Bio

Bio


MD: University of Wisconsin-Madison, 2017
PhD in Biochemistry: University of Wisconsin-Madison, 2015
MEd in Secondary Education: University of Notre Dame, 2008
BS in Biochemistry: University of Notre Dame, 2006

Clinical Focus


  • Residency

Publications

All Publications


  • Systems Biochemistry Approaches to Defining Mitochondrial Protein Function. Cell metabolism Sung, A. Y., Floyd, B. J., Pagliarini, D. J. 2020; 31 (4): 669–78

    Abstract

    Defining functions for the full complement of proteins is a grand challenge in the post-genomic era and is essential for our understanding of basic biology and disease pathogenesis. In recent times, this endeavor has benefitted from a combination of modern large-scale and classical reductionist approaches-a process we refer to as "systems biochemistry"-that helps surmount traditional barriers to the characterization of poorly understood proteins. This strategy is proving to be particularly effective for mitochondria, whose well-defined proteome has enabled comprehensive analyses of the full mitochondrial system that can position understudied proteins for fruitful mechanistic investigations. Recent systems biochemistry approaches have accelerated the identification of new disease-related mitochondrial proteins and of long-sought "missing" proteins that fulfill key functions. Collectively, these studies are moving us toward a more complete understanding of mitochondrial activities and providing a molecular framework for the investigation of mitochondrial pathogenesis.

    View details for DOI 10.1016/j.cmet.2020.03.011

    View details for PubMedID 32268114

  • Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity MOLECULAR CELL Stefely, J. A., Licitra, F., Laredj, L., Reidenbach, A. G., Kemmerer, Z. A., Grangeray, A., Jaeg-Ehret, T., Minogue, C. E., Ulbrich, A., Hutchins, P. D., Wilkerson, E. M., Ruan, Z., Aydin, D., Hebert, A. S., Guo, X., Freiberger, E. C., Reutenauer, L., Jochem, A., Chergova, M., Johnson, I. E., Lohman, D. C., Rush, M. P., Kwiecien, N. W., Singh, P. K., Schlagowski, A. I., Floyd, B. J., Forsman, U., Sindelar, P. J., Westphall, M. S., Pierrel, F., Zoll, J., Dal Peraro, M., Kannan, N., Bingman, C. A., Coon, J. J., Isope, P., Puccio, H., Pagliarini, D. J. 2016; 63 (4): 608–20

    Abstract

    The UbiB protein kinase-like (PKL) family is widespread, comprising one-quarter of microbial PKLs and five human homologs, yet its biochemical activities remain obscure. COQ8A (ADCK3) is a mammalian UbiB protein associated with ubiquinone (CoQ) biosynthesis and an ataxia (ARCA2) through unclear means. We show that mice lacking COQ8A develop a slowly progressive cerebellar ataxia linked to Purkinje cell dysfunction and mild exercise intolerance, recapitulating ARCA2. Interspecies biochemical analyses show that COQ8A and yeast Coq8p specifically stabilize a CoQ biosynthesis complex through unorthodox PKL functions. Although COQ8 was predicted to be a protein kinase, we demonstrate that it lacks canonical protein kinase activity in trans. Instead, COQ8 has ATPase activity and interacts with lipid CoQ intermediates, functions that are likely conserved across all domains of life. Collectively, our results lend insight into the molecular activities of the ancient UbiB family and elucidate the biochemical underpinnings of a human disease.

    View details for DOI 10.1016/j.molcel.2016.06.030

    View details for Web of Science ID 000381620300009

    View details for PubMedID 27499294

    View details for PubMedCentralID PMC5012427

  • Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function MOLECULAR CELL Floyd, B. J., Wilkerson, E. M., Veling, M. T., Minogue, C. E., Xia, C., Beebe, E. T., Wrobel, R. L., Cho, H., Kremer, L. S., Alston, C. L., Gromek, K. A., Dolan, B. K., Ulbrich, A., Stefely, J. A., Bohl, S. L., Werner, K. M., Jochem, A., Westphall, M. S., Rensvold, J. W., Taylor, R. W., Prokisch, H., Kim, J. P., Coon, J. J., Pagliarini, D. J. 2016; 63 (4): 621–32

    Abstract

    Mitochondria are essential for numerous cellular processes, yet hundreds of their proteins lack robust functional annotation. To reveal functions for these proteins (termed MXPs), we assessed condition-specific protein-protein interactions for 50 select MXPs using affinity enrichment mass spectrometry. Our data connect MXPs to diverse mitochondrial processes, including multiple aspects of respiratory chain function. Building upon these observations, we validated C17orf89 as a complex I (CI) assembly factor. Disruption of C17orf89 markedly reduced CI activity, and its depletion is found in an unresolved case of CI deficiency. We likewise discovered that LYRM5 interacts with and deflavinates the electron-transferring flavoprotein that shuttles electrons to coenzyme Q (CoQ). Finally, we identified a dynamic human CoQ biosynthetic complex involving multiple MXPs whose topology we map using purified components. Collectively, our data lend mechanistic insight into respiratory chain-related activities and prioritize hundreds of additional interactions for further exploration of mitochondrial protein function.

    View details for DOI 10.1016/j.molcel.2016.06.033

    View details for Web of Science ID 000381620300010

    View details for PubMedID 27499296

    View details for PubMedCentralID PMC4992456

  • Mitochondrial ADCK3 Employs an Atypical Protein Kinase-like Fold to Enable Coenzyme Q Biosynthesis MOLECULAR CELL Stefely, J. A., Reidenbach, A. G., Ulbrich, A., Oruganty, K., Floyd, B. J., Jochem, A., Saunders, J. M., Johnson, I. E., Minogue, C. E., Wrobel, R. L., Barber, G. E., Lee, D., Li, S., Kannan, N., Coon, J. J., Bingman, C. A., Pagliarini, D. J. 2015; 57 (1): 83–94

    Abstract

    The ancient UbiB protein kinase-like family is involved in isoprenoid lipid biosynthesis and is implicated in human diseases, but demonstration of UbiB kinase activity has remained elusive for unknown reasons. Here, we quantitatively define UbiB-specific sequence motifs and reveal their positions within the crystal structure of a UbiB protein, ADCK3. We find that multiple UbiB-specific features are poised to inhibit protein kinase activity, including an N-terminal domain that occupies the typical substrate binding pocket and a unique A-rich loop that limits ATP binding by establishing an unusual selectivity for ADP. A single alanine-to-glycine mutation of this loop flips this coenzyme selectivity and enables autophosphorylation but inhibits coenzyme Q biosynthesis in vivo, demonstrating functional relevance for this unique feature. Our work provides mechanistic insight into UbiB enzyme activity and establishes a molecular foundation for further investigation of how UbiB family proteins affect diseases and diverse biological pathways.

    View details for DOI 10.1016/j.molcel.2014.11.002

    View details for Web of Science ID 000347711100008

    View details for PubMedID 25498144

    View details for PubMedCentralID PMC4289473

  • SORCS1 is necessary for normal insulin secretory granule biogenesis in metabolically stressed beta cells JOURNAL OF CLINICAL INVESTIGATION Kebede, M. A., Oler, A. T., Gregg, T., Balloon, A. J., Johnson, A., Mitok, K., Rabaglia, M., Schueler, K., Stapleton, D., Thorstenson, C., Wrighton, L., Floyd, B. J., Richards, O., Raines, S., Eliceiri, K., Seidah, N. G., Rhodes, C., Keller, M. P., Coon, J. L., Audhya, A., Attie, A. D. 2014; 124 (10): 4240–56

    Abstract

    We previously positionally cloned Sorcs1 as a diabetes quantitative trait locus. Sorcs1 belongs to the Vacuolar protein sorting-10 (Vps10) gene family. In yeast, Vps10 transports enzymes from the trans-Golgi network (TGN) to the vacuole. Whole-body Sorcs1 KO mice, when made obese with the leptin(ob) mutation (ob/ob), developed diabetes. β Cells from these mice had a severe deficiency of secretory granules (SGs) and insulin. Interestingly, a single secretagogue challenge failed to consistently elicit an insulin secretory dysfunction. However, multiple challenges of the Sorcs1 KO ob/ob islets consistently revealed an insulin secretion defect. The luminal domain of SORCS1 (Lum-Sorcs1), when expressed in a β cell line, acted as a dominant-negative, leading to SG and insulin deficiency. Using syncollin-dsRed5TIMER adenovirus, we found that the loss of Sorcs1 function greatly impairs the rapid replenishment of SGs following secretagogue challenge. Chronic exposure of islets from lean Sorcs1 KO mice to high glucose and palmitate depleted insulin content and evoked an insulin secretion defect. Thus, in metabolically stressed mice, Sorcs1 is important for SG replenishment, and under chronic challenge by insulin secretagogues, loss of Sorcs1 leads to diabetes. Overexpression of full-length SORCS1 led to a 2-fold increase in SG content, suggesting that SORCS1 is sufficient to promote SG biogenesis.

    View details for DOI 10.1172/JCI74072

    View details for Web of Science ID 000342649900022

    View details for PubMedID 25157818

    View details for PubMedCentralID PMC4191024

  • Quantification of Mitochondrial Acetylation Dynamics Highlights Prominent Sites of Metabolic Regulation JOURNAL OF BIOLOGICAL CHEMISTRY Still, A. J., Floyd, B. J., Hebert, A. S., Bingman, C. A., Carson, J. J., Gunderson, D. R., Dolan, B. K., Grimsrud, P. A., Dittenhafer-Reed, K. E., Stapleton, D. S., Keller, M. P., Westphall, M. S., Denu, J. M., Attie, A. D., Coon, J. J., Pagliarini, D. J. 2013; 288 (36): 26209–19

    Abstract

    Lysine acetylation is rapidly becoming established as a key post-translational modification for regulating mitochondrial metabolism. Nonetheless, distinguishing regulatory sites from among the thousands identified by mass spectrometry and elucidating how these modifications alter enzyme function remain primary challenges. Here, we performed multiplexed quantitative mass spectrometry to measure changes in the mouse liver mitochondrial acetylproteome in response to acute and chronic alterations in nutritional status, and integrated these data sets with our compendium of predicted Sirt3 targets. These analyses highlight a subset of mitochondrial proteins with dynamic acetylation sites, including acetyl-CoA acetyltransferase 1 (Acat1), an enzyme central to multiple metabolic pathways. We performed in vitro biochemistry and molecular modeling to demonstrate that acetylation of Acat1 decreases its activity by disrupting the binding of coenzyme A. Collectively, our data reveal an important new target of regulatory acetylation and provide a foundation for investigating the role of select mitochondrial protein acetylation sites in mediating acute and chronic metabolic transitions.

    View details for DOI 10.1074/jbc.M113.483396

    View details for Web of Science ID 000330623300051

    View details for PubMedID 23864654

    View details for PubMedCentralID PMC3764825

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