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Updated: May 3, 2026
08:07
Identification of Plasmodesmal Localization Sequences in Proteins In Planta
Published on: August 15, 2017
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Localizing proteins in the cell from their phylogenetic profiles.
E M Marcotte1, I Xenarios, A M van Der Bliek
1Molecular Biology Institute, University of California Los Angeles, 90095, USA.
Summary
We developed a computational method to predict protein locations using phylogenetic profiles. This approach accurately identifies nucleus-encoded mitochondrial proteins, revealing insights into mitochondrial evolution and function.
Area of Science:
- Computational biology
- Genomics
- Molecular biology
Background:
- Proteins are crucial for cellular function.
- Understanding protein localization is key to cell biology.
- Mitochondria, essential organelles, have complex protein import mechanisms.
Purpose of the Study:
- To develop a computational method for predicting subcellular protein localization.
- To analyze the phylogenetic distribution of mitochondrial proteins.
- To estimate the number of nucleus-encoded mitochondrial genes in model organisms.
Main Methods:
- Phylogenetic profiling of protein homologs.
- Analyzing the evolutionary origins of nucleus-encoded mitochondrial proteins.
- Applying the method to yeast (Saccharomyces cerevisiae) and worm (Caenorhabditis elegans) genomes.
Main Results:
- Identified three groups of nucleus-encoded mitochondrial proteins: prokaryote-derived, eukaryote-derived, and organism-specific.
- Achieved 50% accuracy and 58% coverage in identifying mitochondrial proteins in yeast.
- Estimated ~630 nuclear genes for mitochondrial function in yeast and ~660 in C. elegans.
- Found significant prokaryotic contributions to mitochondrial proteomes, alongside eukaryote-specific and organism-specific genes.
Conclusions:
- Phylogenetic profiles are effective for predicting subcellular protein localization.
- Mitochondria possess specialized functions beyond those inherited from prokaryotic ancestors.
- The computational method provides insights into organellar evolution and genome organization.
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