Plant Proteomics and Peptidomics in Host-Pathogen Interactions: The Weapons Used by Each Side.

Environmental biotic stress factors act continuously on plants, through multiple molecular interactions that eventually lead to the establishment and progress of symbiotic or pathogenic complex interactions. Proteins and peptides play noteworthy roles in such biological processes, usually being the main effectors since the initial recognizing and elicitor functions until the following transduction, gene regulation and physiological responses activities. Ranging from specific regulators to direct antimicrobial agents, plant or pathogen proteins and peptides comprise the arsenal available to each side in this biological war, resulting from the genetic coding potential inherited by each one. Post-translational research tools have widely contributed with valuable information on how the plant proteome works to achieve, maintain and adjust plant immunity in order to properly cope with the challenging pathogenic derived proteomes. These key proteins and peptides have great biotechnological potential since they represent distinctive features of each pathogen group (fungi, bacteria, viruses and other) in response to molecules of defense of host plants.

Proteome responses to nitrate in bioethanol production contaminant Dekkera bruxellensis.

Dekkera bruxellensis is an industrially relevant yeast, especially in bioethanol production. The capacity of D. bruxellensis to assimilate nitrate can confer advantages of this yeast over Saccharomyces cerevisiae at industrial conditions. In the present work we present the consequences of nitrate assimilation, using ammonium as reference, to the proteomics of D. bruxellensis. Thirty-four protein spots were overproduced in nitrate medium and were identified by MS-TOF/TOF analysis and were putatively identified by using local Mascot software. Apart from the overexpression of genes of nitrate metabolism, ATP synthesis and PPP and TCA pathways previously reported, cultivation on nitrate induced overproduction of glycolytic enzymes, which corroborate the high energy demand and NADH availability for nitrate assimilation. Overproduction of alcohol dehydrogenase (Adh) protein was also observed. Proteomic profile of D. bruxellensis cultivated in nitrate and described in the present work agrees with the hypothesis of metabolic flux regulation, making available the energy in the form of NADH to support nitrate assimilation. This work contributes with an initial picture of proteins presenting differential accumulation in industrial contaminant yeast, in strict association with possible metabolic responses to nitrate as sole nitrogen source in cultivation medium. BIOLOGICAL SIGNIFICANCE: The present study investigated the gene expression at translational level of yeast D. bruxellensis for nitrate assimilation. This study corroborated with biological models that consider the ability to assimilate this nitrogen source confers advantages on this yeast during the fermentation process industry. However, larger studies are needed in this way as our group is investigating new proteins under LC-MS/MS approach. Together, these studies will help in understanding the operation of networks and cellular regulation of the process of assimilation of nitrogen sources for the D. bruxellensis, unravelling new aspects of the physiology of this yeast by proteomic analysis. This article is part of a Special Issue entitled: Environmental and structural proteomics.

Differentially delayed root proteome responses to salt stress in sugar cane varieties.

Soil salinity is a limiting factor to sugar cane crop development, although in general plants present variable mechanisms of tolerance to salinity stress. The molecular basis underlying these mechanisms can be inferred by using proteomic analysis. Thus, the objective of this work was to identify differentially expressed proteins in sugar cane plants submitted to salinity stress. For that, a greenhouse experiment was established with four sugar cane varieties and two salt conditions, 0 mM (control) and 200 mM NaCl. Physiological and proteomics analyses were performed after 2 and 72 h of stress induction by salt. Distinct physiological responses to salinity stress were observed in the varieties and linked to tolerance mechanisms. In proteomic analysis, the roots soluble protein fraction was extracted, quantified, and analyzed through bidimensional electrophoresis. Gel images analyses were done computationally, where in each contrast only one variable was considered (salinity condition or variety). Differential spots were excised, digested by trypsin, and identified via mass spectrometry. The tolerant variety RB867515 showed the highest accumulation of proteins involved in growth, development, carbohydrate and energy metabolism, reactive oxygen species metabolization, protein protection, and membrane stabilization after 2 h of stress. On the other hand, the presence of these proteins in the sensitive variety was verified only in stress treatment after 72 h. These data indicate that these stress responses pathways play a role in the tolerance to salinity in sugar cane, and their effectiveness for phenotypical tolerance depends on early stress detection and activation of the coding genes expression.

Cell wall, lignin and fatty acid-related transcriptome in soybean: Achieving gene expression patterns for bioenergy legume.

Increasing efforts to preserve environmental resources have included the development of more efficient technologies to produce energy from renewable sources such as plant biomass, notably through biofuels and cellulosic residues. The relevance of the soybean industry is due mostly to oil and protein production which, although interdependent, results from coordinated gene expression in primary metabolism. Concerning biomass and biodiesel, a comprehensive analysis of gene regulation associated with cell wall components (as polysaccharides and lignin) and fatty acid metabolism may be very useful for finding new strategies in soybean breeding for the expanding bioenergy industry. Searching the Genosoja transcriptional database for enzymes and proteins directly involved in cell wall, lignin and fatty acid metabolism provides gene expression datasets with frequency distribution and specific regulation that is shared among several cultivars and organs, and also in response to different biotic/abiotic stress treatments. These results may be useful as a starting point to depict the Genosoja database regarding gene expression directly associated with potential applications of soybean biomass and/or residues for bioenergy-producing technologies.

Characterization of a new defensin from cowpea (Vigna unguiculata (L.) Walp.).

Using Phaseoleae defensins available in databases, a putative defensin gene was isolated in cowpea (Vigna unguiculata (L.) Walp.) and cloned from genomic cowpea DNA. The putative mature defensin sequence displays the characteristic defensins residues arrangement, secondary and tertiary structures were predicted and splicing analysis was performed. Using RT-PCR, defensin expression and differences in response to biotic stimuli between infected and non infected plants were tested.

Bioinformatics-coupled molecular approaches for unravelling potential antimicrobial peptides coding genes in Brazilian native and crop plant species.

As eukaryotes, plants include in innate defense antimicrobial peptides (AMP), usually small cysteine or glycine-rich peptides effective against a wide range of pathogens. The main classes of AMPs are represented by alpha/beta-defensins, lipid-transfer proteins, thionins, cyclotides, snakins and hevein-like, according to amino acid sequence homology. In spite of increasing number of described AMPs from plants, last decade advances in methodologies for gene expression and the huge amounts of genomic, proteomic and other "-omics" data lead to new prospection strategies of novel potential candidates. Organised user-friendly databases are available to be searched and enlarged with newly discovered plant-derived AMPs. Bioinformatics has allowed the application of in silico-associated molecular tools aiming to screen and identify genes coding for these peptides, starting from genome, transcriptomes, proteome or metabolome from various cultivated or wild plants. As expected, crop plants have been the main target for AMP research and application, also because the higher availability of molecular data. However, wild plant species biodiversity and results for AMP search have increased the importance of characterization in native plants. Enormous plant diversity in Brazilian ecosystems summed to croplands provides potential targets to identify novel candidates for plant AMP. Despite these opportunities, bioinformatics tools are restricted to species whose "-omics" are available, otherwise only heterology-based analyses are feasible, as it has been the case of most Brazilian plant AMP prospection research groups. Still rare, but promising results indicate that this research field on Brazilian crop/native species presents a growing trend of application in agriculture, medicine and industry.