Cytokinin-Regulated Expression of Arabidopsis thaliana PAP Genes and Its Implication for the Expression of Chloroplast-Encoded Genes

Modified Crosstalk between Phytohormones in Arabidopsis Mutants for PEP-Associated Proteins

Plastid-encoded RNA polymerase (PEP) forms a multisubunit complex in operating chloroplasts, where PEP subunits and a sigma factor are tightly associated with 12 additional nuclear-encoded proteins. Mutants with disrupted genes encoding PEP-associated proteins (PAPs) provide unique tools for deciphering mutual relationships among phytohormones. A block of chloroplast biogenesis in Arabidopsis pap mutants specifying highly altered metabolism in white tissues induced dramatic fluctuations in the content of major phytohormones and their metabolic genes, whereas hormone signaling circuits mostly remained functional. Reprogramming of the expression of biosynthetic and metabolic genes contributed to a greatly increased content of salicylic acid (SA) and a concomitant decrease in 1-aminocyclopropane-1-carboxylic acid (ACC) and oxophytodienoic acid (OPDA), precursors of ethylene and jasmonic acid, respectively, in parallel to reduced levels of abscisic acid (ABA). The lack of differences in the free levels of indole-3-acetic acid (IAA) between the pap mutants and wild-type plants was accompanied by fluctuations in the contents of IAA precursors and conjugated forms as well as multilayered changes in the expression of IAA metabolic genes. Along with cytokinin (CK) overproduction, all of these compensatory changes aim to balance plant growth and defense systems to ensure viability under highly modulated conditions.

Phytohormones as Regulators of Mitochondrial Gene Expression in Arabidopsis thaliana

The coordination of activities between nuclei and organelles in plant cells involves information exchange, in which phytohormones may play essential roles. Therefore, the dissection of the mechanisms of hormone-related integration between phytohormones and mitochondria is an important and challenging task. Here, we found that inputs from multiple hormones may cause changes in the transcript accumulation of mitochondrial-encoded genes and nuclear genes encoding mitochondrial (mt) proteins. In particular, treatments with exogenous hormones induced changes in the GUS expression in the reporter line possessing a 5'-deletion fragment of the RPOTmp promoter. These changes corresponded in part to the up- or downregulation of RPOTmp in wild-type plants, which affects the transcription of mt-encoded genes, implying that the promoter fragment of the RPOTmp gene is functionally involved in the responses to IAA (indole-3-acetic acid), ACC (1-aminocyclopropane-1-carboxylic acid), and ABA (abscisic acid). Hormone-dependent modulations in the expression of mt-encoded genes can also be mediated through mitochondrial transcription termination factors 15, 17, and 18 of the mTERF family and genes for tetratricopeptide repeat proteins that are coexpressed with mTERF genes, in addition to SWIB5 encoding a mitochondrial SWI/SNF (nucleosome remodeling) complex B protein. These genes specifically respond to hormone treatment, displaying both negative and positive regulation in a context-dependent manner. According to bioinformatic resources, their promoter region possesses putative cis-acting elements involved in responses to phytohormones. Alternatively, the hormone-related transcriptional activity of these genes may be modulated indirectly, which is especially relevant for brassinosteroids (BS). In general, the results of this study indicate that hormones are essential mediators that are able to cause alterations in the transcript accumulation of mt-related nuclear genes, which, in turn, trigger the expression of mt genes.

A TaSnRK1α Modulates TaPAP6L-Mediated Wheat Cold Tolerance through Regulating Endogenous Jasmonic Acid

Here, a sucrose non-fermenting-1-related protein kinase alpha subunit (TaSnRK1α-1A) is identified as associated with cold stress through integration of genome-wide association study, bulked segregant RNA sequencing, and virus-induced gene silencing. It is confirmed that TaSnRK1α positively regulates cold tolerance by transgenes and ethyl methanesulfonate (EMS) mutants. A plastid-lipid-associated protein 6, chloroplastic-like (TaPAP6L-2B) strongly interacting with TaSnRK1α-1A is screened. Molecular chaperone DJ-1 family protein (TaDJ-1-7B) possibly bridged the interaction of TaSnRK1α-1A and TaPAP6L-2B. It is further revealed that TaSnRK1α-1A phosphorylated TaPAP6L-2B. Subsequently, a superior haplotype TaPAP6L-2B30S /38S is identified and confirmed that both R30S and G38S are important phosphorylation sites that influence TaPAP6L-2B in cold tolerance. Overexpression (OE) and EMS-mutant lines verified TaPAP6L positively modulating cold tolerance. Furthermore, transcriptome sequencing revealed that TaPAP6L-2B-OE lines significantly increased jasmonic acid (JA) content, possibly by improving precursor α-linolenic acid contributing to JA synthesis and by repressing JAR1 degrading JA. Exogenous JA significantly improved the cold tolerance of wheat plants. In summary, TaSnRK1α profoundly regulated cold stress, possibly through phosphorylating TaPAP6L to increase endogenous JA content of wheat plants.

Advances in nanoparticle and organic formulations for prolonged controlled release of auxins

Plant hormones have been well known since Charles Darwin as signaling molecules directing plant metabolism. Their action and transport pathways are at the top of scientific interest and were reviewed in many research articles. Modern agriculture applies phytohormones as supplements to achieve desired physiological plant response. Auxins are a class of plant hormones extensively used for crop management. Auxins stimulate the formation of lateral roots and shoots, seed germination, while extensively high concentrations of these chemicals act as herbicides. Natural auxins are unstable; light or enzyme action leads to their degradation. Moreover, the concentration dependant action of phytohormones denier one-shot injection of these chemicals and require constant slow additive of supplement. It obstructs the direct introduction of auxins. On the other hand, delivery systems can protect phytohormones from degradation and provide a slow release of loaded drugs. Moreover, this release can be managed by external stimuli like pH, enzymes, or temperature. The present review is focused on three auxins: indole-3-acetic, indole-3-butyric, and 1-naphthaleneacetic acids. We collected some examples of inorganic (oxides, Ag, layered double hydroxides) and organic (chitosan, organic formulations) delivery systems. The action of carriers can enhance auxin effects via protection and targeted delivery of loaded molecules. Moreover, nanoparticles can act as nano fertilizers, intensifying the phytohormone effect, providing slow controlled release. So delivery systems for auxins are extremely attractive for modern agriculture opening sustainable management of plant metabolism and morphogenesis.

Cytokinin biosynthesis in cyanobacteria: Insights for crop improvement

Cytokinins, a type of phytohormones that induce division of cytoplasm, have considerable value in agriculture due to their influences on several physiological processes of plants such as morphogenesis, development of chloroplast, seed dormancy, leaf senescence, etc. Previously, it was assumed that plants obtain cytokinin from the soil produced by microbes as these hormones were first discovered in soil-inhabiting bacteria i.e., Agrobacterium tumefaciens. Later, the cytokinin biosynthesis gene, i.e., ipt gene, has been reported in plants too. Though plants synthesize cytokinins, several studies have reported that the exogenous application of cytokinins has numerous beneficial effects including the acceleration of plant growth and boosting economic yield. Cyanobacteria may be employed in the soil not only as the source of cytokinins but also as the source of other plant growth-promoting metabolites. These organisms biosynthesize the cytokinins using the enzyme isopentenyl transferases (IPTs) in a fashion similar to the plants; however, there are few differences in the biosynthesis mechanism of cytokinins in cyanobacteria and plants. Cytokinins are important for the establishment of interaction between plants and cyanobacteria as evidenced by gene knockout experiments. These hormones are also helpful in alleviating the adverse effects of abiotic stresses on plant development. Cyanobacterial supplements in the field result in the induction of adventitious roots and shoots on petiolar as well as internodal segments. The leaf, root, and stem explants of certain plants exhibited successful regeneration when treated with cyanobacterial extract/cell suspension. These successful regeneration practices mark the way of cyanobacterial deployment in the field as a great move toward the goal of sustainable agriculture.

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.

Ontogenetic, Light, and Circadian Regulation of PAP Protein Genes during Seed Germination of Arabidopsis thaliana

The expression profiles of the PAP genes, encoding proteins associated with plastid multisubunit RNA polymerase, were studied in dry seeds, during germination, and at the early stages of Arabidopsis thaliana seedling formation. A detailed analysis of the PAP transcript levels by RT-PCR showed that the transition of seeds from dormancy to active growth is accompanied by a drastic increase in the transcript accumulation of all studied genes on the first day of germination, both in the light and in the dark. Further changes in transcript levels differed among PAP genes and were apparently determined by their functional specificity. It was established for the first time that the expression of individual PAP genes is regulated by circadian rhythms, in addition to factors of ontogenetic and light nature.

Interpreting Cytokinin Action as Anterograde Signaling and Beyond

Among the major phytohormones, the cytokinin exhibits unique features for its ability to positively affect the developmental status of plastids. Even early on in its research, cytokinins were known to promote plastid differentiation and to reduce the loss of chlorophyll in detached leaves. Since the discovery of the components of cytokinin perception and primary signaling, the genes involved in photosynthesis and plastid differentiation have been identified as those directly targeted by type-B response regulators. Furthermore, cytokinins are known to modulate versatile cellular processes such as promoting the division and differentiation of cells and, in concert with auxin, initiating the de novo formation of shoot apical meristem (SAM) in tissue cultures. Yet how cytokinins precisely participate in such diverse cellular phenomena, and how the associated cellular processes are coordinated as a whole, remains unclear. A plausible presumption that would account for the coordinated gene expression is the tight and reciprocal communication between the nucleus and plastid. The fact that cytokinins affect plastid developmental status via gene expression in both the nucleus and plastid is interpreted here to suggest that cytokinin functions as an initiator of anterograde (nucleus-to-plastid) signaling. Based on this viewpoint, we first summarize the physiological relevance of cytokinins to the coordination of plastid differentiation with de novo shoot organogenesis in tissue culture systems. Next, the role of endogenous cytokinins in influencing plastid differentiation within the SAM of intact plants is discussed. Finally, a presumed plastid-derived signal in response to cytokinins for coupled nuclear gene expression is proposed.

A Core Module of Nuclear Genes Regulated by Biogenic Retrograde Signals from Plastids

Chloroplast biogenesis during seedling development of angiosperms is a rapid and highly dynamic process that parallels the light-dependent photomorphogenic programme. Pre-treatments of dark-grown seedlings with lincomyin or norflurazon prevent chloroplast biogenesis upon illumination yielding albino seedlings. A comparable phenotype was found for the Arabidopsis mutant plastid-encoded polymerase associated protein 7 (pap7) being defective in the prokaryotic-type plastid RNA polymerase. In all three cases the defect in plastid function has a severe impact on the expression of nuclear genes representing the influence of retrograde signaling pathway(s) from the plastid. We performed a meta-analysis of recently published genome-wide expression studies that investigated the impact of the aforementioned chemical and genetic blocking of chloroplast biogenesis on nuclear gene expression profiles. We identified a core module of 152 genes being affected in all three conditions. These genes were classified according to their function and analyzed with respect to their implication in retrograde signaling and chloroplast biogenesis. Our study uncovers novel genes regulated by retrograde biogenic signals and suggests the action of a common signaling pathway that is used by signals originating from plastid transcription, translation and oxidative stress.