International Journal of Molecular Sciences

Editorial

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5 pages, 211 KiB

Open AccessEditorial

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 1416

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

Open AccessArticle

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 1 | Viewed by 2403

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

Open AccessArticle

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 1904

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

Open AccessReview

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 2524

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

Open AccessReview

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 3583

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

Open AccessReview

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 16 | Viewed by 3453

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

Open AccessReview

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 12 | Viewed by 3287

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

Open AccessReview

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 12 | Viewed by 3667 | 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

Open AccessReview

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 16 | Viewed by 4521

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

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2 pages, 827 KiB

Open AccessCorrection

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 1371

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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