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. 2021 Jan 8;49(D1):D1541-D1547.
doi: 10.1093/nar/gkaa1011.

MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations

Sneha Rath  1   2   3 , Rohit Sharma  1   2   3 , Rahul Gupta  1   2   3 , Tslil Ast  1   2   3 , Connie Chan  1   2   3 , Timothy J Durham  1   2   3 , Russell P Goodman  1   2   3 , Zenon Grabarek  1   2   3 , Mary E Haas  1   2   3 , Wendy H W Hung  1   2   3 , Pallavi R Joshi  1   2   3 , Alexis A Jourdain  1   2   3 , Sharon H Kim  1   2   3 , Anna V Kotrys  1   2   3 , Stephanie S Lam  1   2   3 , Jason G McCoy  1   2   3 , Joshua D Meisel  1   2   3 , Maria Miranda  1   2   3 , Apekshya Panda  1   2   3 , Anupam Patgiri  1   2   3 , Robert Rogers  1   2   3 , Shayan Sadre  1   2   3 , Hardik Shah  1   2   3 , Owen S Skinner  1   2   3 , Tsz-Leung To  1   2   3 , Melissa A Walker  1   2   3 , Hong Wang  1   2   3 , Patrick S Ward  1   2   3 , Jordan Wengrod  1   2   3 , Chen-Ching Yuan  1   2   3 , Sarah E Calvo  1   2   3 , Vamsi K Mootha  1   2   3
Affiliations

MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations

Sneha Rath et al. Nucleic Acids Res. .

Abstract

The mammalian mitochondrial proteome is under dual genomic control, with 99% of proteins encoded by the nuclear genome and 13 originating from the mitochondrial DNA (mtDNA). We previously developed MitoCarta, a catalogue of over 1000 genes encoding the mammalian mitochondrial proteome. This catalogue was compiled using a Bayesian integration of multiple sequence features and experimental datasets, notably protein mass spectrometry of mitochondria isolated from fourteen murine tissues. Here, we introduce MitoCarta3.0. Beginning with the MitoCarta2.0 inventory, we performed manual review to remove 100 genes and introduce 78 additional genes, arriving at an updated inventory of 1136 human genes. We now include manually curated annotations of sub-mitochondrial localization (matrix, inner membrane, intermembrane space, outer membrane) as well as assignment to 149 hierarchical 'MitoPathways' spanning seven broad functional categories relevant to mitochondria. MitoCarta3.0, including sub-mitochondrial localization and MitoPathway annotations, is freely available at http://www.broadinstitute.org/mitocarta and should serve as a continued community resource for mitochondrial biology and medicine.

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Figures

Figure 1.
Figure 1.
Overview of MitoCarta3.0. MitoCarta2.0 was previously built by Bayesian integration of the enumerated features. MitoCarta3.0 presents a revised inventory which is further annotated for sub-mitochondrial localization based on integrated analysis and MitoPathway membership based on literature curation.
Figure 2.
Figure 2.
Sub-mitochondrial localization of MitoCarta3.0 proteins. (A) Schematic of possible sub-mitochondrial localizations that can be inferred from each type of published experimental evidence, computationally predicted feature, or knowledge of biological pathway. (B) Pie chart of MitoCarta3.0 proteins assigned to one or more sub-mitochondrial compartments.
Figure 3.
Figure 3.
Annotation of MitoCarta3.0 genes to MitoPathways. Listed are a total of 149 MitoPathways organized in a three-tier hierarchy. Genes can be assigned to one or more of these MitoPathways. At the top level are seven overarching categories (color-coded boxes with bold, underlined labels), followed by the second (bold only) and third level of MitoPathways (lighter grey). The underlying treemap was generated in Excel using the number of MitoCarta3.0 genes annotated to each top-level category; this number is also listed in each box.
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