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New Insight into Signaling and Autophagy in Plants 2.0
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New Insight into Signaling and Autophagy in Plants 2.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (31 October 2022) | Viewed by 27527

Special Issue Editors

Dr. Małgorzata Pietrowska-Borek

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Guest Editor
Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, Poznań, Poland
Interests: abiotic and biotic stress; autophagy; cell signaling; cyclic nucleotides; uncommon nucleotides; molecular plant physiology; plant biochemistry; plant biotechnology; plant cell biology; plant molecular biology; plant tissue culture; signal transduction pathways
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Sławomir Borek

E-Mail Website
Guest Editor
Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
Interests: autophagy; autophagic body degradation; plant physiology and biochemistry; programmed cell death (PCD); pexophagy; seed metabolism; selective autophagy; sugar starvation; seed development and germination; storage lipid metabolism; uncommon nucleotides; vacuolar processing enzymes (VPE); vacuole
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

During the entirety of ontogenesis, plants are forced to sense signals and react and adapt to changing and often adverse environmental conditions. Intracellular signal networks are involved in activating, regulating, and silencing various plant responses to environmental stimuli. Plants must also possess systems to exchange information throughout the entire organism to ensure the coordination of development and defense. The signaling systems transmitting this information are complex and involve multiple components, which are far from being understood.

One of the processes that enable plants to respond efficiently to a changing environment, both internal and external, is autophagy. The efficient functioning of autophagy ensures proper growth and development of plants at every stage of ontogenesis. Under normal conditions, autophagy is a housekeeping process, allowing the recycling of damaged or unnecessary organelles and protein complexes, and, under various types of biotic and abiotic stresses, can be an essential element of plant defense responses. The autophagic turnover of organelles and protein complexes occurs in a controlled and selective manner. The attention of many scientists is currently focused on identifying the elements of signaling pathways and the mechanisms of marking, recognizing, and directing particular cell components to autophagic degradation in the vacuole.

This Special Issue will publish original research papers, reviews, short reviews, opinion articles, and hypotheses within the scope of the newest discoveries in signaling and autophagy in plants. In particular, we welcome papers showing molecular data on signal perception and transduction as well as selective types of autophagy in plants

Dr. Małgorzata Pietrowska-Borek
Dr. Sławomir Borek
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Autophagy cargo receptors
  • Autophagy in plant development
  • Autophagy in plant stress
  • Crosstalk between autophagy and phytohormones
  • Plant cell homeostasis
  • Nutrients recycling
  • Plant cell biology
  • Plant signal transduction
  • Selective autophagy
  • Signaling molecules

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Published Papers (9 papers)

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Research

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21 pages, 4136 KiB  
Article
Aux/IAA11 Is Required for UV-AB Tolerance and Auxin Sensing in Arabidopsis thaliana
by Jakub Mielecki, Piotr Gawroński and Stanisław Karpiński
Int. J. Mol. Sci. 2022, 23(21), 13386; https://doi.org/10.3390/ijms232113386 - 02 Nov 2022
Cited by 2 | Viewed by 1896
Abstract
In order to survive, plants have, over the course of their evolution, developed sophisticated acclimation and defense strategies governed by complex molecular and physiological, and cellular and extracellular, signaling pathways. They are also able to respond to various stimuli in the form of [...] Read more.
In order to survive, plants have, over the course of their evolution, developed sophisticated acclimation and defense strategies governed by complex molecular and physiological, and cellular and extracellular, signaling pathways. They are also able to respond to various stimuli in the form of tropisms; for example, phototropism or gravitropism. All of these retrograde and anterograde signaling pathways are controlled and regulated by waves of reactive oxygen species (ROS), electrical signals, calcium, and hormones, e.g., auxins. Auxins are key phytohormones involved in the regulation of plant growth and development. Acclimation responses, which include programmed cell death induction, require precise auxin perception. However, our knowledge of these pathways is limited. The Aux/IAA family of transcriptional corepressors inhibits the growth of the plant under stress conditions, in order to maintain the balance between development and acclimation responses. In this work, we demonstrate the Aux/IAA11 involvement in auxin sensing, survival, and acclimation to UV-AB, and in carrying out photosynthesis under inhibitory conditions. The tested iaa11 mutants were more susceptible to UV-AB, photosynthetic electron transport (PET) inhibitor, and synthetic endogenous auxin. Among the tested conditions, Aux/IAA11 was not repressed by excess light stress, exclusively among its phylogenetic clade. Repression of transcription by Aux/IAA11 could be important for the inhibition of ROS formation or efficiency of ROS scavenging. We also hypothesize that the demonstrated differences in the subcellular localization of the two Aux/IAA11 protein variants might indicate their regulation by alternative splicing. Our results suggest that Aux/IAA11 plays a specific role in chloroplast retrograde signaling, since it is not repressed by high (excess) light stress, exclusively among its phylogenetic clade. Full article
(This article belongs to the Special Issue New Insight into Signaling and Autophagy in Plants 2.0)
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24 pages, 2351 KiB  
Article
Exploring the Contribution of Autophagy to the Excess-Sucrose Response in Arabidopsis thaliana
by Daniel Laloum, Sahar Magen, Yoram Soroka and Tamar Avin-Wittenberg
Int. J. Mol. Sci. 2022, 23(7), 3891; https://doi.org/10.3390/ijms23073891 - 31 Mar 2022
Cited by 2 | Viewed by 2989
Abstract
Autophagy is an essential intracellular eukaryotic recycling mechanism, functioning in, among others, carbon starvation. Surprisingly, although autophagy-deficient plants (atg mutants) are hypersensitive to carbon starvation, metabolic analysis revealed that they accumulate sugars under such conditions. In plants, sugars serve as both an [...] Read more.
Autophagy is an essential intracellular eukaryotic recycling mechanism, functioning in, among others, carbon starvation. Surprisingly, although autophagy-deficient plants (atg mutants) are hypersensitive to carbon starvation, metabolic analysis revealed that they accumulate sugars under such conditions. In plants, sugars serve as both an energy source and as signaling molecules, affecting many developmental processes, including root and shoot formation. We thus set out to understand the interplay between autophagy and sucrose excess, comparing wild-type and atg mutant seedlings. The presented work showed that autophagy contributes to primary root elongation arrest under conditions of exogenous sucrose and glucose excess but not during fructose or mannitol treatment. Minor or no alterations in starch and primary metabolites were observed between atg mutants and wild-type plants, indicating that the sucrose response relates to its signaling and not its metabolic role. Extensive proteomic analysis of roots performed to further understand the mechanism found an accumulation of proteins essential for ROS reduction and auxin maintenance, which are necessary for root elongation, in atg plants under sucrose excess. The analysis also suggested mitochondrial and peroxisomal involvement in the autophagy-mediated sucrose response. This research increases our knowledge of the complex interplay between autophagy and sugar signaling in plants. Full article
(This article belongs to the Special Issue New Insight into Signaling and Autophagy in Plants 2.0)
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15 pages, 3423 KiB  
Article
Nucleoside 5′-Phosphoramidates Control the Phenylpropanoid Pathway in Vitis vinifera Suspension-Cultured Cells
by Małgorzata Pietrowska-Borek, Jędrzej Dobrogojski, Anna Maria Wojdyła-Mamoń, Joanna Romanowska, Justyna Gołębiewska, Sławomir Borek, Koichi Murata, Atsushi Ishihara, Maria Ángeles Pedreño and Andrzej Guranowski
Int. J. Mol. Sci. 2021, 22(24), 13567; https://doi.org/10.3390/ijms222413567 - 17 Dec 2021
Cited by 2 | Viewed by 2333
Abstract
It is known that cells contain various uncommon nucleotides such as dinucleoside polyphosphates (NpnN’s) and adenosine 5′-phosphoramidate (NH2-pA) belonging to nucleoside 5′-phosphoramidates (NH2-pNs). Their cellular levels are enzymatically controlled. Some of them are accumulated in cells under [...] Read more.
It is known that cells contain various uncommon nucleotides such as dinucleoside polyphosphates (NpnN’s) and adenosine 5′-phosphoramidate (NH2-pA) belonging to nucleoside 5′-phosphoramidates (NH2-pNs). Their cellular levels are enzymatically controlled. Some of them are accumulated in cells under stress, and therefore, they could act as signal molecules. Our previous research carried out in Arabidopsis thaliana and grape (Vitis vinifera) showed that NpnN’s induced the expression of genes in the phenylpropanoid pathway and favored the accumulation of their products, which protect plants against stress. Moreover, we found that NH2-pA could play a signaling role in Arabidopsis seedlings. Data presented in this paper show that exogenously applied purine (NH2-pA, NH2-pG) and pyrimidine (NH2-pU, NH2-pC) nucleoside 5′-phosphoramidates can modify the expression of genes that control the biosynthesis of both stilbenes and lignin in Vitis vinifera cv. Monastrell suspension-cultured cells. We investigated the expression of genes encoding for phenylalanine ammonia-lyase (PAL1), cinnamate-4-hydroxylase (C4H1), 4-coumarate:coenzyme A ligase (4CL1), chalcone synthase (CHS1), stilbene synthase (STS1), cinnamoyl-coenzyme A:NADP oxidoreductase (CCR2), and cinnamyl alcohol dehydrogenase (CAD1). Each of the tested NH2-pNs also induced the expression of the trans-resveratrol cell membrane transporter VvABCG44 gene and caused the accumulation of trans-resveratrol and trans-piceid in grape cells as well as in the culture medium. NH2-pC, however, evoked the most effective induction of phenylpropanoid pathway genes such as PAL1, C4H1, 4CL1, and STS1. Moreover, this nucleotide also induced at short times the accumulation of N-benzoylputrescine (BenPut), one of the phenylamides that are derivatives of phenylpropanoid and polyamines. The investigated nucleotides did not change either the lignin content or the cell dry weight, nor did they affect the cell viability throughout the experiment. The results suggest that nucleoside 5′-phosphoramidates could be considered as new signaling molecules. Full article
(This article belongs to the Special Issue New Insight into Signaling and Autophagy in Plants 2.0)
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Review

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14 pages, 3153 KiB  
Review
Vacuolar Processing Enzymes in Plant Programmed Cell Death and Autophagy
by Karolina Wleklik and Sławomir Borek
Int. J. Mol. Sci. 2023, 24(2), 1198; https://doi.org/10.3390/ijms24021198 - 07 Jan 2023
Cited by 4 | Viewed by 2688
Abstract
Vacuolar processing enzymes (VPEs) are plant cysteine proteases that are subjected to autoactivation in an acidic pH. It is presumed that VPEs, by activating other vacuolar hydrolases, are in control of tonoplast rupture during programmed cell death (PCD). Involvement of VPEs has been [...] Read more.
Vacuolar processing enzymes (VPEs) are plant cysteine proteases that are subjected to autoactivation in an acidic pH. It is presumed that VPEs, by activating other vacuolar hydrolases, are in control of tonoplast rupture during programmed cell death (PCD). Involvement of VPEs has been indicated in various types of plant PCD related to development, senescence, and environmental stress responses. Another pathway induced during such processes is autophagy, which leads to the degradation of cellular components and metabolite salvage, and it is presumed that VPEs may be involved in the degradation of autophagic bodies during plant autophagy. As both PCD and autophagy occur under similar conditions, research on the relationship between them is needed, and VPEs, as key vacuolar proteases, seem to be an important factor to consider. They may even constitute a potential point of crosstalk between cell death and autophagy in plant cells. This review describes new insights into the role of VPEs in plant PCD, with an emphasis on evidence and hypotheses on the interconnections between autophagy and cell death, and indicates several new research opportunities. Full article
(This article belongs to the Special Issue New Insight into Signaling and Autophagy in Plants 2.0)
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13 pages, 579 KiB  
Review
Autophagy in the Lifetime of Plants: From Seed to Seed
by Song Wang, Weiming Hu and Fen Liu
Int. J. Mol. Sci. 2022, 23(19), 11410; https://doi.org/10.3390/ijms231911410 - 27 Sep 2022
Cited by 4 | Viewed by 2577
Abstract
Autophagy is a highly conserved self-degradation mechanism in eukaryotes. Excess or harmful intracellular content can be encapsulated by double-membrane autophagic vacuoles and transferred to vacuoles for degradation in plants. Current research shows three types of autophagy in plants, with macroautophagy being the most [...] Read more.
Autophagy is a highly conserved self-degradation mechanism in eukaryotes. Excess or harmful intracellular content can be encapsulated by double-membrane autophagic vacuoles and transferred to vacuoles for degradation in plants. Current research shows three types of autophagy in plants, with macroautophagy being the most important autophagic degradation pathway. Until now, more than 40 autophagy-related (ATG) proteins have been identified in plants that are involved in macroautophagy, and these proteins play an important role in plant growth regulation and stress responses. In this review, we mainly introduce the research progress of autophagy in plant vegetative growth (roots and leaves), reproductive growth (pollen), and resistance to biotic (viruses, bacteria, and fungi) and abiotic stresses (nutrients, drought, salt, cold, and heat stress), and we discuss the application direction of plant autophagy in the future. Full article
(This article belongs to the Special Issue New Insight into Signaling and Autophagy in Plants 2.0)
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15 pages, 825 KiB  
Review
Autophagy-Mediated Regulation of Different Meristems in Plants
by Shan Cheng, Qi Wang, Hakim Manghwar and Fen Liu
Int. J. Mol. Sci. 2022, 23(11), 6236; https://doi.org/10.3390/ijms23116236 - 02 Jun 2022
Cited by 8 | Viewed by 2894
Abstract
Autophagy is a highly conserved cell degradation process that widely exists in eukaryotic cells. In plants, autophagy helps maintain cellular homeostasis by degrading and recovering intracellular substances through strict regulatory pathways, thus helping plants respond to a variety of developmental and environmental signals. [...] Read more.
Autophagy is a highly conserved cell degradation process that widely exists in eukaryotic cells. In plants, autophagy helps maintain cellular homeostasis by degrading and recovering intracellular substances through strict regulatory pathways, thus helping plants respond to a variety of developmental and environmental signals. Autophagy is involved in plant growth and development, including leaf starch degradation, senescence, anthers development, regulation of lipid metabolism, and maintenance of peroxisome mass. More and more studies have shown that autophagy plays a role in stress response and contributes to maintain plant survival. The meristem is the basis for the formation and development of new tissues and organs during the post-embryonic development of plants. The differentiation process of meristems is an extremely complex process, involving a large number of morphological and structural changes, environmental factors, endogenous hormones, and molecular regulatory mechanisms. Recent studies have demonstrated that autophagy relates to meristem development, affecting plant growth and development under stress conditions, especially in shoot and root apical meristem. Here, we provide an overview of the current knowledge about how autophagy regulates different meristems under different stress conditions and possibly provide new insights for future research. Full article
(This article belongs to the Special Issue New Insight into Signaling and Autophagy in Plants 2.0)
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18 pages, 354 KiB  
Review
Linking Autophagy to Potential Agronomic Trait Improvement in Crops
by Jingran Wang, Shulei Miao, Yule Liu and Yan Wang
Int. J. Mol. Sci. 2022, 23(9), 4793; https://doi.org/10.3390/ijms23094793 - 26 Apr 2022
Cited by 1 | Viewed by 2029
Abstract
Autophagy is an evolutionarily conserved catabolic process in eukaryotic cells, by which the superfluous or damaged cytoplasmic components can be delivered into vacuoles or lysosomes for degradation and recycling. Two decades of autophagy research in plants uncovers the important roles of autophagy during [...] Read more.
Autophagy is an evolutionarily conserved catabolic process in eukaryotic cells, by which the superfluous or damaged cytoplasmic components can be delivered into vacuoles or lysosomes for degradation and recycling. Two decades of autophagy research in plants uncovers the important roles of autophagy during diverse biological processes, including development, metabolism, and various stress responses. Additionally, molecular machineries contributing to plant autophagy onset and regulation have also gradually come into people’s sights. With the advancement of our knowledge of autophagy from model plants, autophagy research has expanded to include crops in recent years, for a better understanding of autophagy engagement in crop biology and its potentials in improving agricultural performance. In this review, we summarize the current research progress of autophagy in crops and discuss the autophagy-related approaches for potential agronomic trait improvement in crop plants. Full article
(This article belongs to the Special Issue New Insight into Signaling and Autophagy in Plants 2.0)
24 pages, 3070 KiB  
Review
Phosphatidic Acid in Plant Hormonal Signaling: From Target Proteins to Membrane Conformations
by Yaroslav Kolesnikov, Serhii Kretynin, Yaroslava Bukhonska, Igor Pokotylo, Eric Ruelland, Jan Martinec and Volodymyr Kravets
Int. J. Mol. Sci. 2022, 23(6), 3227; https://doi.org/10.3390/ijms23063227 - 17 Mar 2022
Cited by 15 | Viewed by 2791
Abstract
Cells sense a variety of extracellular signals balancing their metabolism and physiology according to changing growth conditions. Plasma membranes are the outermost informational barriers that render cells sensitive to regulatory inputs. Membranes are composed of different types of lipids that play not only [...] Read more.
Cells sense a variety of extracellular signals balancing their metabolism and physiology according to changing growth conditions. Plasma membranes are the outermost informational barriers that render cells sensitive to regulatory inputs. Membranes are composed of different types of lipids that play not only structural but also informational roles. Hormones and other regulators are sensed by specific receptors leading to the activation of lipid metabolizing enzymes. These enzymes generate lipid second messengers. Among them, phosphatidic acid (PA) is a well-known intracellular messenger that regulates various cellular processes. This lipid affects the functional properties of cell membranes and binds to specific target proteins leading to either genomic (affecting transcriptome) or non-genomic responses. The subsequent biochemical, cellular and physiological reactions regulate plant growth, development and stress tolerance. In the present review, we focus on primary (genome-independent) signaling events triggered by rapid PA accumulation in plant cells and describe the functional role of PA in mediating response to hormones and hormone-like regulators. The contributions of individual lipid signaling enzymes to the formation of PA by specific stimuli are also discussed. We provide an overview of the current state of knowledge and future perspectives needed to decipher the mode of action of PA in the regulation of cell functions. Full article
(This article belongs to the Special Issue New Insight into Signaling and Autophagy in Plants 2.0)
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23 pages, 1453 KiB  
Review
Control of ABA Signaling and Crosstalk with Other Hormones by the Selective Degradation of Pathway Components
by Agnieszka Sirko, Anna Wawrzyńska, Jerzy Brzywczy and Marzena Sieńko
Int. J. Mol. Sci. 2021, 22(9), 4638; https://doi.org/10.3390/ijms22094638 - 28 Apr 2021
Cited by 24 | Viewed by 6026
Abstract
A rapid and appropriate genetic and metabolic acclimation, which is crucial for plants’ survival in a changing environment, is maintained due to the coordinated action of plant hormones and cellular degradation mechanisms influencing proteostasis. The plant hormone abscisic acid (ABA) rapidly accumulates in [...] Read more.
A rapid and appropriate genetic and metabolic acclimation, which is crucial for plants’ survival in a changing environment, is maintained due to the coordinated action of plant hormones and cellular degradation mechanisms influencing proteostasis. The plant hormone abscisic acid (ABA) rapidly accumulates in plants in response to environmental stress and plays a pivotal role in the reaction to various stimuli. Increasing evidence demonstrates a significant role of autophagy in controlling ABA signaling. This field has been extensively investigated and new discoveries are constantly being provided. We present updated information on the components of the ABA signaling pathway, particularly on transcription factors modified by different E3 ligases. Then, we focus on the role of selective autophagy in ABA pathway control and review novel evidence on the involvement of autophagy in different parts of the ABA signaling pathway that are important for crosstalk with other hormones, particularly cytokinins and brassinosteroids. Full article
(This article belongs to the Special Issue New Insight into Signaling and Autophagy in Plants 2.0)
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