First published online September 20, 2002; 10.1104/pp.008052
Plant Physiol, October 2002, Vol. 130, pp. 823-836
The Predicted Candidates of Arabidopsis Plastid Inner
Envelope Membrane Proteins and Their Expression
Profiles1,[w]
Abraham J.K.
Koo and
John B.
Ohlrogge*
Department of Plant Biology, Michigan State University, East
Lansing, Michigan 48824-1312
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.
1
This work was supported by the National Science
Foundation (grant no. MCB98-17882) and by the Michigan Agricultural
Experiment Station.
[w]
The online version of this article contains Web-only
data. The supplemental material is available at www.plantphysiol.org.
*
Corresponding author; e-mail ohlrogge{at}msu.edu; fax
517-353-1926.
© 2002 American Society of Plant Physiologists
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