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Cited by 1,888Bioinformatics and Genomic NetworksMitochondrial Function and PathologyAdvanced Proteomics Techniques and Applications

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

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Rath, Sneha, Sharma, Rohit, Gupta, Rahul, Ast, Tslil, Chan, Connie, Durham, Timothy J, Goodman, Russell P, Grabarek, Zenon +24 more·2021·Nucleic Acids Research
DOI 10.1093/nar/gkaa1011PMC PMC7778944
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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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Authors
Rath, S., Sharma, R., Gupta, R., Ast, T., Chan, C., Durham, T. J., Goodman, R. P., Grabarek, Z., Haas, M. E., Hung, W. H. W., Joshi, P. R., Jourdain, A. A., Kim, S. H., Kotrys, A. V., Lam, S. S., McCoy, J. G., Meisel, J. D., Miranda, M., Panda, A., Patgiri, A., Rogers, R., Sadre, S., Shah, H., Skinner, O. S., To, T.-L., Walker, M. A., Wang, H., Ward, P. S., Wengrod, J., Yuan, C.-C., Calvo, S. E., & Mootha, V. K.
Affiliations
  • Broad Institute (US)
  • Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Corresponding author
  • Calvo, Sarah E
  • Mootha, Vamsi K
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2020-11-11
Volume
49
Issue
D1
Pages
D1541-D1547
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkaa1011
PMC
PMC7778944
OpenAlex
W3106539179
Cited by
1,888
References
1
Citations by year
2026: 444 · 2025: 446 · 2024: 358 · 2023: 347 · 2022: 184 · 2021: 104 · 2020: 5
FWCI
52.79
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • SERVAL (Université de Lausanne) (publishedVersion, cc-by-nc)
  • IRIS (submittedVersion, cc-by-nc)
Funders
  • National Institutes of Health (K00CA212468, T32AG000222, K08DK115881, R01AR071942, F32GM128259, F32GM133047, T32DK007028, R35GM122455)
  • Jane Coffin Childs
  • Deutsche Forschungsgemeinschaft (431313887)
  • Massachusetts General Hospital Department of Neurology
  • Dollis Huntington Endowment Fund for Cancer Research
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Mitochondrial Function and Pathology
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
Keywords
mitochondrial proteome, mitochondrial DNA-encoded proteins, nuclear-encoded mitochondrial proteins, human genes, mitochondrial biology
MeSH terms
Machine Learning, Animals, Bayes Theorem, DNA, Mitochondrial, Humans, Mitochondria, Software, Mass Spectrometry, Internet, Proteome, Mitochondrial Proteins, Databases, Protein, Mitochondrial Membranes, Mice, Molecular Sequence Annotation, Datasets as Topic

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