Bronislava Brejova, Veronika Vozarikova, Ivan Agarsky, Hana Derkova, Matej Fedor, Dominika Harmanova, Lukas Kiss, Andrej Korman, Martin Pasen, Filip Brazdovic, Tomas Vinar, Jozef Nosek, Lubomir Tomaska. y-mtPTM: Yeast mitochondrial posttranslational modification database. Genetics, 224(3):iyad087. 2023.

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Abstract:

One powerful strategy of how to increase the complexity of cellular 
proteomes is through posttranslational modifications (PTMs) of proteins. 
Currently, there are approximately 400 types of PTMs, the different 
combinations of which yield a large variety of  protein isoforms with 
distinct biochemical properties. Although mitochondrial proteins undergoing 
PTMs were identified nearly 6 decades ago, studies on the roles and extent 
of PTMs on mitochondrial functions lagged behind the other cellular 
compartments. The application of mass spectrometry for the characterization 
of the mitochondrial proteome as well as for the detection of various PTMs 
resulted in the identification of thousands of amino acid positions that 
can be modified by different chemical groups. However, the data on 
mitochondrial PTMs are scattered in several data sets, and the available 
databases do not contain a complete list of modified residues. To integrate 
information on PTMs of the mitochondrial proteome of the yeast 
Saccharomyces cerevisiae, we built the yeast mitochondrial 
posttranslational modification (y-mtPTM) database 
(http://compbio.fmph.uniba.sk/y-mtptm/). It lists nearly 20,000 positions 
on mitochondrial proteins affected by  approximately 20 various PTMs, with 
phosphorylated, succinylated, acetylated, and ubiquitylated sites being the 
most abundant. A simple search of a protein of interest reveals the 
modified amino acid residues, their position within the primary sequence as 
well as on its 3D structure, and links to the source reference(s). The 
database will serve yeast mitochondrial researchers as a comprehensive 
platform to investigate the functional significance of the PTMs of 
mitochondrial proteins.

Last update: 09/09/2023