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The interactions between nanoparticles (NPs) and plant cells are one of the most important aspects that are involved in the development of plant nanotechnology. The NPs released in plant cells inevitably interact with the basic organelles of plant cells. Because thousands of studies have addressed plant transformation, conversion, regeneration, accumulation and phytotoxicity of different types of NPs and even their transmission across the food chain, most of the important issues in the field of nanotechnology in plant interactions have remained for a long time. In this review, uptake and translocation pathways of NPs in plants, phytotoxicity, interactions, improvement and transformation are systematically reviewed. In particular, analytical nanotechnology and methodology and future approaches to related fields are proposed. [ABSTRACT FROM AUTHOR]

Oil bodies (OBs) are lipid-storing organelles of plant seeds; they provide energy for seed germination and seedling growth by oxidative degradation as substrate. Soybean OBs are assumed to be involved in the enzymatic oxidation reaction of volatile flavor formation of soymilk. In order to establish a soymilk model system with soybean OBs as the enzymatic oxidation substrate to study the formation mechanism of soymilk flavor, the effects of extraction times and extraction pH on the composition, particle size and volatile flavor of soybean OBs extracted from raw soymilk were studied. The results showed that most of the extrinsic proteins on the surface of the OBs were removed with increasing extraction times. When the extraction pH increased from 7.0 to 11.0, the relative content of neutral lipids in OBs increased by 6.22%, and the relative content of protein and phospholipids in OBs decreased by 3.23% and 2.88%, respectively. The particle sizes of the OBs gradually decreased from 424 nm to 334 nm. The concentrations of volatile flavor components also gradually decreased from 129.29 μg/L to 52.75 μg/L. The integrity and stability of the OBs were compromised when the extraction pH was ≥12.0. The pH 11.0-OBs were the appropriate substrate for the soymilk model system because of their high purity and stability, better emulsion dispersion stability, and weaker flavor. These results are of great significance for exploring the formation mechanism of soymilk flavor in soymilk model systems to further improve the flavor of soymilk. [ABSTRACT FROM AUTHOR]

The appropriate regulation of thylakoid lipid synthesis is essential for the function of chloroplasts. In plant cells, membrane lipids synthesized in the ER are utilized as a precursor for the synthesis of chloroplast glycolipids. This pathway is thought to be mediated by the transport of glycerolipids synthesized in the ER into chloroplasts. However, we have little knowledge about the proteins involved in the lipid transfer between these organelles in plant cells. Here we show a protein, STAR2, containing the START (Steroidogenic acute regulatory protein-related lipid transfer) domain known to function as a lipid transporter, is involved in the incorporation of ER-derived fatty acids into chloroplast glycolipids in Marchantia polymorpha. We found that STAR2 localizes on the chloroplast envelope membrane as a punctuate structure and is required for the increase of C 20 fatty acids, which are synthesized in the ER, in chloroplast glycolipids in response to phosphate deprivation. Our results indicate that STAR2 of M. polymorpha is likely to be involved in the lipid transfer from ER to chloroplast, presumably as a lipid transporter. • Marchantia polymorpha has three START minimal proteins: STAR1, 2, 3. • STAR2 localizes on the chloroplast envelope membrane as a punctuate structure. • STAR2 is essential for optimal growth under phosphate-limited condition. • STAR2 is involved in incorporation of C 20 fatty acids into chloroplast lipids. [ABSTRACT FROM AUTHOR]

Among reactive nitrogen species, nitric oxide (NO) is an important secondary messenger next to reactive oxygen species (ROS) produced under abiotic stress. NO is a small, colorless simple gas but is an important redox active molecule in plants as it has the potential in regulating a wide range of biological processes. Under stress conditions, endogenous synthesis of NO takes place in different plant cell organelles and its accumulation correlates with stress tolerance as it counteracts ROS production by stimulating antioxidant defense response in plants. Several studies have suggested that exogenous application of NO alleviates stress tolerance in most of plant species, although its exact role is unclear. In view of this, an effort has been made in this review to trace steps of NO involvement in different organelles to upgrade the current knowledge. Here, we first discuss the biosynthesis of NO, its sources, targets, signaling pathways, and then advances in NO-mediated biochemical and physiological changes that occur in response to various abiotic stress conditions are also discussed. Furthermore, a brief focus is carried out to determine the mechanism of NO activation in response to ROS production. [ABSTRACT FROM AUTHOR]

RNA cytidine-to-uridine editing is essential for plant organellar gene expression. Pentatricopeptide repeat (PPR)-E+ proteins have been proposed to bind to target sites and recruit the cytidine deaminase AtDYW2, facilitated by AtNUWA. Here we analyze the function of ZmNUWA, ZmDYW2A, and ZmDYW2B and their relationships with other editing factors in maize. The zmdyw2a and zmdyw2b single mutants are normal, but the zmdyw2a::zmdyw2b and zmnuwa mutants are severely arrested in seed development. ZmNUWA, ZmDYW2A, and ZmDYW2B are dual localized in mitochondria and plastids. Loss of ZmNUWA decreases the editing at 99 mitochondrial sites and 8 plastid sites. Surprisingly, loss of ZmDYW2A:ZmDYW2B affects almost the same set of sites targeted by PPR-E+ proteins. ZmNUWA interacts with ZmDYW2A and ZmDYW2B, suggesting that ZmNUWA recruits ZmDYW2A/2B in the editing of PPR-E+-targeted sites in maize. Further protein interaction analyses show that ZmNUWA and ZmDYW2A/2B interact with ZmMORF1, ZmMORF8, ZmMORF2, and ZmMORF9 and that ZmOZ1 interacts with ZmORRM1, ZmDYW2A, ZmDYW2B, ZmMORF8, and ZmMORF9. These results suggest that the maize mitochondrial PPR-E+ editosome contains PPR-E+, ZmDYW2A/2B, ZmNUWA, and ZmMORF1/8, whereas the plastid PPR-E+ editosome is composed of PPR-E+, ZmDYW2A/2B, ZmNUWA, ZmMORF2/8/9, ZmORRM1, and ZmOZ1., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Background: Pentatricopeptide repeat (PPR) proteins compose a large protein family whose members are involved in both RNA processing in organelles and plant growth. Previous reports have shown that E-subgroup PPR proteins are involved in RNA editing. However, the additional functions and roles of the E-subgroup PPR proteins are unknown. Results: In this study, we developed and identified a new maize kernel mutant with arrested embryo and endosperm development, i.e., defective kernel (dek) 55 (dek55). Genetic and molecular evidence suggested that the defective kernels resulted from a mononucleotide alteration (C to T) at + 449 bp within the open reading frame (ORF) of Zm00001d014471 (hereafter referred to as DEK55). DEK55 encodes an E-subgroup PPR protein within the mitochondria. Molecular analyses showed that the editing percentage of 24 RNA editing sites decreased and that of seven RNA editing sites increased in dek55 kernels, the sites of which were distributed across 14 mitochondrial gene transcripts. Moreover, the splicing efficiency of nad1 introns 1 and 4 and nad4 intron 1 significantly decreased in dek55 compared with the wild type (WT). These results indicate that DEK55 plays a crucial role in RNA editing at multiple sites as well as in the splicing of nad1 and nad4 introns. Mutation in the DEK55 gene led to the dysfunction of mitochondrial complex I. Moreover, yeast two-hybrid assays showed that DEK55 interacts with two multiple organellar RNA-editing factors (MORFs), i.e., ZmMORF1 (Zm00001d049043) and ZmMORF8 (Zm00001d048291). Conclusions: Our results demonstrated that a mutation in the DEK55 gene affects the mitochondrial function essential for maize kernel development. Our results also provide novel insight into the molecular functions of E-subgroup PPR proteins involved in plant organellar RNA processing. [ABSTRACT FROM AUTHOR]

Production and expression of RNA requires the action of multiple RNA-binding proteins (RBPs). New RBPs are most often created by novel combinations of dedicated RNA-binding modules. However, recruiting existing genes to create new RBPs is also an important evolutionary strategy. In this report, we analyzed the eightmember uL18 ribosomal protein family in Arabidopsis. uL18 proteins share a short structurally conserved domain that binds the 5S ribosomal RNA (rRNA) and allows its incorporation into ribosomes. Our results indicate that Arabidopsis uL18-Like proteins are targeted to either mitochondria or chloroplasts. While two members of the family are found in organelle ribosomes, we show here that two uL18-type proteins function as factors necessary for the splicing of certain mitochondrial and plastid group II introns. These two proteins do not cosediment with mitochondrial or plastid ribosomes but instead associate with the introns whose splicing they promote. Our study thus reveals that the RNA-binding capacity of uL18 ribosomal proteins has been repurposed to create factors that facilitate the splicing of organellar introns. [ABSTRACT FROM AUTHOR]

Gymnosperms such as ginkgo, conifers, cycads, and gnetophytes are vital components of land ecosystems, and they have significant economic and ecologic value, as well as important roles as forest vegetation. In this study, we investigated the structural variation and evolution of chloroplast transfer RNAs (tRNAs) in gymnosperms. Chloroplasts are important organelles in photosynthetic plants. tRNAs are key participants in translation where they act as adapter molecules between the information level of nucleic acids and functional level of proteins. The basic structures of gymnosperm chloroplast tRNAs were found to have family-specific conserved sequences. The tRNAψ -loop was observed to contain a conforming sequence, i.e., U-U-C-N-A-N2. In gymnosperms, tRNAIle was found to encode a "CAU" anticodon, which is usually encoded by tRNAMet. Phylogenetic analysis suggested that plastid tRNAs have a common polyphyletic evolutionary pattern, i.e., rooted in abundant common ancestors. Analyses of duplication and loss events in chloroplast tRNAs showed that gymnosperm tRNAs have experienced little more gene loss than gene duplication. Transition and transversion analysis showed that the tRNAs are iso-acceptor specific and they have experienced unequal evolutionary rates. These results provide new insights into the structural variation and evolution of gymnosperm chloroplast tRNAs, which may improve our comprehensive understanding of the biological characteristics of the tRNA family. [ABSTRACT FROM AUTHOR]

Pentatricopeptide repeat (PPR) proteins are RNA-binding proteins that function in posttranscriptional regulation as gene-specific regulators of RNA metabolism in plant organelles. Plant PPR proteins are divided into four classes: P, PLS, E and DYW. The E- and DYW-class proteins are mainly implicated in RNA editing, whereas most of the P-class proteins predominantly participate in RNA cleavage, splicing and stabilization. In contrast, the functions of PLS-class proteins still remain obscure. Here, we report the function of PLS-class PpPPR_31 and PpPPR_9 in Physcomitrella patens. The knockout (KO) mutants of PpPPR_31 and PpPPR_9 exhibited slower protonema growth compared to the wild type. The PpPPR_31 KO mutants showed a considerable reduction in the splicing of nad5 intron 3 and atp9 intron 1. The PpPPR_9 KO mutants displayed severely reduced splicing of cox1 intron 3. An RNA electrophoresis mobility shift assay showed that the recombinant PpPPR_31 protein bound to the 5′ region of nad5 exon 4 and the bulged A region in domain VI of atp9 group II intron 1 while the recombinant PpPPR_9 bound to the translated region of ORF622 in cox1 intron 3. These results suggest that a certain set of PLS-class PPR proteins may influence the splicing efficiency of mitochondrial group II introns. [ABSTRACT FROM AUTHOR]

Plastids, the defining organelles of plant cells, undergo physiological and morphological changes to fulfill distinct biological functions. In particular, the differentiation of chloroplasts into chromoplasts results in an enhanced storage capacity for carotenoids with industrial and nutritional value such as beta-carotene (provitamin A). Here, we show that synthetically inducing a burst in the production of phytoene, the first committed intermediate of the carotenoid pathway, elicits an artificial chloroplast-to-chromoplast differentiation in leaves. Phytoene overproduction initially interferes with photosynthesis, acting as a metabolic threshold switch mechanism that weakens chloroplast identity. In a second stage, phytoene conversion into downstream carotenoids is required for the differentiation of chromoplasts, a process that involves a concurrent reprogramming of nuclear gene expression and plastid morphology for improved carotenoid storage. We hence demonstrate that loss of photosynthetic competence and enhanced production of carotenoids are not just consequences but requirements for chloroplasts to differentiate into chromoplasts. [ABSTRACT FROM AUTHOR]

The membrane contact sites (MCSs) enable interorganelle communication by associating organelles at distances of tens of nanometers over extended membrane surfaces and serve to maintain cellular homeostasis through efficient exchange of metabolites, lipid, and calcium between organelles, organelle fission, and movement. Most MCSs and a growing number of tethering proteins especially those involved in mediating the junctions between endoplasmic reticulum (ER) and other organelles have been extensively characterized in mammal and yeast. However, the studies of plant MCSs are still at stages of infancy, at least one reason might be due to the lack of bona fide markers for visualizing these membrane junctions in plant cells. In this study, a series of genetically encoded reporters using split super-folder GFP protein were designed to detect the possible MCSs between ER and three other cellular compartments including chloroplast, mitochondria and plasma membrane (PM) in plant cell. By expressing these genetically encoded reporter in Arabidopsis protoplasts as well as Nicotiana benthamiana leaf, we could intuitively observe the punctate signal surrounding chloroplast upon expression of ER-chloroplast MCS reporter, punctate signal of ER-mitochondria MCS reporter and punctate signal close to the PM upon expression of ER-PM MCS reporter. We also showed that the ER-chloroplast MCSs were dynamic structures that undergo active remodeling with concomitant occurrence of chloroplast dysfunction inside plant cells. This study demonstrates that ER associates with various organelles in close proximity in plant cells and provides tools that might be applicable for visualizing MCSs in plants. [ABSTRACT FROM AUTHOR]

In plants, pathogen triggered programmed cell death (PCD) is frequently mediated by polar lipid molecules referred as long chain bases (LCBs) or ceramides. PCD interceded by LCBs is a well-organized process where several cell organelles play important roles. In fact, light-dependent reactions in the chloroplast have been proposed as major players during PCD, however, the functional aspects of the chloroplast during PCD are largely unknown. For this reason, we investigated events that lead to disassembly of the chloroplast during PCD mediated by LCBs. To do so, LCB elevation was induced with Pseudomonas syringae pv. tomato (a non-host pathogen) or Fumonisin B1 in Phaseolus vulgaris. Then, we performed biochemical tests to detect PCD triggering events (phytosphingosine rises, MPK activation and H2O2 generation) followed by chloroplast structural and functional tests. Observations of the chloroplast, via optical phenotyping methods combined with microscopy, indicated that the loss of photosynthetic linear electron transport coincides with the organized ultrastructure disassembly. In addition, structural changes occurred in parallel with accumulation of H2O2 inside the chloroplast. These features revealed the collapse of chloroplast integrity and function as a mechanism leading to the irreversible execution of the PCD promoted by LCBs. [ABSTRACT FROM AUTHOR]

The twin‐arginine protein transport (Tat pathway) is found in prokaryotes and plant organelles and transports folded proteins across membranes. Targeting of substrates to the Tat system is mediated by the presence of an N‐terminal signal sequence containing a highly conserved twin‐arginine motif. The Tat machinery comprises membrane proteins from the TatA and TatC families. Assembly of the Tat translocon is dynamic and is triggered by the interaction of a Tat substrate with the Tat receptor complex. This review will summarise recent advances in our understanding of Tat transport, focusing in particular on the roles played by Tat signal peptides in protein targeting and translocation. [ABSTRACT FROM AUTHOR]

Vesicle trafficking between the membrane-bound organelles in plant cells plays crucial roles in the precise transportation of various materials, and thus supports cell proliferation and cellular polarization. Conventionally, plant prevacuolar compartments (PVCs), identified as multivesicular bodies (MVBs), play important roles in both the secretory pathway as intermediate compartments and the endocytic pathway as late endosomes. In recent years, the PVC/MVBs have been proposed to play important roles in both protein vacuolar delivery and unconventional secretion, but several important questions on the new regulators and environmental cues that coordinate the PVC/MVB–organelle membrane interactions and their biological significances remain. In this review, we first summarize the identity and nature of the plant PVC/MVBs, and then we present an update on our current understanding on the interaction of PVC/MVBs with other organelles in the plant endomembrane system with focus on the vacuole, autophagosome, and plasma membrane (PM) in plant development and stress responses. Finally, we raise some open questions and present future perspectives in the study of PVC/MVB–organelle interactions and associated biological functions. [ABSTRACT FROM AUTHOR]

Current approaches for nanomaterial delivery in plants are unable to target specific subcellular compartments with high precision, limiting our ability to engineer plant function. We demonstrate a nanoscale platform that targets and delivers nanomaterials with biochemicals to plant photosynthetic organelles (chloroplasts) using a guiding peptide recognition motif. Quantum dot (QD) fluorescence emission in a low background window allows confocal microscopy imaging and quantitative detection by elemental analysis in plant cells and organelles. QD functionalization with β-cyclodextrin molecular baskets enables loading and delivery of diverse chemicals, and nanoparticle coating with a rationally designed and conserved guiding peptide targets their delivery to chloroplasts. Peptide biorecognition provides high delivery efficiency and specificity of QD with chemical cargoes to chloroplasts in plant cells in vivo (74.6 ± 10.8%) and more specific tunable changes of chloroplast redox function than chemicals alone. Targeted delivery of nanomaterials with chemical cargoes guided by biorecognition motifs has a broad range of nanotechnology applications in plant biology and bioengineering, nanoparticle-plant interactions, and nano-enabled agriculture. Targeted delivery of nanomaterials to subcellular compartments could allow precision engineering of plant function. Here, Santana et al. show that quantum dots functionalized with a rationally-designed targeting peptide are preferentially delivered to chloroplasts where they can be used to tune organellar redox status. [ABSTRACT FROM AUTHOR]

Autophagy is an intracellular trafficking and degradation system for recycling of damaged organelles, mis-folded proteins and cytoplasmic constituents. Autophagy can be divided into non-selective autophagy and selective autophagy according to the cargo specification. Key to the process is the timely formation of the autophagosome, a double-membrane structure which is responsible for the delivery of damaged organelles and proteins to lysosomes or vacuoles for their turnover. Autophagosomes are formed by the closure of cup-shaped phagophore which depends on the proper communication with membrane contributors. The endoplasmic reticulum (ER) is a major membrane source for autophagosome biogenesis whereby the ER connects with phagophore through membrane contact sites (MCSs). MCSs are closely apposed domains between organelle membranes where lipids and signals are exchanged. Lipid transfer proteins (LTPs) are a large family of proteins including Oxysterol-binding protein related proteins (ORP) which can be found at MCSs and mediate lipid transfer in mammals and yeast. In addition, interaction between autophagosomes and other organelles can also be detected in selective autophagy for selection and degradation of various damaged organelles. Selective autophagy is mediated by the binding of a receptor or an adaptor between a cargo and an autophagosome. Here we summarize what we know about the MCS between autophagosomes and other organelles in eukaryotes. We then discuss progress in our understanding about ORPs at MCSs in plants and the underlying mechanisms of selective autophagy in plants with a focus on receptors/adaptors that are involved in the interaction of the autophagosome with other cytoplasmic constituents, including the Neighbor of BRCA1 gene 1 (NBR1), ATG8-interacting protein 1 (ATI1), Regulatory Particle Non-ATPase 10 (RPN10), and Dominant Suppressor of KAR2 (DSK2). [ABSTRACT FROM AUTHOR]

Background: Chloroplasts are essential organelles of plant cells for not only being the energy factory but also making plant cells adaptable to different environmental stimuli. The nuclear genome encodes most of the chloroplast proteins, among which a large percentage of membrane proteins have yet to be functionally characterized. Results: We report here functional characterization of two nuclear-encoded chloroplast proteins, Chloroplast protein for Growth and Fertility (CGF1) and CGF2. CGF1 and CGF2 are expressed in diverse tissues and developmental stages. Proteins they encode are associated with chloroplasts through a N-terminal chloroplast-targeting signal in green tissues but also located at plastids in roots and seeds. Mutants of CGF1 and CGF2 generated by CRISPR/Cas9 exhibited vegetative defects, including reduced leaf size, dwarfism, and abnormal cell death. CGF1 and CGF2 redundantly mediate female gametogenesis, likely by securing local energy supply. Indeed, mutations of both genes impaired chloroplast integrity whereas exogenous sucrose rescued the growth defects of the CGF double mutant. Conclusion: This study reports that two nuclear-encoded chloroplast proteins, Chloroplast protein for Growth and Fertility (CGF1) and CGF2, play important roles in vegetative growth, in female gametogenesis, and in embryogenesis likely by mediating chloroplast integrity and development. [ABSTRACT FROM AUTHOR]

Increased temperatures caused by global warming threaten agricultural production, as warmer conditions can inhibit plant growth and development or even destroy crops in extreme circumstances. Extensive research over the past several decades has revealed that chloroplasts, the photosynthetic organelles of plants, are highly sensitive to heat stress, which affects a variety of photosynthetic processes including chlorophyll biosynthesis, photochemical reactions, electron transport, and CO2 assimilation. Important mechanisms by which plant cells respond to heat stress to protect these photosynthetic organelles have been identified and analyzed. More recent studies have made it clear that chloroplasts play an important role in inducing the expression of nuclear heat-response genes during the heat stress response. In this review, we summarize these important advances in plant-based research and discuss how the sensitivity, responses, and signaling roles of chloroplasts contribute to plant heat sensitivity and tolerance. [ABSTRACT FROM AUTHOR]

Summary: The central dogma in biology defines the flow of genetic information from DNA to RNA to protein. Accordingly, RNA molecules generally accurately follow the sequences of the genes from which they are transcribed. This rule is transgressed by RNA editing, which creates RNA products that differ from their DNA templates. Analyses of the RNA landscapes of terrestrial plants have indicated that RNA editing (in the form of C‐U base transitions) is highly prevalent within organelles (that is, mitochondria and chloroplasts). Numerous C→U conversions (and in some plants also U→C) alter the coding sequences of many of the organellar transcripts and can also produce translatable mRNAs by creating AUG start sites or eliminating premature stop codons, or affect the RNA structure, influence splicing and alter the stability of RNAs. RNA‐binding proteins are at the heart of post‐transcriptional RNA expression. The C‐to‐U RNA editing process in plant mitochondria involves numerous nuclear‐encoded factors, many of which have been identified as pentatricopeptide repeat (PPR) proteins that target editing sites in a sequence‐specific manner. In this review we report on major discoveries on RNA editing in plant organelles, since it was first documented 30 years ago. Significance Statement: The basic principle of molecular biology, in which RNAs faithfully follow the primary sequences of the genes from which they are transcribed, has been challenged by RNA editing, which creates RNA products that differ from their DNA templates, and affects many of the mtRNAs in plants. In accordance with the huge progress made concerning the characterization of the molecular basis of RNA editing in plants, we report here on major discoveries on RNA editing in plant organelles, since first documented 30 years ago. [ABSTRACT FROM AUTHOR]

Biosensors based on organic electrochemical transistors (OECT) are attractive devices for real‐time monitoring of biological processes. The direct coupling between the channel of the OECT and the electrolyte enables intimate interfacing with biological environments at the same time bringing signal amplification and fast sensor response times. So far, these devices are mainly applied to mammalian systems; cells or body fluids for the development of diagnostics and various health status monitoring technology. Yet, no direct detection of biomolecules from cells or organelles is reported. Here, an OECT glucose sensor applied to chloroplasts, which are the plant organelles responsible for the light‐to‐chemical energy conversion of the photosynthesis, is reported. Real‐time monitoring of glucose export from chloroplasts in two distinct metabolic phases is demonstrated and the transfer dynamics with a time resolution of 1 min is quantified, thus reaching monitoring dynamics being an order of magnitude better than conventional methods. [ABSTRACT FROM AUTHOR]

Plants are naturally abundant and display high sensitivity to ecological factors to thrive in diverse environmental conditions. As sessile organisms, they have evolved complex, internal, and interplant signaling pathways with distinct structures to promptly adjust to the constantly changing environment. In the past five years, the unique ways in which they exchange information with and function in the environment have inspired an emerging field of plant nanobionics, which describes the interface between living plants and nanotechnology to impart the former with novel and useful functions. The structural merits of plant organs and organelles have also inspired the creation of plant‐derived structures through biointerfacing with nanoparticles containing electronic and optical properties. Here, the emerging applications and vision of plant nanobionics are highlighted together with related plant‐inspired materials in potentially replacing the myriad devices in the everyday lives stamped out of plastic, containing circuit boards and consuming power from the electrical grid. Applications in environmental sensing, communication devices, and energy harvesting and conversion are comprehensively discussed. [ABSTRACT FROM AUTHOR]

Plant organelles cope with endogenous DNA damaging agents, byproducts of respiration and photosynthesis, and exogenous agents like ultraviolet light. Plant organellar DNA polymerases (DNAPs) are not phylogenetically related to yeast and metazoan DNAPs and they harbor three insertions not present in any other DNAPs. Plant organellar DNAPs from Arabidopsis thaliana (AtPolIA and AtPolIB) are translesion synthesis (TLS) DNAPs able to bypass abasic sites, a lesion that poses a strong block to replicative polymerases. Besides abasic sites, reactive oxidative species and ionizing radiation react with thymine resulting in thymine glycol (Tg), a DNA adduct that is also a strong block to replication. Here, we report that AtPolIA and AtPolIB bypass Tg by inserting an adenine opposite the lesion and efficiently extend from a Tg-A base pair. The TLS ability of AtPolIB is mapped to two conserved lysine residues: K593 and K866. Residue K593 is situated in insertion 1 and K866 is in insertion 3. With basis on the location of both insertions on a structural model of AtPolIIB, we hypothesize that the two positively charged residues interact to form a clamp around the primer-template. In contrast with nuclear and bacterial replication, where lesion bypass involves an interplay between TLS and replicative DNA polymerases, we postulate that plant organellar DNAPs evolved to exert replicative and TLS activities. [ABSTRACT FROM AUTHOR]

In plant cells, cadmium (Cd) and arsenic (As) exert toxicity mainly by inducing oxidative stress through an imbalance between the production of reactive oxygen species (ROS) and reactive nitrogen species (RNS), and their detoxification. Nitric oxide (NO) is a RNS acting as signalling molecule coordinating plant development and stress responses, but also as oxidative stress inducer, depending on its cellular concentration. Peroxisomes are versatile organelles involved in plant metabolism and signalling, with a role in cellular redox balance thanks to their antioxidant enzymes, and their RNS (mainly NO) and ROS. This study analysed Cd or As effects on peroxisomes, and NO production and distribution in the root system, including primary root (PR) and lateral roots (LRs). Arabidopsis thaliana wild-type and transgenic plants enabling peroxisomes to be visualized in vivo , through the expression of the 35S-cyan fluorescent protein fused to the peroxisomal targeting signal1 (PTS1) were used. Peroxisomal enzymatic activities including the antioxidant catalase, the H 2 O 2 -generating glycolate oxidase, and the hydroxypyruvate reductase, and root system morphology were also evaluated under Cd/As exposure. Results showed that Cd and As differently modulate these activities, however, catalase activity was inhibited by both. Moreover, Arabidopsis root system was altered, with the pollutants differently affecting PR growth, but similarly enhancing LR formation. Only in the PR apex, and not in LR one, Cd more than As caused significant changes in peroxisome distribution, size, and in peroxisomal NO content. By contrast, neither pollutant caused significant changes in peroxisomes size and peroxisomal NO content in the LR apex. • Cd and As at 60 μM differently affect PR in Arabidopsis, but similarly enhance LRs. • Cd and As alter peroxisome distribution and peroxisomal NO in the PR but not in the LR. • Cd negatively affects the indeterminate growth of the PR altering peroxisome activity. [ABSTRACT FROM AUTHOR]

Chloroplasts are photosynthetic plant organelles descended from a bacterial ancestor. The vast majority of chloroplast proteins are synthesized in the cytosol and then imported into the chloroplast post-translationally. Translocation complexes exist in the organelle's outer and inner envelope membranes (termed TOC and TIC, respectively) to facilitate protein import. These systems recognize chloroplast precursor proteins and mediate their import in an energy-dependent manner. However, many unanswered questions remain regarding mechanistic details of the import process and the participation and functions of individual components; for example, the cytosolic events that mediate protein delivery to chloroplasts, the composition of the TIC apparatus, and the nature of the protein import motor all require resolution. The flux of proteins through TOC and TIC varies greatly throughout development and in response to specific environmental cues. The import process is, therefore, tightly regulated, and it has emerged that the ubiquitin-proteasome system (UPS) plays a key role in this regard, acting at several different steps in the process. The UPS is involved in: the selective degradation of transcription factors that co-ordinate the expression of chloroplast precursor proteins; the removal of unimported chloroplast precursor proteins in the cytosol; the inhibition of chloroplast biogenesis pre-germination; and the reconfiguration of the TOC apparatus in response to developmental and environmental signals in a process termed chloroplast-associated protein degradation. In this review, we highlight recent advances in our understanding of protein import into chloroplasts and how this process is regulated by the UPS. [ABSTRACT FROM AUTHOR]

In agriculture, plant transformation is a versatile platform for crop improvement with the aim of increased pest resistance and an improved nutrient profile. Nanotechnology can overcome several challenges that face conventional methods of gene delivery. Specifically, nanomaterials offer an optimal platform for biomolecule delivery with unique physiochemical properties as well as the ability to traverse the challenging barrier of the plant cell wall. We review the potential of diverse nanovehicles for biomolecule delivery in plant systems to obtain desired genetic traits. The efficacy of nanoparticles against pests or pathogens is also explored, as well as the interaction of nanovehicles with plant organelles, with due consideration of the effects and toxic profile of nanoparticles. To enhance crop productivity, genetic engineering is an important technique for introducing traits of interest into plant species. The desired trait can provide increased pest resistance and an improved nutrient profile, ultimately ensuring food security. Compared with conventional methods of biomolecule delivery, modern nanotechnology offers high efficiency and diverse cargo delivery options. The unique properties of nanomaterials, such as tunable physicochemical properties and the ability to traverse the plant cell wall, can be exploited to deliver species-dependent biomolecules. Nanoparticles are also effective as micronutrients and as agents against pests or bacterial infections. [ABSTRACT FROM AUTHOR]

Fluorescent materials and technologies have become widely used in scientific research, and due to the ability to convert light wavelengths, their application to photosynthetic organisms can affect their development by altering light quality. However, the impacts of fluorescent materials on aquatic plants and their environmental risks remain unclear. To assess the effects of luminescent materials on floating aquatic macrophytes and their rhizosphere microorganisms, 4-(di-p-tolylamino)benzaldehyde-A (DTB-A) and 4-(di-p-tolylamino)benzaldehyde-M (DTB-M) (emitting blue-green and orange-red light, respectively) were added individually and jointly to Spirodela polyrhiza cultures and set at different concentrations (1, 10, and 100 μM). Both DTB-A and DTB-M exhibited phytotoxicity, which increased with concentration under separate treatment. Moreover, the combined group exhibited obvious stress relief at 10 μM compared to the individually treated group. Fluorescence imaging showed that DTB-A and DTB-M were able to enter the cell matrix and organelles of plant leaves and roots. Peroxidation induced cellular damage, contributing to a decrease in superoxide dismutase (SOD) and peroxidase (POD) activities and malondialdehyde (MDA) accumulation. Decomposition of organelle structures, starch accumulation in chloroplasts, and plasmolysis were observed under the ultrastructure, disrupting photosynthetic pigment content and photosynthesis. DTB-A and DTB-M exposure resulted in growth inhibition, dry weight loss, and leaf yellowing in S. polyrhiza. A total of 3519 Operational Taxonomic Units (OTUs) were identified in the rhizosphere microbiome. The microbial communities were dominated by Alphaproteobacteria , Oxyphotobacteria , and Gammaproteobacteria , with the abundance and diversity varied significantly among treatment groups according to Shannon, Simpson, and Chao1 indices. This study revealed the stress defense response of S. polyrhiza to DTB-A and DTB-M exposures, which provides a broader perspective for the bioremediation of pollutants using aquatic plants and supports the further development of fluorescent materials for applications. [Display omitted] • Two fluorescent materials caused toxic effects on S. polyrhiza both singly and in combination. • The structures of leaf cells and rhizosphere microbiota showed distinctive changes. • Composite fluorescent materials mitigated the negative impacts of single treatments. • Fluorescent images showed transportation of materials into the cell interior. [ABSTRACT FROM AUTHOR]

Oil bodies, which are lipid-storage organelles in plant seeds, are stabilized by monolayer of phospholipids and oil body associated proteins (OBAPs). OBAPs have unique interfacial characteristics but poor water-solubility because they contain long hydrophobic segments. In this paper, dextran with different molecular weights (5, 10, and 20 kDa) was grafted onto the C- and N-terminal ends of OBAPs through in situ Maillard reaction on the surface of oil bodies. Grafting of dextran increases the length of the hydrophilic region of OBAPs, which improves their solubility and function as interfacial stabilizers. Changes in chemical bonds after grafting were observed via confocal-Raman microscopy. After de-lipidization, the physicochemical properties of OBAPs–dextran conjugates were analyzed using solubility and infrared spectroscopy. The interfacial behavior was evaluated using critical micelle concentration and interfacial rheology. The results showed that grafting of dextran improved the solubility of the OBAPs by 20-fold. The contents of α-helix and β-sheet in the OBAPs–dextran conjugates decreased, when compared with OBAPs. The critical micelle concentration of OBAPs–dextran conjugates ranged from 1.20 to 4.92 μg/mL. Grafting of dextran, especially high molecular weight, improved the capacity of the OBAPs to increase the interfacial pressure. Our results provide an efficient and eco-friend method for modification of membrane proteins. [Display omitted] • Glycosylation at the oil–water interface through Maillard reaction is green and efficient. • Water-solubility of oil body associated proteins increased 20-fold after glycosylation. • Obtained protein–dextran conjugates have a very low critical micelle concentration. • Glycosylation at the interface is monitored using confocal-Raman spectroscopy in situ. [ABSTRACT FROM AUTHOR]

Electron transfer chains of plant organelles (both chloroplasts and mitochondria) contain their own special set of ferredoxins. The relatively recently described adrenodoxin-like [2Fe-2S]-ferredoxins MFDX1 and MFDX2 of plant mitochondria are among the least studied of these. Until now, the only established function for them is participation in the final stage of biotin biosynthesis. In this work, using genetic and biochemical approaches, we searched for possible partners of these proteins in the genomes and proteomes of tobacco (Nicotiana tabacum L.) and foxglove (Digitalis purpurea L.) plants. MORF9 protein, one of the auxiliary components of the RNA editing complex of organelles (editosome), was found among the most prominent protein partners of adrenodoxin-like [2Fe-2S] tobacco ferredoxins. According to the results obtained from the yeast two-hybrid system, NtMFDX1 and NtMFDX2 of tobacco also bind and interact productively with the previously uncharacterised long non-coding polyadenylated RNA, which, based on its structural features, is capable of regulating the function of a number of components of complexes I (Nad1, Nad5) and III (protein of the cytochrome c synthesis system CcmF) and contributes to the formation of Fe/S-clusters in the corresponding protein complexes of the respiratory chain of plant mitochondria. We found one of the main components of the thiazol synthase complex (mitochondrial protein DpTHI1) to be the partner of ferredoxin DpMFDX2 of Digitalis purpurea. Finally, additional arguments were obtained in favour of the possible participation of MFDX1 and MFDX2 in the very ancient, but only recently described 'progesterone' steroid hormonal regulatory system: in leaves of the previously constructed CYP11A1-transgenic tomato plants, only the mature form of mitochondrial cytochrome P450scc (CYP11A1) of mammals is able to enter the mitochondria, where the above-mentioned components of the electron transport chain are localised. In summary, all of the newly revealed interactions of adrenodoxin-like [2Fe-2S] ferredoxins MFDX1 and MFDX2 indicate their participation in a wide range of functions in plant mitochondria. [ABSTRACT FROM AUTHOR]

Recent evidence for intimate relationship of plants with their microbiota shows that plants host individual and diverse microbial communities that are essential for their survival. Understanding their relatedness using genome-based and high-throughput techniques remains a hot topic in microbiome research. Molecular analysis of the plant holobiont necessitates the application of specific sampling and preparatory steps that also consider sources of unwanted information, such as soil, co-amplified plant organelles, human DNA, and other contaminations. Here, we review state-of-the-art and present practical guidelines regarding experimental and computational aspects to be considered in molecular plant–microbiome studies. We discuss sequencing and "omics" techniques with a focus on the requirements needed to adapt these methods to individual research approaches. The choice of primers and sequence databases is of utmost importance for amplicon sequencing, while the assembly and binning of shotgun metagenomic sequences is crucial to obtain quality data. We discuss specific bioinformatic workflows to overcome the limitation of genome database resources and for covering large eukaryotic genomes such as fungi. In transcriptomics, it is necessary to account for the separation of host mRNA or dual-RNAseq data. Metaproteomics approaches provide a snapshot of the protein abundances within a plant tissue which requires the knowledge of complete and well-annotated plant genomes, as well as microbial genomes. Metabolomics offers a powerful tool to detect and quantify small molecules and molecular changes at the plant–bacteria interface if the necessary requirements with regard to (secondary) metabolite databases are considered. We highlight data integration and complementarity which should help to widen our understanding of the interactions among individual players of the plant holobiont in the future. [ABSTRACT FROM AUTHOR]

Vacuoles are essential organelles in plants, playing crucial roles, such as cellular material degradation, ion and metabolite storage, and turgor maintenance. Vacuoles receive material via the endocytic, secretory, and autophagic pathways. Membrane fusion is the last step during which prevacuolar compartments (PVCs) and autophagosomes fuse with the vacuole membrane (tonoplast) to deliver cargoes. Protein components of the canonical intracellular fusion machinery that are conserved across organisms, including Arabidopsis thaliana, include complexes, such as soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs), that catalyze membrane fusion, and homotypic fusion and vacuole protein sorting (HOPS), that serve as adaptors which tether cargo vesicles to target membranes for fusion under the regulation of RAB-GTPases. The mechanisms regulating the recruitment and assembly of tethering complexes are not well-understood, especially the role of RABs in this dynamic regulation. Here, we report the identification of the small synthetic molecule Endosidin17 (ES17), which interferes with synthetic, endocytic, and autophagic traffic by impairing the fusion of late endosome compartments with the tonoplast. Multiple independent target identification techniques revealed that ES17 targets the VPS35 subunit of the retromer tethering complex, preventing its normal interaction with the Arabidopsis RAB7 homolog RABG3f. ES17 interference with VPS35-RABG3f interaction prevents the retromer complex to endosome anchoring, resulting in retention of RABG3f. Using multiple approaches, we show that VPS35-RABG3f-GTP interaction is necessary to trigger downstream events like HOPS complex assembly and fusion of late compartments with the tonoplast. Overall, our results support a role for the interaction of RABG3f-VPS35 as a checkpoint in the control of traffic toward the vacuole. [ABSTRACT FROM AUTHOR]

Amborella trichopoda is placed close to the base of the angiosperm lineage (basal angiosperm). By genome-wide RNA sequencing, we identified 184C-to-U RNA editing sites in the plastid genome of Amborella. This number is much higher than that observed in other angiosperms including maize (44 sites), rice (39 sites) and grape (115 sites). Despite the high frequency of RNA editing, the biased distribution of RNA editing sites in the genome, target codon preference and nucleotide preference adjacent to the edited cytidine are similar to that in other angiosperms, suggesting a common editing machinery. Consistent with this idea, the Amborella nuclear genome encodes 2–3 times more of the E- and DYW-subclass members of pentatricopeptide repeat proteins responsible for RNA editing site recognition in plant organelles. Among 165 editing sites in plastid protein coding sequences in Amborella , 100 sites were conserved at least in one out of 38 species selected to represent key branching points of the angiosperm phylogenetic tree. We assume these 100 sites represent at least a subset of the sites in the plastid editotype of ancestral angiosperms. We then mapped the loss and gain of editing sites on the phylogenetic tree of angiosperms. Our results support the idea that the evolution of angiosperms has led to the loss of RNA editing sites in plastids. [ABSTRACT FROM AUTHOR]

Summary: Structural analyses of organelles and localization of proteins in their confines are essential to investigate inner workings of eukaryotic cells. Electron tomography (ET) is a three‐dimensional electron microscopy method with which we can extract sliced views of organelles from any direction and quantify their structural parameters at nanometer‐level resolution. This advanced electron microscopy tool is suited for characterization of convoluted membrane compartments and of cellular constituents of dimensions smaller than 100 nm. ET studies of plant cells fixed by rapid freezing have expanded our understanding of the biogenesis and functions of plant organelles. Here we describe how the molecular imaging capacity of correlative light and electron microscopy can be integrated with ET in studies of plant organelles. [ABSTRACT FROM AUTHOR]

• Phosphorus, an essential macronutrient for plant growth and development, is taken up from the rhizosphere in form of inorganic phosphate (Pi). • Five families of phosphate transporter proteins (PHTs) facilitate uptake of Pi from soil and its allocation to below- and above-ground organs. • PHTs also mediate the subcellular Pi distribution between various organelles of a cell, like plastids, mitochondria, vacuoles, or golgi. • The orchestration of PHT and plastidial phosphate translocator (PT) activities enables maintenance of cellular/subcellular Pi homeostasis. • Besides their role in metabolism, PHTs and PTs may contribute to signaling processes in sensory plastids of the vasculature. Phosphorus in plant cells occurs in inorganic form as both ortho- and pyrophosphate or bound to organic compounds, like e.g. , nucleotides, phosphorylated metabolites, phospholipids, phosphorylated proteins, or phytate as P storage in the vacuoles of seeds. Individual compartments of the cell are surrounded by membranes that are selective barriers to avoid uncontrolled solute exchange. A controlled exchange of phosphate or phosphorylated metabolites is accomplished by specific phosphate transporters (PHTs) and the plastidial phosphate translocator family (PTs) of the inner envelope membrane. Plastids, in particular chloroplasts, are the site of various anabolic sequences of enzyme-catalyzed reactions. Apart from their role in metabolism PHTs and PTs are presumed to be also involved in communication between organelles and plant organs. Here we will focus on the integration of phosphate transport and homeostasis in signaling processes. Recent developments in this field will be critically assessed and potential future developments discussed. In particular, the occurrence of various plastid types in one organ (i.e. the leaf) with different functions with respect to metabolism or sensing, as has been documented recently following a tissue-specific proteomics approach (Beltran et al., 2018), will shed new light on functional aspects of phosphate homeostasis. [ABSTRACT FROM AUTHOR]

Besause MTs are highly conserved protein structures, the interaction of MT elements with MT-associated proteins and post-translational modifiers is fully dependent on protein interfaces, and almost all MT modifications are well described except acetylation. Another plant tubulin post-translational modification - phosphorylation - plays very important role in MT structuration, tubulin interaction with other MT-related proteins as well as in intracellular signaling (Yemets et al., [50]). In this study, 6 -tubulin genes, 13 -tubulin genes, 2 -tubulin genes, and 15 actin genes were identified in the flax genome and the phylogenetic relationships between flax and I A. thaliana i tubulin and actin genes were analyzed. Exon-intron structure analysis has shown intron length polymorphism within the -tubulin genes and intron number variation among the -tubulin gene: three or four introns are found in two or four genes, respectively. [Extracted from the article]

The tRNA molecules, in addition to translating the genetic code into protein and defining the second genetic code via their aminoacylation by aminoacyl‐tRNA synthetases, act in many other cellular functions and dysfunctions. This article, illustrated by personal souvenirs, covers the history of ~60 years tRNA research in Strasbourg. Typical examples point up how the work in Strasbourg was a two‐way street, influenced by and at the same time influencing investigators outside of France. All along, research in Strasbourg has nurtured the structural and functional diversity of tRNA. It produced massive sequence and crystallographic data on tRNA and its partners, thereby leading to a deeper physicochemical understanding of tRNA architecture, dynamics, and identity. Moreover, it emphasized the role of nucleoside modifications and in the last two decades, highlighted tRNA idiosyncrasies in plants and organelles, together with cellular and health‐focused aspects. The tRNA field benefited from a rich local academic heritage and a strong support by both university and CNRS. Its broad interlinks to the worldwide community of tRNA researchers opens to an exciting future. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1066–1087, 2019 [ABSTRACT FROM AUTHOR]

The chloroplast is an essential photosynthetic apparatus that is more sensitive to low temperatures than other organelles. Sigma factors were revealed regulating specific gene expression for maintaining photosynthetic efficiency and adapting to physiological and environmental conditions. However, the regulatory mechanisms of SIG genes supporting chloroplast development under low temperature in rice have not yet been reported. Here, we uncovered the essential role of OsSIG2A in rice chloroplast development at low temperatures by a newly reported thermo - sensitive chlorophyll deficient 12 (tcd12) mutant, which exhibited albino leaves with decreased chlorophyll content and malformed chloroplasts at seedling stage under low temperature. OsSIG2A is a typical chloroplast-localised RNA polymerase sigma factor, and constitutively expresses in different rice tissues, especially for young leaves and stems. Moreover, the transcription level of both PEP- and NEP- dependent genes, which are necessary for chloroplast development at early leaf development stage, was greatly affected in the tcd12 mutant under low temperature. Taken together, our findings indicate that OsSIG2A is required for early chloroplast differentiation under low temperatures by regulating plastid genes expression. Chloroplasts are essential organelles for photosynthesis in plants, but they are more sensitive to low temperature than other cellular organs. The role of OsSIG2A in chloroplast development at low temperature is of great significance and cannot be replaced by the other endogenously expressed sigma factors. This suggests a new function of sigma factors in protecting plant development under low temperature. [ABSTRACT FROM AUTHOR]

Fungal plant diseases are controlled by a complex molecular dialogue that involves pathogen effectors able to manipulate plant susceptibility factors at the earliest stages of the interaction. By probing the wheat–Fusarium graminearum pathosystem, we profiled the coregulations of the fungal and plant proteins shaping the molecular responses of a 96‐hr‐long infection's dynamics. Although no symptoms were yet detectable, fungal biomass swiftly increased along with an extremely diverse set of secreted proteins and candidate effectors supposed to target key plant organelles. Some showed to be early accumulated during the interaction or already present in spores, otherwise stored in germinating spores and detectable in an in vitro F. graminearum exudate. Wheat responses were swiftly set up and were evidenced before any visible symptom. Significant wheat protein abundance changes co‐occurred along with the accumulation of putative secreted fungal proteins and predicted effectors. Regulated wheat proteins were closely connected to basal cellular processes occurring during spikelet ontogeny, and particular coregulation patterns were evidenced between chloroplast proteins and fungal proteins harbouring a predicted chloroplast transit peptide. The described plant and fungal coordinated responses provide a resourceful set of data and expand our understanding of the wheat–F. graminearum interaction. The wheat and Fusarium graminearum proteomes depict the co‐occurrence of fine‐tuned regulations of plant and fungal proteins involving putative fungal effectors already accumulated in spores and plant metabolic functions that could constitute new FHB susceptibility factors. [ABSTRACT FROM AUTHOR]

Bacteriochlorophyll and chlorophyll serve as the most abundant and essential tetrapyrroles in photoautotrophs, while heme is indispensable for all organisms. However, some parasites of metazoan are characterized by a reduced genome, in particular for the metabolic pathway of heme synthesis and their blood feeding provide heme from the host organism. Nevertheless, it is sensible to juxtapose the heme metabolism of non-photosynthetic organisms with that of algae and plants, which require a more complex control of the entire tetrapyrrole metabolism to allocate the metabolic intermediates for the production of the chlorophyll and heme-synthesizing branch of tetrapyrrole biosynthesis. This chapter surveys recent biochemical and structural information of the enzymes of the entire heme-synthesizing pathway. A final section of this chapter highlights the functional, structural and regulatory divergences of the plant ferrochelatase in comparison to the common properties of the homologs in bacteria and animals. It is hypothesized that the two naturally occurring genes encoding isoforms of ferrochelatase are evolved to enable an appropriate and balanced heme synthesis for the supply of heme in all organelles of plant cells. [ABSTRACT FROM AUTHOR]

Chloroplasts, mitochondria and vacuoles represent characteristic organelles of the plant cell, with a predominant function in cellular metabolism. Chloroplasts are the site of photosynthesis and therefore basic and essential for photoautotrophic growth of plants. Mitochondria produce energy during respiration and vacuoles act as internal waste and storage compartments. Moreover, chloroplasts and mitochondria are sites for the biosynthesis of various compounds of primary and secondary metabolism. For photosynthesis and energy generation, the internal membranes of chloroplasts and mitochondria are equipped with electron transport chains. To perform proper electron transfer and several biosynthetic functions, both organelles contain transition metals and here iron is by far the most abundant. Although iron is thus essential for plant growth and development, it becomes toxic when present in excess and/or in its free, ionic form. The harmful effect of the latter is caused by the generation of oxidative stress. As a consequence, iron transport and homeostasis have to be tightly controlled during plant growth and development. In addition to the corresponding transport and homeostasis proteins, the vacuole plays an important role as an intracellular iron storage and release compartment at certain developmental stages. In this review, we will summarize current knowledge on iron transport and homeostasis in chloroplasts, mitochondria and vacuoles. In addition, we aim to integrate the physiological impact of intracellular iron homeostasis on cellular and developmental processes. [ABSTRACT FROM AUTHOR]

Polyphenols present in different plant cell organelles increase the resistance of plants to various types of environmental stresses. We investigated the possibility of increasing the content of bioactive compounds in the seed of yellow soybean variety Laura. The soybean was treated during vegetation with five products based on plant extracts, on the assumption of enrichment of plants with various nutrients. Soybean flour extracts were screened spectrophotometrically for total phenolic content and antioxidant activity. The antioxidant activity was evaluated using three methods. The content of phenolic acids was determined by HPLC, and the raw protein content was estimated by the Kjeldahl method. Depending on the treatment, variations in the quantity of individual phenolic acids with up to 90% higher concentration as compared to the control were observed. Controlled usage of certain plant extracts can increase the concentration of the target group of bioactive compounds in the samples. The synergistic effect of proteins and phenolic compounds on the antioxidant activity of extracts was detected. The results of this study are not only important from the aspect of plant resistance to various types of stress, but also when considering soybean as a functional food. [ABSTRACT FROM AUTHOR]

The dynamic behavior of organelles is essential for plant survival under various environmental conditions. Plant organelles, with various functions, migrate along actin filaments and contact other types of organelles, leading to physical interactions at a specific site called the membrane contact site. Recent studies have revealed the importance of physical interactions in maintaining efficient metabolite flow between organelles. In this review, we first summarize peroxisome function under different environmental conditions and growth stages to understand organelle interactions. We then discuss current knowledge regarding the interactions between peroxisome and other organelles, i.e., the oil bodies, chloroplast, and mitochondria from the perspective of metabolic and physiological regulation, with reference to various organelle interactions and techniques for estimating organelle interactions occurring in plant cells. [ABSTRACT FROM AUTHOR]

Peroxisomes are small multi‐functional organelles essential for plant development and growth. Plant peroxisomes play various physiological roles, including phytohormone biosynthesis, lipid catabolism, reactive oxygen species metabolism and many others. Mutant analysis demonstrated key roles for peroxisomes in plant reproduction, seed development and germination and post‐germinative seedling establishment; however, the underlying mechanisms remain to be fully elucidated. This review summarizes findings that reveal the importance and complexity of the role of peroxisomes in the pertinent processes. The β‐oxidation pathway plays a central role, whereas other peroxisomal pathways are also involved. Understanding the biochemical and molecular mechanisms of these peroxisomal functions will be instrumental to the improvement of crop plants. [ABSTRACT FROM AUTHOR]

Summary: In mammals and yeast, tail‐anchored (TA) membrane proteins destined for the post‐translational pathway are safely delivered to the endoplasmic reticulum (ER) membrane by a well‐known targeting factor, TRC40/Get3. In contrast, the underlying mechanism for translocation of TA proteins in plants remains obscure. How this unique eukaryotic membrane‐trafficking system correctly distinguishes different subsets of TA proteins destined for various organelles, including mitochondria, chloroplasts and the ER, is a key question of long standing. Here, we present crystal structures of algal ArsA1 (the Get3 homolog) in a distinct nucleotide‐free open state and bound to adenylyl‐imidodiphosphate. This approximately 80‐kDa protein possesses a monomeric architecture, with two ATPase domains in a single polypeptide chain. It is capable of binding chloroplast (TOC34 and TOC159) and mitochondrial (TOM7) TA proteins based on features of its transmembrane domain as well as the regions immediately before and after the transmembrane domain. Several helices located above the TA‐binding groove comprise the interlocking hook‐like motif implicated by mutational analyses in TA substrate recognition. Our data provide insights into the molecular basis of the highly specific selectivity of interactions of algal ArsA1 with the correct sets of TA substrates before membrane targeting in plant cells. Significance Statement: The molecular and cellular mechanisms responsible for targeting tail‐anchored (TA) proteins in plant cells remain insufficiently understood, despite the likelihood that they play essential roles in metabolic regulation and responses to environmental stress, amongst other processes, in different membrane‐bound organelles during plant growth and development. Here, we propose a model of the TA pathway that is based on structural and biochemical data to explain how these diverse organelle‐targeting signals are appropriately recognized by a targeting factor(s) in plant cells. [ABSTRACT FROM AUTHOR]

Summary: Subcellular compartmentation of plant biosynthetic pathways in the mitochondria and plastids requires coordinated regulation of nuclear encoded genes, and the role of these genes has been largely ignored by wood researchers.In this study, we constructed a targeted systems genetics coexpression network of xylogenesis in Eucalyptus using plastid and mitochondrial carbon metabolic genes and compared the resulting clusters to the aspen xylem developmental series.The constructed network clusters reveal the organization of transcriptional modules regulating subcellular metabolic functions in plastids and mitochondria. Overlapping genes between the plastid and mitochondrial networks implicate the common transcriptional regulation of carbon metabolism during xylem secondary growth.We show that the central processes of organellar carbon metabolism are distinctly coordinated across the developmental stages of wood formation and are specifically associated with primary growth and secondary cell wall deposition. We also demonstrate that, during xylogenesis, plastid‐targeted carbon metabolism is partially regulated by the central clock for carbon allocation towards primary and secondary xylem growth, and we discuss these networks in the context of previously established associations with wood‐related complex traits. This study provides a new resolution into the integration and transcriptional regulation of plastid‐ and mitochondrial‐localized carbon metabolism during xylogenesis. [ABSTRACT FROM AUTHOR]

In animal and yeast system, subcellular fractionation has been widely used in studies of protein localization and organelle proteomics. Alternatively, it has not been an effective way of study in plant system because of some experimental limitations. The main aim of this study is to optimize subcellular and subnuclear fractionation of wild-type of Arabidopsis thaliana ecotype Colombia (Col-0) leaves by comparing three different methods to isolate nuclear membrane. In the study, we at first optimized nuclear washing steps to remove chloroplast contents from nuclear fractions. By optimizing speed of centrifugation and chemical component of the nuclear washing buffer, purified nuclear fractions was obtained. After measurement of protein amount for each fraction, purity of the fractions was analyzed by western blot assay with some specific cell compartment markers such as anti-Histone3 for nuclear fraction and anti-Rubisco for cytoplasmic fraction. Also, lactate dehydrogenase enzyme assay was used to confirm purity of the fractions. Then, subnuclear fractionation was done to isolate purified nuclear membrane. Three different methods were used to separate the nuclear membrane from whole purified nucleus. Nuclear compartment markers such as anti-Histone3 and anti-Fibrillarin was used in this step. In the study, Inner Nuclear Membrane protein (AtSUN2) was used as a nuclear membrane marker. All things considered, we conclude that the method with DNase digestion and high centrifugation speed (first method) is a more effective way in separation of nuclear membrane fractions because the low centrifugal speed (second method) does not appear to be sufficient for separating the nuclear membrane, and the third method does not seem to be a very effective way as it requires a high centrifugal speed. [ABSTRACT FROM AUTHOR]

Abstract RNA editing is a widespread epitranscriptomic mechanism by which primary RNAs are specifically modified through insertions/deletions or nucleotide substitutions. In plants, RNA editing occurs in organelles (plastids and mitochondria), involves the cytosine to uridine modification (rarely uridine to cytosine) within protein-coding and non-protein-coding regions of RNAs and affects organelle biogenesis, adaptation to environmental changes and signal transduction. High-throughput sequencing technologies have dramatically improved the detection of RNA editing sites at genomic scale. Consequently, different bioinformatics resources have been released to discovery and/or collect novel events. Here, we review and describe the state-of-the-art bioinformatics tools devoted to the characterization of RNA editing in plant organelles with the aim to improve our knowledge about this fascinating but yet under investigated process. Highlights • RNA editing is a relevant epitranscriptomic process. • RNA editing in plants occurs in organelles and affects coding and non-coding transcripts. • Detecting C-to-U editing events in organelles is a challenging task. • Several bioinformatics resources for RNA editing detection are now available. • Bioinformatics tools devoted to RNA editing improve our knowledge about this fascinating but yet under investigated process. [ABSTRACT FROM AUTHOR]

Abstract Tissue temperature rather than ambient air temperature determines the rate of the processes that affect plant growth and development at molecular and cellular scales. Therefore, the use of air temperature to represent the temperature at which these processes occur within a plant organ implies a critical, yet poorly tested, assumption for most eco-physiological studies. The goal of this study was to determine whether the temperature of the tissues of field-grown grapevines differs significantly from the air temperature measured at a standard weather station. Thermocouples and infrared thermometers were used to measure the temperature of xylem at different heights in the west and east sides of the trunk of the vines, compound buds, and leaf surface in a vineyard between 2015 and 2017. The temperature of these tissues was compared with the air temperature measured at a standard weather station located at a distance of 410 m from the vineyard. Significant differences (p < 0.05) were determined between the temperature series. The significance and magnitude of the differences depended on the time of day and season of the year. In general, the tissue temperatures measured during the day were significantly higher than the air temperature recorded at the same time, and this difference was more than 2 °C in several cases. During the night, the tissue temperature was lower than the air temperature, but the difference was not greater than 2 °C. The higher thermal amplitude in the tissues due to these differences could explain some site- and time-specific patterns observed by viticulturists, such as the deacclimation or loss of cold hardiness during the day at higher than expected rates based on air temperature. [ABSTRACT FROM AUTHOR]

Nuclear-encoded pentatricopeptide repeat (PPR) proteins are site-specific factors for C-to-U RNA editing in plant organelles coevolving with their targets. Losing an editing target by C-to-T conversion allows for eventual loss of its editing factor, as recently confirmed for editing factors CLB19, CRR28, and RARE1 targeting ancient chloroplast editing sites in flowering plants. Here, we report on alternative evolutionary pathways for DOT4 addressing rpoC1eU488SL, a chloroplast editing site in the RNA polymerase β′ subunit mRNA. Upon loss of rpoC1eU488SL by C-to-T conversion, DOT4 got lost multiple times independently in angiosperm evolution with intermediate states of DOT4 orthologs in various stages of degeneration. Surprisingly, we now also observe degeneration and loss of DOT4 despite retention of a C in the editing position (in Carica, Coffea, Vicia, and Spirodela). We find that the cytidine remains unedited, proving that DOT4 was not replaced by another editing factor. Yet another pathway of DOT4 evolution is observed among the Poaceae. Although the rpoC1eU488SL edit has been lost through C-to-T conversion, DOT4 orthologs not only remain conserved but also have their array of PPRs extended by six additional repeats. Here, the loss of the ancient target has likely allowed DOT4 to adapt for a new function. We suggest rps3 antisense transcripts as previously demonstrated in barley (Hordeum vulgare) arising from promotor sequences newly emerging in the rpl16 intron of Poaceae as a new candidate target for the extended PPR stretch of DOT4. Altogether, DOT4 and its target show more flexible pathways for evolution than the previously explored editing factors CLB19, CRR28, and RARE1. Certain plant clades (e.g. Amaranthus, Vaccinium, Carica, the Poaceae, Fabales, and Caryophyllales) show pronounced dynamics in the evolution of editing sites and corresponding factors. [ABSTRACT FROM AUTHOR]

The haploid gametophyte generation of ferns is an excellent experimental material for cell biology studies because of its simple structure and high sensitivity to light. Each step of the developmental process, such as cell growth, cell cycle and the direction of cell division, is controlled, step by step, by light, unlike what happens in complex seed plant tissues. To perform analyses at the cell or organelle level, we have developed special tools, instruments and techniques, such as a cuvette suitable for repeated centrifugation in particular directions, microbeam irradiators for partial cell irradiation and single-cell ligation technique to create enucleated cells. Some of our main discoveries are as follows: (1) changes in the intracellular position of the nucleus in long protonemal cells by centrifugation revealed that the nuclear position or a factor(s) that is/are co-centrifuged with the nucleus is important for the decision regarding the place of the formation of preprophase bands and the timing of their disappearance, which determines the position where the new cell wall attaches to the mother cell wall; (2) even within a single cell, various phenomena could be induced by blue or red light, with the localization of the blue or red light receptors being different depending on the phenomenon; (3) de novo mRNA synthesis is not involved in the signal transduction pathways underlying light-induced chloroplast movements. In this review article, various microscopic techniques, in addition to the results of physiology studies in fern gametophytes, are described. [ABSTRACT FROM AUTHOR]

Abstract In terrestrial plants, RNA editing converts specific cytidines to uridines in mitochondrial and plastidic transcripts. Most of these events appear to be important for proper function of organellar encoded genes, since translated proteins from edited mRNAs show higher similarity with evolutionary conserved polypeptide sequences. So far about 100 nuclear encoded proteins have been characterized as RNA editing factors in plant organelles. Respective RNA editing mutants reduce or lose editing activity at different sites and display various macroscopic phenotypes from pale or albino in the case of chloroplasts to growth retardation or even embryonic lethality. Therefore, RNA editing mutants can be a useful resource of surrogate mutants for organellar encoded genes, especially for mitochondrially encoded genes that it is so far unfeasible to manipulate. However, connections between RNA editing defects and observed phenotypes in the mutants are often hard to elucidate, since RNA editing factors often target multiple RNA sites in different genes simultaneously. In this review article, we summarize the physiological aspects of respective RNA editing mutants and discuss them as surrogate mutants for functional analysis of mitochondrially encoded genes. Highlights • RNA editing in plant organelles converts specific cytidines to uridines. • RNA editing mutants can be surrogates for single nucleotide substituted mutants in mitochondrially encoded genes. • PPR proteins are specificity factor for respective editing sites. • Mutants for PPR type RNA editing factors are useful for detailed functional analysis on mitochondrially encoded genes. [ABSTRACT FROM AUTHOR]