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Type: Journal article
Title: Differential use of signal peptides and membrane domains is a common occurrence in the protein output of transcriptional units
Author: Davis, M.
Hanson, K.
Clark, F.
Fink, L.
Zhang, F.
Kasukawa, T.
Kai, C.
Kawai, J.
Carninci, P.
Hayashizaki, Y.
Teasdale, R.
Citation: PLoS Genetics, 2006; 2(4):554-563
Publisher: Public Library of Science
Issue Date: 2006
ISSN: 1553-7390
Editor: Blake, J.
Hancock, J.
Pavan, B.
Stubbs, L.
Statement of
Melissa J. Davis, Kelly A. Hanson, Francis Clark, J. Lynn Fink, Fasheng Zhang, Takeya Kasukawa, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki and Rohan D. Teasdale
Abstract: Membrane organization describes the orientation of a protein with respect to the membrane and can be determined by the presence, or absence, and organization within the protein sequence of two features: endoplasmic reticulum signal peptides and alpha-helical transmembrane domains. These features allow protein sequences to be classified into one of five membrane organization categories: soluble intracellular proteins, soluble secreted proteins, type I membrane proteins, type II membrane proteins, and multi-spanning membrane proteins. Generation of protein isoforms with variable membrane organizations can change a protein's subcellular localization or association with the membrane. Application of MemO, a membrane organization annotation pipeline, to the FANTOM3 Isoform Protein Sequence mouse protein set revealed that within the 8,032 transcriptional units (TUs) with multiple protein isoforms, 573 had variation in their use of signal peptides, 1,527 had variation in their use of transmembrane domains, and 615 generated protein isoforms from distinct membrane organization classes. The mechanisms underlying these transcript variations were analyzed. While TUs were identified encoding all pairwise combinations of membrane organization categories, the most common was conversion of membrane proteins to soluble proteins. Observed within our high-confidence set were 156 TUs predicted to generate both extracellular soluble and membrane proteins, and 217 TUs generating both intracellular soluble and membrane proteins. The differential use of endoplasmic reticulum signal peptides and transmembrane domains is a common occurrence within the variable protein output of TUs. The generation of protein isoforms that are targeted to multiple subcellular locations represents a major functional consequence of transcript variation within the mouse transcriptome.
Keywords: Animals
Protein Sorting Signals
Membrane Proteins
Protein Isoforms
Transcription, Genetic
Genetic Variation
Rights: © 2006 Davis et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
DOI: 10.1371/journal.pgen.0020046
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Earth and Environmental Sciences publications
Environment Institute publications

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