Challenges and Prospects of Plant Proteomics

Wijk, Klaas J. van

doi:10.1104/pp.126.2.501

Cited by 207 publications

(116 citation statements)

References 29 publications

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“…As the word "candidates" implies, the results of our study are not definitive due to the nature of prediction software and due to the possibility of errors in protein annotations in the genome databases (van Wijk, 2001). Although it is likely that at least 10% of the AtPEM candidates represent incorrect predictions, it is reasonable to assume that the selected candidates represent a large portion of the real envelope proteome.…”

Section: Discussionmentioning

confidence: 88%

The Predicted Candidates of Arabidopsis Plastid Inner Envelope Membrane Proteins and Their Expression Profiles,

Koo

Ohlrogge

2002

Plant Physiology

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Plastid envelope proteins from the Arabidopsis nuclear genome were predicted using computational methods. Selection criteria were: first, to find proteins with NH 2 -terminal plastid-targeting peptides from all annotated open reading frames from Arabidopsis; second, to search for proteins with membrane-spanning domains among the predicted plastidial-targeted proteins; and third, to subtract known thylakoid membrane proteins. Five hundred forty-one proteins were selected as potential candidates of the Arabidopsis plastid inner envelope membrane proteins (AtPEM candidates). Only 34% (183) of the AtPEM candidates could be assigned to putative functions based on sequence similarity to proteins of known function (compared with the 69% function assignment of the total predicted proteins in the genome). Of the 183 candidates with assigned functions, 40% were classified in the category of "transport facilitation," indicating that this collection is highly enriched in membrane transporters. Information on the predicted proteins, tissue expression data from expressed sequence tags and microarrays, and publicly available T-DNA insertion lines were collected. The data set complements proteomic-based efforts in the increased detection of integral membrane proteins, low-abundance proteins, or those not expressed in tissues selected for proteomic analysis. Digital northern analysis of expressed sequence tags suggested that the transcript levels of most AtPEM candidates were relatively constant among different tissues in contrast to stroma and the thylakoid proteins. However, both digital northern and microarray analyses identified a number of AtPEM candidates with tissue-specific expression patterns.Plastids exist in a wide range of differential forms, including proplastids, chloroplasts, etioplasts, amyloplasts, leucoplasts, and chromoplasts, depending on the developmental stage and function of the plant cells in which they reside. To a large extent, the types of plastids that are carried by cells determine the metabolic function and products of the particular plant tissue (Kirk and Tilney-Bassett, 1978).One constant feature among the various types of plastids is the double membrane envelope structure that surrounds the organelle. The envelope, especially the inner envelope, effectively separates plastid metabolism from that of the cytosol. At the same time, almost all carbon and a major flux of other metabolites, various polypeptides, and signals must move through the envelope to coordinate and integrate metabolism with the entire cell. Plastid envelopes contain protein transport machinery (Schnell, 1995;Cline and Henry, 1996;Heins et al., 1998), and are a major site for membrane biogenesis. Metabolite transporters from chloroplast and/or nongreen plastids accommodate the requirements of the different photosynthetic or heterotrophic tissues (Kammerer et al., 1998;Neuhaus and Emes, 2000). Membrane constituents (glycerolipids, pigments, and prenylquinones) are synthesized on the envelope membrane as well as the porphyrin ring ...

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Section: Discussionmentioning

confidence: 88%

The Predicted Candidates of Arabidopsis Plastid Inner Envelope Membrane Proteins and Their Expression Profiles,

Koo

Ohlrogge

2002

Plant Physiology

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“…Many biological researchers investigating proteomes have already experienced the lack of genomic resources as an inability to identify proteins by MS. For example, proteomic studies in maize, an economically important organism, have been compromised due to the lack of database resources and an inability to use available database resources effectively [47]. However, plant scientists have begun to realize the limitations of non-error-tolerant methods of protein identification and now see the prospects of sequence similarity methods to contribute to proteomics [47,55].…”

Section: Perspective: Proteomics and Phylogenetic Considerations For mentioning

confidence: 99%

Expanding the organismal scope of proteomics: Cross‐species protein identification by mass spectrometry and its implications

2003

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“…Plant proteomics, when compared with proteomic analyses of prokaryotes, yeast, and humans, is in its infancy, which is partly due to the lack of availability of completed genomic or cDNA sequences from plants (11). The completion of the draft sequence of the rice (Oryza sativa) genome and subsequent prediction of the protein complement (12) provided us with the unique opportunity to study the metabolic pathways common to multiple tissues and those uniquely expressed in particular tissues.…”

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confidence: 99%

Proteomic survey of metabolic pathways in rice

Koller

Washburn

Lange

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

372

224

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A systematic proteomic analysis of rice (Oryza sativa) leaf, root, and seed tissue using two independent technologies, two-dimensional gel electrophoresis followed by tandem mass spectrometry and multidimensional protein identification technology, allowed the detection and identification of 2,528 unique proteins, which represents the most comprehensive proteome exploration to date. A comparative display of the expression patterns indicated that enzymes involved in central metabolic pathways are present in all tissues, whereas metabolic specialization is reflected in the occurrence of a tissue-specific enzyme complement. For example, tissuespecific and subcellular compartment-specific isoforms of ADPglucose pyrophosphorylase were detected, thus providing proteomic confirmation of the presence of distinct regulatory mechanisms involved in the biosynthesis and breakdown of separate starch pools in different tissues. In addition, several previously characterized allergenic proteins were identified in the seed sample, indicating the potential of proteomic approaches to survey food samples with regard to the occurrence of allergens.

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Challenges and Prospects of Plant Proteomics

Cited by 207 publications

References 29 publications

The Predicted Candidates of Arabidopsis Plastid Inner Envelope Membrane Proteins and Their Expression Profiles,

The Predicted Candidates of Arabidopsis Plastid Inner Envelope Membrane Proteins and Their Expression Profiles,

Expanding the organismal scope of proteomics: Cross‐species protein identification by mass spectrometry and its implications

Proteomic survey of metabolic pathways in rice

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