Plant Cell Wall Proteomes: Bioinformatics and Cell Biology Tools to Assess the Bona Fide Cell Wall Localization of Proteins.

The purification of plant cell walls is challenging because they constitute an open compartment which is not limited by a membrane like the cell organelles. Different strategies have been established to limit the contamination by proteins of other compartments in cell wall proteomics studies. Non-destructive methods rely on washing intact cells with various types of solutions without disrupting the plasma membrane in order to elute cell wall proteins.

Localizing proteins by tissue printing.

The simple technique of making tissue prints on appropriate substrate material has made possible the easy localization of proteins, nucleic acids, carbohydrates, and small molecules in a tissue-specific mode. Plant tissues can be used to produce prints revealing a remarkable amount of anatomical detail, even without staining, which might be used to record developmental changes over time. In this chapter we will focus on the protocols for the localization of proteins and glycans using antibodies or lectins, probably the most frequently used application, but the localization of other molecules is reported and the sources indicated.

Calmodulin and calmodulin-like proteins in plant calcium signaling.

Calmodulin (CaM) is a primary calcium sensor in all eukaryotes. It binds calcium and regulates the activity of a wide range of effector proteins in response to calcium signals. The list of CaM targets includes plant-specific proteins whose functions are progressively being elucidated.

Localizing proteins by tissue printing.

The simple technique of making tissue prints on appropriate substrate material has made possible the easy localization of proteins, nucleic acids, carbohydrates, and small molecules in a tissue-specific mode. Plant tissues can be used to produce prints revealing a remarkable amount of anatomical detail, even without staining, which might be used to record developmental changes over time. In this chapter we will focus on the protocols for the localization of proteins and glycans using antibodies or lectins, probably the most frequently used application, but the localization of other molecules is reported and the sources indicated.

Isolation of plant cell wall proteins.

The quality of a proteomic analysis of a cell compartment strongly depends on the reliability of the isolation procedure for the cell compartment of interest. Plant cell walls possess specific drawbacks: (1) the lack of a surrounding membrane may result in the loss of cell wall proteins (CWP) during the isolation procedure; (2) polysaccharide networks of cellulose, hemicelluloses, and pectins form potential traps for contaminants such as intracellular proteins; (3) the presence of proteins interacting in many different ways with the polysaccharide matrix require different procedures to elute them from the cell wall. Three categories of CWP are distinguished: labile proteins that have little or no interactions with cell wall components, weakly bound proteins extractable with salts, and strongly bound proteins.

Transcriptome of Aphanomyces euteiches: new oomycete putative pathogenicity factors and metabolic pathways.

Aphanomyces euteiches is an oomycete pathogen that causes seedling blight and root rot of legumes, such as alfalfa and pea. The genus Aphanomyces is phylogenically distinct from well-studied oomycetes such as Phytophthora sp., and contains species pathogenic on plants and aquatic animals.

AphanoDB: a genomic resource for Aphanomyces pathogens.

Background: The Oomycete genus Aphanomyces comprises devastating plant and animal pathogens. However, little is known about the molecular mechanisms underlying pathogenicity of Aphanomyces species. In this study, we report on the development of a public database called AphanoDB which is dedicated to Aphanomyces genomic data.

Root rot disease of legumes caused by Aphanomyces euteiches.

Unlabelled: The Oomycete genus Aphanomyces houses plant and animal pathogens found in both terrestrial and aquatic habitats. Aphanomyces euteiches Drechs. causes seedling damping off and root rot diseases on many legumes.

Regulation and role of a STE12-like transcription factor from the plant pathogen Colletotrichum lindemuthianum.

In phytopathogenic fungi, STE12-like genes encode transcription factors essential for appressorium-mediated host penetration. However, their regulation and downstream targets are still unknown. In the present study, a STE12-like gene (CLSTE12) from Colletotrichum lindemuthianum was isolated.

Towards the molecular understanding of glycogen elongation by amylosucrase.

Amylosucrase from Neisseria polysaccharea (AS) is a transglucosidase from the glycoside-hydrolase family 13 that catalyzes the synthesis of an amylose-like polymer from sucrose, without any primer. Its affinity towards glycogen is particularly noteworthy since glycogen is the best D-glucosyl unit acceptor and the most efficient activator (98-fold k(cat) increase) known for this enzyme. Glycogen-enzyme interactions were modeled starting from the crystallographic AS: maltoheptaose complex, where two key oligosaccharide binding sites, OB1 and OB2, were identified.

Evaluation of cell wall preparations for proteomics: a new procedure for purifying cell walls from Arabidopsis hypocotyls.

Background: The ultimate goal of proteomic analysis of a cell compartment should be the exhaustive identification of resident proteins; excluding proteins from other cell compartments. Reaching such a goal closely depends on the reliability of the isolation procedure for the cell compartment of interest. Plant cell walls possess specific difficulties: (i) the lack of a surrounding membrane may result in the loss of cell wall proteins (CWP) during the isolation procedure, (ii) polysaccharide networks of cellulose, hemicelluloses and pectins form potential traps for contaminants such as intracellular proteins.

Transcript profiling of a xylem vs phloem cDNA subtractive library identifies new genes expressed during xylogenesis in Eucalyptus.

Eucalyptus is one of the world's main sources of biomass. The genus includes species representing the principle hardwood trees used for pulp and paper. Here, we aimed to identify genes specifically expressed in differentiating secondary xylem compared with phloem.