Differential degradation of RNA species by autophagy-related pathways in Arabidopsis

Post-transcriptional dynamics and RNA homeostasis in autophagy and cancer

Autophagy is an essential recycling and quality control pathway which preserves cellular and organismal homeostasis. As a catabolic process, autophagy degrades damaged and aged intracellular components in response to conditions of stress, including nutrient deprivation, oxidative and genotoxic stress. Autophagy is a highly adaptive and dynamic process which requires an intricately coordinated molecular control. Here we provide an overview of how autophagy is regulated post-transcriptionally, through RNA processing events, epitranscriptomic modifications and non-coding RNAs. We further discuss newly revealed RNA-binding properties of core autophagy machinery proteins and review recent indications of autophagy's ability to impact cellular RNA homeostasis. From a physiological perspective, we examine the biological implications of these emerging regulatory layers of autophagy, particularly in the context of nutrient deprivation and tumorigenesis.

The vacuolar phosphatases purple acid phosphatase 26 and haloacid dehalogenase IIA2.1 hydrolyze 5'-, 3'-, and 2'-nucleotides derived from RNA degradation

The vacuole is an important site for RNA degradation. Autophagy delivers RNA to the vacuole, where the vacuolar T2 RNase ribonuclease 2 (RNS2) plays a major role in RNA catabolism. The presumed products of RNS2 activity are 3'-nucleoside monophosphates (3'-NMPs). Vacuolar phosphatases that carry out 3'-NMP hydrolysis are required to metabolize 3'-NMPs, but the specific players remain unknown. Using a mutant of RNS2 and mutants of the autophagy-related genes 5 and 9 (atg5 and atg9), we confirmed that 3'-NMPs are products of vacuolar RNS2-mediated RNA degradation in Arabidopsis (Arabidopsis thaliana). Moreover, we identified purple acid phosphatase 26 (PAP26) and haloacid dehalogenase IIA2.1 (HIIA2.1) as vacuolar 3'-NMP phosphatases. Based on phylogenetic analysis, we propose systematic nomenclature for HADIIA enzymes, some of which were previously named vegetative storage proteins, which we critically discuss. PAP26 and HIIA2.1 differ in their NMP specificity and activity in vitro. However, hiia2.1 pap26 double mutant plants, but generally not the respective single mutants, accumulate 3'-NMPs in addition to 5'-NMPs and, surprisingly, also 2'-NMPs. These findings suggest that PAP26 and HIIA2.1 have overlapping NMP substrate spectra in vivo. Excess 3'- and 2'-NMPs accumulate in plants exposed to a prolonged night, presumably because carbon limitation enhances autophagy-mediated vacuolar RNA degradation. We conclude that vacuolar RNA catabolism releases 3'-NMPs and 2'-NMPs through RNS2 and other RNases that also generate 5'-NMPs. PAP26 and HIIA2.1 are required to dephosphorylate these NMPs, so that they can enter general nucleotide metabolism outside the vacuole.

Nucleotides and nucleotide derivatives as signal molecules in plants

In reaction to a stimulus, signaling molecules are made, generate a response, and are then degraded. Nucleotides are classically associated with central metabolism and nucleic acid biosynthesis, but there are a number of nucleotides and nucleotide derivatives in plants to which this simple definition of a signaling molecule applies in whole or at least in part. These include cytokinins and chloroplast guanosine tetraposphate (ppGpp), as well as extracellular canonical nucleotides such as extracellular ATP (eATP) and NAD+ (eNAD+). In addition, there is a whole series of compounds derived from NAD+ such as ADP ribose (ADPR), and ATP-ADPR dinucleotides and their hydrolysis products (e.g. pRib-AMP) together with different variants of cyclic ADPR (cADPR, 2´-cADPR, 3´-cADPR), and also cyclic nucleotides such as 3´,5´-cAMP and 2´,3´-cyclic nucleoside monophosphates. Interestingly, some of these compounds have recently been shown to play a central role in pathogen defense. In this review, we highlight these exciting new developments. We also review nucleotide derivatives that are considered as candidates for signaling molecules, for example purine deoxynucleosides, and discuss more controversial cases.

RNA pseudouridine modification in plants

Pseudouridine is one of the well-known chemical modifications in various RNA species. Current advances to detect pseudouridine show that the pseudouridine landscape is dynamic and affects multiple cellular processes. Although our understanding of this post-transcriptional modification mainly depends on yeast and human models, the recent findings provide strong evidence for the critical role of pseudouridine in plants. Here, we review the current knowledge of pseudouridine in plant RNAs, including its synthesis, degradation, regulatory mechanisms, and functions. Moreover, we propose future areas of research on pseudouridine modification in plants.

Canonical and non-canonical roles for ATG8 proteins in autophagy and beyond

During autophagy, the ATG8 family proteins have several well-characterized roles in facilitating early, mid, and late steps of autophagy, including autophagosome expansion, cargo recruitment and autophagosome-lysosome fusion. Their discovery has importantly allowed for precise experimental monitoring of the pathway, bringing about a huge expansion of research in the field over the last decades. In this review, we discuss both canonical and non-canonical roles of the autophagic lipidation machinery, with particular focus on the ATG8 proteins, their post-translational modifications and their increasingly uncovered alternative roles mediated through their anchoring at different membranes. These include endosomes, macropinosomes, phagosomes and the plasma membrane, to which ATG8 proteins can bind through canonical or alternative lipidation. Beyond new ATG8 binding partners and cargo types, we also explore several open questions related to alternative outcomes of autophagic machinery engagement beyond degradation. These include their roles in plasma membrane repair and secretion of selected substrates as well as the physiological implications hereof in health and disease.

Regulatory roles of selective autophagy through targeting of native proteins in plant adaptive responses

Selective autophagy functions as a regulatory mechanism by targeting native and functional proteins to ensure their proper levels and activities in plant adaptive responses. Autophagy is a cellular degradation and recycling pathway with a key role in cellular homeostasis and metabolism. Autophagy is initiated with the biogenesis of autophagosomes, which fuse with the lysosomes or vacuoles to release their contents for degradation. Under nutrient starvation or other adverse environmental conditions, autophagy usually targets unwanted or damaged proteins, organelles and other cellular components for degradation and recycling to promote cell survival. Over the past decade, however, a substantial number of studies have reported that autophagy in plants also functions as a regulatory mechanism by targeting enzymes, structural and regulatory proteins that are not necessarily damaged or dysfunctional to ensure their proper abundance and function to facilitate cellular changes required for response to endogenous and environmental conditions. During plant-pathogen interactions in particular, selective autophagy targets specific pathogen components as a defense mechanism and pathogens also utilize autophagy to target functional host factors to suppress defense mechanisms. Autophagy also targets native and functional protein regulators of plant heat stress memory, hormone signaling, and vesicle trafficking associated with plant responses to abiotic and other conditions. In this review, we discuss advances in the regulatory roles of selective autophagy through targeting of native proteins in plant adaptive responses, what questions remain and how further progress in the analysis of these special regulatory roles of autophagy can help understand biological processes important to plants.

Eating the messenger (RNA): autophagy shapes the cellular RNA landscape

This article comments on: Hickl D, Drews F, Girke C, Zimmer D, Mühlhaus T, Hauth J, Nordström K, Trentmann O, Neuhaus EH, Scheuring D, Fehlmann T, Keller A, Simon M, Möhlmann T. 2021. Differential degradation of RNA species by autophagy-related pathways in Arabidopsis. Journal of Experimental Botany 72, 6867–6881.