Alternative workflows for plant proteomic analysis

Increasing Coverage of Proteome Identification of the Fruiting Body of Agaricus bisporus by Shotgun Proteomics

To increase coverage of protein identification of an Agaricus bisporus fruiting body, we analyzed the crude protein fraction of the fruiting body by using a shotgun proteomics approach where 7 MudPIT (Multi-Protein identification Technology) runs were conducted and the MS/MS spectra from the 7 MudPIT runs were merged. Overall, 3093 non-redundant proteins were identified to support the expression of those genes annotated in the genome database of Agaricus bisporus. The physicochemical properties of the identified proteins, i.e., wide pI value range and molecular mass range, were indicative of unbiased protein identification. The relative quantification of the identified proteins revealed that K5XI50 (Aldedh domain-containing protein) and K5XEW1 (Ubiquitin-like domain-containing protein) were highly abundant in the fruiting body. Based on the information in the Uniprot (Universal Protein Resource) database for A. bisporus, only approximately 53% of the 3093 identified proteins have been functionally described and approximately 47% of the proteins remain uncharacterized. Gene Ontology analysis revealed that the majority of proteins were annotated with a biological process, and proteins associated with coiled-coil (12.8%) and nucleotide binding (8.21%) categories were dominant. The Kyoto Encyclopedia of Genes and Genome analysis revealed that proteins involved in biosynthesis of secondary metabolites and tyrosine metabolism were enriched in a fruiting body of Agaricus bisporus, suggesting that the proteins are associated with antioxidant metabolites.

Putative Rust Fungal Effector Proteins in Infected Bean and Soybean Leaves

The plant-pathogenic fungi Uromyces appendiculatus and Phakopsora pachyrhizi cause debilitating rust diseases on common bean and soybean. These rust fungi secrete effector proteins that allow them to infect plants, but their effector repertoires are not understood. The discovery of rust fungus effectors may eventually help guide decisions and actions that mitigate crop production loss. Therefore, we used mass spectrometry to identify thousands of proteins in infected beans and soybeans and in germinated fungal spores. The comparative analysis between the two helped differentiate a set of 24 U. appendiculatus proteins targeted for secretion that were specifically found in infected beans and a set of 34 U. appendiculatus proteins targeted for secretion that were found in germinated spores and infected beans. The proteins specific to infected beans included family 26 and family 76 glycoside hydrolases that may contribute to degrading plant cell walls. There were also several types of proteins with structural motifs that may aid in stabilizing the specialized fungal haustorium cell that interfaces the plant cell membrane during infection. There were 16 P. pachyrhizi proteins targeted for secretion that were found in infected soybeans, and many of these proteins resembled the U. appendiculatus proteins found in infected beans, which implies that these proteins are important to rust fungal pathology in general. This data set provides insight to the biochemical mechanisms that rust fungi use to overcome plant immune systems and to parasitize cells.

Studies of a biochemical factory: tomato trichome deep expressed sequence tag sequencing and proteomics

Shotgun proteomics analysis allows hundreds of proteins to be identified and quantified from a single sample at relatively low cost. Extensive DNA sequence information is a prerequisite for shotgun proteomics, and it is ideal to have sequence for the organism being studied rather than from related species or accessions. While this requirement has limited the set of organisms that are candidates for this approach, next generation sequencing technologies make it feasible to obtain deep DNA sequence coverage from any organism. As part of our studies of specialized (secondary) metabolism in tomato (Solanum lycopersicum) trichomes, 454 sequencing of cDNA was combined with shotgun proteomics analyses to obtain in-depth profiles of genes and proteins expressed in leaf and stem glandular trichomes of 3-week-old plants. The expressed sequence tag and proteomics data sets combined with metabolite analysis led to the discovery and characterization of a sesquiterpene synthase that produces beta-caryophyllene and alpha-humulene from E,E-farnesyl diphosphate in trichomes of leaf but not of stem. This analysis demonstrates the utility of combining high-throughput cDNA sequencing with proteomics experiments in a target tissue. These data can be used for dissection of other biochemical processes in these specialized epidermal cells.

Establishment of a protein reference map for soybean root hair cells

Root hairs are single tubular cells formed from the differentiation of epidermal cells on roots. They are involved in water and nutrient uptake and represent the infection site on leguminous roots by rhizobia, soil bacteria that establish a nitrogen-fixing symbiosis. Root hairs develop by polar cell expansion or tip growth, a unique mode of plant growth shared only with pollen tubes. A more complete characterization of root hair cell biology will lead to a better understanding of tip growth, the rhizobial infection process, and also lead to improvements in plant water and nutrient uptake. We analyzed the proteome of isolated soybean (Glycine max) root hair cells using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and shotgun proteomics (1D-PAGE-liquid chromatography and multidimensional protein identification technology) approaches. Soybean was selected for this study due to its agronomic importance and its root size. The resulting soybean root hair proteome reference map identified 1,492 different proteins. 2D-PAGE followed by mass spectrometry identified 527 proteins from total cell contents. A complementary shotgun analysis identified 1,134 total proteins, including 443 proteins that were specific to the microsomal fraction. Only 169 proteins were identified by the 2D-PAGE and shotgun methods, which highlights the advantage of using both methods. The proteins identified are involved not only in basic cell metabolism but also in functions more specific to the single root hair cell, including water and nutrient uptake, vesicle trafficking, and hormone and secondary metabolism. The data presented provide useful insight into the metabolic activities of a single, differentiated plant cell type.

Quantitative proteomic analysis of bean plants infected by a virulent and avirulent obligate rust fungus

Plants appear to have two types of active defenses, a broad-spectrum basal system and a system controlled by R-genes providing stronger resistance to some pathogens that break the basal defense. However, it is unknown if the systems are separate entities. Therefore, we analyzed proteins from leaves of the dry bean crop plant Phaseolus vulgaris using a high-throughput liquid chromatography tandem mass spectrometry method. By statistically comparing the amounts of proteins detected in a single plant variety that is susceptible or resistant to infection, depending on the strains of a rust fungus introduced, we defined basal and R-gene-mediated plant defenses at the proteomic level. The data reveal that some basal defense proteins are potential regulators of a strong defense weakened by the fungus and that the R-gene modulates proteins similar to those in the basal system. The results satisfy a new model whereby R-genes are part of the basal system and repair disabled defenses to reinstate strong resistance.

A systems biology investigation of the MEP/terpenoid and shikimate/phenylpropanoid pathways points to multiple levels of metabolic control in sweet basil glandular trichomes

The glandular trichome is an excellent model system for investigating plant metabolic processes and their regulation within a single cell type. We utilized a proteomics-based approach with isolated trichomes of four different sweet basil (Ocimum basilicum L.) lines possessing very different metabolite profiles to clarify the regulation of metabolism in this single cell type. Significant differences in the distribution and accumulation of the 881 highly abundant and non-redundant protein entries demonstrated that although the proteomes of the glandular trichomes of the four basil lines shared many similarities they were also each quite distinct. Correspondence between proteomic, expressed sequence tag, and metabolic profiling data demonstrated that differential gene expression at major metabolic branch points appears to be responsible for controlling the overall production of phenylpropanoid versus terpenoid constituents in the glandular trichomes of the different basil lines. In contrast, post-transcriptional and post-translational regulation of some enzymes appears to contribute significantly to the chemical diversity observed within compound classes for the different basil lines. Differential phosphorylation of enzymes in the 2-C-methyl-d-erythritol 4-phosphate (MEP)/terpenoid and shikimate/phenylpropanoid pathways appears to play an important role in regulating metabolism in this single cell type. Additionally, precursors for different classes of terpenoids, including mono- and sesquiterpenoids, appear to be almost exclusively supplied by the MEP pathway, and not the mevalonate pathway, in basil glandular trichomes.

Tandem mass spectrometry for the detection of plant pathogenic fungi and the effects of database composition on protein inferences

LC-MS/MS has demonstrated potential for detecting plant pathogens. Unlike PCR or ELISA, LC-MS/MS does not require pathogen-specific reagents for the detection of pathogen-specific proteins and peptides. However, the MS/MS approach we and others have explored does require a protein sequence reference database and database-search software to interpret tandem mass spectra. To evaluate the limitations of database composition on pathogen identification, we analyzed proteins from cultured Ustilago maydis, Phytophthora sojae, Fusarium graminearum, and Rhizoctonia solani by LC-MS/MS. When the search database did not contain sequences for a target pathogen, or contained sequences to related pathogens, target pathogen spectra were reliably matched to protein sequences from nontarget organisms, giving an illusion that proteins from nontarget organisms were identified. Our analysis demonstrates that when database-search software is used as part of the identification process, a paradox exists whereby additional sequences needed to detect a wide variety of possible organisms may lead to more cross-species protein matches and misidentification of pathogens.

Subcellular shotgun proteomics in plants: looking beyond the usual suspects

In this review we examine the current state of analytical methods used for shotgun proteomics experiments in plants. The rapid advances in this field in recent years are discussed, and contrasted with experiments performed using current widely used procedures. We also examine the use of subcellular fractionation approaches as they apply to plant proteomics, and discuss how appropriate sample preparation can produce a great increase in proteome coverage in subsequent analysis. We conclude that the conjunction of these two techniques represents a significant advance in plant proteomics, and the future of plant biology research will continue to be enriched by the ongoing development of proteomic analytical technology.

Protein accumulation in the germinating Uromyces appendiculatus uredospore

Uromyces appendiculatus is a rust fungus that causes disease on beans. To understand more about the biology of U. appendiculatus, we have used multidimensional protein identification technology to survey proteins in germinating asexual uredospores and have compared this data with proteins discovered in an inactive spore. The relative concentrations of proteins were estimated by counting the numbers of tandem mass spectra assigned to peptides for each detected protein. After germination, there were few changes in amounts of accumulated proteins involved in glycolysis, acetyl Co-A metabolism, citric acid cycle, ATP-coupled proton transport, or gluconeogenesis. Moreover, the total amount of translation elongation factors remained high, supporting a prior model that suggests that germlings acquire protein translation machinery from uredospores. However, germlings contained a higher amount of proteins involved in mitochondrial ADP:ATP translocation, which is indicative of increased energy production. Also, there were more accumulating histone proteins, pointing to the reorganization of the nuclei that occurs after germination prior to appressorium formation. Generally, these changes are indicative of metabolic transition from dormancy to germination and are supported by cytological and developmental models of germling growth.