Large-scale plant proteomics

Kersten, Birgit; Bürkle, Lukas; Kuhn, Eckehard J.; Giavalisco, Patrick; Konthur, Zoltán; Lueking, Angelika; Walter, Gerald; Eickhoff, Holger; Schneider, Ulrich

doi:10.1007/978-94-010-0448-0_9

Cited by 29 publications

(33 citation statements)

References 80 publications

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“…Genes expressed only after induction with phytohormones were included by also isolating and combining RNA from seedlings treated with one of the five classical phytohormones (auxin, abscisic acid, cytokinin, ethylene and gibberellic acid). For the construction of the libraries we used the Gateway™ in vitro cloning system as this system has been proven to be very efficient in large scale approaches and is used in many functional genomic experiments (Kersten et al 2002;Vincentelli et al 2003;Li et al 2004). All sequenced clones were assigned to the GO process ontology to check if all these functional categories are represented within the library and to compare this functional distribution to the whole annotated Arabidopsis genome.…”

Section: Discussionmentioning

confidence: 99%

“…Unicellular organisms and animal model systems, like Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, or Drosophila melanogaster have been the focus of attention in the first of these large-scale experiments. However the sequencing of the model plants Arabidopsis and rice have enabled large-scale approaches to also be conducted in plants (Arabidopsis Genome 2000; Bürkle et al 2003;Fang et al 2002;Goff et al 2002;Kersten et al 2002;Roberts 2002;Yu et al 2002). The need for large-scale investigation of biological processes becomes especially evident when considering the high number of genes of unknown function and often inaccurate bioinformatic predictions.…”

Section: Introductionmentioning

confidence: 99%

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In vitro recombination cloning of entire cDNA libraries in Arabidopsis thaliana and its application to the yeast two-hybrid system

Bürkle

Meyer²,

Dortay³

et al. 2005

Funct Integr Genomics

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In the postgenomic era many experiments rely on the availability of transcript sequence for cloning. As these clones usually originate from cDNA libraries, the quality of these libraries is crucial. If a good library is generated it is desirable to use a versatile cloning system suitable for many different kinds of applications. The cloning systems based on in vitro recombination proves fitting for this task. However, the use of this method for shuttling entire cDNA libraries between different vectors has not yet been studied in great detail. Here we describe the construction of four cDNA libraries from different tissues of Arabidopsis thaliana, the shuttling of the libraries into expression vectors, and evaluation of this method as well as its suitability for downstream applications. Libraries were constructed from seedlings, hormone treated seedlings, flowers, developing seeds and primary leaves in the "entry vector" of the Gateway™ cloning system. After initial characterization of the libraries, they were shuttled into an expression vector (a yeast two-hybrid prey vector). To monitor for a size bias generally assumed to be inherent to in vitro recombination methods, the libraries were characterized before and after the transfer into the expression vector. However no significant difference could be detected. The functionality of the in vitro recombination system for the shuttling of entire libraries was then further tested by protein-protein interaction screens. The results of the library characterization and of the yeast two-hybrid screens and their implications for large-scale proteomic approaches are discussed.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

In vitro recombination cloning of entire cDNA libraries in Arabidopsis thaliana and its application to the yeast two-hybrid system

Bürkle

Meyer²,

Dortay³

et al. 2005

Funct Integr Genomics

Self Cite

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“…While proteomics research is advanced in animals and yeast, plant proteomics is still in the initial phase (Kersten et al, 2002;van Wijk, 2001;Zivy and de Vienne, 2000). Several proteomics groups have studied subcellular proteomes and protein complexes in plants, e.g.…”

Section: Introductionmentioning

confidence: 99%

Analysis of the Arabidopsis nuclear proteome and its response to cold stress

Bae¹,

Cho²,

et al. 2003

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These authors contributed equally to the work. SummaryThe nucleus is the subcellular organelle that contains nearly all the genetic information required for the regulated expression of cellular proteins. In this study, we comprehensively characterized the Arabidopsis nuclear proteome. Nuclear proteins were isolated and analyzed using two-dimensional (2D) gel electrophoresis and matrix-assisted laser desorption/ionization time-of-¯ight mass spectrometry (MALDI-TOF MS). Approximately 500±700 spots were detected in reference 2D gels of nuclear proteins. Proteomic analyses led to the identi®cation of 184 spots corresponding to 158 different proteins implicated in a variety of cellular functions. We additionally analyzed the changes in the nuclear proteome in response to cold stress. Of the 184 identi®ed proteins, 54 were up-or downregulated with a greater than twofold change in response to cold treatment. Among these, six proteins were selected for further characterization. Northern analysis data revealed that gene expression of these proteins was also altered by cold stress. Following transient expression in BY-2 protoplasts, two proteins were detected in both the cytoplasm and the nucleus and four others were detected exclusively in the nucleus, which correlates well with the nuclear localization patterns of the proteomic data. Our study provides an initial insight into the Arabidopsis nuclear proteome and its response to cold stress.

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“…Proteomics has become an important tool in the study of plant biology (Heazlewood and Millar 2003;Kersten et al 2002;Rossignol 2001;Thiellement et al 1999;van Wijk 2001). In the last decade, proteomics has succeeded in identifying approximately 400 proteins associated with the development and functioning of both mycorrhizal and rhizobial symbioses (Bestel-Corre et al 2004;Rolfe et al 2003;Trevaskis et al 2002).…”

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confidence: 99%

Proteomic Analysis of Soybean Root Hairs After Infection by Bradyrhizobium japonicum

Wan¹,

Torres²,

Ganapathy³

et al. 2005

MPMI

124

122

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Infection of soybean root hairs by Bradyrhizobium japonicum is the first of several complex events leading to nodulation. In the current proteomic study, soybean root hairs after inoculation with B. japonicum were separated from roots. Total proteins were analyzed by two-dimensional (2-D) polyacrylamide gel electrophoresis. In one experiment, 96 protein spots were analyzed by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) to compare protein profiles between uninoculated roots and root hairs. Another 37 spots, derived from inoculated root hairs over different timepoints, were also analyzed by tandem MS (MS/MS). As expected, some proteins were differentially expressed in root hairs compared with roots (e.g., a chitinase and phosphoenolpyruvate carboxylase). Out of 37 spots analyzed by MS/MS, 27 candidate proteins were identified by database comparisons. These included several proteins known to respond to rhizobial inoculation (e.g., peroxidase and phenylalanine-ammonia lyase). However, novel proteins were also identified (e.g., phospholipase D and phosphoglucomutase). This research establishes an excellent system for the study of root-hair infection by rhizobia and, in a more general sense, the functional genomics of a single, plant cell type. The results obtained also indicate that proteomic studies with soybean, lacking a complete genome sequence, are practical.

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Large-scale plant proteomics

Cited by 29 publications

References 80 publications

In vitro recombination cloning of entire cDNA libraries in Arabidopsis thaliana and its application to the yeast two-hybrid system

In vitro recombination cloning of entire cDNA libraries in Arabidopsis thaliana and its application to the yeast two-hybrid system

Analysis of the Arabidopsis nuclear proteome and its response to cold stress

Proteomic Analysis of Soybean Root Hairs After Infection by Bradyrhizobium japonicum

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