Special Issue: Ubiquitination and Sumoylation   

January 2013, Volume 55 Issue 1, Pages 2C120.

Cover Caption: Ubiquitination and Sumoylation
About the cover: This Special Issue focuses on protein ubiquitination and Sumoylation in plants. On the cover, we have used a cartoon of a Japanese sumo wrestler to represent Small Ubiquitin-like Modifier (SUMO) proteins, which are the same proteins in Sumoylation. The box has F-BOX printed on it, which is a reference to the F-box proteins in ubiquitination. Likewise, the golden ring refers to RING finger proteins (cover design by Qi Xie and Ying Wang).


First Issue of 2013: What's New for JIPB  
Author: Chun-Ming Liu
Journal of Integrative Plant Biology 2013 55(1): 2-4
Published Online: January 21, 2013
DOI: 10.1111/jipb.12023

It is no exaggeration to say that 2012 was an eventful year. China has a new president, Xi Jinping, and the US re-elected Barack Obama. Gmail was ranked as the world's number one email service, and astronomers measured light from the universe's first stars. JIPB has also undergone great transformative changes as we move forward into the new year.

Abstract (Browse 1272)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
The Ever Expanding Role of Ubiquitin and SUMO in Plant Biology  
Author: Giovanna Serino and Qi Xie
Journal of Integrative Plant Biology 2013 55(1): 5-6
Published Online: January 21, 2013
DOI: 10.1111/jipb.12020

When it was discovered in the 1970s as a ubiquitous protein, ubiquitin, a 76-aminoacid peptide, had no assigned function. It was not until later that ubiquitin was found to be a necessary cofactor in a vital cellular process: the degradation of proteins. Work by Avram Hershko, Aaron Ciechanover, and Irwin Rose (for which they received the 2004 Nobel Prize in Chemistry) showed that the covalent attachment of ubiquitin provide proteins with a tag that dispatches them to the proteasome, the main cell degradation machinery.

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          Invited Expert Reviews
Emerging Role of the Ubiquitin Proteasome System in the Control of Shoot Apical Meristem Function  
Author: Elisabetta Di Giacomo, Giovanna Serino and Giovanna Frugis
Journal of Integrative Plant Biology 2013 55(1): 7-20
Published Online: January 21, 2013
DOI: 10.1111/jipb.12010

The shoot apical meristem (SAM) is a population of undifferentiated cells at the tip of the shoot axis that establishes early during plant embryogenesis and gives rise to all shoot organs throughout the plant's life. A plethora of different families of transcription factors (TFs) play a key role in establishing the equilibrium between cell differentiation and stem cell maintenance in the SAM. Fine tuning of these regulatory proteins is crucial for a proper and fast SAM response to environmental and hormonal cues, and for development progression. One effective way to rapidly inactivate TFs involves regulated proteolysis by the ubiquitin/26S proteasome system (UPS). However, a possible role of UPS-dependent protein degradation in the regulation of key SAM TFs has not been thoroughly investigated. Here, we summarize recent evidence supporting a role for the UPS in SAM maintenance and function. We integrate this survey with an in silico analysis of publicly-available microarray databases which identified ubiquitin ligases that are expressed in specific areas within the SAM, suggesting that they may regulate or act downstream of meristem-specific factors.

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Cullin-RING Ubiquitin Ligase Family in Plant Abiotic Stress Pathways  
Author: Liquan Guo, Cynthia D. Nezames, Lianxi Sheng, Xingwang Deng and Ning Wei
Journal of Integrative Plant Biology 2013 55(1): 21-30
Published Online: January 21, 2013
DOI: 10.1111/jipb.12019

The ubiquitin-proteasome system is a key mechanism that plants use to generate adaptive responses in coping with various environmental stresses. Cullin-RING (CRL) complexes represent a predominant group of ubiquitin E3 ligases in this system. In this review, we focus on the CRL E3s that have been implicated in abiotic stress signaling pathways in Arabidopsis. By comparing and analyzing these cases, we hope to gain a better understanding on how CRL complexes work under various settings in an attempt to decipher the clues about the regulatory mechanism of CRL E3s.

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New Role for an Old Rule: N-end Rule-Mediated Degradation of Ethylene Responsive Factor Proteins Governs Low Oxygen Response in Plants  
Author: Francesco Licausi, Chiara Pucciariello and Pierdomenico Perata
Journal of Integrative Plant Biology 2013 55(1): 31-39
Published Online: January 21, 2013
DOI: 10.1111/jipb.12011

The N-end rule pathway regulates protein degradation, which depends on exposed N-terminal sequences in prokaryotes and eukaryotes. In plants, conserved and specific enzymes stimulate selective proteolysis. Although a number of developmental and growth phenotypes have been reported for mutants in the N-end rule, its function has remained unrelated to specific physiological pathways. The first report of the direct involvement of the N-end rule in stress responses focused on hypoxic signaling and how the oxygen-dependent oxidation of cystein promotes the N-end rule-mediated degradation of ethylene responsive factor (ERF)-VII proteins, the master regulators of anaerobic responses. It has been suggested that plants have evolved specific mechanisms to tune ERF-VII availability in the nucleus. In this review, we speculate that ERF-VII proteins are reversibly protected from degradation via membrane sequestration. The oxidative response in plants subjected to anoxic conditions suggests that reactive oxygen and nitrogen species (reactive oxygen species and reactive nitrogen species) may interact or interfere with the N-end rule pathway-mediated response to hypoxia.

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Roles of Ubiquitination in the Control of Phosphate Starvation Responses in Plants  
Author: Mónica Rojas-Triana, Regla Bustos, Ana Espinosa-Ruiz, Salomé Prat, Javier Paz-Ares and Vicente Rubio
Journal of Integrative Plant Biology 2013 55(1): 40-53
Published Online: January 21, 2013
DOI: 10.1111/jipb.12017

Throughout evolution, plants have evolved sophisticated adaptive responses that allow them to grow with a limited supply of phosphate, the preferential form in which the essential macronutrient phosphorus is absorbed by plants. Most of these responses are aimed to increase phosphate availability and acquisition through the roots, to optimize its usage in metabolic processes, and to protect plants from the deleterious effects of phosphate deficiency stress. Regulation of these adaptive responses requires fine perception of the external and internal phosphate levels, and a complex signal transduction pathway that integrates information on the phosphate status at the whole-plant scale. The molecular mechanisms that participate in phosphate homeostasis include transcriptional control of gene expression, RNA silencing mediated by microRNAs, regulatory non-coding RNAs of miRNA activity, phosphate transporter trafficking, and post-translational modification of proteins, such as phosphorylation, sumoylation and ubiquitination. Such a varied regulatory repertoire reflects the complexity intrinsic to phosphate surveying and signaling pathways. Here, we describe these regulatory mechanisms, emphasizing the increasing importance of ubiquitination in the control of phosphate starvation responses.

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Non-26S Proteasome Proteolytic Role of Ubiquitin in Plant Endocytosis and Endosomal Trafficking  
Author: Miaomiao Tian and Qi Xie
Journal of Integrative Plant Biology 2013 55(1): 54-63
Published Online: January 21, 2013
DOI: 10.1111/jipb.12007

The 76 amino acid protein ubiquitin (Ub) is highly conserved in all eukaryotic species. It plays important roles in many cellular processes by covalently attaching to the target proteins. The best known function of Ub is marking substrate proteins for degradation by the 26S proteasome. In fact, other consequences of ubiquitination have been discovered in yeast and mammals, such as membrane trafficking, DNA repair, chromatin modification, and protein kinase activation. The common mechanism underlying these processes is that Ub serves as a signal to sort proteins to the vacuoles or lysosomes for degradation as opposed to 26S proteasome-dependent degradation. To date, several reports have indicated that a similar function of Ub also exists in plants. This review focuses on a summary and analysis of the recent research progress on Ub acting as a signal to mediate endocytosis and endosomal trafficking in plants.

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          Research Articles
The Arabidopsis Anaphase-Promoting Complex/Cyclosome Subunit 1 is Critical for Both Female Gametogenesis and Embryogenesis  
Author: Yanbing Wang, Yingnan Hou, Hongya Gu, Dingming Kang, Zhang-Liang Chen, Jingjing Liu and Li-Jia Qu
Journal of Integrative Plant Biology 2013 55(1): 64-74
Published Online: January 21, 2013
DOI: 10.1111/jipb.12018

Anaphase-promoting complex/cyclosome (APC/C), a multisubunit E3 ligase, plays a critical role in cell cycle control, but the functional characterization of each subunit has not yet been completed. To investigate the function of APC1 in Arabidopsis, we analyzed four mutant alleles of APC1, and found that mutation in APC1 resulted in significantly reduced plant fertility, accumulation of cyclin B, and disrupted auxin distribution in embryos. The three mutant alleles apc1–1, apc1–2 and apc1–3 shared variable defects in female gametogenesis including degradation, abnormal nuclear number, and disrupted polarity of nuclei in the embryo sac as well as in embryogenesis, in which embryos were arrested at multiple stages. All of these defects are similar to those previously identified in apc4. The mutant apc1–4, in which the T-DNA was inserted after the transmembrane domain at the C-terminus, showed much more severe phenotypes; that is, most of the ovules were arrested at the one-nucleate female gametophyte stage (stage FG1). In the apc1 apc4 double mutants, the fertility was further reduced by one-third in apc1–1/+ apc4–1/+, and in some cases no ovules even survived in siliques of apc1–4/+ apc4–1/+. Our data thus suggest that APC1, an essential component of APC/C, plays a synergistic role with APC4 both in female gametogenesis and in embryogenesis.

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Small Ubiquitin-Like Modifier Conjugating Enzyme with Active Site Mutation Acts as Dominant Negative Inhibitor of SUMO Conjugation in Arabidopsis  
Author: Konstantin Tomanov, Christian Hardtke, Ruchika Budhiraja, Rebecca Hermkes, George Coupland and Andreas Bachmair
Journal of Integrative Plant Biology 2013 55(1): 75-82
Published Online: January 21, 2013
DOI: 10.1111/jipb.12016

Small ubiquitin-like modifier (SUMO) conjugation affects a broad range of processes in plants, including growth, flower initiation, pathogen defense, and responses to abiotic stress. Here, we investigate in vivo and in vitro a SUMO conjugating enzyme with a Cys to Ser change in the active site, and show that it has a dominant negative effect. In planta expression significantly perturbs normal development, leading to growth retardation, early flowering and gene expression changes. We suggest that the mutant protein can serve as a probe to investigate sumoylation, also in plants for which poor genetic infrastructure precludes analysis via loss-of-function mutants.

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SUMO E3 Ligase AtMMS21 Regulates Drought Tolerance in Arabidopsis thaliana  
Author: Shengchun Zhang, Yanli Qi, Ming Liu and Chengwei Yang
Journal of Integrative Plant Biology 2013 55(1): 83-95
Published Online: January 21, 2013
DOI: 10.1111/jipb.12024

Post-translational modifications of proteins by small ubiquitin-like modifiers (SUMOs) play crucial roles in plant growth and development, and in stress responses. The MMS21 is a newly-identified Arabidopsis thaliana L. SUMO E3 ligase gene aside from the SIZ1, and its function requires further elucidation. Here, we show that MMS21 deficient plants display improved drought tolerance, and constitutive expression of MMS21 reduces drought tolerance. The expression of MMS21 was reduced by abscisic acid (ABA), polyethylene glycol (PEG) or drought stress. Under drought conditions, mms21 mutants showed the highest survival rate and the slowest water loss, and accumulated a higher level of free proline compared to wild-type (WT) and MMS21 over-expression plants. Stomatal aperture, seed germination and cotyledon greening analysis indicated that mms21 was hypersensitive to ABA. Molecular genetic analysis revealed that MMS21 deficiency led to elevated expression of a series of ABA-mediated stress-responsive genes, including COR15A, RD22, and P5CS1 The ABA and drought-induced stress-responsive genes, including RAB18, RD29A and RD29B, were inhibited by constitutive expression of MMS21. Moreover, ABA-induced accumulation of SUMO-protein conjugates was blocked in the mms21 mutant. We thus conclude that MMS21 plays a role in the drought stress response, likely through regulation of gene expression in an ABA-dependent pathway.

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Identification of SUMO Targets by a Novel Proteomic Approach in Plants  
Author: Gema López-Torrejón, Davide Guerra, Rafael Catalá, Julio Salinas and Juan C. del Pozo
Journal of Integrative Plant Biology 2013 55(1): 96-107
Published Online: January 21, 2013
DOI: 10.1111/jipb.12012

Post-translational modifications (PTMs) chemically and physically alter the properties of proteins, including their folding, subcellular localization, stability, activity, and consequently their function. In spite of their relevance, studies on PTMs in plants are still limited. Small Ubiquitin-like Modifier (SUMO) modification regulates several biological processes by affecting protein-protein interactions, or changing the subcellular localizations of the target proteins. Here, we describe a novel proteomic approach to identify SUMO targets that combines 2-D liquid chromatography, immunodetection, and mass spectrometry (MS) analyses. We have applied this approach to identify nuclear SUMO targets in response to heat shock. Using a bacterial SUMOylation system, we validated that some of the targets identified here are, in fact, labeled with SUMO1. Interestingly, we found that GIGANTEA (GI), a photoperiodic-pathway protein, is modified with SUMO in response to heat shock both in vitro and in vivo.

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Arabidopsis RING Peroxins are E3 Ubiquitin Ligases that Interact with Two Homologous Ubiquitin Receptor Proteins  
Author: Navneet Kaur, Qingzhen Zhao, Qi Xie and Jianping Hu
Journal of Integrative Plant Biology 2013 55(1): 108-120
Published Online: January 21, 2013
DOI: 10.1111/jipb.12014

Peroxisomes are essential eukaryotic organelles that mediate various metabolic processes. Peroxisome import depends on a group of peroxisome biogenesis factors called peroxins, many of which are evolutionarily conserved. PEX2, PEX10, and PEX12 are three RING-finger-domain-containing integral membrane peroxins crucial for protein import. In yeast (Saccharomyces cerevisae), RING peroxins act as E3 ligases, facilitating the recycling of the peroxisome import receptor protein PEX5 through ubiquitination. In plants, RING peroxins are essential to plant vitality. To elucidate the mode of action of the plant RING peroxins, we employed in vitro assays to show that the Arabidopsis RING peroxins also have E3 ligase activities. We also identified a PEX2-interacting protein, DSK2b, which is a member of the ubiquitin receptor family known to function as shuttle factors ferrying polyubiquitinated substrates to the proteasome for degradation. DSK2b and its tandem duplicate DSK2a are localized in the cytosol and the nucleus, and both interact with the RING domain of PEX2 and PEX12. DSK2 artificial microRNA lines did not display obvious defects in plant growth or peroxisomal processes, indicating functional redundancies among Arabidopsis ubiquitin receptor proteins. Our results suggest that Arabidopsis RING peroxins can function as E3 ligases and act together with the ubiquitin receptor protein DSK2 in the peroxisomal membrane-associated protein degradation system.

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