoded product. Transmission electron microscopy revealed that chloroplast development was impaired in the ygl2 mutant. The expression levels of plastid-encoded genes were significantly altered in the ygl2 mutant. Furthermore, in a yeast two-hybrid assay, we found that YGL2 interacted with the RNA editing factor MORF8.

Albino seedling lethality 4; Chloroplast 30S Ribosomal Protein S1 is Required for Chloroplast Ribosome Biogenesis and Early Chloroplast Development in Rice

BackgroundRibosomes responsible for transcription and translation of plastid-encoded proteins in chloroplasts are essential for chloroplast development and plant growth. Although most ribosomal proteins in plastids have been identified, the molecular mechanisms regulating chloroplast biogenesis remain to be investigated.ResultsHere, we identified albinic seedling mutant albino seedling lethality 4 (asl4) caused by disruption of 30S ribosomal protein S1 that is targeted to the chloroplast. The mutant was defective in early chloroplast development and chlorophyll (Chl) biosynthesis. A 2855-bp deletion in the ASL4 allele was verified as responsible for the mutant phenotype by complementation tests. Expression analysis revealed that the ASL4 allele was highly expressed in leaf 4 sections and newly expanded leaves during early leaf development. Expression levels were increased by exposure to light following darkness. Some genes involved in chloroplast biogenesis were up-regulated and others down-regulated in asl4 mutant tissues compared to wild type. Plastid-encoded plastid RNA polymerase (PEP)-dependent photosynthesis genes and nuclear-encoded phage-type RNA polymerase (NEP)-dependent housekeeping genes were separately down-regulated and up-regulated, suggesting that plastid transcription was impaired in the mutant. Transcriptome and western blot analyses showed that levels of most plastid-encoded genes and proteins were reduced in the mutant. The decreased contents of chloroplast rRNAs and ribosomal proteins indicated that chloroplast ribosome biogenesis was impaired in the asl4 mutant.ConclusionsRice ASL4 encodes 30S ribosomal protein S1, which is targeted to the chloroplast. ASL4 is essential for chloroplast ribosome biogenesis and early chloroplast development. These data will facilitate efforts to further elucidate the molecular mechanism of chloroplast biogenesis.

OsMORF9 is necessary for chloroplast development and seedling survival in rice

Chloroplasts are closely associated with the growth and development of higher plants. Accumulating evidence has revealed that the multiple organellar RNA editing factors (MORF) family of proteins influences plastidic and mitochondrial development through post-transcriptional regulation. However, the role of MORFs in regulating the development of chloroplasts in rice is still unclear. The OsMORF9 gene belongs to a small family of 7 genes in rice and is highly expressed in young leaves. We used the CRISPR/Cas9 system to mutate OsMORF9. The resulting knockout lines osmorf9−1 and osmorf9−2 exhibited an albino seedling lethal phenotype. Besides, the expression of many plastid-encoded genes involved in photosynthesis, the biogenesis of plastidic ribosomes and the editing and splicing of specific plastidic RNA molecules were severely affected in these two OsMORF9 mutants. Furthermore, yeast two-hybrid analysis revealed that OsMORF9 could interact with OsSLA4 and DUA1 which are members of the pentatricopeptide repeat (PPR) family of proteins. Analysis of subcellular localization of OsMORF9 also suggested that it might function in chloroplasts. The findings from the present study demonstrated the critical role of OsMORF9 in the biogenesis of chloroplast ribosomes, chloroplast development and seedling survival. This therefore provides new insights on the function of MORF proteins in rice.

Nuclear-Ecoded Plastid RNA Polymerases Are Components of Anterograde Control in Hormonal Regulation of Chloroplast Gene Expression

Phytohormones are known to play an important role in the regulation of chloroplast biogenesis. However, information on the pathways of hormonal signal perception by chloroplasts is limited. In order to analyze the possible mechanisms of hormone action, the response to abscisic acid (ABA) and cytokinin (CKs) treatment of Arabidopsis thaliana (L.) Heynh. scabra3-2 (sca3-2) and rpotmp mutants with defective genes for nuclear-encoded plastid RNA polymerases was studied. The reaction of the rpotmp mutant usually did not differ from the response of wild-type plants: trans-zeatin activated the accumulation of transcripts of genes encoding the transcription apparatus and genes encoded by the plastid genome, while ABA weakly suppressed their expression or had no significant effect. However, the steady-state levels of gene templates of the plastid-encoded RNA polymerase (PEP-A) enzyme complex in the rpotmp mutant were higher than in wild-type plants, probably due to a compensatory mechanism that allows the mutant to enhance PEP-dependent transcription in the absence of the RPOTmp enzyme. Dysfunction of the plastid RNA polymerase RPOTp enzyme in the sca3-2 mutant induced an altered hormonal response of the genes for plastid transcriptional complex and plastid-encoded genes in comparison with the response of wild-type plants. The absence of a significant up-regulating effect of CKs on the expression of genes encoding the transcription apparatus correlated with the retention of the steady-state levels of transcripts for chloroplast genes and plastid proteins. In addition, the sca3-2 mutant had an increased steady-state expression of genes for CK metabolism: IPT3, IPT5, and CKX5. However, the response to the inhibitory effect of ABA in this mutant, on the contrary, was more pronounced, which is possibly caused by the changes in the steady-state levels of the transcripts of a number of genes encoding of ABA signaling and metabolism proteins. Thus, changes in the expression of NEP (nuclear-encoded RNA polymerases) genes under the action of hormones can be transformed into activation or inhibition in the expression of chloroplast genes of nuclear or plastome coding, providing the regulation of chloroplast functions through the mechanisms of anterograde signaling.