In plants, membrane compartmentalization requires vesicle trafficking for communication among distinct organelles. Membrane proteins involved in vesicle trafficking are highly dynamic and can respond rapidly to changes in the environment and to cellular signals. Capturing their localization and dynamics is thus essential for understanding the mechanisms underlying vesicular trafficking pathways. Quantitative mass spectrometry and imaging approaches allow a system-wide dissection of the vesicular proteome, the characterization of ligand-receptor pairs and the determination of secretory, endocytic, recycling and vacuolar trafficking pathways. In this review, we highlight major proteomics and imaging methods employed to determine the location, distribution and abundance of proteins within given trafficking routes. We focus in particular on methodologies for the elucidation of vesicle protein dynamics and interactions and their connections to downstream signalling outputs. Finally, we assess their biological applications in exploring different cellular and subcellular processes.

• Klíčová slova
• Golgi, endocytosis, exocytosis, microscopy, proteomics, vesicle,
• MeSH
• biologický transport MeSH
• endocytóza MeSH
• hmotnostní spektrometrie metody   MeSH
• proteom * analýza   metabolismus   MeSH
• proteomika * metody   MeSH
• transport proteinů MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• proteom * MeSH

Phospholipase D alpha 1 (PLDα1) is a phospholipid hydrolyzing enzyme playing multiple regulatory roles in stress responses of plants. Its signaling activity is mediated by phosphatidic acid (PA) production, capacity to bind, and modulate G-protein complexes or by interaction with other proteins. This work presents a quantitative proteomic analysis of two T-DNA insertion pldα1 mutants of Arabidopsis thaliana. Remarkably, PLDα1 knockouts caused differential regulation of many proteins forming protein complexes, while PLDα1 might be required for their stability. Almost one third of differentially abundant proteins (DAPs) in pldα1 mutants are implicated in metabolism and RNA binding. Latter functional class comprises proteins involved in translation, RNA editing, processing, stability, and decay. Many of these proteins, including those regulating chloroplast protein import and protein folding, share common functions in chloroplast biogenesis and leaf variegation. Consistently, pldα1 mutants showed altered level of TIC40 (a major regulator of protein import into chloroplast), differential accumulation of photosynthetic protein complexes and changed chloroplast sizes as revealed by immunoblotting, blue-native electrophoresis, and microscopic analyses, respectively. Our proteomic analysis also revealed that genetic depletion of PLDα1 also affected proteins involved in cell wall architecture, redox homeostasis, and abscisic acid signaling. Taking together, PLDα1 appears as a protein integrating cytosolic and plastidic protein translations, plastid protein degradation, and protein import into chloroplast in order to regulate chloroplast biogenesis in Arabidopsis.

• Klíčová slova
• Arabidopsis, chloroplast biogenesis, chloroplast protein import, phospholipase D alpha 1, proteomics, translation,
• Publikační typ
• časopisecké články MeSH

Phospholipase Dα1 (PLDα1) belongs to phospholipases, a large phospholipid hydrolyzing protein family. PLDα1 has a substrate preference for phosphatidylcholine leading to enzymatic production of phosphatidic acid, a lipid second messenger with multiple cellular functions. PLDα1 itself is implicated in biotic and abiotic stress responses. Here, we present a shot-gun differential proteomic analysis on roots of two Arabidopsis pldα1 mutants compared to the wild type. Interestingly, PLDα1 deficiency leads to altered abundances of proteins involved in diverse processes related to membrane transport including endocytosis and endoplasmic reticulum-Golgi transport. PLDα1 may be involved in the stability of attachment sites of endoplasmic reticulum to the plasma membrane as suggested by increased abundance of synaptotagmin 1, which was validated by immunoblotting and whole-mount immunolabelling analyses. Moreover, we noticed a robust abundance alterations of proteins involved in mitochondrial import and electron transport chain. Notably, the abundances of numerous proteins implicated in glucosinolate biosynthesis were also affected in pldα1 mutants. Our results suggest a broader biological involvement of PLDα1 than anticipated thus far, especially in the processes such as endomembrane transport, mitochondrial protein import and protein quality control, as well as glucosinolate biosynthesis.

• Klíčová slova
• Arabidopsis, cytoskeleton, mitochondrial protein import, phospholipase D alpha1, proteomics, quality control, vesicular transport,
• MeSH
• Arabidopsis metabolismus   MeSH
• endocytóza MeSH
• fosfolipasa D genetika   metabolismus   MeSH
• genová ontologie MeSH
• glukosinoláty biosyntéza   MeSH
• kořeny rostlin metabolismus   MeSH
• mitochondriální proteiny metabolismus   MeSH
• proteiny huseníčku genetika   metabolismus   MeSH
• proteom metabolismus   MeSH
• proteomika * MeSH
• synaptotagmin I metabolismus   MeSH
• tandemová hmotnostní spektrometrie MeSH
• transport proteinů MeSH
• uncoupling protein 1 metabolismus   MeSH
• vysokoúčinná kapalinová chromatografie MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• fosfolipasa D MeSH
• glukosinoláty MeSH
• mitochondriální proteiny MeSH
• PLDA1 protein, Arabidopsis MeSH Prohlížeč
• proteiny huseníčku MeSH
• proteom MeSH
• synaptotagmin I MeSH
• SYT1 protein, Arabidopsis MeSH Prohlížeč
• uncoupling protein 1 MeSH

BACKGROUND: Processes of anterograde and retrograde membrane trafficking play an important role in cellular homeostasis and dynamic rearrangements of the plasma membrane (PM) in all eukaryotes. These processes depend on the activity of adenosine ribosylation factors (ARFs), a family of GTP-binding proteins and their guanine exchange factors (GEFs). However, knowledge on the function and specificity of individual ARF-GEFs for individual steps of membrane trafficking pathways is still limited in plants. RESULTS: In this work, treatments with various trafficking inhibitors showed that the endocytosis of FM 4-64 is largely dynamin-dependent and relies on proteins containing endocytic tyrosine-based internalization motif and intact cytoskeleton. Interestingly, brefeldin A (BFA), reported previously as an inhibitor of anterograde membrane trafficking in plants, appeared to be the most potent inhibitor of endocytosis in tobacco. In concert with this finding, we demonstrate that the point mutation in the Sec7 domain of the GNOM-LIKE protein1a (NtGNL1a) confers intracellular trafficking pathway-specific BFA resistance. The internalization of FM 4-64 and trafficking of PIN-FORMED1 (PIN1) auxin efflux carrier in BY-2 tobacco cells were studied to reveal the function of the ARF-GEF NtGNL1a in these. CONCLUSIONS: Altogether, our observations uncovered the role of NtGNL1a in endocytosis, including endocytosis of PM proteins (as PIN1 auxin efflux carrier). Moreover these data emphasize the need of careful evaluation of mode of action of non-native inhibitors in various species. In addition, they demonstrate the potential of tobacco BY-2 cells for selective mapping of ARF-GEF-regulated endomembrane trafficking pathways.

• MeSH
• endocytóza MeSH
• kvartérní amoniové sloučeniny metabolismus   MeSH
• pyridinové sloučeniny metabolismus   MeSH
• rostlinné buňky fyziologie   MeSH
• rostlinné proteiny genetika   metabolismus   MeSH
• tabák genetika   fyziologie   MeSH
• transport proteinů MeSH
• výměnné faktory guaninnukleotidů genetika   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• FM 4-64 MeSH Prohlížeč
• kvartérní amoniové sloučeniny MeSH
• pyridinové sloučeniny MeSH
• rostlinné proteiny MeSH
• výměnné faktory guaninnukleotidů MeSH

Disentanglement of functional complexity associated with plant mitogen-activated protein kinase (MAPK) signaling has benefited from transcriptomic, proteomic, phosphoproteomic, and genetic studies. Published transcriptomic analysis of a double homozygous recessive anp2anp3 mutant of two MAPK kinase kinase (MAPKKK) genes called Arabidopsis thaliana Homologues of Nucleus- and Phragmoplast-localized Kinase 2 (ANP2) and 3 (ANP3) showed the upregulation of stress-related genes. In this study, a comparative proteomic analysis of anp2anp3 mutant against its respective Wassilevskaja ecotype (Ws) wild type background is provided. Such differential proteomic analysis revealed overabundance of core enzymes such as FeSOD1, MnSOD, DHAR1, and FeSOD1-associated regulatory protein CPN20, which are involved in the detoxification of reactive oxygen species in the anp2anp3 mutant. The proteomic results were validated at the level of single protein abundance by Western blot analyses and by quantitative biochemical determination of antioxidant enzymatic activities. Finally, the functional network of proteins involved in antioxidant defense in the anp2anp3 mutant was physiologically linked with the increased resistance of mutant seedlings against paraquat treatment.

• Klíčová slova
• ANP2, ANP3, Arabidopsis, antioxidant defense, mitogen-activated protein kinase kinase kinase, oxidative stress, proteomics, signaling,
• MeSH
• antioxidancia metabolismus   MeSH
• Arabidopsis účinky léků   genetika   metabolismus   MeSH
• biologické modely MeSH
• chromatografie kapalinová MeSH
• herbicidy farmakologie   MeSH
• imunoblotting MeSH
• MAP kinasy kinas (kinas) genetika   metabolismus   MeSH
• mutace MeSH
• paraquat farmakologie   MeSH
• proteiny huseníčku genetika   metabolismus   MeSH
• proteom genetika   metabolismus   MeSH
• proteomika metody   MeSH
• reaktivní formy kyslíku metabolismus   MeSH
• semenáček účinky léků   genetika   metabolismus   MeSH
• signální transdukce účinky léků   MeSH
• superoxiddismutasa metabolismus   MeSH
• tandemová hmotnostní spektrometrie MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Názvy látek
• ANP2 protein, Arabidopsis MeSH Prohlížeč
• ANP3 protein, Arabidopsis MeSH Prohlížeč
• antioxidancia MeSH
• herbicidy MeSH
• MAP kinasy kinas (kinas) MeSH
• paraquat MeSH
• proteiny huseníčku MeSH
• proteom MeSH
• reaktivní formy kyslíku MeSH
• superoxiddismutasa MeSH

Dual-specificity mitogen-activated protein kinases kinases (MAPKKs) are the immediate upstream activators of MAPKs. They simultaneously phosphorylate the TXY motif within the activation loop of MAPKs, allowing them to interact with and regulate multiple substrates. Often, the activation of MAPKs triggers their nuclear translocation. However, the spatiotemporal dynamics and the physiological consequences of the activation of MAPKs, particularly in plants, are still poorly understood. Here, we studied the activation and localization of the Medicago sativa stress-induced MAPKK (SIMKK)-SIMK module after salt stress. In the inactive state, SIMKK and SIMK co-localized in the cytoplasm and in the nucleus. Upon salt stress, however, a substantial part of the nuclear pool of both SIMKK and SIMK relocated to cytoplasmic compartments. The course of nucleocytoplasmic shuttling of SIMK correlated temporally with the dual phosphorylation of the pTEpY motif. SIMKK function was further studied in Arabidopsis plants overexpressing SIMKK-yellow fluorescent protein (YFP) fusions. SIMKK-YFP plants showed enhanced activation of Arabidopsis MPK3 and MPK6 kinases upon salt treatment and exhibited high sensitivity against salt stress at the seedling stage, although they were salt insensitive during seed germination. Proteomic analysis of SIMKK-YFP overexpressors indicated the differential regulation of proteins directly or indirectly involved in salt stress responses. These proteins included catalase, peroxiredoxin, glutathione S-transferase, nucleoside diphosphate kinase 1, endoplasmic reticulum luminal-binding protein 2, and finally plasma membrane aquaporins. In conclusion, Arabidopsis seedlings overexpressing SIMKK-YFP exhibited higher salt sensitivity consistent with their proteome composition and with the presumptive MPK3/MPK6 hijacking of the salt response pathway.

• Klíčová slova
• Arabidopsis, MAPK, Medicago, SIMK, SIMKK, proteomics, salt stress, subcellular relocation.,
• MeSH
• aktivace enzymů MeSH
• Arabidopsis genetika   růst a vývoj   metabolismus   MeSH
• exprese genu MeSH
• geneticky modifikované rostliny genetika   růst a vývoj   metabolismus   MeSH
• Medicago sativa enzymologie   genetika   MeSH
• mitogenem aktivované proteinkinasy kinas genetika   metabolismus   MeSH
• rostlinné proteiny genetika   metabolismus   MeSH
• semenáček genetika   růst a vývoj   metabolismus   MeSH
• soli metabolismus   MeSH
• transport proteinů MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• mitogenem aktivované proteinkinasy kinas MeSH
• rostlinné proteiny MeSH
• soli MeSH

LY294002 is a synthetic quercetin-like compound, which, unlike wortmannin, is more specific inhibitor of phosphatidylinositol 3-kinase (PI3K). It inhibits endocytosis and vacuolar transport. We report here on the proteome-wide effects of LY294002 on Arabidopsis roots focusing on proteins involved in vesicular trafficking and stress response. At the subcellular level, LY294002 caused swelling and clustering of late endosomes leading to inhibition of vacuolar transport. At the proteome level, this compound caused changes in abundances of proteins categorized to 10 functional classes. Among proteins involved in vesicular trafficking, a small GTPase ARFA1f was more abundant, indicating its possible contribution to the aggregation and fusion of late endosomes triggered by LY294002. Our study provides new information on storage proteins and vacuolar hydrolases in vegetative tissues treated by LY294002. Vacuolar hydrolases were downregulated, while storage proteins were more abundant, suggesting that storage proteins were protected from degradation in swollen multivesicular bodies upon LY294002 treatment. Upregulation of 2S albumin was validated by immunoblotting and immunolabeling analyses. Our study also pointed to the control of antioxidant enzyme machinery by PI3K because LY294002 downregulated two isozymes of superoxide dismutase. This most likely occurred via PI3K-mediated downregulation of protein AtDJ1A. Finally, we discuss specificity differences of LY294002 and wortmannin against PI3K, which are reflected at the proteome level. Compared with wortmannin, LY294002 showed more narrow and perhaps also more specific effects on proteins, as suggested by gene ontology functional annotation.

• MeSH
• anotace sekvence MeSH
• Arabidopsis cytologie   účinky léků   metabolismus   MeSH
• biologický transport MeSH
• chromony farmakologie   MeSH
• fosfatidylinositol-3-kinasy metabolismus   MeSH
• fyziologický stres MeSH
• inhibitory fosfoinositid-3-kinasy * MeSH
• kořeny rostlin cytologie   účinky léků   metabolismus   MeSH
• morfoliny farmakologie   MeSH
• proteiny huseníčku antagonisté a inhibitory   genetika   metabolismus   MeSH
• proteom genetika   metabolismus   MeSH
• regulace genové exprese u rostlin účinky léků   MeSH
• trans-Golgiho síť metabolismus   MeSH
• transportní vezikuly metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• Research Support, N.I.H., Extramural MeSH
• Názvy látek
• 2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one MeSH Prohlížeč
• chromony MeSH
• inhibitory fosfoinositid-3-kinasy * MeSH
• morfoliny MeSH
• proteiny huseníčku MeSH
• proteom MeSH