Granular bodies in root primary meristem cells of Zea mays L. var. Cuscoensis K. (Poaceae) that enter young vacuoles by invagination: a novel ribophagy mechanism

Picky eaters: selective autophagy in plant cells

Autophagy, a fundamental cellular process, plays a vital role in maintaining cellular homeostasis by degrading damaged or unnecessary components. While selective autophagy has been extensively studied in animal cells, its significance in plant cells has only recently gained attention. In this review, we delve into the intriguing realm selective autophagy in plants, with specific focus on its involvement in nutrient recycling, organelle turnover, and stress response. Moreover, recent studies have unveiled the interesting interplay between selective autophagy and epigenetic mechanisms in plants, elucidating the significance of epigenetic regulation in modulating autophagy-related gene expression and finely tuning the selective autophagy process in plants. By synthesizing existing knowledge, this review highlights the emerging field of selective autophagy in plant cells, emphasizing its pivotal role in maintaining nutrient homeostasis, facilitating cellular adaptation, and shedding light on the epigenetic regulation that governs these processes. Our comprehensive study provides the way for a deeper understanding of the dynamic control of cellular responses to nutrient availability and stress conditions, opening new avenues for future research in this field of autophagy in plant physiology.

Intracellular phosphate recycling systems for survival during phosphate starvation in plants

Phosphorus (P) is an essential nutrient for plant growth and plants use inorganic phosphate (Pi) as their P source, but its bioavailable form, orthophosphate, is often limited in soils. Hence, plants have several mechanisms for adaptation to Pi starvation. One of the most common response strategies is "Pi recycling" in which catabolic enzymes degrade intracellular constituents, such as phosphoesters, nucleic acids and glycerophospholipids to salvage Pi. Recently, several other intracellular degradation systems have been discovered that salvage Pi from organelles. Also, one of sphingolipids has recently been identified as a degradation target for Pi recycling. So, in this mini-review we summarize the current state of knowledge, including research findings, about the targets and degradation processes for Pi recycling under Pi starvation, in order to further our knowledge of the whole mechanism of Pi recycling.

RCB-mediated chlorophagy caused by oversupply of nitrogen suppresses phosphate-starvation stress in plants

Inorganic phosphate (Pi) and nitrogen (N) are essential nutrients for plant growth. We found that a five-fold oversupply of nitrate rescues Arabidopsis (Arabidopsis thaliana) plants from Pi-starvation stress. Analyses of transgenic plants that overexpressed GFP-AUTOPHAGY8 showed that an oversupply of nitrate induced autophagy flux under Pi-depleted conditions. Expression of DIN6 and DIN10, the carbon (C) starvation-responsive genes, was upregulated when nitrate was oversupplied under Pi starvation, which suggested that the plants recognized the oversupply of nitrate as C starvation stress because of the reduction in the C/N ratio. Indeed, formation of Rubisco-containing bodies (RCBs), which contain chloroplast stroma and are induced by C starvation, was enhanced when nitrate was oversupplied under Pi starvation. Moreover, autophagy-deficient mutants did not release Pi (unlike wild-type plants), exhibited no RCB accumulation inside vacuoles, and were hypersensitive to Pi starvation, indicating that RCB-mediated chlorophagy is involved in Pi starvation tolerance. Thus, our results showed that the Arabidopsis response to Pi starvation is closely linked with N and C availability and that autophagy is a key factor that controls plant growth under Pi starvation.

Three-dimensional digital image construction of metaxylem vessels in root tips of Zea mays subsp. mexicana from thin transverse sections

PREMISE

Young plant roots share a common architecture: a central vascular cylinder surrounded by enveloping cylinders of ground and dermal tissue produced by an apical promeristem. Roots with closed apical organization can be studied to explore how ontogeny is managed. The analysis of transverse and longitudinal sections has been the most useful approach for this, but suffers from limitations. We developed a new method that utilizes digital photography of transverse sections and three-dimensional (3D) computer virtual reconstructions to overcome the limitations of other techniques.

METHODS

Serial transverse sections of teosinte root tips (Zea mays subsp. mexicana) were used to construct longitudinal images, 3D images, and an animated 3D model. The high-resolution, high-contrast, and low-distortion sectioning method developed previously by the authors enabled high-quality virtual image construction with the aid of a standard laptop computer.

RESULTS

The resulting 3D images allowed greater insight into root tissue ontogeny and organization, especially specific cellular structures such as histogen layers, xylem vessels, pericycle, and meristematic initials.

DISCUSSION

This new method has advantages over confocal laser scanning microscopy and magnetic resonance imaging for visualizing anatomy, and includes a procedure to correct for sectioning distortion. An additional advantage of this method, developed to produce better knowledge about the developmental anatomy of procambium in roots, is its applicability to a wide range of anatomical subjects.

Immunoprofiling of Cell Wall Carbohydrate Modifications During Flooding-Induced Aerenchyma Formation in Fabaceae Roots

Understanding plant adaptation mechanisms to prolonged water immersion provides options for genetic modification of existing crops to create cultivars more tolerant of periodic flooding. An important advancement in understanding flooding adaptation would be to elucidate mechanisms, such as aerenchyma air-space formation induced by hypoxic conditions, consistent with prolonged immersion. Lysigenous aerenchyma formation occurs through programmed cell death (PCD), which may entail the chemical modification of polysaccharides in root tissue cell walls. We investigated if a relationship exists between modification of pectic polysaccharides through de-methyl esterification (DME) and the formation of root aerenchyma in select Fabaceae species. To test this hypothesis, we first characterized the progression of aerenchyma formation within the vascular stele of three different legumes-Pisum sativum, Cicer arietinum, and Phaseolus coccineus-through traditional light microscopy histological staining and scanning electron microscopy. We assessed alterations in stele morphology, cavity dimensions, and cell wall chemistry. Then we conducted an immunolabeling protocol to detect specific degrees of DME among species during a 48-hour flooding time series. Additionally, we performed an enzymatic pretreatment to remove select cell wall polymers prior to immunolabeling for DME pectins. We were able to determine that all species possessed similar aerenchyma formation mechanisms that begin with degradation of root vascular stele metaxylem cells. Immunolabeling results demonstrated DME occurs prior to aerenchyma formation and prepares vascular tissues for the beginning of cavity formation in flooded roots. Furthermore, enzymatic pretreatment demonstrated that removal of cellulose and select hemicellulosic carbohydrates unmasks additional antigen binding sites for DME pectin antibodies. These results suggest that additional carbohydrate modification may be required to permit DME and subsequent enzyme activity to form aerenchyma. By providing a greater understanding of cell wall pectin remodeling among legume species, we encourage further investigation into the mechanism of carbohydrate modifications during aerenchyma formation and possible avenues for flood-tolerance improvement of legume crops.

The Ins and Outs of Autophagic Ribosome Turnover

Ribosomes are essential for protein synthesis in all organisms and their biogenesis and number are tightly controlled to maintain homeostasis in changing environmental conditions. While ribosome assembly and quality control mechanisms have been extensively studied, our understanding of ribosome degradation is limited. In yeast or animal cells, ribosomes are degraded after transfer into the vacuole or lysosome by ribophagy or nonselective autophagy, and ribosomal RNA can also be transferred directly across the lysosomal membrane by RNautophagy. In plants, ribosomal RNA is degraded by the vacuolar T2 ribonuclease RNS2 after transport by autophagy-related mechanisms, although it is unknown if a selective ribophagy pathway exists in plants. In this review, we describe mechanisms of turnover of ribosomal components in animals and yeast, and, then, discuss potential pathways for degradation of ribosomal RNA and protein within the vacuole in plants.

A novel thin section preparation and staining protocol to increase contrast and resolution of cell details for light microscopy

We developed a novel sectioning and staining method to make high contrast, high resolution sections of plant tissue for light microscopy. Specimens of teosinte (Zea mays L., ssp. mexicana) root tips were fixed and embedded in Technovit 7100™ plastic resin. Thin sections, 1-2.5 μm, were cut and mounted on glass slides. The sections were either treated with RNase or not, then stained with 0.1% toluidine blue O and observed through ∞/0 objective lenses. For light microscopy, the enzyme staining procedure increased resolution and contrast. High magnification ∞/0 objective lenses produced high quality images for digital photography without using a coverslip or immersion oil. Our slide preparation and microscopic analysis were less labor intensive and more rapid than previous methods and enabled rapid and precise alignment of serial transverse sections for both tracking cell lineages and tissue measurements.

Does functional specialization of ribosomes really exist?

It has recently become clear that ribosomes are much more heterogeneous than previously thought, with diversity arising from rRNA sequence and modifications, ribosomal protein (RP) content and posttranslational modifications (PTMs), as well as bound nonribosomal proteins. In some cases, the existence of these diverse ribosome populations has been verified by biochemical or structural methods. Furthermore, knockout or knockdown of RPs can diversify ribosome populations, while also affecting the translation of some mRNAs (but not others) with biological consequences. However, the effects on translation arising from depletion of diverse proteins can be highly similar, suggesting that there may be a more general defect in ribosome function or stability, perhaps arising from reduced ribosome numbers. Consistently, overall reduced ribosome numbers can differentially affect subclasses of mRNAs, necessitating controls for specificity. Moreover, in order to study the functional consequences of ribosome diversity, perturbations including affinity tags and knockouts are introduced, which can also affect the outcome of the experiment. Here we review the available literature to carefully evaluate whether the published data support functional diversification, defined as diverse ribosome populations differentially affecting translation of distinct mRNA (classes). Based on these observations and the commonly observed cellular responses to perturbations in the system, we suggest a set of important controls to validate functional diversity, which should include gain-of-function assays and the demonstration of inducibility under physiological conditions.

Molecular mechanisms underpinning phosphorus-use efficiency in rice

Orthophosphate (H₂ PO₄^- , Pi) is an essential macronutrient integral to energy metabolism as well as a component of membrane lipids, nucleic acids, including ribosomal RNA, and therefore essential for protein synthesis. The Pi concentration in the solution of most soils worldwide is usually far too low for maximum growth of crops, including rice. This has prompted the massive use of inefficient, polluting, and nonrenewable phosphorus (P) fertilizers in agriculture. We urgently need alternative and more sustainable approaches to decrease agriculture's dependence on Pi fertilizers. These include manipulating crops by (a) enhancing the ability of their roots to acquire limiting Pi from the soil (i.e. increased P-acquisition efficiency) and/or (b) increasing the total biomass/yield produced per molecule of Pi acquired from the soil (i.e. increased P-use efficiency). Improved P-use efficiency may be achieved by producing high-yielding plants with lower P concentrations or by improving the remobilization of acquired P within the plant so as to maximize growth and biomass allocation to developing organs. Membrane lipid remodelling coupled with hydrolysis of RNA and smaller P-esters in senescing organs fuels P remobilization in rice, the world's most important cereal crop.

Degradation of cytosolic ribosomes by autophagy-related pathways

Ribosomes are essential molecular machines that require a large cellular investment, yet the mechanisms of their turnover are not well understood in any eukaryotic organism. Recent advances in Arabidopsis suggest that plants utilize selective mechanisms to transport rRNA or ribosomes to the vacuole, where rRNA is degraded and the breakdown products recycled to maintain cellular homeostasis. This review focuses on known mechanisms of rRNA turnover and explores unanswered questions on the specificity and pathways of ribosome turnover and the role of this process in maintenance of cellular homeostasis.

Molecular definitions of autophagy and related processes

Over the past two decades, the molecular machinery that underlies autophagic responses has been characterized with ever increasing precision in multiple model organisms. Moreover, it has become clear that autophagy and autophagy-related processes have profound implications for human pathophysiology. However, considerable confusion persists about the use of appropriate terms to indicate specific types of autophagy and some components of the autophagy machinery, which may have detrimental effects on the expansion of the field. Driven by the overt recognition of such a potential obstacle, a panel of leading experts in the field attempts here to define several autophagy-related terms based on specific biochemical features. The ultimate objective of this collaborative exchange is to formulate recommendations that facilitate the dissemination of knowledge within and outside the field of autophagy research.

Cytoplasmic RNA decay pathways - Enzymes and mechanisms

RNA decay plays a crucial role in post-transcriptional regulation of gene expression. Work conducted over the last decades has defined the major mRNA decay pathways, as well as enzymes and their cofactors responsible for these processes. In contrast, our knowledge of the mechanisms of degradation of non-protein coding RNA species is more fragmentary. This review is focused on the cytoplasmic pathways of mRNA and ncRNA degradation in eukaryotes. The major 3' to 5' and 5' to 3' mRNA decay pathways are described with emphasis on the mechanisms of their activation by the deprotection of RNA ends. More recently discovered 3'-end modifications such as uridylation, and their relevance to cytoplasmic mRNA decay in various model organisms, are also discussed. Finally, we provide up-to-date findings concerning various pathways of non-coding RNA decay in the cytoplasm.

Methods for analysis of autophagy in plants

The plant vacuole is a major site for the breakdown and recycling of cellular macromolecules. Cytoplasmic components destined for degradation are delivered to the vacuole in vesicles termed autophagosomes, and the breakdown products are transported back into the cytosol for reuse, with the overall process termed autophagy. In plants, autophagy is required for nutrient remobilization and recycling during senescence and nutrient deficiency, for clearance of protein aggregates and damaged organelles during environmental stress, for pathogen defense, and for general cellular maintenance under normal growth conditions. There is growing interest in autophagy in plants due to the wide range of processes in which it functions. While much of the work thus far has used the model plant Arabidopsis thaliana, autophagy is now under investigation in a number of other plants, particularly in economically important crop species. Here, I discuss methods for assessing autophagy activity in plant cells. Microscopic and biochemical assays are described, along with ways to distinguish the steady-state number of autophagosomes from flux through the autophagic pathway. Some deficiencies still exist in plant autophagy analysis, and there is a particular need for more accurate methods of quantifying autophagic flux in plants.