Headshot of Jonathan Stefely

Undergraduate education

University of Notre Dame - BS (2009)

Years in MSTP

2009-

PhD Program

Biochemistry

Mentor

Dave Pagliarini, PhD

Thesis title

Biochemical Functions of Mitochondrial ADCK3 and Other Coenzyme Q Biosynthesis Proteins

Undergraduate and/or masters publications

Stefely JA, Palchaudhuri R, Miller PA, Peterson RJ, Moraski GC, Hergenrother PJ, Miller MJ. N-((1-benzyl-1H-1,2,3-triazol-4-yl)methyl)arylamide as a new scaffold that provides rapid access to antimicrotubule agents: synthesis and evaluation of antiproliferative activity against select cancer cell lines. J Med Chem. 2010 Apr 22;53(8):3389-95. PMID: 20334421; PMCID: PMC2859177.

PhD publications

Stefely JA, Reidenbach AG, Ulbrich A, Oruganty K, Floyd BJ, Jochem A, Saunders JM, Johnson IE, Minogue CE, Wrobel RL, Barber GE, Lee D, Li S, Kannan N, Coon JJ, Bingman CA, Pagliarini DJ. Mitochondrial ADCK3 Employs an Atypical Protein
Kinase-like Fold to Enable Coenzyme Q Biosynthesis. Mol Cell. 2015 Jan 8;57(1):83-94. PMID: 25498144; PMCID: PMC4289473.

Hebert AS, Merrill AE, Stefely JA, Bailey DJ, Wenger CD, Westphall MS, Pagliarini DJ, Coon JJ. Amine-reactive neutron-encoded labels for highly-plexed proteomic quantitation. Mol Cell Proteomics. 2013 Nov;12(11):3360-9. PMID: 23882030; PMCID: PMC3820946.

Khadria AS, Mueller BK, Stefely JA, Tan CH, Pagliarini DJ, Senes A. A Gly-zipper motif mediates homo-dimerization of the transmembrane domain of the mitochondrial kinase ADCK3. J Am Chem Soc. 2014 Oct 8;136(40):14068-14077. PMID: 25216398; PMCID: PMC4195374.

Lohman DC, Forouhar F, Beebe ET, Stefely MS, Minogue CE, Ulbrich A, Stefely JA, Sukumar S, Luna-Sánchez M, Jochem A, Lew S, Seetharaman J, Xiao R, Wang H, Westphall MS, Wrobel RL, Everett JK, Mitchell JC, López LC, Coon JJ, Tong L, Pagliarini DJ. Mitochondrial COQ9 is a lipid-binding protein that associates with COQ7 to enable coenzyme Q biosynthesis. Proc Natl Acad Sci U S A. 2014 Nov 4;111(44):E4697-705. PMID: 25339443; PMCID: PMC4226113.

Floyd BJ, Wilkerson EM, Veling MT, Minogue CE, Xia C, Beebe ET, Wrobel RL, Cho H, Kremer LS, Alston CL, Gromek KA, Dolan BK, Ulbrich A, Stefely JA, Bohl SL, Werner KM, Jochem A, Westphall MS, Rensvold JW, Taylor RW, Prokisch H, Kim JP, Coon JJ, Pagliarini DJ. Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function. Mol Cell. 2016 Aug 18;63(4):621-32. PMID: 27499296; PMCID: PMC4992456.

Stefely JA, Licitra F, Laredj L, Reidenbach AG, Kemmerer ZA, Grangeray A, Jaeg-Ehret T, Minogue CE, Ulbrich A, Hutchins PD, Wilkerson EM, Ruan Z, Aydin D, Hebert AS, Guo X, Freiberger EC, Reutenauer L, Jochem A, Chergova M, Johnson IE, Lohman DC, Rush MJ, Kwiecien NW, Singh PK, Schlagowski AI, Floyd BJ, Forsman U, Sindelar PJ, Westphall MS, Pierrel F, Zoll J, Dal Peraro M, Kannan N, Bingman CA, Coon JJ, Isope P, Puccio H, Pagliarini DJ. Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity. Mol Cell. 2016 Aug 18;63(4):608-20. PMID: 27499294;PMCID: PMC5012427.

Stefely JA, Kwiecien NW, Freiberger EC, Richards AL, Jochem A, Rush MJ, Ulbrich A, Robinson KP, Hutchins PD, Veling MT, Guo X, Kemmerer ZA, Connors KJ, Trujillo EA, Sokol J, Marx H, Westphall MS, Hebert AS, Pagliarini DJ, Coon JJ. Mitochondrial protein functions elucidated by multi-omic mass spectrometry profiling. Nat Biotechnol. 2016 Nov;34(11):1191-1197. PMID: 27669165; PMCID: PMC5101133. Y3K Project Resource

Stefely JA, Pagliarini DJ. Biochemistry of Mitochondrial Coenzyme Q Biosynthesis. Trends Biochem Sci. 2017 Oct;42(10):824-843. PMID: 28927698; PMCID: PMC5731490.

Sanjana N, Zhang F, Fulco C, Lander E, Engreitz J, Costanzo M, Myers CL, Andrews B, Boone C, Kwiecien N, Coon J, Stefely J, Pagliarini D, Lewitus E, Morlon H, Zhang RH, Heyde KC, Scott FY, Paek SH, Ruder WC, Liang K, Doonan C, Falcaro P. Principles of Systems Biology-No. 10. Cell Syst. 2016 Oct 26;3(4):318-320. PMID: 27788354.

Reidenbach AG, Kemmerer ZA, Aydin D, Jochem A, McDevitt MT, Hutchins PD, Stark JL, Stefely JA, Reddy T, Hebert AS, Wilkerson EM, Johnson IE, Bingman CA, Markley JL, Coon JJ, Dal Peraro M, Pagliarini DJ. Conserved Lipid and Small-Molecule Modulation of COQ8 Reveals Regulation of the Ancient Kinase-like UbiB Family. Cell Chem Biol. 2018 Feb 15:25(2):154-165. PMID: 29198567; PMCID: PMC5879996.

Lapointe CP, Stefely JA, Jochem A, Hutchins PD, Wilson GM, Kwiecien NW, Coon JJ, Wickens M, Pagliarini DJ. Multi-omics Reveal Specific Targets of the RNA-Binding Protein Puf3p and Its Orchestration of Mitochondrial Biogenesis. Cell Syst. 2018 Jan 24;6(1):125-135. PMID: 29248374; PMCID: PMC5799006.