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The Predicted Candidates of Arabidopsis Plastid Inner Envelope Membrane Proteins and Their Expression Profiles1(w)

The Predicted Candidates of Arabidopsis Plastid Inner Envelope Membrane Proteins and Their Expression Profiles1(w),Abraham J. K. Koo,John B. Ohlrogge

The Predicted Candidates of Arabidopsis Plastid Inner Envelope Membrane Proteins and Their Expression Profiles1(w)   (Citations: 20)
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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 NH2-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, amy- loplasts, 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, espe- cially 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 inte- grate metabolism with the entire cell. Plastid enve- lopes 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 plas- tids accommodate the requirements of the different
Published in 2002.
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    • ...Although the recently finished sequence of the Arabidopsis genome indicates the existence of some 150 putative metabolite transporters in the plastid envelope membrane (Ferro et al., 2002; Koo and Ohlrogge, 2002; Schwacke et al., 2003), up to now only a small number of these transporters have been identified at the molecular level (Table 1). For the majority of these proteins, their functions have been confirmed by in vitro studies using ...
    • ...Systematic approaches, such as mining of plant genomes sequences for putative plastidic transporters (Koo and Ohlrogge, 2002; Schwacke et al., 2003), phenotypic analysis of corresponding knockout mutants, and functional analysis of recombinant candidate proteins will certainly lead to the discovery of novel transporters...

    Andreas P. M. Weberet al. Using mutants to probe the in vivo function of plastid envelope membra...

    • ...The localization of SAMT1 in the chloroplast envelope membranes has been suggested previously by bioinformatic analysis (Koo and Ohlrogge, 2002) and demonstrated by proteomics (Ferro et al., 2002, 2003), supporting the localization data presented in this study...

    Florence Bouvieret al. Arabidopsis SAMT1 Defines a Plastid Transporter Regulating Plastid Bio...

    • ...This observation confirms (i) the interest of putative membraneassociated plant-specific proteins for future functional studies and (ii) the importance of bioinformatics for analysing plant membrane proteomes (see also Barbier-Brygoo et al., 2001; Ferro et al., 2002; Koo and Ohlrogge, 2002; Durand et al., 2003; Chew and Whelan, 2004; Friso et al., 2004; Sun et al., 2004; Vandenbrouck et al., 2005)...

    Norbert Rollandet al. A versatile method for deciphering plant membrane proteomes

    • ...(Kruft et al., 2001; Koo and Ohlrogge, 2002; Peltier et al., 2002; Leister, 2003)...

    Alexey V. Kochetovet al. Translational polymorphism as a potential source of plant proteins var...

    • ...Nevertheless, evidence suggests that the outer membrane is characterised by the presence of beta-barrel proteins, and that the inner membrane is dominated by transporters with multiple, helical transmembrane domains (Koo and Ohlrogge 2002; Schleiff et al. 2003)...

    Paul Jarvis. The Proteomes of Chloroplasts and other Plastids

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