{"doi":"10.1016/j.jbc.2021.100880","title":"The extensive and functionally uncharacterized mitochondrial phosphoproteome","abstract":"More than half a century ago, reversible protein phosphorylation was linked to mitochondrial metabolism through the regulation of pyruvate dehydrogenase. Since this discovery, the number of identified mitochondrial protein phosphorylation sites has increased by orders of magnitude, driven largely by technological advances in mass spectrometry-based phosphoproteomics. However, the majority of these modifications remain uncharacterized, rendering their function and relevance unclear. Nonetheless, recent studies have shown that disruption of resident mitochondrial protein phosphatases causes substantial metabolic dysfunction across organisms, suggesting that proper management of mitochondrial phosphorylation is vital for organellar and organismal homeostasis. While these data suggest that phosphorylation within mitochondria is of critical importance, significant gaps remain in our knowledge of how these modifications influence organellar function. Here, we curate publicly available datasets to map the extent of protein phosphorylation within mammalian mitochondria and to highlight the known functions of mitochondrial-resident phosphatases. We further propose models by which phosphorylation may affect mitochondrial enzyme activities, protein import and processing, and overall organellar homeostasis. More than half a century ago, reversible protein phosphorylation was linked to mitochondrial metabolism through the regulation of pyruvate dehydrogenase. Since this discovery, the number of identified mitochondrial protein phosphorylation sites has increased by orders of magnitude, driven largely by technological advances in mass spectrometry-based phosphoproteomics. However, the majority of these modifications remain uncharacterized, rendering their function and relevance unclear. Nonetheless, recent studies have shown that disruption of resident mitochondrial protein phosphatases causes substantial metabolic dysfunction across organisms, suggesting that proper management of mitochondrial phosphorylation is vital for organellar and organismal homeostasis. While these data suggest that phosphorylation within mitochondria is of critical importance, significant gaps remain in our knowledge of how these modifications influence organellar function. Here, we curate publicly available datasets to map the extent of protein phosphorylation within mammalian mitochondria and to highlight the known functions of mitochondrial-resident phosphatases. We further propose models by which phosphorylation may affect mitochondrial enzyme activities, protein import and processing, and overall organellar homeostasis. Metabolism must respond to dynamic shifts in nutrient availability and energy demands. Phosphorylation, being a rapid and reversible posttranslational modification (PTM), is well suited to calibrate these needs. Indeed, phosphorylation has long been known to modulate metabolic signaling: the first protein associated with phosphorylation-based regulation was glycogen phosphorylase (1Fischer E.H. Krebs E.G. Conversion of phosphorylase b to phosphorylase a in muscle extracts.J. Biol. Chem. 1955; 216: 121-132Abstract Full Text PDF PubMed Google Scholar)—a discovery first reported in 1955 by Edwin Krebs and Edmond Fischer that earned them the 1992 Nobel Prize in Physiology and Medicine (2Cohen P. The origins of protein phosphorylation.Nat. Cell Biol. 2002; 4: E127-130Crossref PubMed Scopus (724) Google Scholar). Early observations also linked phosphorylation to mitochondria. Albert Lehninger's group noted in the mid-1940s that incorporation of radioactive phosphate into rat liver phosphoproteins was dependent upon oxidative phosphorylation (3Friedkin M. Lehninger A.L. Oxidation-coupled incorporation of inorganic radiophosphate into phospholipide and nucleic acid in a cell-free system.J. Biol. Chem. 1949; 177: 775-788Abstract Full Text PDF PubMed Google Scholar), and Eugene Kennedy and colleagues first demonstrated cellular kinase activity against ca","journal":"Journal of Biological Chemistry","year":2021,"id":164240,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":39,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9269,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":253457,"name":"David J. Pagliarini","orcid":"0000-0002-0001-0087","position":1,"is_corresponding":false},{"id":253456,"name":"Natalie M. Niemi","orcid":"0000-0002-5174-4005","position":0,"is_corresponding":true}],"reference_count":53,"raw_metadata":null,"created_at":"2026-07-18T23:45:27.031465Z","pmid":"34144036","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}