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Ubiquitylation in Plant Developmental and Physiological Processes
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Ubiquitylation in Plant Developmental and Physiological Processes

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 (30 June 2022) | Viewed by 33185

Special Issue Editors

Dr. Zhihua Hua

E-Mail Website
Guest Editor
Plant Ubiquitylation Laboratory, Ohio University, Athens, OH 45701, USA
Interests: protein ubiquitylation; plant hormone signaling; chloroplast development; gene superfamily evolution
Dr. Richard S. Marshall

E-Mail Website
Guest Editor
Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
Interests: protein ubiquitylation; protein degradation; proteostasis; 26S proteasome; autophagy

Special Issue Information

Dear Colleagues,

Advances in genome sequencing have revealed large groups of plant genes whose protein products are involved in the process of protein ubiquitylation, where the 76-amino-acid ubiquitin protein is attached to (typically) a lysine residue within a target protein. This biochemical reaction is catalyzed by a highly polymorphic E1–E2–E3 enzymatic cascade consisting of a conserved E1 ubiquitin-activating enzyme, multiple E2 ubiquitin-conjugating enzymes and, in plants, a remarkable number of E3 ubiquitin ligases. The consequences of ubiquitylation are diverse, including altering the activity and/or localization of a protein or targeting it for degradation. Recently developed mass spectrometry-based proteome-wide analyses have uncovered an incredibly broad scope of ubiquitylation substrates, many of which are recognized and degraded by either the 26S proteasome or autophagy. As such, emerging hypotheses argue that this post-translational modification rivals gene transcription in both depth and breadth as a dominant regulatory mechanism controlling protein activity and abundance. Not surprisingly, studies from mutants of multiple core components of the ubiquitylation system, such as Cullin-RING E3 ligases or 26S proteasome subunits, display either lethal or severe pleiotropic phenotypes relating to plant growth and development. Unfortunately, these types of studies are often not helpful in revealing the functions of individual pathways involving different E3 ligases, the majority of which remain unknown.

Reverse genetics has demonstrated enormous power in functional genomic studies. However, uncovering the specific functions of a large system such as protein ubiquitylation requires more innovative approaches. For example, redundant functions among E3 ligase homologs pose challenges for characterizing their function(s) using insertion mutants but could be solved by recently emerging multiplex CRISPR/Cas9-based knock-out or knock-in approaches. In addition, genomic and evolutionary studies have helped to prioritize research directions. To encourage teamwork and discovery in the field of plant protein ubiquitylation, we here solicit contributions from the community on this topic. For example, if your favorite protein is potentially ubiquitylated or is an E3 ubiquitin ligase, we encourage such research articles to be submitted to this Special Issue, with novel approaches being highly encouraged. In addition, we welcome experts in the field to contribute a review article, thus bringing varied perspectives to the community.

Dr. Zhihua Hua
Dr. Richard S. Marshall
Guest Editors

Manuscript Submission Information

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Keywords

  • ubiquitylation
  • degradation
  • proteasome
  • autophagy
  • chloroplast
  • E3 ligase
  • germination
  • growth
  • hormone signaling
  • flowering
  • reproductive development

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Published Papers (10 papers)

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Editorial

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5 pages, 211 KiB  
Editorial
The Ubiquitin–26S Proteasome System—A Versatile Player Worthy of Close Attention in Plants
by Zhihua Hua
Int. J. Mol. Sci. 2023, 24(9), 8185; https://doi.org/10.3390/ijms24098185 - 3 May 2023
Cited by 1 | Viewed by 1699
Abstract
In the crowded and confined space of a cell, numerous proteins work collaboratively in various subsystems, such as metabolic pathways, organelle compartments, and complexes, to regulate cell growth and development [...] Full article
(This article belongs to the Special Issue Ubiquitylation in Plant Developmental and Physiological Processes)

Research

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33 pages, 7632 KiB  
Article
The Arabidopsis Deubiquitylase OTU5 Suppresses Flowering by Histone Modification-Mediated Activation of the Major Flowering Repressors FLC, MAF4, and MAF5
by Ramalingam Radjacommare, Shih-Yun Lin, Raju Usharani, Wen-Dar Lin, Guang-Yuh Jauh, Wolfgang Schmidt and Hongyong Fu
Int. J. Mol. Sci. 2023, 24(7), 6176; https://doi.org/10.3390/ijms24076176 - 24 Mar 2023
Cited by 2 | Viewed by 2733
Abstract
Distinct phylogeny and substrate specificities suggest that 12 Arabidopsis Ovarian Tumor domain-containing (OTU) deubiquitinases participate in conserved or plant-specific functions. The otu5-1 null mutant displayed a pleiotropic phenotype, including early flowering, mimicking that of mutants harboring defects in subunits (e.g., ARP6) of the [...] Read more.
Distinct phylogeny and substrate specificities suggest that 12 Arabidopsis Ovarian Tumor domain-containing (OTU) deubiquitinases participate in conserved or plant-specific functions. The otu5-1 null mutant displayed a pleiotropic phenotype, including early flowering, mimicking that of mutants harboring defects in subunits (e.g., ARP6) of the SWR1 complex (SWR1c) involved in histone H2A.Z deposition. Transcriptome and RT-qPCR analyses suggest that downregulated FLC and MAF4-5 are responsible for the early flowering of otu5-1. qChIP analyses revealed a reduction and increase in activating and repressive histone marks, respectively, on FLC and MAF4-5 in otu5-1. Subcellular fractionation, GFP-fusion expression, and MNase treatment of chromatin showed that OTU5 is nucleus-enriched and chromatin-associated. Moreover, OTU5 was found to be associated with FLC and MAF4-5. The OTU5-associated protein complex(es) appears to be distinct from SWR1c, as the molecular weights of OTU5 complex(es) were unaltered in arp6-1 plants. Furthermore, the otu5-1 arp6-1 double mutant exhibited synergistic phenotypes, and H2A.Z levels on FLC/MAF4-5 were reduced in arp6-1 but not otu5-1. Our results support the proposition that Arabidopsis OTU5, acting independently of SWR1c, suppresses flowering by activating FLC and MAF4-5 through histone modification. Double-mutant analyses also indicate that OTU5 acts independently of the HUB1-mediated pathway, but it is partially required for FLC-mediated flowering suppression in autonomous pathway mutants and FRIGIDA-Col. Full article
(This article belongs to the Special Issue Ubiquitylation in Plant Developmental and Physiological Processes)
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15 pages, 16983 KiB  
Article
Endosomally Localized RGLG-Type E3 RING-Finger Ligases Modulate Sorting of Ubiquitylation-Mimic PIN2
by Katarzyna Retzer, Jeanette Moulinier-Anzola, Rebecca Lugsteiner, Nataliia Konstantinova, Maximilian Schwihla, Barbara Korbei and Christian Luschnig
Int. J. Mol. Sci. 2022, 23(12), 6767; https://doi.org/10.3390/ijms23126767 - 17 Jun 2022
Cited by 3 | Viewed by 2150
Abstract
Intracellular sorting and the abundance of sessile plant plasma membrane proteins are imperative for sensing and responding to environmental inputs. A key determinant for inducing adjustments in protein localization and hence functionality is their reversible covalent modification by the small protein modifier ubiquitin, [...] Read more.
Intracellular sorting and the abundance of sessile plant plasma membrane proteins are imperative for sensing and responding to environmental inputs. A key determinant for inducing adjustments in protein localization and hence functionality is their reversible covalent modification by the small protein modifier ubiquitin, which is for example responsible for guiding proteins from the plasma membrane to endosomal compartments. This mode of membrane protein sorting control requires the catalytic activity of E3 ubiquitin ligases, amongst which members of the RING DOMAIN LIGASE (RGLG) family have been implicated in the formation of lysine 63-linked polyubiquitin chains, serving as a prime signal for endocytic vacuolar cargo sorting. Nevertheless, except from some indirect implications for such RGLG activity, no further evidence for their role in plasma membrane protein sorting has been provided so far. Here, by employing RGLG1 reporter proteins combined with assessment of plasma membrane protein localization in a rglg1 rglg2 loss-of-function mutant, we demonstrate a role for RGLGs in cargo trafficking between plasma membrane and endosomal compartments. Specifically, our findings unveil a requirement for RGLG1 association with endosomal sorting compartments for fundamental aspects of plant morphogenesis, underlining a vital importance for ubiquitylation-controlled intracellular sorting processes. Full article
(This article belongs to the Special Issue Ubiquitylation in Plant Developmental and Physiological Processes)
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Review

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24 pages, 2897 KiB  
Review
To Kill or to Be Killed: How Does the Battle between the UPS and Autophagy Maintain the Intracellular Homeostasis in Eukaryotes?
by Peifeng Yu and Zhihua Hua
Int. J. Mol. Sci. 2023, 24(3), 2221; https://doi.org/10.3390/ijms24032221 - 22 Jan 2023
Cited by 3 | Viewed by 2880
Abstract
The ubiquitin-26S proteasome system and autophagy are two major protein degradation machineries encoded in all eukaryotic organisms. While the UPS is responsible for the turnover of short-lived and/or soluble misfolded proteins under normal growth conditions, the autophagy-lysosomal/vacuolar protein degradation machinery is activated under [...] Read more.
The ubiquitin-26S proteasome system and autophagy are two major protein degradation machineries encoded in all eukaryotic organisms. While the UPS is responsible for the turnover of short-lived and/or soluble misfolded proteins under normal growth conditions, the autophagy-lysosomal/vacuolar protein degradation machinery is activated under stress conditions to remove long-lived proteins in the forms of aggregates, either soluble or insoluble, in the cytoplasm and damaged organelles. Recent discoveries suggested an integrative function of these two seemly independent systems for maintaining the proteome homeostasis. One such integration is represented by their reciprocal degradation, in which the small 76-amino acid peptide, ubiquitin, plays an important role as the central signaling hub. In this review, we summarized the current knowledge about the activity control of proteasome and autophagosome at their structural organization, biophysical states, and turnover levels from yeast and mammals to plants. Through comprehensive literature studies, we presented puzzling questions that are awaiting to be solved and proposed exciting new research directions that may shed light on the molecular mechanisms underlying the biological function of protein degradation. Full article
(This article belongs to the Special Issue Ubiquitylation in Plant Developmental and Physiological Processes)
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13 pages, 1013 KiB  
Review
The Role of E3 Ubiquitin Ligases in Chloroplast Function
by Katherine A. Hand and Nitzan Shabek
Int. J. Mol. Sci. 2022, 23(17), 9613; https://doi.org/10.3390/ijms23179613 - 25 Aug 2022
Cited by 7 | Viewed by 4017
Abstract
Chloroplasts are ancient organelles responsible for photosynthesis and various biosynthetic functions essential to most life on Earth. Many of these functions require tightly controlled regulatory processes to maintain homeostasis at the protein level. One such regulatory mechanism is the ubiquitin-proteasome system whose fundamental [...] Read more.
Chloroplasts are ancient organelles responsible for photosynthesis and various biosynthetic functions essential to most life on Earth. Many of these functions require tightly controlled regulatory processes to maintain homeostasis at the protein level. One such regulatory mechanism is the ubiquitin-proteasome system whose fundamental role is increasingly emerging in chloroplasts. In particular, the role of E3 ubiquitin ligases as determinants in the ubiquitination and degradation of specific intra-chloroplast proteins. Here, we highlight recent advances in understanding the roles of plant E3 ubiquitin ligases SP1, COP1, PUB4, CHIP, and TT3.1 as well as the ubiquitin-dependent segregase CDC48 in chloroplast function. Full article
(This article belongs to the Special Issue Ubiquitylation in Plant Developmental and Physiological Processes)
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15 pages, 899 KiB  
Review
Ubiquitination of Receptorsomes, Frontline of Plant Immunity
by Yongming Chen, Yingying Song, Jing Liu, Guangyuan Xu and Daolong Dou
Int. J. Mol. Sci. 2022, 23(6), 2937; https://doi.org/10.3390/ijms23062937 - 9 Mar 2022
Cited by 18 | Viewed by 3873
Abstract
Sessile plants are constantly exposed to myriads of unfavorable invading organisms with different lifestyles. To survive, plants have evolved plasma membrane-resident pattern recognition receptors (PRRs) and intracellular nucleotide-binding domain leucine-rich repeat receptors (NLRs) to initiate sophisticated downstream immune responses. Ubiquitination serves as one [...] Read more.
Sessile plants are constantly exposed to myriads of unfavorable invading organisms with different lifestyles. To survive, plants have evolved plasma membrane-resident pattern recognition receptors (PRRs) and intracellular nucleotide-binding domain leucine-rich repeat receptors (NLRs) to initiate sophisticated downstream immune responses. Ubiquitination serves as one of the most important and prevalent posttranslational modifications (PTMs) to fine-tune plant immune responses. Over the last decade, remarkable progress has been made in delineating the critical roles of ubiquitination in plant immunity. In this review, we highlight recent advances in the understanding of ubiquitination in the modulation of plant immunity, with a particular focus on ubiquitination in the regulation of receptorsomes, and discuss how ubiquitination and other PTMs act in concert to ensure rapid, proper, and robust immune responses. Full article
(This article belongs to the Special Issue Ubiquitylation in Plant Developmental and Physiological Processes)
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23 pages, 670 KiB  
Review
How Many Faces Does the Plant U-Box E3 Ligase Have?
by Xinguo Mao, Chunmei Yu, Long Li, Min Wang, Lili Yang, Yining Zhang, Yanfei Zhang, Jingyi Wang, Chaonan Li, Matthew Paul Reynolds and Ruilian Jing
Int. J. Mol. Sci. 2022, 23(4), 2285; https://doi.org/10.3390/ijms23042285 - 18 Feb 2022
Cited by 18 | Viewed by 3651
Abstract
Ubiquitination is a major type of post-translational modification of proteins in eukaryotes. The plant U-Box (PUB) E3 ligase is the smallest family in the E3 ligase superfamily, but plays a variety of essential roles in plant growth, development and response to diverse environmental [...] Read more.
Ubiquitination is a major type of post-translational modification of proteins in eukaryotes. The plant U-Box (PUB) E3 ligase is the smallest family in the E3 ligase superfamily, but plays a variety of essential roles in plant growth, development and response to diverse environmental stresses. Hence, PUBs are potential gene resources for developing climate-resilient crops. However, there is a lack of review of the latest advances to fully understand the powerful gene family. To bridge the gap and facilitate its use in future crop breeding, we comprehensively summarize the recent progress of the PUB family, including gene evolution, classification, biological functions, and multifarious regulatory mechanisms in plants. Full article
(This article belongs to the Special Issue Ubiquitylation in Plant Developmental and Physiological Processes)
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12 pages, 6123 KiB  
Review
Nitric Oxide Signaling and Its Association with Ubiquitin-Mediated Proteasomal Degradation in Plants
by Anjali Pande, Bong-Gyu Mun, Murtaza Khan, Waqas Rahim, Da-Sol Lee, Geun-Mo Lee, Tiba Nazar Ibrahim Al Azawi, Adil Hussain and Byung-Wook Yun
Int. J. Mol. Sci. 2022, 23(3), 1657; https://doi.org/10.3390/ijms23031657 - 31 Jan 2022
Cited by 13 | Viewed by 4038 | Correction
Abstract
Nitric oxide (NO) is a versatile signaling molecule with diverse roles in plant biology. The NO-mediated signaling mechanism includes post-translational modifications (PTMs) of target proteins. There exists a close link between NO-mediated PTMs and the proteasomal degradation of proteins via ubiquitylation. In some [...] Read more.
Nitric oxide (NO) is a versatile signaling molecule with diverse roles in plant biology. The NO-mediated signaling mechanism includes post-translational modifications (PTMs) of target proteins. There exists a close link between NO-mediated PTMs and the proteasomal degradation of proteins via ubiquitylation. In some cases, ubiquitin-mediated proteasomal degradation of target proteins is followed by an NO-mediated post-translational modification on them, while in other cases NO-mediated PTMs can regulate the ubiquitylation of the components of ubiquitin-mediated proteasomal machinery for promoting their activity. Another pathway that links NO signaling with the ubiquitin-mediated degradation of proteins is the N-degron pathway. Overall, these mechanisms reflect an important mechanism of NO signal perception and transduction that reflect a close association of NO signaling with proteasomal degradation via ubiquitylation. Therefore, this review provides insight into those pathways that link NO-PTMs with ubiquitylation. Full article
(This article belongs to the Special Issue Ubiquitylation in Plant Developmental and Physiological Processes)
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11 pages, 873 KiB  
Review
Ubiquitylation of ABA Receptors and Protein Phosphatase 2C Coreceptors to Modulate ABA Signaling and Stress Response
by Alberto Coego, Jose Julian, Jorge Lozano-Juste, Gaston A. Pizzio, Abdulwahed F. Alrefaei and Pedro L. Rodriguez
Int. J. Mol. Sci. 2021, 22(13), 7103; https://doi.org/10.3390/ijms22137103 - 1 Jul 2021
Cited by 18 | Viewed by 4910
Abstract
Post-translational modifications play a fundamental role in regulating protein function and stability. In particular, protein ubiquitylation is a multifaceted modification involved in numerous aspects of plant biology. Landmark studies connected the ATP-dependent ubiquitylation of substrates to their degradation by the 26S proteasome; however, [...] Read more.
Post-translational modifications play a fundamental role in regulating protein function and stability. In particular, protein ubiquitylation is a multifaceted modification involved in numerous aspects of plant biology. Landmark studies connected the ATP-dependent ubiquitylation of substrates to their degradation by the 26S proteasome; however, nonproteolytic functions of the ubiquitin (Ub) code are also crucial to regulate protein interactions, activity, and localization. Regarding proteolytic functions of Ub, Lys-48-linked branched chains are the most common chain type for proteasomal degradation, whereas promotion of endocytosis and vacuolar degradation is triggered through monoubiquitylation or Lys63-linked chains introduced in integral or peripheral plasma membrane proteins. Hormone signaling relies on regulated protein turnover, and specifically the half-life of ABA signaling components is regulated both through the ubiquitin-26S proteasome system and the endocytic/vacuolar degradation pathway. E3 Ub ligases have been reported that target different ABA signaling core components, i.e., ABA receptors, PP2Cs, SnRK2s, and ABFs/ABI5 transcription factors. In this review, we focused specifically on the ubiquitylation of ABA receptors and PP2C coreceptors, as well as other post-translational modifications of ABA receptors (nitration and phosphorylation) that result in their ubiquitination and degradation. Full article
(This article belongs to the Special Issue Ubiquitylation in Plant Developmental and Physiological Processes)
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Other

2 pages, 827 KiB  
Correction
Correction: Pande et al. Nitric Oxide Signaling and Its Association with Ubiquitin-Mediated Proteasomal Degradation in Plants. Int. J. Mol. Sci. 2022, 23, 1657
by Anjali Pande, Bong-Gyu Mun, Murtaza Khan, Waqas Rahim, Da-Sol Lee, Geun-Mo Lee, Tiba Nazar Ibrahim Al Azawi, Adil Hussain and Byung-Wook Yun
Int. J. Mol. Sci. 2022, 23(10), 5628; https://doi.org/10.3390/ijms23105628 - 18 May 2022
Cited by 3 | Viewed by 1530
Abstract
The authors wish to make the following corrections to the original publication [...] Full article
(This article belongs to the Special Issue Ubiquitylation in Plant Developmental and Physiological Processes)
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