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

Abstract

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 ...

ArabidopsisSAMT1 Defines a Plastid Transporter Regulating Plastid Biogenesis and Plant Development

“…As would be predicted for an integral protein, SAMT1 was completely solubilized by treatment with 2% Triton X-100 ( Figure 2E). 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(Ferro et al, , 2003, supporting the localization data presented in this study. Collectively, these data demonstrate that SAMT1 is an integral membrane protein that is localized in the chloroplast envelope membranes.…”

AtOSA1, a Member of the Abc1-Like Family, as a New Factor in Cadmium and Oxidative Stress Response

“…Sequence analysis of the AtOSA1 protein with Target P (http://www.cbs.dtu.dk/services/TargetP/; Emanuelsson et al, 2000), used for proteomic analyses and theoretical predictions of protein localization (Koo and Ohlrogge, 2002;Peltier et al, 2002), revealed the presence of a 28-amino acid N-terminal chloroplast targeting presequence (Supplemental Fig. S1).…”

Proteomic Characterization of A Triton-Insoluble Fraction from Chloroplasts Defines A Novel Group of Proteins Associated with Macromolecular Structures

“…6,7 Although over 3600 proteins are predicted to be targeted to plastids, the number of characterized plastid proteins represents only a small percentage of this predicted number. 4,8 Despite significant efforts to characterize chloroplasts and subfractions therein, less than one-fifth of the predicted number of plastid proteins have been confirmed.…”

“…2 The remainder of the estimated 3600 plastid proteins are nuclear encoded. 3,4 The estimated number of plastid proteins for a higher plant is based upon subcellular target prediction analyses of open reading frames from the Arabidopsis thaliana genome using organelle targeting algorithms. 5 Nuclear-encoded chloroplast proteins are transcribed from the nuclear genome, translated in the cytosol and imported into chloroplasts through the envelope membrane via an amino-terminal targeting peptide.…”