Root Membrane Ubiquitinome under Short-Term Osmotic Stress

Berger, Nathalie; Demolombe, Vincent; Hem, Sonia; Rofidal, Valérie; Steinmann, Laura; Krouk, Gabriel; Crabos, Amandine; Nacry, Philippe; Verdoucq, Lionel; Santoni, Véronique

doi:10.3390/ijms23041956

Cited by 9 publications

(4 citation statements)

References 58 publications

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“…Most diUb cleavage profiles included Lys6, Lys11, Lys48, and Lys63 preferences, which are reminiscent of those seen in bacterial OTU enzymes (Schubert et al, 2020). The seven Lys residues of ubiquitin are conserved among all eukaryotes, and indeed, linkages through all Lys residues coexist in humans, yeast, and Arabidopsis (Peng et al, 2003;Xu et al, 2009;Berger et al, 2022). The only chain types previously detected in Toxoplasma are Lys11-, Lys48-, and Lys63-linked polyubiquitin chains (Dhara & Sinai, 2016).…”

Section: Discussionmentioning

confidence: 84%

Characterisation of the OTU domain deubiquitinase complement ofToxoplasma gondii

et al. 2023

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The phylum Apicomplexa contains several parasitic species of medical and agricultural importance. The ubiquitination machinery remains, for the most part, uncharacterised in apicomplexan parasites, despite the important roles that it plays in eukaryotic biology. Bioinformatic analysis of the ubiquitination machinery in apicomplexan parasites revealed an expanded ovarian tumour domain–containing (OTU) deubiquitinase (DUB) family inToxoplasma, potentially reflecting functional importance in apicomplexan parasites. This study presents comprehensive characterisation ofToxoplasmaOTU DUBs. AlphaFold-guided structural analysis not only confirmed functional orthologues found across eukaryotes, but also identified apicomplexan-specific enzymes, subsequently enabling discovery of a cryptic OTU DUB inPlasmodiumspecies. Comprehensive biochemical characterisation of 11ToxoplasmaOTU DUBs revealed activity against ubiquitin- and NEDD8-based substrates and revealed ubiquitin linkage preferences for Lys6-, Lys11-, Lys48-, and Lys63-linked chain types. We show that accessory domains inToxoplasmaOTU DUBs impose linkage preferences, and in case of apicomplexan-specific TgOTU9, we discover a cryptic ubiquitin-binding domain that is essential for TgOTU9 activity. Using the auxin-inducible degron (AID) to generate knockdown parasite lines, TgOTUD6B was found to be important forToxoplasmagrowth.

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Section: Discussionmentioning

confidence: 84%

Characterisation of the OTU domain deubiquitinase complement ofToxoplasma gondii

et al. 2023

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“…For the MDHs (Table 2), the predicted S-palmitoylation may guide the proteins to the PM. Other post-translational modifications, e.g., ubiquitination, alter the abundances of proteins via proteasomal degradation, which was shown for Na + /K + -ATPase under hypoxia in eukaryotic cell lines [148] and Arabidopsis root microsomes under osmotic stress [149]. An effect of hypoxia on decreased protein degradation also seems possible.…”

Section: Transcriptome To Proteome Regulationmentioning

confidence: 89%

Hypoxia-Induced Aquaporins and Regulation of Redox Homeostasis by a Trans-Plasma Membrane Electron Transport System in Maize Roots

2022

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In plants, flooding-induced oxygen deficiency causes severe stress, leading to growth reduction and yield loss. It is therefore important to understand the molecular mechanisms for adaptation to hypoxia. Aquaporins at the plasma membrane play a crucial role in water uptake. However, their role during hypoxia and membrane redox changes is still not fully understood. The influence of 24 h hypoxia induction on hydroponically grown maize (Zea mays L.) was investigated using an oil-based setup. Analyses of physiological parameters revealed typical flooding symptoms such as increased ethylene and H2O2 levels, an increased alcohol dehydrogenase activity, and an increased redox activity at the plasma membrane along with decreased oxygen of the medium. Transcriptomic analysis and shotgun proteomics of plasma membranes and soluble fractions were performed to determine alterations in maize roots. RNA-sequencing data confirmed the upregulation of genes involved in anaerobic metabolism, biosynthesis of the phytohormone ethylene, and its receptors. Transcripts of several antioxidative systems and other oxidoreductases were regulated. Mass spectrometry analysis of the plasma membrane proteome revealed alterations in redox systems and an increased abundance of aquaporins. Here, we discuss the importance of plasma membrane aquaporins and redox systems in hypoxia stress response, including the regulation of plant growth and redox homeostasis.

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“…For LC-MS/MS analysis, ubiquitinated peptides of pomelo juice sacs were conducted as previously studied [45]. The ubiquitinated peptides dissolved into solvent A (0.1% formic acid, 2% acetonitrile) and the peptides were separated by gradient in 8% -80% solvent B (0.1% formic acid, 90% acetonitrile).…”

Section: Lc-ms/ms Analysismentioning

confidence: 99%

A multilevel investigation to reveal the regulatory mechanism of lignin accumulation in juice sac granulation of pomelo

LIU,

Chen,

et al. 2024

Preprint

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Granulation of juice sacs is a physiological disorder, which affects pomelo fruit quality. Here, the transcriptome and ubiquitinome of the granulated juice sacs were analyzed in Guanxi pomelo. We found that lignin accumulation in the granulated juice sacs was regulated at transcription and protein modification levels. In transcriptome data, we found that the genes in lignin biosynthesis pathway and antioxidant enzyme system of the granulated juice sacs were significantly up-regulated. However, in ubiquitinome data, we found that ubiquitinated antioxidant enzymes increased in abundance but the enzyme activities decreased after the modification, which gave rise to reactive oxygen species (ROS) contents in granulated juice sacs. This finding suggests that ubiquitination level of the antioxidant enzymes is negatively correlated with the enzyme activities. Increased H2O2 is considered to be a signalling molecule to activate the key gene expressions in lignin biosynthesis pathway, which leads to the lignification in granulated juice sacs of pomelo. This regulatory mechanism in juice sac granulation of pomelo was further confirmed through the verification experiment using tissue culture by adding H2O2 or dimethylthiourea (DMTU). Our findings suggest that scavenging H2O2 and other ROS are important for reducing lignin accumulation, alleviating juice sac granulation and improving pomelo fruit quality.

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Root Membrane Ubiquitinome under Short-Term Osmotic Stress

Cited by 9 publications

References 58 publications

Characterisation of the OTU domain deubiquitinase complement ofToxoplasma gondii

Characterisation of the OTU domain deubiquitinase complement ofToxoplasma gondii

Hypoxia-Induced Aquaporins and Regulation of Redox Homeostasis by a Trans-Plasma Membrane Electron Transport System in Maize Roots

A multilevel investigation to reveal the regulatory mechanism of lignin accumulation in juice sac granulation of pomelo

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