Maize (Zea mays L.) root cap cells secrete a large variety of compounds including proteins via an amorphous gel structure called mucilage into the rhizosphere. In the present study, mucilage secreted by primary roots of 3-4 day old maize seedlings was collected under axenic conditions, and the constitutively secreted proteome was analyzed. A total of 2848 distinct extracellular proteins were identified by nanoLC-MS/MS. Among those, metabolic proteins (approximately 25%) represented the largest class of annotated proteins. Comprehensive sets of proteins involved in cell wall metabolism, scavenging of reactive oxygen species, stress response, or nutrient acquisition provided detailed insights in functions required at the root-soil interface. For 85-94% of the mucilage proteins previously identified in the relatively small data sets of the dicot species pea, Arabidopsis, and rapeseed, a close homologue was identified in the mucilage proteome of the monocot model plant maize, suggesting a considerable degree of conservation between mono and dicot mucilage proteomes. Homologues of a core set of 12 maize proteins including three superoxide dismutases and four chitinases, which provide protection from fungal infections, were present in all three mucilage proteomes investigated thus far in the dicot species Arabidopsis, rapeseed, and pea and might therefore be of particular importance.
"These proteins are believed to play an important role in the rhizosphere and a relatively high number (54%) had predicted signal peptides. Ma et al. (2010) collected proteins secreted in the mucilage of primary maize roots. Using a combination of 1D SDS-PAGE and HPLC-MS/MS, the presence of 2848 proteins were reported, which is over 50 times more compared to earlier quantitative studies of root mucilage based on 2D-PAGE or MudPIT (Basu et al., 2006; Wen et al., 2007). "
[Show abstract][Hide abstract] ABSTRACT: The plant secretome refers to the set of proteins secreted out of the plant cell into the surrounding extracellular space commonly referred to as the apoplast. Secreted proteins maintain cell structure and acts in signaling and are crucial for stress responses where they can interact with pathogen effectors and control the extracellular environment. Typically, secreted proteins contain an N-terminal signal peptide and are directed through the endoplasmic reticulum/Golgi pathway. However, in plants many proteins found in the secretome lack such a signature and might follow alternative ways of secretion. This review covers techniques to isolate plant secretomes and how to identify and quantify their constituent proteins. Furthermore, bioinformatical tools to predict secretion signals and define the putative secretome are presented. Findings from proteomic studies and important protein families of plant secretomes, such as proteases and hydrolases, are highlighted.
"Over the past decade, mass spectrometry (MS)-based shotgun proteomics has emerged as a high-throughput, unbiased method for the identification of proteins in complex samples , . Its application holds great potential in identifying comprehensive proteins profile in all kinds of species , . Brechenmacher, L. analyzed the proteome of isolated soybean root hair cells using shotgun proteomics approaches. "
[Show abstract][Hide abstract] ABSTRACT: Shotgun proteomics data analysis usually relies on database search. Because commonly employed protein sequence databases of most species do not contain sufficient protein information, the application of shotgun proteomics to the research of protein sequence profile remains a big challenge, especially to the species whose genome has not been sequenced yet.
In this paper, we present a workflow with integrated database to partly address this problem. First, we downloaded the homologous species database. Next, we identified the transcriptome of the sample, created a protein sequence database based on the transcriptome data, and integtrated it with homologous species database. Lastly, we developed a workflow for identifying peptides simultaneously from shotgun proteomics data.
We used datasets from orange leaves samples to demonstrate our workflow. The results showed that the integrated database had great advantage on orange shotgun proteomics data analysis compared to the homologous species database, an 18.5% increase in number of proteins identification.
PLoS ONE 10/2012; 7(6):e39494. DOI:10.1371/journal.pone.0039494 · 3.23 Impact Factor
"However, it was not possible to detect ear preferential fungal infection (Fig. 5B). Previously, a large number of proteins related to plant defence or diseases were detected in root mucilage even if all maize plants were healthy and grown in an axenic environment (Ma et al., 2010). Therefore, it was concluded that nitrogen nutritional imbalance, rather than bacterial or fungal pathogen infection, resulted in significant differential accumulation of proteins related to plant defence in the present study. "
[Show abstract][Hide abstract] ABSTRACT: Optimal nitrogen (N) supply is critical for achieving high grain yield of maize. It is well established that N deficiency
significantly reduces grain yield and N oversupply reduces N use efficiency without significant yield increase. However, the
underlying proteomic mechanism remains poorly understood. The present field study showed that N deficiency significantly reduced
ear size and dry matter accumulation in the cob and grain, directly resulting in a significant decrease in grain yield. The
N content, biomass accumulation, and proteomic variations were further analysed in young ears at the silking stage under different
N regimes. N deficiency significantly reduced N content and biomass accumulation in young ears of maize plants. Proteomic
analysis identified 47 proteins with significant differential accumulation in young ears under different N treatments. Eighteen
proteins also responded to other abiotic and biotic stresses, suggesting that N nutritional imbalance triggered a general
stress response. Importantly, 24 proteins are involved in regulation of hormonal metabolism and functions, ear development,
and C/N metabolism in young ears, indicating profound impacts of N nutrition on ear growth and grain yield at the proteomic
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