LC-MSMS identification of Arabidopsis thaliana heat-stable seed proteins: enriching for LEA-type proteins by acid treatment

Protein identification in systems containing very highly abundant proteins is not always efficient and usually requires previous enrichment or fractionation steps in order to uncover minor proteins. In plant seeds, identification of late embryogenesis abundant (LEA) proteins is often masked by the presence of the large family of storage proteins. LEA-proteins are predicted to play a role in plant stress tolerance. They are highly hydrophilic proteins, generally heat-stable, and correlate with dehydration in seeds or vegetative tissues. In the present work, we analyze the protein composition of heat-stable Arabidopsis thaliana seed extracts after treatment with trichloroacetic acid (TCA). The composition of the proteins that precipitate and those that remain in solution in 3% TCA was analyzed by two different approaches: 1D SDS-PAGE coupled to LC-ESI-MSMS analysis and a gel-free protocol associated with LC-MALDI-MSMS. Our results indicate that treating total heat-soluble extracts with 3% TCA is an effective procedure to remove storage proteins by selective precipitation and this fractionation step provides a soluble fraction highly enriched in Lea-type proteins. The analysis and determination of protein identities in this acid-soluble fraction by MS technology is a suitable system for large-scale identification of Lea-proteins present in seeds.     

Recombination proteins and telomere stability in plants

Repair of DNA damage is essential for the maintenance of the integrity and transmission of the genome in development and reproduction. Telomeres are nucleoprotein structures which protect the ends of (linear) eukaryotic chromosomes. Telomere dysfunction results in loss of this protection and the telomeres being recognised as DNA damage by the cellular DNA Damage Repair and Response (DDR) machinery, leading to senescence or cell death. Telomeric homeostasis is thus tightly controlled and many specific and non-specific proteins are involved in its regulation. Among these, DNA damage and Repair proteins contribute both to the recognition of telomere dysfunction and more surprisingly, are directly implicated in telomere homeostasis itself. Plants offer a great opportunity to study these mechanisms due to the fact that many key DNA repair and recombination proteins are non-essential in plants, in contrast to vertebrates. In the following text, after a brief summary of the current state of knowledge on telomere-specific proteins in plants, we review the DDR processes and the related proteins implicated in plant telomere stability. We focus specifically on telomere signalling and on recombination events induced by unprotected telomeres, at the origin of genome rearrangements and instability when telomere function is affected.     

Ultrafast excitation relaxation dynamics of lutein in solution and in the light-harvesting complexes II isolated from Arabidopsis thaliana

Ultrafast excitation relaxation dynamics and energy-transfer processes in the light-harvesting complex II (LHC II) of Arabidopsis thaliana were examined at physiological temperature using femtosecond time-resolved fluorescence spectroscopy. Energy transfer from lutein to Chl a proceeded with a rate constant of k(ET) = 1.8-1.9 x 10(13) s(-1) and a yield of approximately Phi(ET) = 0.70, whereas that from neoxanthin to Chl a had a rate constant of k(ET) = 6.5 x 10(11) s(-1) and a yield at the most of Phi(ET) = 0.09. Fluorescence anisotropic decay of lutein in LHC II showed a value larger than 0.4 at the initial state and decayed to approximately 0.1 in 0.3 ps, indicating that two lutein molecules interact with each other in LHC II. In solution, anisotropy of lutein remained constant (0.38) independent of time, and thus a new excited state inferred between the S(2) (1B(u)) state and the S(1) (2A(g)) state was not applicable for lutein in solution. Energy migration processes among Chl a or Chl b molecules were clearly resolved by kinetic analysis. On the basis of these results, relaxation processes and energy-transfer kinetics in LHC II of A. thaliana are discussed.     

Shotgun proteomic analysis of Arabidopsis thaliana leaves

Two shotgun tandem MS proteomics approaches, multidimensional protein identification technology (MudPIT) and 1-D gel-LC-MS/MS, were used to identify Arabidopsis thaliana leaf proteins. These methods utilize different protein/peptide separation strategies. Detergents not compatible with MudPIT were used with 1-D gel-LC-MS/MS to help enrich for the detection of membrane-spanning and hydrophobic proteins. By combining the data from all MudPIT and 1-D gel-LC-MS/MS experiments, 2342 nonredundant proteins spanning a broad range of molecular weights and pI values were detected. With the exception of unknown proteins, the distribution of gene ontology (GO) classifications for the detected proteins was similar to that encoded by the genome, which shows that these extraction and separation procedures are useful for a broad proteomic survey of plant cells. Unknown proteins will likely have to be targeted by using additional methods, some of which should be compatible with separation strategies taken here.     

Proteomics of loosely bound cell wall proteins of Arabidopsis thaliana cell suspension cultures: a critical analysis

The complete sequencing of the Arabidopsis thaliana genome allows the use of the recently developed mass spectrometry techniques to identify the cell wall proteins (CWPs). Most proteomic approaches depend on the quality of sample preparation. Extraction of CWPs is particularly complex since the proteins may be free in the apoplast or are embedded in a polysaccharide matrix where they are retained by Van der Waals interactions, hydrogen bonds, hydrophobic or ionic interactions, or cross-linked by covalent bonds. Specific and sequential extraction procedures thus need to be developed. We report on the sequential extraction of loosely bound CWPs from living A. thaliana cells in culture. Different salts and chelating agents were used for releasing the proteins from the wall. Their effects on the extraction of CWPs and on the integrity of the plasma membrane were evaluated. Bioinformatic software was used to identify proteins and to predict their sub-cellular localization. The obtained data show that the plasma membrane of cells in culture was easily damaged by some steps of the extraction procedure, leading to the release of increasing amounts of intracellular proteins. Nevertheless, we identified fifty CWPs among which thirteen were new proteins for the cell wall. In addition, 76% of these CWPs were basic proteins not resolved in two-dimensional (2-D) gel electrophoresis. The existence of two hypothetical proteins was confirmed. The structure of three proteins could be confirmed using mass spectrometry data.     

Proteomic analysis of the Arabidopsis thaliana cell wall

With the completion of the Arabidopsis genome, many hypothetical proteins have been predicted without any information on their expression, subcellular localisation and function. We have performed proteomic analysis of proteins sequentially extracted from enriched Arabidopsis cell wall fractions and separated by two-dimensional gel electrophoresis (2-DE). The proteins were identified by peptide mass fingerprinting using matrix-assisted laser desorption/ionisation-time of flight (MALDI-TOF) mass spectrometry and genomic database searches. This is part of a targeted exercise to establish the entire Arabidopsis secretome database. We report evidence for new proteins of unknown function whose existence had been predicted from genomic sequences and, furthermore, localise them to the cell wall. In addition, we observed an unexpected presence in the cell wall preparations of proteins whose known biochemical activity has never been associated with this compartment hitherto. We discuss the implications of these findings and present results suggesting a possible involvement of cell wall kinases in plant responses to pathogen attack.     

A proteomic analysis of organelles from Arabidopsis thaliana

We introduce the use of Arabidopsis thaliana callus culture as a system for proteomic analysis of plant organelles using liquid-grown callus. This callus is relatively homogeneous, reproducible and cytoplasmically rich, and provides organelles in sufficient quantities for proteomic studies. A database was generated of mitochondrial, endoplasmic reticulum (ER), Golgi/prevacuolar compartment and plasma membrane (PM) markers using two-dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoresis (2-D SDS-PAGE) and peptide sequencing or mass spectrometric methods. The major callus membrane-associated proteins were characterised as being integral or peripheral by Triton X-114 phase partitioning. The database was used to define specific proteins at the Arabidopsis callus plasma membrane. This database of organelle proteins provides the basis for future characterisation of the expression and localisation of novel plant proteins.     

Identification and Quantification of Coumarins by UHPLC-MS in Arabidopsis thaliana Natural Populations

Coumarins are phytochemicals occurring in the plant kingdom, which biosynthesis is induced under various stress factors. They belong to the wide class of specialized metabolites well known for their beneficial properties. Due to their high and wide biological activities, coumarins are important not only for the survival of plants in changing environmental conditions, but are of great importance in the pharmaceutical industry and are an active source for drug development. The identification of coumarins from natural sources has been reported for different plant species including a model plant Arabidopsis thaliana. In our previous work, we demonstrated a presence of naturally occurring intraspecies variation in the concentrations of scopoletin and its glycoside, scopolin, the major coumarins accumulating in Arabidopsis roots. Here, we expanded this work by examining a larger group of 28 Arabidopsis natural populations (called accessions) and by extracting and analysing coumarins from two different types of tissues–roots and leaves. In the current work, by quantifying the coumarin content in plant extracts with ultra-high-performance liquid chromatography coupled with a mass spectrometry analysis (UHPLC-MS), we detected a significant natural variation in the content of simple coumarins like scopoletin, umbelliferone and esculetin together with their glycosides: scopolin, skimmin and esculin, respectively. Increasing our knowledge of coumarin accumulation in Arabidopsis natural populations, might be beneficial for the future discovery of physiological mechanisms of action of various alleles involved in their biosynthesis. A better understanding of biosynthetic pathways of biologically active compounds is the prerequisite step in undertaking a metabolic engineering research.     

Classifying substrate specificities of membrane transporters from Arabidopsis thaliana

Membrane transporters catalyze the active transport of molecules across biological barriers such as lipid bilayer membranes. Currently, the experimental annotation of which proteins transport which substrates is far from complete and will likely remain so for much longer. Therefore, it is highly desirable to develop computational methods that may aid in the substrate annotation of putative membrane transport proteins. Here, we measured the similarity of membrane transporters from Arabidopsis thaliana by their amino acid composition, higher sequence order information, amino acid characteristics, or sequence conservation. We considered the substrate classes amino acids, oligopeptides, phosphates, and hexoses. Substrate classification based on the amino acid frequency yielded an accuracy of 75% or higher. Integrating additional information improved the prediction performance to 90% and higher.     

Ligand migration in nonsymbiotic hemoglobin AHb1 from Arabidopsis thaliana

AHb1 is a hexacoordinated type 1 nonsymbiotic hemoglobin recently discovered in Arabidopsis thaliana. To gain insight into the ligand migration inside the protein, we studied the CO rebinding kinetics of AHb1 encapsulated in silica gels, in the presence of glycerol. The CO rebinding kinetics after nanosecond laser flash photolysis exhibits complex ligand migration patterns, consistent with the existence of discrete docking sites in which ligands can temporarily be stored before rebinding to the heme at different times. This finding may be of relevance to the physiological NO dioxygenase activity of this protein, which requires sequential binding of two substrates, NO and O2, to the heme.     

Absorption and fluorescence spectroscopic characterization of cryptochrome 3 from Arabidopsis thaliana

The blue light photoreceptor cryptochrome 3 (cry3) from Arabidopsis thaliana was characterized at room temperature in vitro in aqueous solution by optical absorption and emission spectroscopic studies. The protein non-covalently binds the chromophores flavin adenine dinucleotide (FAD) and N5,N10-methenyl-5,6,7,8-tetrahydrofolate (MTHF). In the dark-adapted state of cry3, the bound FAD is present in the oxidized form (FAD(ox), ca. 38.5%), in the semiquinone form (FADH., ca. 5%), and in the fully reduced neutral form (FAD(red)H2) or fully reduced anionic form (FAD(red)H-, ca. 55%). Some amount of FAD (ca. 1.5%) in the oxidized state remains unbound probably caused by chromophore release and/or denaturation. F?rster-type energy transfer from MTHF to FAD(ox) is observed. Photo-excitation reversibly modifies the protein conformation causing a slight rise of the MTHF absorption strength and an increase of the MTHF fluorescence efficiency (efficient protein conformation photo-cycle). Additionally there occurs reversible reduction of bound FAD(ox) to FAD(red)H2 (or FAD(red)H-, FAD(ox) photo-cycle of moderate efficiency), reversible reduction of FADH. to FAD(red)H2 (or FAD(red)H-, FADH. photo-cycle of high efficiency), and modification of re-oxidable FAD(red)H2 (or FAD(red)H-) to permanent FAD(red)H2 (or FAD(red)H-) with low quantum efficiency. Photo-excitation of MTHF causes the reversible formation of a MTHF species (MTHF', MTHF photo-cycle, moderate quantum efficiency) with slow recovery to the initial dark state, and also the formation of an irreversible photoproduct (MTHF').     

Insight into herbicide resistance of W574L mutant Arabidopsis thaliana acetohydroxyacid synthase: molecular dynamics simulations and binding free energy calculations

Acetohydroxyacid synthase (AHAS) is the target enzyme of several classes of herbicides, such as sulfonylureas and imidazolinones. Now many mutant AHASs with herbicide resistance have emerged along with extensive use of herbicides, therefore it is imperative to understand the detailed interaction mechanism and resistance mechanism so as to develop new potent inhibitors for wild-type or resistant AHAS. With the aid of available crystal structures of the Arabidopsis thaliana (At) AHAS-inhibitor complex, molecular dynamics (MD) simulations were used to investigate the interaction and resistance mechanism directly and dynamically at the atomic level. Nanosecond-level MD simulations were performed on six systems consisting of wild-type or W574L mutant AtAHAS in the complex with three sulfonylurea inhibitors, separately, and binding free energy was calculated for each system using the MM-GBSA method. Comprehensive analyses from structural and energetic aspects confirmed the importance of residue W574, and also indicated that W574L mutation might alert the structural charactersistic of the substrate access channel and decrease the binding affinity of inhibitors, which cooperatively weaken the effective channel-blocked effect and finally result in weaker inhibitory effect of inhibitor and corresponding herbicide resistance of W574L mutant. To our knowledge, it is the first report about MD simulations study on the AHAS-related system, which will pave the way to study the interactions between herbicides and wild-type or mutant AHAS dynamically, and decipher the resistance mechanism at the atomic level for better designing new potent anti-resistance herbicides.     

Insight into herbicide resistance of W574L mutant Arabidopsis thaliana acetohydroxyacid synthase:molecular dynamics simulations and binding free energy calculations

Acetohydroxyacid synthase(AHAS) is the target enzyme of several classes of herbicides,such as sulfonylureas and imidazolinones.Now many mutant AHASs with herbicide resistance have emerged along with extensive use of herbicides,therefore it is imperative to understand the detailed interaction mechanism and resistance mechanism so as to develop new potent inhibitors for wild-type or resistant AHAS.With the aid of available crystal structures of the Arabidopsis thaliana(At) AHAS-inhibitor complex,molecular dyn...     

Ultraviolet wavelength dependence of photomorphological and photosynthetic responses in Brassica napus and Arabidopsis thaliana

Among the photomorphological responses in plants induced by ultraviolet-B radiation (UVB; 290 nm-320 nm) are leaf asymmetry, leaf thickening and cotyledon curling. We constructed an action spectrum of cotyledon curling in light-grown Brassica napus to characterize the UVB photoreceptor that initiates this response. Cotyledon curling was also characterized in Arabidopsis thaliana. Peak efficiency for this response occurred between 285 and 290 nm. Additionally, UVB-induced changes in epidermal cells from A. thaliana cotyledons were assessed because they are the likely site of UVB photoreception that leads to curling. Investigation of cellular structure, chlorophyll a fluorescence and chlorophyll concentration indicated that cotyledon curling is not concomitant with gross cellular damage or inhibition of photosynthesis, which only occurred in response to wavelengths <280 nm. Many UVB effects are apparently an indirect consequence of UVB radiation, dependent on UVB-mediated increases in reactive oxygen species (ROS) that either act as a signal in the UVB transduction pathway or cause oxidative damage. The cotyledon curling response was impeded by ascorbate and cystine, ROS scavengers and was promoted by H(2)O(2), a ROS. We suggest that following absorption by a UVB chromophore, ROS are generated via photosensitization, ultimately leading to cotyledon curling.     

Computational prediction of protein ubiquitination sites mapping on Arabidopsis thaliana

Among the protein post-translational modifications (PTMs), ubiquitination is considered as one of the most significant processes which can regulate the cellular functions and various diseases. Identification of ubiquitination sites becomes important for understanding the mechanisms of ubiquitination-related biological processes. Both experimental and computational approaches are available for identifying ubiquitination sites based on protein sequences of different species. The experimental approaches are time-consuming, laborious and costly. In silico prediction is an alternative time saving, easier and cost-effective approach for identifying ubiquitination sites. Moreover, the sequence patterns in the different species around the ubiquitination sites are not similar which demands species-specific predictors. Therefore, in this study, we have proposed a novel computational method for identifying ubiquitination sites based on protein sequences of A. thaliana species which will be robust against outlying observations also. Through the comparative study of two encoding schemes and three classifiers, the random forest (RF) based predictor was selected as the best predictor under the CKSAAP encoding scheme with 1:1 ratio of positive and negative samples (i.e. ubiquitinated and non-ubiquitinated) in training dataset. The proposed predictor produced the area under the ROC curve (AUC score) as 0.91 and 0.86 for 5-fold cross-validation test with the training dataset and the independent test dataset of A. thaliana respectively. The proposed RF based predictor also performed much better than the other existing ubiquitination sites predictors for A. thaliana.     

Monitoring of isothiocyanates emanating from Arabidopsis thaliana upon paraquat spraying

Arabidopsis thaliana plants were sprayed with the superoxide-generating herbicide paraquat. The headspace of sprayed plants was characterized by a number of compounds, which were absent in the headspace of untreated plants. They were identified as isothiocyanates (ITCs) with 4-methylthiobutyl isothiocyanate as main compound. After identification, a GC-system, based on PDMS sorption, was used to continuously monitor the ITC emissions. The specificity of isothiocyanate emission was also determined by subjecting the Arabidopsis thaliana plants to in vitro mechanical wounding. Again, 4-methylthiobutyl isothiocyanate was the main component, but the emission profile was completely different since the compound was emitted immediately, i.e., during wounding itself.     

Application of sequence Fourier analysis to a specific interaction in Arabidopsis thaliana

The sequence Fourier analysis reported previously seems to be applicable to elucidating a simple and concerted interaction in Arabidopsis thaliana, similar to that in Homo sapiens.