ProMEX – a mass spectral reference database for plant proteomics

The ProMEX database is one of the main collection of annotated tryptic peptides in plant proteomics. The main objective of the ProMEX database is to provide experimental MS/MS-based information for cell type-specific or sub-cellular proteomes in Arabidopsis thaliana, Medicago truncatula, Chlamydomonas reinhardtii, Lotus japonicus, Lotus corniculatus, Phaseolus vulgaris, Lycopersicon esculentum, Solanum tuberosum, Nicotiana tabacum, Glycine max, Zea mays, Bradyrhizobium japonicum, and Sinorhizobium meliloti. Direct links at the protein level to the most relevant databases are present in ProMEX. Furthermore, the spectral sequence information are linked to their respective pathways and can be viewed in pathway maps

Comparative expression profiling reveals a role of the root apoplast in local phosphate response

BACKGROUND Plant adaptation to limited phosphate availability comprises a wide range of responses to conserve and remobilize internal phosphate sources and to enhance phosphate acquisition. Vigorous restructuring of root system architecture provides a developmental strategy for topsoil exploration and phosphate scavenging. Changes in external phosphate availability are locally sensed at root tips and adjust root growth by modulating cell expansion and cell division. The functionally interacting Arabidopsis genes, LOW PHOSPHATE RESPONSE 1 and 2 (LPR1/LPR2) and PHOSPHATE DEFICIENCY RESPONSE 2 (PDR2), are key components of root phosphate sensing. We recently demonstrated that the LOW PHOSPHATE RESPONSE 1 - PHOSPHATE DEFICIENCY RESPONSE 2 (LPR1-PDR2) module mediates apoplastic deposition of ferric iron (Fe3+) in the growing root tip during phosphate limitation. Iron deposition coincides with sites of reactive oxygen species generation and triggers cell wall thickening and callose accumulation, which interfere with cell-to-cell communication and inhibit root growth. RESULTS We took advantage of the opposite phosphate-conditional root phenotype of the phosphate deficiency response 2 mutant (hypersensitive) and low phosphate response 1 and 2 double mutant (insensitive) to investigate the phosphate dependent regulation of gene and protein expression in roots using genome-wide transcriptome and proteome analysis. We observed an overrepresentation of genes and proteins that are involved in the regulation of iron homeostasis, cell wall remodeling and reactive oxygen species formation, and we highlight a number of candidate genes with a potential function in root adaptation to limited phosphate availability. Our experiments reveal that FERRIC REDUCTASE DEFECTIVE 3 mediated, apoplastic iron redistribution, but not intracellular iron uptake and iron storage, triggers phosphate-dependent root growth modulation. We further highlight expressional changes of several cell wall-modifying enzymes and provide evidence for adjustment of the pectin network at sites of iron accumulation in the root. CONCLUSION Our study reveals new aspects of the elaborate interplay between phosphate starvation responses and changes in iron homeostasis. The results emphasize the importance of apoplastic iron redistribution to mediate phosphate-dependent root growth adjustment and suggest an important role for citrate in phosphate-dependent apoplastic iron transport. We further demonstrate that root growth modulation correlates with an altered expression of cell wall modifying enzymes and changes in the pectin network of the phosphate-deprived root tip, supporting the hypothesis that pectins are involved in iron binding and/or phosphate mobilization

Variabilität der Proteine der Augenlinse und ihre Auswirkung auf Kataraktbildung und Kataraktentwicklung

Die Variabilität der Proteine der Augenlinse der Maus wurde in der Spezies Mus spretus und in zwei Stämmen der Spezies Mus musculus untersucht. Die Linsenproteine von Mus musculus und Mus spretus wurden mit hochauflösender Flüssigkeitschromatographie und Massenspektrometrie (nano LC-MS/MS) analysiert. Mit der iTRAQ Strategie wurden 36 Proteine identifiziert und quantifiziert, darunter 11 der 16 ubiquitären Crystalline, die 90% der Gesamtheit der Linsenproteine ausmachen sowie die meisten anderen reichlich vorhandenen Linsenproteine. Sequenzpolymorphismen in vier Crystallinen (Alpha B, Gamma B, Gamma F und Gamma S) wurden entdeckt. Die Variabilität der Proteine der Augenlinse in den beiden Mus musculus Stämmen wurden mit hochauflösender zweidimensionaler Gelelektrophorese und Massenspektrometrie (2DE und MS/MS) analysiert und komplett erfasst. Vierundneunzig (94) Proteine zeigten einen 2-fachen oder größeren Unterschied in ihrer Menge in den zwei Stämmen. Dreiundsechzig (63) der Proteine wurden identifiziert, die übrigen lagen außerhalb des Sensitivitätsbereiches der angewandten Methoden. Die Mengen der identifizierten Proteine in den Linsen von transgenen Tieren der beiden Stämme mit einer Knockout-Mutation in dem Alpha 3 connexin Gen die zu der stammesspezifisch unterschiedlich gravierenden Bildung einer Katarakt in dem Nucleus der Linse führte wurden ebenfalls analysiert. Der Einfluss der unterschiedlichen Proteinkomposition auf die Linsenerkrankung Katarakt wurde festgestellt. Sieben Proteine und verwandte Proteinspecies wurden als Faktoren (CP49, HSP27/25, Chaperonin subunit 6A, Hsc70 homolog, ERp29, Syntaxin binding protein und Annexin A1) die die Entwicklung der Krankheit modifizieren eindeutig festgestellt. Die funktionellen Implikationen der Proteinspezies, der modifizierten und unmodifizierten Genprodukte, wurden aufgezeigt.In an attempt to determine the variability in the proteins of the eye lens of the mouse, a discovery-type approach with proteomics methods was used. The lens is composed almost entirely of proteins in various stages of solution. Around 90% of lens proteins belong to the crystallin protein superfamily, which is loosely classified into Alpha, Beta and Gamma crystallins. There are sixteen primary crystallin gene translation products in the eye lens of the mouse, so the unmodified proteome is easily managed. The variability in two species, Mus musculus and Mus spretus, was examined using liquid chromatography (LC) and mass spectrometry (MS). Two types of isotope coded protein labeling reagents, the cleavable ICAT reagent and the iTRAQ reagent were used for the detection of variability and polymorphisms. The iTRAQ label was used in conjunction with nano-LC, automated MALDI plate spotting and MALDI/TOF/TOF-MS. The iTRAQ methodology proved superior to the ICAT based approach employing nano-LC and on-line ESI-MS. The investigation with the iTRAQ reagent identified and quantified 11 of the 16 crystallins ubiquitous to mammals and many of the major non-crystallin proteins in the lens fiber cells. Four polymorphisms in the crystallins (Alpha B, Gamma B, Gamma F and Gamma S crystallin) were also detected in the two mouse species, using the iTRAQ methodology. The variability in two strains, C57BL/6J and 129/SvJ of the Mus musculus species, and its effects on the onset and severity of cataract of the lens nucleus (because of loss of the Alpha 3 connexin protein due to knockout of the Alpha 3 connexin gene Gja3) was analyzed using two-dimensional electrophoresis (2-DE), 2-DE image analysis software and MALDI-MS. This produced the largest and most comprehensive investigation of mouse lens proteins to date, comprising more than 100 identified proteins each in the two strains and in the mutants of both strains. The variability in the lens proteins was completely established. Seven factors (CP49, HSP27/25, Chaperonin subunit 6A, DnaK-type molecular chaperone hsc70 homolog, Endoplasmatic reticulum protein 29, Syntaxin binding protein and Annexin A1) which specifically determine the onset and severity of nuclear cataract in the two strains are identified. The investigation shows that the healthy and pathological development in the lens • cannot be attributed to certain proteins alone, but that • similar but distinct networks of interactions, specific to the two mouse strains, are responsible for these phenomena in each of them. • The view has to be extended to the protein species level. A basis for the detailed understanding of the processes in healthy lens and cataract development is established