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Profiling of Methyltransferases and Other S-adenosyl-L-homocysteine-binding Proteins by Capture Compound Mass Spectrometry (CCMS)
Published on: December 20, 2010
Automated identification of putative methyltransferases from genomic open reading frames
Jonathan E Katz1, Mensur Dlakić, Steven Clarke
1Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, California 90095-1569, USA.
Molecular & Cellular Proteomics : MCP
|July 23, 2003
Summary
Researchers developed a new method to identify S-adenosylmethionine (AdoMet)-dependent methyltransferases, crucial enzymes in many organisms. This approach improves the prediction of methyltransferase genes across diverse genomes.
Area of Science:
- Genomics
- Bioinformatics
- Enzymology
Background:
- S-adenosylmethionine (AdoMet)-dependent methyltransferases are essential enzymes.
- These enzymes share conserved structural motifs for AdoMet cofactor binding.
- Identifying these enzymes computationally is challenging.
Purpose of the Study:
- To develop and validate novel computational methods for identifying AdoMet-dependent methyltransferases.
- To analyze the prevalence of these methyltransferases across various genomes.
- To identify novel candidate methyltransferase genes for further study.
Main Methods:
- Analysis of existing and development of new methodologies for functional assignment.
- Utilized methyltransferase signature motifs based on conserved AdoMet binding structures.
- Employed a novel "sensitized matrices for scoring methyltransferases" (SM2) method using modified MEME and MAST tools.
Main Results:
- Simple motif pattern matching showed limited utility.
- The SM2 method significantly improved methyltransferase identification in the Saccharomyces cerevisiae genome.
- AdoMet-dependent methyltransferases constitute approximately 0.6-1.6% of genes in yeast, human, mouse, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, and Escherichia coli.
Conclusions:
- The SM2 method offers a significant advancement in identifying AdoMet-dependent methyltransferases.
- This enzyme class is conserved across a wide range of organisms.
- Provided a list of high-probability uncharacterized methyltransferase genes for future research.
