Differential use of signal peptides and membrane domains is a common occurrence in the protein output of transcriptional units.

PLoS Genet 2006 Apr 28;2(4):e46. Epub 2006 Apr 28.

Institute for Molecular Bioscience and ARC Centre in Bioinformatics, University of Queensland, St. Lucia, Queensland, Australia.

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.

Download full-text PDF

Source
https://dx.plos.org/10.1371/journal.pgen.0020046
Publisher Site
http://dx.doi.org/10.1371/journal.pgen.0020046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449889PMC
April 2006
3 Reads

Publication Analysis

Top Keywords

membrane proteins
24
membrane organization
20
protein isoforms
16
signal peptides
16
membrane
15
transmembrane domains
12
protein
11
proteins
9
reticulum signal
8
protein sequence
8
soluble membrane
8
proteins soluble
8
generation protein
8
type membrane
8
proteins type
8
transcriptional units
8
organization categories
8
endoplasmic reticulum
8
common occurrence
8
domains common
8

Similar Publications