scholarly journals Root membrane ubiquitinome under short-term osmotic stress

2021 ◽  
Author(s):  
Nathalie Berger ◽  
Vincent Demolombe ◽  
Sonia Hem ◽  
Valérie Rofidal ◽  
Laura Steinmann ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Osmotic Stress ◽  
High Resolution Mass Spectrometry ◽  
Primary Root ◽  
In Silico Analysis ◽  
Post Translational Modification ◽  
Positive Role ◽  
Protein Ubiquitination ◽  
Cargo Proteins ◽  
Osmotic Treatment

Osmotic stress can be detrimental to plants, whose survival relies heavily on proteomic plasticity. Protein ubiquitination is a central post-translational modification in osmotic mediated stress. Plants use the ubiquitin (Ub) proteasome system to modulate protein content, and a role for Ub in mediating endocytosis and trafficking plant plasma membrane proteins has recently emerged. In this study, we used the K-ε-GG antibody enrichment method integrated with high-resolution mass spectrometry to compile a list of 719 ubiquitinated lysine (K-Ub) residues from 450 Arabidopsis root membrane proteins (58% of which are transmembrane proteins), thereby adding to the database of ubiquitinated substrates in plants. Although no Ub motifs could be identified, the presence of acidic residues close to K-Ub was revealed. Our ubiquitinome analysis pointed to a broad role of ubiquitination in the internalization and sorting of cargo proteins. Moreover, the simultaneous proteome and ubiquitinome quantification showed that ubiquitination is mostly not involved in membrane protein degradation in response to short osmotic treatment, but putatively in protein internalization as described for the aquaporin PIP2;1. Our in silico analysis of ubiquitinated proteins shows that two E2 Ub ligases, UBC32 and UBC34, putatively target membrane proteins under osmotic stress. Finally, we revealed a positive role for UBC32 and UBC34 in primary root growth under osmotic stress.

Towards Computational Models of Identifying Protein Ubiquitination Sites

2019 ◽  
Vol 20 (5) ◽  
pp. 565-578 ◽  
Author(s):  
Lidong Wang ◽  
Ruijun Zhang
Keyword(s):  
Computational Methods ◽  
Computational Models ◽  
Feature Representation ◽  
Biological Sequence ◽  
Post Translational Modification ◽  
Test Dataset ◽  
Protein Ubiquitination ◽  
Protein Functions ◽  
Independent Test Dataset ◽  
Benchmark Datasets

Ubiquitination is an important post-translational modification (PTM) process for the regulation of protein functions, which is associated with cancer, cardiovascular and other diseases. Recent initiatives have focused on the detection of potential ubiquitination sites with the aid of physicochemical test approaches in conjunction with the application of computational methods. The identification of ubiquitination sites using laboratory tests is especially susceptible to the temporality and reversibility of the ubiquitination processes, and is also costly and time-consuming. It has been demonstrated that computational methods are effective in extracting potential rules or inferences from biological sequence collections. Up to the present, the computational strategy has been one of the critical research approaches that have been applied for the identification of ubiquitination sites, and currently, there are numerous state-of-the-art computational methods that have been developed from machine learning and statistical analysis to undertake such work. In the present study, the construction of benchmark datasets is summarized, together with feature representation methods, feature selection approaches and the classifiers involved in several previous publications. In an attempt to explore pertinent development trends for the identification of ubiquitination sites, an independent test dataset was constructed and the predicting results obtained from five prediction tools are reported here, together with some related discussions.

scholarly journals The Arabidopsis TETRATRICOPEPTIDE THIOREDOXIN-LIKE 1 Gene Is Involved in Anisotropic Root Growth during Osmotic Stress Adaptation

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 236
Author(s):  
María Belén Cuadrado-Pedetti ◽  
Inés Rauschert ◽  
María Martha Sainz ◽  
Vítor Amorim-Silva ◽  
Miguel Angel Botella ◽  
...  
Keyword(s):  
Osmotic Stress ◽  
Root Growth ◽  
Cell Walls ◽  
Primary Root ◽  
Stress Adaptation ◽  
Elongation Zone ◽  
Cortical Cells ◽  
Force Microscopy ◽  
Atomic Force ◽  
The Mean

Mutations in the Arabidopsis TETRATRICOPEPTIDE THIOREDOXIN-LIKE 1 (TTL1) gene cause reduced tolerance to osmotic stress evidenced by an arrest in root growth and root swelling, which makes it an interesting model to explore how root growth is controlled under stress conditions. We found that osmotic stress reduced the growth rate of the primary root by inhibiting the cell elongation in the elongation zone followed by a reduction in the number of cortical cells in the proximal meristem. We then studied the stiffness of epidermal cell walls in the root elongation zone of ttl1 mutants under osmotic stress using atomic force microscopy. In plants grown in control conditions, the mean apparent elastic modulus was 448% higher for live Col-0 cell walls than for ttl1 (88.1 ± 2.8 vs. 16.08 ± 6.9 kPa). Seven days of osmotic stress caused an increase in the stiffness in the cell wall of the cells from the elongation zone of 87% and 84% for Col-0 and ttl1, respectively. These findings suggest that TTL1 may play a role controlling cell expansion orientation during root growth, necessary for osmotic stress adaptation.

scholarly journals Mechanisms of membrane protein biogenesis

2014 ◽  
Vol 70 (a1) ◽  
pp. C1161-C1161
Author(s):  
Irmgard Sinning
Keyword(s):  
Membrane Proteins ◽  
Signal Sequence ◽  
Signal Recognition Particle ◽  
Signal Recognition ◽  
Protein Biogenesis ◽  
Cargo Proteins ◽  
Target Membrane ◽  
Hydrophobic Nature ◽  
Correct Target ◽  
Srp Rna

More than 25% of the cellular proteome comprise membrane proteins that have to be inserted into the correct target membrane. Most membrane proteins are delivered to the membrane by the signal recognition particle (SRP) pathway which relies on the recognition of an N-terminal signal sequence. In contrast to this co-translational mechanism, which avoids problems due to the hydrophobic nature of the cargo proteins, tail-anchored (TA) membrane proteins utilize a post-translational mechanism for membrane insertion – the GET pathway (guided entry of tail-anchored membrane proteins). The SRP and GET pathways are both regulated by GTP and ATP binding proteins of the SIMIBI family. However, in the SRP pathway the SRP RNA plays a unique regulatory role. Recent insights into eukaryotic SRP will be discussed.

scholarly journals Some Mechanisms Modulating the Root Growth of Various Wheat Species under Osmotic-Stress Conditions

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1545
Author(s):  
Nina V. Terletskaya ◽  
Tamara E. Lee ◽  
Nazira A. Altayeva ◽  
Nataliya O. Kudrina ◽  
Irina V. Blavachinskaya ◽  
...  
Keyword(s):  
Osmotic Stress ◽  
Water Deficit ◽  
Apical Meristem ◽  
Primary Root ◽  
Triticum Aestivum L ◽  
Root Diameter ◽  
Wheat Species ◽  
Drought Tolerant ◽  
Primary Roots ◽  
Species Specific

The role of the root in water supply and plant viability is especially important if plants are subjected to stress at the juvenile stage. This article describes the study of morphophysiological and cytological responses, as well as elements of the anatomical structure of primary roots of three wheat species, Triticum monococcum L., Triticum dicoccum Shuebl., and Triticum aestivum L., to osmotic stress. It was shown that the degree of plasticity of root morphology in water deficit affected the growth and development of aboveground organs. It was found that in conditions of osmotic stress, the anatomical root modulations were species-specific. In control conditions the increase in absolute values of root diameter was reduced with the increase in the ploidy of wheat species. Species-specific cytological responses to water deficit of apical meristem cells were also shown. The development of plasmolysis, interpreted as a symptom of reduced viability apical meristem cells, was revealed. A significant increase in enzymatic activity of superoxide dismutase under osmotic stress was found to be one of the mechanisms that could facilitate root elongation in adverse conditions. The tetraploid species T. dicoccum Shuebl. were confirmed as a source of traits of drought tolerant primary root system for crosses with wheat cultivars.

scholarly journals Negatively charged amino acids in the stalk region of membrane proteins reduce ectodomain shedding

2020 ◽  
Vol 295 (35) ◽  
pp. 12343-12352 ◽  
Author(s):  
Ryo Iwagishi ◽  
Rika Tanaka ◽  
Munenosuke Seto ◽  
Tomoyo Takagi ◽  
Naoko Norioka ◽  
...  
Keyword(s):  
Amino Acids ◽  
Membrane Proteins ◽  
Molecular Mechanisms ◽  
Alternative Exon ◽  
Ectodomain Shedding ◽  
Post Translational Modification ◽  
Charged Amino Acids ◽  
Juxtamembrane Region ◽  
Protein Variants ◽  
Variant Protein

Ectodomain shedding is a post-translational modification mechanism by which the entire extracellular domain of membrane proteins is liberated through juxtamembrane processing. Because shedding rapidly and irreversibly alters the characteristics of cells, this process is properly regulated. However, the molecular mechanisms governing the propensity of membrane proteins to shedding are largely unknown. Here, we present evidence that negatively charged amino acids within the stalk region, an unstructured juxtamembrane region at which shedding occurs, contribute to shedding susceptibility. We show that two activated leukocyte cell adhesion molecule (ALCAM) protein variants produced by alternative splicing have different susceptibilities to ADAM metallopeptidase domain 17 (ADAM17)-mediated shedding. Of note, the inclusion of a stalk region encoded by a 39-bp-long alternative exon conferred shedding resistance. We found that this alternative exon encodes a large proportion of negatively charged amino acids, which we demonstrate are indispensable for conferring the shedding resistance. We also show that the introduction of negatively charged amino acids into the stalk region of shedding-susceptible ALCAM variant protein attenuates its shedding. Furthermore, we observed that negatively charged amino acids residing in the stalk region of Erb-B2 receptor tyrosine kinase 4 (ERBB4) are indispensable for its shedding resistance. Collectively, our results indicate that negatively charged amino acids within the stalk region interfere with the shedding of multiple membrane proteins. We conclude that the composition of the stalk region determines the shedding susceptibility of membrane proteins.

scholarly journals The Yeast vps Class E Mutants: The Beginning of the Molecular Genetic Analysis of Multivesicular Body Biogenesis

2010 ◽  
Vol 21 (23) ◽  
pp. 4057-4060 ◽  
Author(s):  
Emily M. Coonrod ◽  
Tom H. Stevens
Keyword(s):  
Membrane Proteins ◽  
Molecular Genetic ◽  
Multivesicular Body ◽  
Molecular Genetic Analysis ◽  
Vacuolar Membrane ◽  
Multivesicular Bodies ◽  
Golgi Membrane ◽  
Cargo Proteins ◽  
Vacuolar Protein ◽  
Class E

In 1992, Raymond et al. published a compilation of the 41 yeast vacuolar protein sorting (vps) mutant groups and described a large class of mutants (class E vps mutants) that accumulated an exaggerated prevacuolar endosome-like compartment. Further analysis revealed that this “class E compartment” contained soluble vacuolar hydrolases, vacuolar membrane proteins, and Golgi membrane proteins unable to recycle back to the Golgi complex, yet these class E vps mutants had what seemed to be normal vacuoles. The 13 class E VPS genes were later shown to encode the proteins that make up the complexes required for formation of intralumenal vesicles in late endosomal compartments called multivesicular bodies, and for the sorting of ubiquitinated cargo proteins into these internal vesicles for eventual delivery to the vacuole or lysosome.

scholarly journals Methylation of aquaporins in plant plasma membrane

2006 ◽  
Vol 400 (1) ◽  
pp. 189-197 ◽  
Author(s):  
Véronique Santoni ◽  
Lionel Verdoucq ◽  
Nicolas Sommerer ◽  
Joëlle Vinh ◽  
Delphine Pflieger ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Membrane Proteins ◽  
Water Permeability ◽  
Plant Root ◽  
Ectopic Expression ◽  
Regulatory Mechanisms ◽  
Wild Type ◽  
Post Translational Modification ◽  
Suspension Cells ◽  
Plant Plasma Membrane

A thorough analysis, using MS, of aquaporins expressed in plant root PM (plasma membrane) was performed, with the objective of revealing novel post-translational regulations. Here we show that the N-terminal tail of PIP (PM intrinsic protein) aquaporins can exhibit multiple modifications and is differentially processed between members of the PIP1 and PIP2 subclasses. Thus the initiating methionine was acetylated or cleaved in native PIP1 and PIP2 isoforms respectively. In addition, several residues were detected to be methylated in PIP2 aquaporins. Lys3 and Glu6 of PIP2;1, one of the most abundant aquaporins in the PM, occurred as di- and mono-methylated residues respectively. Ectopic expression in Arabidopsis suspension cells of PIP2;1, either wild-type or with altered methylation sites, revealed an interplay between methylation at the two sites. Measurements of water transport in PM vesicles purified from these cells suggested that PIP2;1 methylation does not interfere with the aquaporin intrinsic water permeability. In conclusion, the present study identifies methylation as a novel post-translational modification of aquaporins, and even plant membrane proteins, and may represent a critical advance towards the identification of new regulatory mechanisms of membrane transport.

scholarly journals Osmoregulation and the Anthozoan-Dinoflagellate Symbiosis

2021 ◽  
Author(s):  
◽  
Michael Cowlin
Keyword(s):  
Osmotic Stress ◽  
Stress Responses ◽  
High Performance ◽  
Stable State ◽  
Organic Osmolytes ◽  
Physiological Indicators ◽  
Host Cytoplasm ◽  
Saline Treatment ◽  
Tropical Coral ◽  
Osmotic Treatment

<p>This study investigated the responses of the temperate anemone Anthopleura aureoradiata, and the tropical coral Acropora aspera to osmotic stress and the role that free amino acids (FAAs) may play in the osmoregulatory mechanism of these anthozoan-dinoflagellate symbioses. Specimens were exposed to a range of hypo- and hyper-saline conditions for durations of 1, 12, 48 and 96 hours, whereupon respiration and photosynthetic rates were measured as physiological indicators of osmotic stress. High performance liquid chromatography was used to quantify 15 FAAs within the anthozoan host tissues to establish the response of FAA pools to osmotic stress and whether FAAs are used in an osmoregulatory capacity. Aposymbiotic specimens of A. aureoradiata were similarly tested to establish if the presence of symbiotic dinoflagellates alters the host’s capacity to respond to osmotic stress given that the symbionts are known to release FAAs into the host cytoplasm. In A. aureoradiata, significant changes in respiration were only observed with exposure to the extreme hypo-osmotic salinity of 12‰, with respiration decreasing by 67% after 1 hour of exposure. No significant changes in respiration were seen at 25, 43 or 50‰, despite a 52% decrease in respiration seen at the hyper-saline treatment of 50‰. The response of the coral A. aspera was markedly different, showing an increase in respiration in response to hypo-salinity (22 and 28‰). Interestingly, the most pronounced respiratory increase of up to 460% occurred in the less extreme hypo-saline treatment of 28‰. The response of photosynthesis also showed differences between the two species. In the symbiotic A. aureoradiata, photosynthesis declined by 61% after the 1 hour exposure to 12‰ and further decreased to 72% below control rates after 96 hours. While in A. aspera, photosynthesis showed no significant deviation from control levels at any of the treatment salinities. FAA pools in both A. aureoradiata and A. aspera showed significant responses to osmotic stress. In symbiotic A. aureoradiata, exposure to 12‰ caused total FAA pools to decline by 50% after 1 hour, after which a seemingly stable state was reached. A hyper-osmotic treatment of 50‰ resulted in a similar trend with a more than 50% decrease after 1 hour of exposure. In A. aspera, the response of the FAA pool was markedly different, with the concentration increasing by up to 200% with exposure to 22‰ and by more than 260% at 28‰. Interestingly, one on the main constituents of FAA pools in A. aureoradiata, Taurine (15% of FAA pools at 35‰), was not present in measurable quantities within A. aspera host tissue. In aposymbiotic individuals of A. aureoradiata exposed to extreme hypo- and hyper-saline treatments of 12 and 50‰ a significant impact on respiration was only observed at 12‰, with a 77% decrease in respiration after 96 hours. Changes in FAA pools of aposymbiotic A. aureoradiata were only seen after 12 hours exposure to 50‰ with a significant 26% decrease. However, the direct comparison between symbiotic and aposymbiotic A. aureoradiata did serve to highlight the contribution of symbiont-derived FAAs to the host pool of FAAs, with FAA pools in aposymbiotic anemones up to 41% lower than those found in symbiotic anemones. The results seen here were not suggestive of FAAs being regulated for the explicit use as compatible organic osmolytes. Rather, changes in FAA pools showed changes consistent with other stress responses. Moreover, the response of anthozoan-dinoflagellate symbioses to osmotic stress appears to be species specific, or at least taxa specific, as the responses of respiration, photosynthesis and FAA pools were very different between the temperate anemone A. aureoradiata and the tropical coral A. aspera. Nevertheless, differences in the respiratory response between symbiotic and apo-symbiotic anemones did indicate some influence of the dinoflagellate symbionts on the ability of the anthozoan host to mediate osmotic stress. It may therefore be that other symbiont-derived compounds are utilised as compatible organic osmolytes (COOs), with a primary candidate being glycerol. This warrants further investigation.</p>

scholarly journals TGN/EE SNARE protein SYP61 is ubiquitinated and required for carbon/nitrogen-nutrient responses in Arabidopsis

2020 ◽  
Author(s):  
Yoko Hasegawa ◽  
Thais Huarancca Reyes ◽  
Tomohiro Uemura ◽  
Akari Fujimaki ◽  
Yongming Luo ◽  
...  
Keyword(s):  
Membrane Trafficking ◽  
Critical Role ◽  
Snare Protein ◽  
Post Translational Modification ◽  
Cellular Processes ◽  
Protein Receptor ◽  
Sensitive Factor ◽  
Cargo Proteins ◽  
Golgi Network

AbstractUbiquitination is a post-translational modification with reversible attachment of the small protein ubiquitin, which is involved in numerous cellular processes including membrane trafficking. For example, ubiquitination of cargo proteins is known to regulate their subcellular dynamics, and plays important roles in plant growth and stress adaptation. However, the regulatory mechanism of the trafficking machinery components remains elusive. Here, we report Arabidopsis trans-Golgi network/early endosome (TGN/EE) localized soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) protein SYP61 as a novel ubiquitination target of a membrane localized ubiquitin ligase ATL31. SYP61 is a key component of membrane trafficking in Arabidopsis. SYP61 was ubiquitinated with K63-linked chain by ATL31 in vitro and in plants. The knockdown mutants of SYP61 were hypersensitive to the disrupted carbon (C)/nitrogen (N)-nutrient stress, suggesting its critical role in plant homeostasis in response to nutrients. We also found the ubiquitination status of SYP61 is affected by C/N-nutrient availability. These results provided possibility that ubiquitination of SNARE protein has important role in plant physiology.

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