Ubiquitination: a tool for plant adaptation to changing environments

Mandal, Arunava; Sharma, Namisha; Muthamilarasan, Mehanathan; Prasad, Manoj

doi:10.1007/s13237-018-0255-6

Cited by 14 publications

(12 citation statements)

References 81 publications

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“…These enzymes bind to ubiquitin and form multimers that attach to proteins, targeting them for degradation by 26S proteasomes. This ubiquitin-proteasome system interacts with key components of plant immunity to positively or negatively regulate resistance to plant pathogens [71]. Genes encoding RING proteins in the E3 ubiquitin pathway were upregulated in Rcr1-mediated clubroot resistance and downregulated in susceptible Arabidopsis following P. brassicae infection [32,72].…”

Section: Protein Degradationmentioning

confidence: 99%

Comparative Transcriptome Analysis of Rutabaga (Brassica napus) Cultivars Indicates Activation of Salicylic Acid and Ethylene-Mediated Defenses in Response to Plasmodiophora brassicae

Zhou

Galindo‐González

Manolii

et al. 2020

IJMS

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Clubroot, caused by Plasmodiophora brassicae Woronin, is an important soilborne disease of Brassica napus L. and other crucifers. To improve understanding of the mechanisms of resistance and pathogenesis in the clubroot pathosystem, the rutabaga (B. napus subsp. rapifera Metzg) cultivars ‘Wilhelmsburger’ (resistant) and ‘Laurentian’ (susceptible) were inoculated with P. brassicae pathotype 3A and their transcriptomes were analyzed at 7, 14, and 21 days after inoculation (dai) by RNA sequencing (RNA-seq). Thousands of transcripts with significant changes in expression were identified in each host at each time-point in inoculated vs. non-inoculated plants. Molecular responses at 7 and 14 dai supported clear differences in the clubroot response mechanisms of the two genotypes. Both the resistant and the susceptible cultivars activated receptor-like protein (RLP) genes, resistance (R) genes, and genes involved in salicylic acid (SA) signaling as clubroot defense mechanisms. In addition, genes related to calcium signaling and genes encoding leucine-rich repeat (LRR) receptor kinases, the respiratory burst oxidase homolog (RBOH) protein, and transcription factors such as WRKYs, ethylene responsive factors, and basic leucine zippers (bZIPs), appeared to be upregulated in ‘Wilhelmsburger’ to restrict P. brassicae development. Some of these genes are essential components of molecular defenses, including ethylene (ET) signaling and the oxidative burst. Our study highlights the importance of activation of genes associated with SA- and ET-mediated responses in the resistant cultivar. A set of candidate genes showing contrasting patterns of expression between the resistant and susceptible cultivars was identified and includes potential targets for further study and validation through approaches such as gene editing.

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Section: Protein Degradationmentioning

confidence: 99%

Comparative Transcriptome Analysis of Rutabaga (Brassica napus) Cultivars Indicates Activation of Salicylic Acid and Ethylene-Mediated Defenses in Response to Plasmodiophora brassicae

Zhou

Galindo‐González

Manolii

et al. 2020

IJMS

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“…Besides, E3-ubiquitin protein ligases were significantly upregulated during salt stress (Figure 11). E3-ubiquitin ligase mediated protein ubiquitination is one of the main posttranslation modification pathways for protein which regulates various intracellular processes such as hormone signaling and stress resistance (Duplan and Rivas, 2014;Shu and Yang, 2017;Mandal et al, 2018;Kelley, 2018). The E3-ubiquitin ligases are known to regulate salt stress by participating in SOS pathway, MAPK Cascade, ABA signaling pathway, flowering pathway and ROS homeostasis (Wang et al, 2022).…”

Section: ; Jimenezmentioning

confidence: 99%

Transcriptome profiling revealed salt stress-responsive genes in Lilium pumilum bulbs

Pak

Sun

et al. 2022

Front. Plant Sci.

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Lilium pumilum is an important ornamental, culinary and medicinal bulbous plants with salt tolerance. However, salt tolerance of lily, particularly the bulb, has been studied relatively little, which brings challenges to the cultivation of lily varieties with high salt tolerance. Here, we performed transcriptome sequencing on the bulb organs of L. pumilum under salt stress treatment, analyzed differential gene expressed levels and then identified several key genes associated with salt stress tolerance at genome-wide scale. For the first time, we revealed the obvious response against salt stress for L. pumilum bulb organs, while distinct from those for root organs. Several key genes obtained through transcriptome analysis and DEG screening include NF-YB3 transcription factor, metallothionein type 2 protein, vicilin like seed storage protein and bidirectional sugar transporter SWEET14. Rather than typical ROS scavengers like superoxide dismutase, peroxidase, and glutathione transferase, non-typical ROS scavengers such as the metallothionein type 2 protein, and vicilin like seed storage protein were upregulated in our work. The bidirectional sugar transporter SWEET14 protein and the hormone signaling proteins such as E3-ubiquitin protein ligases, PYL4 and protein phosphatase 2C were also upregulated, suggesting the role of sugars and hormones in the bulb organ responses to salt stress. Co-expression analysis of the DEGs further confirmed that NF-YB3 transcription factor acted as a hub gene, suggesting that salt stress can promote flowering of L. pumilum. Taken together, we identified important candidate genes associated with salt tolerance of the L. pumilum bulb organs, which may provide the excellent basis for further in-depth salt tolerance mechanisms of the lily bulbs.

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“…Ubiquitination modifications include conventional ubiquitination modification (with ubiquitin as the substrate) and SUMO-type ubiquitination modification (with the ubiquitin-like SUMO molecule as the substrate) ( Zhou and Zeng, 2017 ). Conventional ubiquitination typically involves defined steps: (1) first, E1 ubiquitin activase (UBA) activates ubiquitin in the presence of ATP, allowing the cysteine residues of UBA to form the thioester-linked intermediate E1-ubiquitin (E1-Ub) ( Mandal et al, 2018 ); (2) subsequently, the E2 ubiquitin-binding enzyme (UBC) interacts with UAB-Ub and transfers activated Ub to an active cysteine residue of UBC to form a thioester-linked UBC-Ub intermediate ( Mandal et al, 2018 ); (3) finally, the ubiquitin ligase (E3) interacts with the target protein and E2-Ub to create an isopeptide bond between the C-terminal glycine residue and the lysine residue of Ub. The establishment of an isopeptide bond between this glycine residue and the lysine residue of the target protein results in the transfer of Ub to the target protein by ubiquitin ligase (E3) ( Mandal et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

“…Conventional ubiquitination typically involves defined steps: (1) first, E1 ubiquitin activase (UBA) activates ubiquitin in the presence of ATP, allowing the cysteine residues of UBA to form the thioester-linked intermediate E1-ubiquitin (E1-Ub) ( Mandal et al, 2018 ); (2) subsequently, the E2 ubiquitin-binding enzyme (UBC) interacts with UAB-Ub and transfers activated Ub to an active cysteine residue of UBC to form a thioester-linked UBC-Ub intermediate ( Mandal et al, 2018 ); (3) finally, the ubiquitin ligase (E3) interacts with the target protein and E2-Ub to create an isopeptide bond between the C-terminal glycine residue and the lysine residue of Ub. The establishment of an isopeptide bond between this glycine residue and the lysine residue of the target protein results in the transfer of Ub to the target protein by ubiquitin ligase (E3) ( Mandal et al, 2018 ). The ubiquitination modification system includes a large protein family, with ∼10 E1 ubiquitin activating enzymes, ∼50 E2 ubiquitin conjugating enzymes, and ∼400 E3 ubiquitin ligases in plants ( Richard, 2009 ).…”

Section: Introductionmentioning

confidence: 99%

“…Among them, E3 ubiquitin ligase is the most abundant, and it also influences ubiquitinated substrate diversity ( Rennie et al, 2020 ). The numerous substrate-selective E3 ubiquitin ligases are mainly classified into RING-finger, HECT, and U-box structural domain classes ( Mandal et al, 2018 ). Due to their specific non-spontaneous ubiquitination activity and their ability to participate in the degradation of unfolded or misfolded proteins upon activation by cofactors, U-box-like proteins are important, but they are complex and more difficult to control than other E3 ubiquitin ligases.…”

Section: Introductionmentioning

confidence: 99%

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Identification, characterization, and expression profiling of the putative U-box E3 ubiquitin ligase gene family in Sorghum bicolor

Fang

Yang

et al. 2022

Front. Microbiol.

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The U-box family is one of the main E3 ubiquitin ligase families in plants. The U-box family has been characterized in several species. However, genome-wide gene identification and expression profiling of the U-box family in response to abiotic stress in Sorghum bicolor remain unclear. In this study, we broadly identified 68 U-box genes in the sorghum genome, including 2 CHIP genes, and 1 typical UFD2 (Ub fusion degradation 2) gene. The U-box gene family was divided into eight subclasses based on homology and conserved domain characteristics. Evolutionary analysis identified 14, 66, and 82 U-box collinear gene pairs in sorghum compared with arabidopsis, rice, and maize, respectively, and a unique tandem repeat pair (SbPUB26/SbPUB27) is present in the sorghum genome. Gene Ontology (GO) enrichment analysis showed that U-box proteins were mainly related to ubiquitination and modification, and various stress responses. Comprehensive analysis of promoters, expression profiling, and gene co-regulation networks also revealed that many sorghum U-box genes may be correlated with multiple stress responses. In summary, our results showed that sorghum contains 68 U-box genes, which may be involved in multiple abiotic stress responses. The findings will support future gene functional studies related to ubiquitination in sorghum.

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Ubiquitination: a tool for plant adaptation to changing environments

Cited by 14 publications

References 81 publications

Comparative Transcriptome Analysis of Rutabaga (Brassica napus) Cultivars Indicates Activation of Salicylic Acid and Ethylene-Mediated Defenses in Response to Plasmodiophora brassicae

Comparative Transcriptome Analysis of Rutabaga (Brassica napus) Cultivars Indicates Activation of Salicylic Acid and Ethylene-Mediated Defenses in Response to Plasmodiophora brassicae

Transcriptome profiling revealed salt stress-responsive genes in Lilium pumilum bulbs

Identification, characterization, and expression profiling of the putative U-box E3 ubiquitin ligase gene family in Sorghum bicolor

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