Updates from the Metabolism Community

As part of the new Morgridge Metabolism Initiative, we want to share news and publications from campus. We hope these communications familiarize you with new findings and increase the awareness of our experimental capabilities.

Please send along information on your latest published work in this format to metabolismdirector@morgridge.org to be included in the next update!

July 2020 A Bacterial Biosynthetic Pathway for Methylated Furan Fatty Acids.

Lemke RA, Olson SM, Morse K, Karlen SD, Higbee A, Beebe ET, Ralph J, Coon JJ, Fox BG, Donohue TJ

J. Biol. Chem. 2020 Jul 17; 295(29):9786-9801 Epub 2020 May 20

Furan fatty acids (FuFAs), characterized by the presence of a furan ring within the molecule’s hydrophobic core, are found at low levels in many cells, and have properties that make them attractive in industrial, medical and other applications, but their biosynthetic origins are not clear. In this study, an interdisciplinary research team deployed a suite of genetic, genomics, biochemical, and high-resolution analytical techniques (GC-MS and NMR) to identify the chemical structures of intermediates in the FuFA acid biosynthetic pathway and isotopic studies to determine the source of the oxygen in the furan ring. These findings lay the foundation for detailed study of novel biosynthetic enzymes, obtaining new insights into cellular FuFA functions, and engineering cells that overproduce these fatty acids for various applications.

July 2020 21-plex DiLeu isobaric tags for high-throughput quantitative proteomics.

Frost DC, Feng Y, Li L.

Anal Chem. 2020 June 16; 92(12):8228-8234. doi: 10.1021acs.analchem.0c00473. ePub 2020 May 13.

Quantitative mass spectrometry has emerged as a central technology for biomedical research and provides deep insights into complex biological mechanisms and disease states. Multiplexed isobaric tagging is a particularly powerful tool that enables broad investigation of many samples in a single LC-MS/MS experiment, but the cost of employing commercial tagging reagents for large-scale, discovery-based studies is often prohibitive. As a practical alternative, we previously developed our own isobaric tags, dimethylated leucine (DiLeu), that we synthesize in-house at a fraction of the cost. In this work, we devise a novel synthetic avenue to generate additional isotopic variants that allow us to greatly increase multiplexing capability, beyond that of established isobaric tags, while preserving the existing design and its advantages. The result is a new generation of DiLeu tags that permits simultaneous identification and quantification of 21 samples in parallel on mainstream Orbitrap MS platforms. As such, the 21-plex DiLeu isobaric tags offer the potential to substantially facilitate the high-throughput analyses and large-scale experiments that are increasingly being conducted in discovery-based quantitative proteomics and metabolomics workflows.

  • Novel chemical tag design and synthesis
  • Stable isotope labeling of complex biological samples
  • Highly multiplexed quantitative analysis by mass spectrometry
July 2020 Postpartum Supplementation with Fermented Ammoniated Condensed Whey Altered Nutrient Partitioning to Support Hepatic Metabolism.

Caputo Oliveira R, Erb SJ, Pralle RS, Holdorf HT, Seely CR, White HM.

J Dairy Sci. 2020 Aug;103(8):7055-7067. doi: 10.3168/jds.2019-17790. Epub 2020 Jun 10.

General Background:
In ruminant animals, carbohydrates are fermented in the rumen and absorbed as volatile fatty acids rather than glucose and other monomers, therefore nearly all glucose must be generated via gluconeogenesis in the liver and then transported to the mammary gland as a lactose precursor. In the lactating dairy cow, this glucose need can range from 10 to 20 lb of glucose daily and lactose is a key limiter of milk production.

Study summary:
Shifting nutrient partitioning to support the glucose and energy needs during the peripartum period in lactating dairy cows can contribute to improved feed efficiency and improved metabolic health. While lactate is a known gluconeogenic precursor, previous attempts to feed lactate sources led to rumen acidosis. Supplementation of ammoniated lactate to postpartum dairy cows resulted in improved feed efficiency and decreased incidence of hyperketonemia and hepatic lipid content. Examining hepatic gene expression and protein abundance supported a multi-faceted mechanism of increasing gluconeogenic precursors to support glucose production and increasing the TCA cycle oxidative capacity which together may have supported the improvements in feed efficiency and metabolic health.

  • Bovine liver biopsies
  • Liver lipid quantification
  • Real-time quantitative PCR
  • Western blot analysis
  • Metabolite quantification
April 2020 Automated Extraction and Visualization of Protein-Protein Interaction Networks and Beyond: A Text-Mining Protocol.

Raja K, Natarajan J, Kuusisto F, Steill J, Ross I, Thomson J, Stewart R.

Methods Mol Biol. 2020;2074:13-34. doi: 10.1007/978-1-4939-9873-9_2.

Proteins perform their function by interacting with other proteins. Protein-protein interaction (PPI) analysis allows us to better understand the functions of individual proteins, the mechanisms of biological processes, and disease mechanisms. In many metabolic reactions, PPI is essential for electron transfer reactions (ex. electron transfer from ferredoxin to lipoic acid synthase). Information on PPI are abundant in published PubMed articles and their extraction is possible only through automated approaches. We describe the standard text-mining protocol that includes four major tasks, namely, recognizing protein mentions, normalizing protein names and aliases to unique identifiers such as gene symbol, extracting PPIs, and visualizing the PPI network using Cytoscape or other visualization tools. We show the application of KinderMiner, our recent text-mining tool on retrieving significant co-occurring protein pairs from ~30 million PubMed articles. KinderMiner retrieved known and new PPIs from PubMed articles and performed better than String and PolySearch2, the well-known PPI resources, on extracting mitochondrial PPIs. KinderMiner is a general text mining system applicable to a wide range of metabolic and other biological queries.

  • Automated approach to replace abbreviations with respective original text in ~30 million PubMed articles
  • Many new features were added to KinderMiner
  • For applications other than PPI using KinderMiner, we generated diseases lexicon, phenotypes lexicon, and drugs lexicon from existing resources.
April 2020 Systematically Sifting Big Data to Identify Novel Causal Genes for Human Traits.

Nicholas J. Hand and Daniel J. Rader

Cell Metab. 2020 Apr 7;31(4):658-659. doi: 10.1016/j.cmet.2020.03.013.

Identifying the causal gene(s) that connects genetic variation to a phenotype is a challenging problem in genome-wide association studies (GWASs). Here, we develop a systematic approach that integrates mouse liver co-expression networks with human lipid GWAS data to identify regulators of cholesterol and lipid metabolism. Through our approach, we pinpoint Sestrin1 as a causal gene associated with plasma cholesterol levels in humans. Our validation studies demonstrate that Sestrin1 influences plasma cholesterol in multiple mouse models and regulates cholesterol biosynthesis. Our results highlight the power of combining mouse and human datasets for prioritization of human lipid GWAS loci and discovery of lipid genes.

  • Co-expression network analysis with the Center for High Throughput Computing (CHTC)
  • Radio-label tracing of cholesterol biosynthesis
April 2020 Integrating Mouse and Human Genetic Data to Move beyond GWAS and Identify Causal Genes in Cholesterol Metabolism.

Zhonggang Li, James A. Votava, Gregory J.M. Zajac, Jenny N. Nguyen, Fernanda B. Leyva Jaimes, Sophia M. Ly, Jacqueline A. Brinkman, Marco De Giorgi, Sushma Kaul, Cara L. Green, Samantha L. St. Clair, Sabrina L. Belisle, Julia M. Rios, David W. Nelson, Mary G. Sorci-Thomas, William R. Lagor, Dudley W. Lamming, Chi-Liang Eric Yen, and Brian W. Parks

Cell Metab. 2020 Apr 7;31(4):741-754.e5. doi: 10.1016/j.cmet.2020.02.015. Epub 2020 Mar 19.

April 2020 Dual metabolomic profiling uncovers Toxoplasma manipulation of the host metabolome and the discovery of a novel parasite metabolic capability.

Olson WJ, Martorelli Di Genova B, Gallego-Lopez G, Dawson AR, Stevenson D, Amador-Noguez D, Knoll LJ.

PLoS Pathog. 2020 Apr 7;16(4):e1008432. doi: 10.1371/journal.ppat.1008432. eCollection 2020 Apr.

Toxoplasma gondii is an obligate intracellular parasite that is auxotrophic for several key metabolites and must scavenge these from the host. It is unclear how Toxoplasma manipulates host metabolism for its overall growth rate and non-essential metabolites. To address this question, we measured changes in the joint host-parasite metabolome over a time course of infection. These experiments led to the discovery of a Toxoplasma sedoheptulose bisphosphatase, which funnels carbon from glycolysis into ribose synthesis through an energetically driven dephosphorylation reaction. This second route for ribose synthesis resolves a conflict between the Toxoplasma tricarboxylic acid cycle and pentose phosphate pathway, which are both NADP+ dependent. Sedoheptulose bisphosphatase represents a novel step in Toxoplasma central carbon metabolism that allows Toxoplasma to satisfy its ribose demand without using NADP+. Sedoheptulose bisphosphatase is not present in humans, highlighting its potential as a drug target.

  • Discovery mass spectrometry metabolomics and RNAseq
  • CRISPR-mediated genome edited Toxoplasma
  • Stable isotope labeling with mass spectrometry
April 2020 Contributions of Spore Secondary Metabolites to UV-C Protection and Virulence Vary in Different Aspergillus fumigatus Strains.

Blachowicz A, Raffa N, Bok JW, Choera T, Knox B, Lim FY, Huttenlocher A, Wang CCC, Venkateswaran K, Keller NP

mBio. 2020 Feb 18;11(1):e03415-19

The opportunistic human pathogen Aspergillus fumigatus synthesizes spore specific secondary metabolites, several of which (DHN melanin, trypacidin) are virulence factors in invasive aspergillosis. This article demonstrates that DHN melanin and other spore metabolites serve as UV protectants for the fungus dependent on fungal isolate. This work supports previous hypotheses that secondary metabolites which evolved for protection against environmental stresses can serve as double edged swords in pathogenesis.

  • Creation of Aspergillus mutants
  • Zebrafish virulence assays
April 2020 Beta Cell Dedifferentiation Induced by IRE1α Deletion Prevents Type 1 Diabetes.

Lee H, Lee YS, Harenda Q, Pietrzak S, Oktay HZ, Schreiber S, Liao Y, Sonthalia S, Ciecko AE, Chen YG, Keles S, Sridharan R, Engin F.

Cell Metab. 2020 Apr 7;31(4):822-836.e5. doi: 10.1016/j.cmet.2020.03.002. Epub 2020 Mar 26.

Immune-mediated destruction of insulin-producing β-cells causes type 1 diabetes (T1D). However, how β-cells participate in their own destruction during the disease process is poorly understood. Here, we report that modulating the unfolded protein response (UPR) in β-cells of non-obese diabetic (NOD) mice by deleting the UPR sensor IRE1α prior to insulitis induced a transient dedifferentiation of the β-cells, resulting in substantially reduced islet immune cell infiltration and β-cell apoptosis. Single-cell and whole-islet transcriptomics analyses of immature β-cells revealed remarkably diminished expression of β-cell autoantigens, MHC class I components and upregulation of immune inhibitory markers. IRE1α-deficient mice exhibited significantly less cytotoxic CD8+ T-cells in their pancreata and adoptive transfer of their total T-cells did not induce diabetes in Rag1-/- mice. Our results indicate that inducing β-cell dedifferentiation, prior to insulitis, allows these cells to escape immune-mediated destruction and may be used as a novel preventive strategy for T1D in high-risk individuals.

  • Bulk-RNAseq
  • Single cell RNAseq
  • Adoptive transfer experiments
  • Immunophenotyping
  • Inflammation scoring
  • Metabolic assays
  • Islet histomorphometry
April 2020 A Genetic Toggle for Chemical Control of Individual Plk1 Substrates.

Johnson JM, Hebert AS, Drane QH, Lera RF, Wan J, Weaver BA, Coon JJ, Burkard ME.

Cell Chem Biol. 2020 Mar 19;27(3):350-362.e8. doi: 10.1016/j.chembiol.2020.01.007. Epub 2020 Feb 3.

Enzymes like kinases can often catalyze many molecular events, each setting off a separate signaling cascade. However, disentangling the complex diversity of the signaling events can be a challenge. James Johnson (Burkard lab) in collaboration with Alex Hebert (Coon lab) built and tested a new chemical genetic tool. By manipulating the kinase under study, Polo-like kinase 1, he was able to reprogram it to selectively identify either serine or threonine amino acids. Next, he recoded the substrate proteins to ‘toggle’ serine-and-threonine, thereby placing desired phosphorylation events under genetic control. This was validated with deep phosphoproteomics.

February 2020 The Rise of Physiologic Media.

Cantor JR.

Trends Cell Biol. 2019 Nov;29(11):854-861. doi: 10.1016/j.tcb.2019.08.009. Epub 2019 Oct 14. Review.

Conventional cell culture media has been a staple in scientific research for over 70 years. This media has remained relatively unchanged during this time. The major goal of this media is to keep cells alive and have them grow rapidly, but is this the best way? This review published by the Cantor looks at cell culture media from a different view point and articulates the importance of understanding how cells work in the human body. Further summary.

February 2020 Real-time health monitoring through urine metabolomics.

Miller IJ, Peters SR, Overmyer KA, Paulson BR, Westphall MS, Coon JJ.

NPJ Digit Med. 2019 Nov 11;2:109. doi: 10.1038/s41746-019-0185-y. eCollection 2019.

The advent of wearable devices for health monitoring is ushering in an era of more personalized and preventive medicine. However, most consumer-grade health data is currently limited to metrics such as step count and heart rate. We imagine technology that could enable the passive and continuous monitoring of metabolic health by measuring the diverse set of metabolites in urine. There are over 4,500 metabolites in human urine that are known to be associated with more than 600 human conditions. These metabolites can further reflect lifestyle choices, such as alcohol and tobacco consumption, in addition to exercise and physical activity. In this small pilot study, we collected every urine sample from two healthy volunteers for 10 days along with biohealth data (diet, sleep, exercise) from smart phone applications. Using gas chromatography and mass spectrometry we measured the relative levels of hundreds of individual metabolites and found patterns in the urine metabolites that reflected the ebb and flow of daily life. For instance, we could see associations with nutrition, OTC drug metabolism, exercise, and sleep. We plan to expand this type of study to a larger cohort and to develop technology that could be integrated into a “smart bathroom” and achieve passive measurements of metabolic health at scale.

  • Longitudinal metabolomics analysis using gas chromatography and mass spectrometry
  • Collection and integration of digital health data collected from smartphones and wearable devices.
February 2020 Hepatic stearoyl CoA desaturase 1 deficiency increases glucose uptake in adipose tissue partially through the PGC-1α-FGF21 axis in mice.

Aljohani A, Khan MI, Bonneville A, Guo C, Jeffery J, O'Neill L, Syed DN, Lewis SA, Burhans M, Mukhtar H, Ntambi JM

J Biol Chem. 2019 Dec 20;294(51):19475-19485. doi: 10.1074/jbc.RA119.009868. Epub 2019 Nov 5.

Increased carbohydrate consumption increases hepatic de novo lipogenesis, which has been linked to the development of chronic metabolic diseases, including obesity, hepatic steatosis, and insulin resistance. Stearoyl CoA desaturase 1 (SCD1) is a critical lipogenic enzyme that catalyzes the synthesis of two monounsaturated fatty acids, oleate and palmitoleate, from the saturated fatty acids stearate and palmitate, respectively. SCD1-deficient mouse models are protected against diet-induced adiposity, hepatic steatosis, and hyperglycemia. However, the mechanism of this protection by SCD1 deficiency is unclear. Using liver-specific SCD1 knockout (LKO) mice fed a high-carbohydrate, low-fat diet, we show that hepatic SCD1 deficiency increases systemic glucose uptake. Hepatic SCD1 deficiency enhanced glucose transporter type 1 (GLUT1) expression in the liver and also up-regulated GLUT4 and adiponectin expression in adipose tissue. The enhanced glucose uptake correlated with increased liver expression and elevated plasma levels of fibroblast growth factor 21 (FGF21), a hepatokine known to increase systemic insulin sensitivity and regulate whole-body lipid metabolism. Feeding LKO mice a triolein-supplemented but not tristearin-supplemented high-carbohydrate, low-fat diet reduced FGF21 expression and plasma levels. Consistently, SCD1 inhibition in primary hepatocytes induced FGF21 expression, which was repressed by treatment with oleate but not palmitoleate. Moreover, deletion of the transcriptional coactivator PPARγ coactivator 1α (PGC-1α) reduced hepatic and plasma FGF21 and white adipocyte tissue-specific GLUT4 expression and raised plasma glucose levels in LKO mice. These results suggest that hepatic oleate regulates glucose uptake in adipose tissue either directly or partially by modulating the hepatic PGC-1α-FGF21 axis.

  • Measurements of Plasma FGF21 levels using the FGF-21 Quantikine ELISA Kit.
  • in vivo 2-[3H] deoxyglucose uptake assays.
  • Positron Emission Tomography-computed tomography (PET/CT) imaging analysis.
February 2020 Quantitative Spatial Analysis of Metabolic Heterogeneity Across in vivo and in vitro Tumor Models.

Heaster TM, Landman BA, Skala MC.

Front Oncol. 2019 Nov 1;9:1144. doi: 10.3389/fonc.2019.01144. eCollection 2019.

The goal of this paper was to quantify the spatial distribution of tumor cells with distinct cell metabolism using multivariate spatial statistical tools. Autofluorescence images of tumors in vivo and in 3D culture revealed spatial patterns of cell metabolism specific to drug response and resistance. This quantitative analysis framework can be used to assess the effect of drugs on cell-level heterogeneity in tumors.

  • Two photon fluorescence lifetime imaging of NAD(P)H and FAD
  • Single cell segmentation
  • Multivariate spatial statistical analysis
November 2019 Evaporative cooling provides a major metabolic energy sink.

Kasza I, Adler D, Nelson DW, Eric Yen CL, Dumas S, Ntambi JM, MacDougald OA, Hernando D, Porter WP, Best FA, Alexander CM.

Mol Metab. 2019 Sep;27:47-61. doi: 10.1016/j.molmet.2019.06.023. Epub 2019 Jul 1. PMID: 31302039

Heat production (thermogenesis) in mammalian bodies creates the so-called b-adrenergic lipolytic environment which also serves to modify disease progression and inflammatory conditions. Furthermore, stimulation of thermogenesis could be used to combat obesity. However, the total demand for heat production is offset by heat losses through skin; this manuscript therefore focuses on the key properties of skin that determine heat loss. This interdisciplinary project relied on space science engineering collaborators to calculate the total energy sink through all modes of heat transfer. We found that a large fraction of total energy expenditure in mice can be accounted for by evaporative cooling, especially for mice with genetic lesions in skin lipogenesis. These mice are also resistant to diet-induced obesity, prompting us to speculate that skin cooling is a significant player in calorie disposition.

  • Analysis of heat transfer processes in biological systems, using infrared thermography (FLIR) and assay of trans-epidermal water loss (TEWL)
  • Assay of skins of genetically- and environmentally- modified mice
  • Evaluation of dermal white adipose tissues by immunofluorescent stains
  • Energy expenditure assays
November 2019 Metabolic Remodeling during Biofilm Development of Bacillus subtilis.

Pisithkul T, Schroeder JW, Trujillo EA, Yeesin P, Stevenson DM, Chaiamarit T, Coon JJ, Wang JD, Amador-Noguez D.

MBio. 2019 May 21;10(3). pii: e00623-19. doi: 10.1128/mBio.00623-19.

The ability to form biofilms, multicellular communities encapsulated by an extracellular matrix, is a widespread trait in bacteria. Using time-resolved metabolomic, fluxomic, and proteomic analyses we discovered a surprisingly widespread and dynamic remodeling of both primary and secondary metabolism during biofilm development in Bacillus subtilis. This work represents the most comprehensive and systematic characterization of metabolic alterations during bacterial biofilm development ever undertaken. Our results demonstrate that dynamic remodeling of metabolism is a critical, and heretofore unreported, component of the highly coordinated response that leads to biofilm development.

  • Targeted metabolomics
  • Shotgun proteomics
  • 13C isotope tracer experiments
November 2019 Gene loci associated with insulin secretion in islets from non-diabetic mice.

Keller MP, Rabaglia ME, Schueler KL, Stapleton DS, Gatti DM, Vincent M, Mitok KA, Wang Z, Ishimura T, Simonett SP, Emfinger CH, Das R, Beck T, Kendziorski C, Broman KW, Yandell BS, Churchill GA, Attie AD.

J Clin Invest. 2019 Jul 25;130:4419-4432. doi: 10.1172/JCI129143.

Type 2 diabetes occurs when pancreatic ß-cells are unable to keep up with the demand for insulin, often a consequence of insulin resistance. Human genetic studies show that most of the genetic predisposition to T2D results in a reduction of ß-cell insulin secretion or ß-cell mass. We used a genetically divers outbred population of mice to screen for genes that affect ß-cell insulin secretion. This was a heroic effort carried out by Mary Rabaglia, Kiki Schueler, Donnie Stapleton, and Shane Simonett and carefully supervised by Mark Keller. We collaborated with Gary Churchill at the Jackson Lab. The work identified multiple loci associated with insulin secretion. In three cases, we derived knockout mouse models and all showed an insulin secretion phenotype. With Josh Coon, we carried out proteomic and lipidomic analysis and have identified gene loci controlling protein and lipid abundance. With Federico Rey, we have connected the intestinal microbiome with genetic differences in serum bile acids. We now have multiple projects testing interesting candidate genes that have emerged from this screen.

  • insulin secretion measurements in isolated islets
  • mass spectrometry of proteins, lipids, and metabolites
  • systems biology analysis of pathways associated with metabolic disease
November 2019 Intestinal delta-6-desaturase activity determines host range for Toxoplasma sexual reproduction.

Martorelli Di Genova B, Wilson SK, Dubey JP, Knoll LJ.

PLoS Biol. 2019 Aug 20;17(8):e3000364. doi: 10.1371/journal.pbio.3000364. eCollection 2019 Aug.

It has long been a puzzle why felines are the only mammal permissive of the sexual cycle of Toxoplasma gondii. Cats lack intestinal delta-6-desaturase activity and as a consequence, they have systemic increases in linoleic acid. In this study, Morgridge Metabolism Interdisciplinary (MMI) fellow Bruno Martorelli Di Genova determined that inhibition of murine delta-6-desaturase and dietary supplementation with linoleic acid allowed Toxoplasma sexual development to occur in mice.

  • Intestinal organoid culture of cat and mouse cells
  • CRISPR-mediated genome edited mouse model
  • High resolution microscopy for Toxoplasma sexual stages 
November 2019 Hypothalamic mTORC2 is essential for metabolic health and longevity.

Chellappa K, Brinkman JA, Mukherjee S, Morrison M, Alotaibi MI, Carbajal KA, Alhadeff AL, Perron IJ, Yao R, Purdy CS, DeFelice DM, Wakai MH, Tomasiewicz J, Lin A, Meyer E, Peng Y, Arriola Apelo SI, Puglielli L, Betley JN, Paschos GK, Baur JA, Lamming DW.

Aging Cell. 2019 Oct; 18(5): e13014.

The mechanistic target of rapamycin (mTOR) is a conserved protein kinase that regulates growth and metabolism. Rapamycin, a drug that extends lifespan, promotes longevity through inhibition of mTORC1, but we have found that rapamycin also inhibits mTORC2. We find that hypothalamic mTORC2 signaling normally increases with age, and that mice genetically engineered to lack hypothalamic mTORC2 signaling display higher fat mass and impaired glucose homeostasis throughout life, become more frail with age, and have decreased overall survival. We conclude that hypothalamic mTORC2 is essential for the normal metabolic health, fitness, and lifespan of mice.

  • Phenotyping of glucoregulatory control, including in vivo glucose and insulin tolerance tests
  • Determination of body composition, activity and energy expenditure using metabolic chambers
  • Determination of lifespan and longitudinal assessment of frailty
November 2019 Pptc7 is an essential phosphatase for promoting mammalian mitochondrial metabolism and biogenesis.

Niemi NM, Wilson GM, Overmyer KA, Vogtle FN, Myketin L, Lohman DC, Schueler KL, Attie AD, Meisinger C, Coon JJ, and DJ Pagliarini

Nat Commun. 2019 Jul 19;10(1):3197. doi: 10.1038/s41467-019-11047-6.

Mitochondrial proteins are replete with phosphorylation, yet its functional relevance remains largely unclear. The presence of multiple resident mitochondrial phosphatases, however, suggests that protein dephosphorylation may be broadly important for calibrating mitochondrial activities. Here, we use CRISPR to delete the mitochondrial phosphatase Pptc7 in Mus musculus and find these mice exhibit hypoketotic hypoglycemia, elevated acylcarnitines and serum lactate, and die soon after birth. Pptc7−/− tissues have markedly diminished mitochondrial size and protein content despite normal transcript levels, and aberrantly elevated phosphorylation on select mitochondrial proteins. Overall, our data define Pptc7 as a protein phosphatase essential for proper mitochondrial function and biogenesis during the extrauterine transition.

  • Generation of a knockout mouse using CRISPR
  • Acylcarnitine profiling coupled with unbiased metabolomic and lipidomic analysis of perinatal mouse tissue
  • Phosphoproteomic and proteomic analysis of perinatal mouse tissue
  • Electron microscopy of mitochondria in perinatal mouse tissue
  • Mitochondrial import assays
November 2019 Acetyl-CoA flux regulates the proteome and acetyl-proteome to maintain intracellular metabolic crosstalk.

Dieterich IA, Lawton AJ, Peng Y, Yu Q, Rhoads TW, Overmyer KA, Cui Y, Armstrong EA, Howell PR, Burhans MS, Li L, Denu JM, Coon JJ, Anderson RM, Puglielli L.

Nature Communications. 2019; 10: 3929 (doi: 10.1038/s41467-019-11945-9).

AT-1/SLC33A1 is a key member of the endoplasmic reticulum (ER) acetylation machinery, transporting acetyl-CoA from the cytosol into the ER lumen where acetyl-CoA serves as the acetyl-group donor for Nε-lysine acetylation. Dysfunctional ER acetylation, as caused by heterozygous or homozygous mutations as well as gene duplication events of AT-1/SLC33A1, has been linked to both developmental and degenerative diseases. Here, we used two mouse models of AT-1 dysregulation to study how the cytosol-to-ER flux of acetyl-CoA promotes functional crosstalk between different intracellular organelles and compartments.

  • New mouse models
  • Biochemistry, histology, EM and diet manipulation
  • Quantitative proteomics
  • Stoichiometry of acetylation
  • Metabolomics
  • Primary cell isolation and culture
  • SIM microscopy
June 2019 Growth factor stimulation promotes multivesicular endosome biogenesis by prolongingrecruitment of the late-acting ESCRT machinery.

Quinney KB, Frankel EB, Shankar R, Kasberg W, Luong P, Audhya A.

Proc Natl Acad Sci U S A. 2019 Apr 2;116(14):6858-6867. doi: 10.1073/pnas.1817898116. Epub 2019 Mar 20.

Growth factor signaling plays a key role in directing metabolic flux within cells. In this work, we demonstrate a mechanism by which the mammalian ESCRT machinery acts to attenuate growth factor driven changes in metabolism using a combination of CRISPR-mediated genome editing, lattice light sheet microscopy, and super resolution STED microscopy.

  • CRISPR-mediated genome editing using mammalian cell lines
  • FACS sorting to identify clonal edited cell populations
  • Stimulated emission depletion (STED) microscopy at the UW-Madison Optical Imaging Core
  • Thin section electron microscopy in collaboration with the SMPH EM facility
  • Electron tomography using the TF30 transmission electron microscope
June 2019 Capturing site-specific heterogeneity with large-scale N-glycoproteome analysis.

Riley NM, Hebert AS, Westphall MS, Coon JJ.

Nat Commun. 2019 Mar 21;10(1):1311. doi: 10.1038/s41467-019-09222-w.

New technology is needed to advance the characterization of protein glycosylation, which is a prevalent, chemically complex, and biologically diverse post-translational modification that plays particularly important roles at the cell surface. Here we applied a new technology we developed called activated ion electron transfer dissociation (AI-ETD) to improve the identification of intact N-glycopeptides, and we also designed new visualization approaches to capture the heterogeneity of the glycoproteome at a systems scale.

  • Mass spectrometer instrumentation modifications
  • MS-based glycoproteomics
  • Development of new visualization tools
June 2019 A heterodimeric glutathione S-transferase that stereospecifically breaks lignin's β(R)-aryl ether bond reveals the diversity of bacterial β-etherases.

Kontur WS, Olmsted CN, Yusko LM, Niles AV, Walters KA, Beebe ET, Vander Meulen KA, Karlen SD, Gall DL, Noguera DR, Donohue TJ.

J Biol Chem. 2019 Feb 8;294(6):1877-1890. doi: 10.1074/jbc.RA118.006548. Epub 2018 Dec 12.

In this study, GLBRC researchers identified and characterized a new type of enzyme that specifically cleaves β-aryl ether bonds. This work demonstrates that there is more variability in the bacterial pathway for cleaving the β-aryl ether bond than previously thought, and illustrates the importance of studying this pathway – as well as other pathways involved in metabolizing lignin-derived compounds – in multiple species to better understand and be able to capitalize on this diversity. Characterizing microbial strategies for lignin breakdown is important for understanding plant biomass turnover in nature, and could aid in developing industrial systems for producing commodity chemicals from this abundant renewable resource.

  • Expression and purification of proteins from recombinant hosts and cell free systems
  • Kinetic analysis of wild type and mutant proteins (including determine of Km, Vmax and kcat)
  • Modeling of enzyme active site
  • HPLC of aromatic compounds and glutathione-aromatic conjugates
  • Phylogenetic analysis of protein databases
June 2019 Evolution of a novel chimeric maltotriose transporter in Saccharomyces eubayanus from parent proteins unable to perform this function.

Baker EP, Hittinger CT.

PLoS Genet. 2019 Apr 4;15(4):e1007786. doi: 10.1371/journal.pgen.1007786. eCollection 2019 Apr.

Here the Hittinger lab showed how the genes encoding maltose transporters could undergo ectopic gene conversion to produce genes encoding transporters for the bulkier sugar maltotriose, a critical sugar in wort or the malt extract used to brew beer. This adaptive laboratory evolution experiment showed how Saccharomyces eubayanus, the wild, cold-tolerant parent of hybrid lager yeasts, could gain this industrially important function.

  • Illumina sequencing (Biotechnology Center)
  • Bulk segregant analysis (Hittinger Lab)
  • Adaptive laboratory evolution (Hittinger Lab)
  • Phylogenetic analysis (Hittinger Lab)
June 2019 Fungal secondary metabolism: regulation, function and drug discovery.

Keller NP.

Nat Rev Microbiol. 2019 Mar;17(3):167-180. doi: 10.1038/s41579-018-0121-1.

The fungal secondary metabolome is both a primary source of new pharmaceuticals and an endogenous source of secondary metabolites important for fungal warfare, defense and development. This review provides up-to-date insights into how to harvest bioactive fungal secondary metabolites and to elucidate their roles in fungal ecology.

  • Fungal molecular biology (deletion, over-expression and mutation of genes)
  • Culture growth and extraction of fungal metabolites
  • Liquid chromatography, high resolution mass spectrometry, NMR analysis
  • Bioinfomatics
June 2019 The Metabolic Response to a Low Amino Acid Diet is Independent of Diet-Induced Shifts in the Composition of the Gut Microbiome.

Heidi H. Pak, Nicole E. Cummings, Cara L. Green, Jacqueline A. Brinkman, Deyang Yu, Jay L. Tomasiewicz, Shany E. Yang, Colin Boyle, Elizabeth N. Konon, Irene M. Ong & Dudley W. Lamming.

Sci Rep. 2019 Jan 11;9(1):67. doi: 10.1038/s41598-018-37177-3.

Low protein diets promote metabolic health in both humans and mice, but the mechanisms that drive the physiological benefits of these diets have not been determined. Here, we find that reducing dietary protein significantly alters the taxonomic composition of the gut microbiome, but that this shift does not mediate the metabolic benefits of a low protein diet.

  • 16S rRNA profiling, RNA-seq and all gene expression analysis
  • Phenotyping of glucoregulatory control, including in vivo glucose and insulin tolerance tests
  • Determination of body composition, activity and energy expenditure using metabolic chambers
June 2019 TAT1 and TAT2 tyrosine aminotransferases have both distinct and shared functions in tyrosine metabolism and degradation in Arabidopsis thaliana.

Wang M, Toda K, Block A, Maeda HA.

J Biol Chem. 2019 Mar 8;294(10):3563-3576. doi: 10.1074/jbc.RA118.006539. Epub 2019 Jan 10.

This study demonstrated that two tyrosine aminotransferases play key roles in tyrosine degradation and metabolism in Arabidopsis thaliana, by combining reverse genetics, metabolite profiling, and 13C-precursor time course feeding experiments.

  • 13C labeling measurement using GC-MS
  • Dark respiration measurement using LI-COR LI-6400XT
June 2019 Obesity-dependent CDK1 signaling stimulates mitochondrial respiration at complex I in pancreatic β-cells.

Gregg T, Sdao SM, Dhillon RS, Rensvold JW, Lewandowski SL, Pagliarini DJ, Denu JM, Merrins MJ.

J Biol Chem. 2019 Mar 22;294(12):4656-4666. doi: 10.1074/jbc.RA118.006085. Epub 2019 Jan 30.

Beta cell mitochondria play a central role in coupling glucose metabolism with insulin secretion. These studies identify a novel role for complex I in mediating the effects of obesity on the beta cell secretory pathway, and implicate cyclin-dependent kinase 1 (CDK1) signaling as the mechanism driving this effect. Two graduate students in the Merrins lab, Trilly Gregg and Sophie Sdao, spearheaded the project (https://www.merrinslab.org/publications).

  • Live-cell imaging of the beta cell secretory pathway, including real-time measurements of cytosolic citrate, ATP/ADP, and calcium
  • 2-photon fluorescence lifetime imaging of mitochondrial NAD(P)H
  • Direct measurements of electron transport chain fluxes using oxygen consumption rate measurements
June 2019 An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis.

Lohman DC, Aydin D, Von Bank HC, Smith RW, Linke V, Weisenhorn E, McDevitt MT, Hutchins P, Wilkerson EM, Wancewicz B, Russell J, Stefely MS, Beebe ET, Jochem A, Coon JJ, Bingman CA, Dal Peraro M, Pagliarini DJ.

Mol Cell. 2019 Feb 21;73(4):763-774.e10. doi: 10.1016/j.molcel.2018.11.033. Epub 2019 Jan 17.

Coenzyme Q is among the most hydrophobic molecules in nature, which presents challenges for its biosynthesis and delivery. In this paper, we describe how COQ9 uses accesses, binds, and presents CoQ precursors to another member of the biosynthesis machinery.

  • MS-based lipidomics with Josh Coon’s group
  • Protein purification
  • Crystallography with Craig Bingman and Bob Smith from the crystallography core
  • Liposome flotation assays (to assess protein binding to membranes of varying lipid composition)
  • Yeast growth assays
March 2018 Caloric Restriction Engages Hepatic RNA Processing Mechanisms in Rhesus Monkeys.

Rhoads TW, Burhans MS, Chen VB, Hutchins PD, Rush MJP, Clark JP, Stark JL, McIlwain SJ, Eghbalnia HR, Pavelec DM, Ong IM, Denu JM, Markley JL, Coon JJ, Colman RJ, Anderson RM.

Cell Metabolism. 2018 Mar 6;27(3):677-688.e5. doi: 10.1016/j.cmet.2018.01.014. PMCID: PMC5844481

A multi-disciplinary research team has uncovered new clues about calorie restriction and how it works to delay aging and age-related diseases. The researchers used a range of molecular profiling techniques to catalog over 20,000 molecules in rhesus liver. Data were analyzed using complex statistical approaches including machine learning techniques. The team showed that CR reprogrammed metabolism by harnessing distinct control mechanisms including RNA processing.

**Special Note: This publication was highlighted on the cover of the March 6, 2018 issue of Cell Metabolism.

    Next Generation Sequencing - Biotech Center
  • Mass Spectrometry Metabolomics/Proteomics - Coon Lab/Denu Lab
  • Nuclear Magnetic Resonance John Markely (NMR Fam)
  • Higher Order Statistical Modeling - Ong/McIlwain CPCP
March 2018 Ist1 regulates ESCRT-III assembly and function during multivesicular endosome biogenesis in Caenorhabditis elegans embryos.

Frankel EB, Shankar R, Moresco JJ, Yates JR 3rd, Volkmann N, Audhya A.

Nature Communications. 2017 Nov 13;8(1):1439. doi: 10.1038/s41467-017-01636-8. PMCID: PMC5682282.

The normal turnover of many integral membrane proteins is mediated by the formation of multivesicular endosomes, which sequester cargoes destined for degradation within intralumenal vesicles that bud away from the cytoplasm. In this work, we demonstrate a direct role for the ESCRT-III complex during membrane bending that is necessary to create intralumenal vesicles and define a new regulatory mechanism that preserves the continual action of the ESCRT machinery in repetitive cycles of vesicle biogenesis.

  • Immunogold labeling for electron microscopy
  • Super resolution (stimulated emission depletion) fluorescence microscopy
  • Electron tomography
March 2018 Broadening the functionality of a J-protein/Hsp70 molecular chaperone system.

Schilke BA, Ciesielski SJ, Ziegelhoffer T, Kamiya E, Tonelli M, Lee W, Cornilescu G, Hines JK, Markley JL, Craig EA.

PLoS Genet. 2017 Oct 30;13(10):e1007084. doi: 10.1371/journal.pgen.1007084. eCollection 2017 Oct. PMCID: PMC5679652.

This publication describes the isolation and analysis of gain-of-function mutations that overcome the requirement for an essential, conserved molecular chaperone. Results of analyses of isolated suppressor variants point to the idea that fine-tuning of Hsp70’s interaction cycle with substrate proteins can have major, unexpected consequences in vivo.

  • Yeast gain-of-function genetic selections
  • Structural analysis using NMR through National Magnetic Resonance Facility at Madison (NMRFAM)
  • Interaction studies using fluorescence anisotropy
March 2018 NRPS-Derived Isoquinolines and Lipopetides Mediate Antagonism between Plant Pathogenic Fungi and Bacteria.

Khalid S, Baccile JA, Spraker JE, Tannous J, Imran M, Schroeder FC, Keller NP.

ACS Chem Biol. 2018 Jan 19;13(1):171-179. doi: 10.1021/acschembio.7b00731. Epub 2017 Dec 18. PMID: 29182847

This work identifies antagonistic small molecule communication between two agricultural pathogens, the bacterium Ralstonia solanacearum and the fungus Aspergillus flavus. The fungal alkaloid product enhances fungal germination and slows bacterial growth but is inhibited in production by a bacterial lipopeptide.

  • Creation of genetic mutant strains of bacteria and fungi
  • RNA-seq and all gene expression analysis
  • Microbial physiology and statistical analysis
March 2018 Restoration of metabolic health by decreased consumption of branched-chain amino acids.

Cummings NE, Williams EM, Kasza I, Konon EN, Schaid MD, Schmidt BA, Poudel C, Sherman DS, Yu D, Arriola Apelo SI, Cottrell SE, Geiger G, Barnes ME, Wisinski JA, Fenske RJ, Matkowskyj KA, Kimple ME, Alexander CM, Merrins MJ, Lamming DW.

J Physiol. 2017 Dec 19. doi: 10.1113/JP275075. [Epub ahead of print]. PMID: 29266268

The branched-chain amino acids (BCAAs) leucine, isoleucine, and valine are elevated in the blood of obese, insulin-resistant humans and rodents. In this work, we show that specifically reducing dietary BCAAs rapidly reverses diet-induced obesity and improves glucose tolerance and insulin sensitivity in diet-induced obese mice. Significantly, this occurs even in mice continuing to eat an otherwise unhealthy high-calorie, high-sugar “Western” diet. Reducing dietary levels of the BCAAs promotes leanness by increasing energy expenditure. Our results link dietary BCAAs with the regulation of metabolic health and energy balance in obese animals, and suggest that specifically reducing dietary BCAAs may represent a highly translatable option for the treatment of obesity and insulin resistance.

  • Feeding of amino acid defined diets to diet-induced obese mice
  • Phenotyping of glucoregulatory control, including in vivo glucose and insulin tolerance tests, and ex vivo characterization of pancreatic islet function and metabolism
  • Determination of body composition, activity and energy expenditure using metabolic chambers
March 2018 UCP1 deficiency increases adipose tissue monounsaturated fatty acid synthesis and trafficking to the liver.

Bond LM, Ntambi JM.

J Lipid Res. 2018 Feb;59(2):224-236. doi: 10.1194/jlr.M078469. Epub 2017 Dec 3. PMCID: PMC5794418.

This publication demonstrates that brown adipose tissue thermogenesis regulates whole body lipid homeostasis. Using mice lacking uncoupling protein-1, a protein critical for heat production, we revealed that loss of brown adipose tissue thermogenesis elevates the synthesis of monounsaturated fatty acids in white adipose tissue and causes triglyceride accumulation in the liver.

  • Analysis of fatty acid composition using gas chromatography
  • in vivo lipid synthesis and export assays
March 2018 Multi-omic mitoprotease profiling defines a role for Oct1p in coenzyme Q production.

Veling MT, Reidenbach AG, Freiberger EC, Kwiecien NW, Hutchins PD, Drahnak MJ, Jochem A, Ulbrich A, Rush JPR, Russell JD, Coon JJ, and Pagliarini DJ

Molecular Cell, 2017 doi: 10.1016/j.molcel.2017.11.023

March 2018 Multi-Omics Reveal Specific Targets of the RNA-Binding Protein Puf3p and Its Orchestration of Mitochondrial Biogenesis.

Lapointe CP, Stefely JA, Jochem A, Hutchins PD, Wilson G, Kwiecien NW, Coon JJ, Wickens MP, and Pagliarini DJ

Cell Systems, 2017 doi: 10.1016/j.cels.2017.11.012

March 2018 Conserved lipid and small molecule modulation of COQ8 reveals regulation of the ancient kinase-like UbiB family.

Reidenbach AG, Kemmerer ZA, Aydin D, Jochem A, McDevitt MT, Hutchins PD, Stark JL, Stefely, Reddy T, Hebert AS, Wilkerson EM, JA, Johnson IE, Bingman CA, Markley JL, Coon JJ, Dal Peraro M, and Pagliarini DJ

Cell Chemical Biology, 2017 doi.org/10.1016/j.chembiol.2017.11.001

In a three-paper series, we established new post-transcriptional regulatory processes for coenzyme Q (CoQ) metabolism. First, we discovered small- molecule and lipid activators for the atypical kinase-like protein COQ8 and developed an analog- sensitive version that can be selectively inhibited in vivo. Second, we used a multi-omic approach that incorporates measurements of mRNAs, proteins, lipids, and metabolites to identify endogenous targets for the mRNA binding protein, Puf3p, including the CoQ-related methyltransferase, COQ5. Finally, using a similar approach, we reveal numerous connections between mitoproteases and their biological functions, including a direct role for Oct1p in processes COQ5.

UW Collaborators: Josh Coon’s group, Marv Wicken’s group, John Markley’s group, and Craig Bingman

Further summary: https://morgridge.org/story/cracking-the-code-of-coenzyme-q-biosynthesis/

  • One-dimensional (1D) 1H nuclear magnetic resonance (NMR) ligand-affinity screen
  • Mass spec-based proteomics, metabolomics, and lipidomicsa
  • Liposome flotation analyses (i.e., protein interactions with liposomes)
  • Molecular modeling
  • Recombinant protein purification and various yeast growth assays
  • RNA binding protein analyses (RNA Tagging and HITS/CLIP)
October 2017 TFG facilitates outer coat disassembly on COPII transport carriers to promote tethering and fusion with ER-Golgi intermediate compartments.

Hanna MG 4th, Block S, Frankel EB, Hou F, Johnson A, Yuan L, Knight G, Moresco JJ, Yates JR 3rd, Ashton R, Schekman R, Tong Y, Audhya A.
Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):E7707-E7716. doi: 10.1073/pnas.1709120114. Epub 2017 Aug 29. PMID: 28851831; PMCID: PMC5604033.

The endoplasmic reticulum (ER) serves as a platform for the packaging of most secretory proteins into conserved COPII-coated transport carriers destined for ER-Golgi intermediate compartments (ERGIC) in animal cells. In this work, we demonstrate that Trk-fused gene (TFG) simultaneously captures and concentrates COPII transport carriers at the ER/ERGIC interface to enable the rapid movement of secretory cargoes to the ERGIC.

  • CRISPR-mediated genome editing
  • Super resolution (stimulated emission depletion) fluorescence microscopy
  • In vitro reconstitution of vesicle tethering
October 2017 Chemical Genomics, Structure Elucidation, and in Vivo Studies of the Marine-Derived Anticlostridial Ecteinamycin.

Wyche TP, Alvarenga RFR, Piotrowski JS, Duster MN, Warrack SR, Cornilescu G, De Wolfe TJ, Hou Y, Braun DR, Ellis GA, Simpkins SW, Nelson J, Myers CL, Steele J, Mori H, Safdar N, Markley JL, Rajski SR, Bugni TS.
ACS Chem. Biol. 2017 Sep 15; 12(9):2287-2295 doi:10.1021/acschembio.7b00388. PMID: 28708379

This paper describes the isolation and structural characterization of the natural product ecteinamycin, the product of a marine-derived bacterium. Additionally, this paper strongly supports the hypothesis that ionophore antibiotics such as ecteinamycin and other more well established ionophores such as commonly used feed additives have tremendous potential as therapeutics for treating Clostridium difficile infections in humans. Ecteinamycin showed exceptional potency toward C. difficile, and yeast chemical genomics suggested that ecteinamycin disrupts vesicular trafficking pathways in eukaryotic cells that are required for C. difficile toxin maturation; impairment of such pathways appears to protect humans from the toxin effects of C. difficile.

  • LCMS-based metabolomics
  • Yeast chemical genomics using a DNA-barcoded knockout library
  • E. coli chemical genomics using DNA-barcoded knockout library
  • Residual Dipolar Couplings (RDCs) to assist with configurational analysis
October 2017 WBSCR16 is a Guanine Nucleotide Exchange Factor Important for Mitochondrial Fusion.

Huang G, Massoudi D, Muir AM, Joshi DC, Zhang C-L, Chiu, SY, Greenspan DS.
Cell Reports. 2017 July 25; 20(4): 923-934. doi: 10.1016/j.celrep.2017.06.090. PMID:28746876

This study identifies WBSCR16 as a protein that co-localizes with OPA1 on the outer surface of the inner mitochondrial membrane. It also shows WBSCR16 to act as a GEF for OPA1, a dynamin-like GTPase essential to mitochondrial fusion, which is in turn essential to mitochondrial function.

  • Gene mapping and deep sequencing to identify a spontaneous mutation in the Wbscr16 gene in mice
  • Mitochondrial subfractionation to localize proteins within different mitochondrial compartments
  • Use of a proximity ligation assay to demonstrate close enough proximity of WBSCR16 and OPA1 in situ for direct protein-protein interactions
  • GEF activity assays, in vitro and for intact mitochondria, to demonstrate a role for WBSCR16 as an intramitochondrial GEF with specific activity for OPA1
October 2017 A kidney-specific genetic control module in mice governs endocrine regulation of the cytochrome P450 gene Cyp27b1 essential for vitamin D3 activation..

Meyer MB, Benkusky NA, Kaufmann M, Lee SM, Onal M, Jones G, Pike JW.
J Biol Chem. 2017 Aug 14. pii: jbc.M117.806901. doi: 10.1074/jbc.M117.806901. PMID: 28808057

In this paper, we describe the functional identification of a kidney-specific genomic regulatory region in the mouse that controls the expression of the Cyp27b1 gene whose enzymatic product is responsible for the final synthesis of 1α,25-dihydroxyvitamin D3, the biologically active hormonal form of vitamin D3.

  • ChIP-seq analysis of genetic and epigenetic features of mouse kidney tissue to define the locations and activity of novel regulatory regions of the Cyp27b1 gene
  • CRISPR/Cas9 gene-editing methods to delete potential regulatory regions in the mouse for subsequent loss-of-function analyses
  • Extensive systemic, regulatory and skeletal phenotyping to describe the consequence of aberrant Cyp27b1 regulation by mineral regulating hormones
July 2017 Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae.

Sato TK, Tremaine M, Parreiras LS, Hebert AS, Myers KS, Higbee AJ, Sardi M, McIlwain SJ, Ong IM, Breuer RJ, Avanasi Narasimhan R, McGee MA, Dickinson Q, La Reau A, Xie D, Tian M, Reed JL, Zhang Y, Coon JJ, Hittinger CT, Gasch AP, Landick R.
PLoS Genetics. 2016 Oct 14;12(10):e1006372. doi: 10.1371/journal.pgen.1006372. eCollection 2016 Oct. PMID: 27741250; PMCID: PMC5065143.

This publication describes the identification and molecular characterization of mutations in yeast that were engineering and evolved to ferment xylose, a pentose sugar that the organism does not normally metabolize. Using genetic, proteomic and metabolomic comparisons, it was determined that inactivating mutations in Fe-S cluster mitochondrial biogenesis, cAMP/Protein Kinase A and MAP Kinase signaling pathways enabled the conversion of xylose to ethanol.

  • High throughput genome resequencing (UW Biotech Center) and sequence analysis
  • Yeast genetic engineering and directed evolution
  • Proteome quantification
  • Intracellular and extracellular metabolite quantification
July 2017 Dual interaction of scaffold protein Tim44 of mitochondrial import motor with channel-forming translocase subunit Tim23.

Ting SY, Yan NL, Schilke BA, Craig EA.
Elife. 2017 Apr 25;6. pii: e23609. doi: 10.7554/eLife.23609. PMID: 28440746; PMCID: PMC5422074.

This publication reveals functional attributes of Tim44 the "hub" protein of the Hsp70 chaperone-based “import motor”, which is located in the matrix of mitochondria and required for the translocation of proteins into that subcompartment from the cytosol.

  • Site-specific in vivo crosslinking using photoactivatable alternative amino acid Bpa
  • in organellar mitochondria import assays
  • Yeast genetic suppressor analysis
July 2017 Inference and Evolutionary Analysis of Genome-Scale Regulatory Networks in Large Phylogenies.

Koch C, Konieczka J, Delorey T, Lyons A, Socha A, Davis K, Knaack SA, Thompson D, O'Shea EK, Regev A, Roy S.
Cell Systems. 2017 May 24;4(5):543-558.e8. doi: 10.1016/j.cels.2017.04.010. PMID: 28544882.

In this paper, we developed a new computational method to infer gene regulatory networks in multiple non-model species from global transcriptomic profiles. We used this approach to study how regulatory networks, associated with stress response, evolve across six yeast species.

  • Design and implementation of the multi-species network inference algorithm
  • Analytical measures used to study regulatory network evolution at the structure and function level.
July 2017 SCnorm: robust normalization of single-cell RNA-seq data.

Bacher R, Chu LF, Leng N, Gasch AP, Thomson JA, Stewart RM, Newton M, Kendziorski C.
Nat Methods. 2017 Jun;14(6):584-586. doi: 10.1038/nmeth.4263. Epub 2017 Apr 17. PMID: 28418000; PMCID: PMC5473255.

This publication presents a statistical method for normalizing data from single-cell RNA sequencing experiments. Normalization is a critical step required prior to downstream analysis to ensure that technical artifacts are removed and that gene expression profiles can be compared across cells.

  • Quality control, normalization, and downstream analysis of bulk and single-cell RNA-sequencing data.
July 2017 Molecular basis of the evolution of alternative tyrosine biosynthetic routes in plants.

Schenck C.A., Holland C.K., Schneider M., Men Y., Lee S.G., Jez J. and Maeda H.A.
Nature Chemical Biology 2017 Jun 26. doi: 10.1038/nchembio.2414. PMID: 28671678.

This study conducted phylogeny-guided structure-function analyses of key regulatory enzymes of tyrosine biosynthesis (prephenate and arogenate dehydrogenases), discovered a single amino acid residue that confers their substrate specificity and feedback inhibition, and provided molecular basis of long-known two alternative tyrosine biosynthetic pathways.

  • Structure-guided phylogenetic analysis of proteins from distantly-related organisms.
  • Prephenate and arogenate dehydrogenase assays using a plate reader and LC-fluorescence detection.
  • Key amino acid residue identification by defining a precise evolutionary timing of enzyme neofunctionalization, followed by primary sequence and structure comparisons, and site-directed mutagenesis.
April 2017 Ongoing resolution of duplicate gene functions shapes the diversification of a metabolic network.

Kuang MC, Hutchins PD, Russell JD, Coon JJ, Hittinger CT. Elife. 2016 Sep 30;5. pii: e19027. doi: 10.7554/eLife.19027. PubMed PMID: 27690225; PubMed Central PMCID: PMC5089864.

In this publication, we showed that more active metabolic networks also require more robust repression systems. The paper also showcases some of the metabolomic capabilities of the LBMS facility.

  • Liquid chromatography-mass spectrometry (LC-MS) assays to measure central carbon metabolites by the Laboratory of Biomolecular Mass Spectrometry (LBMS)
  • Custom galactose-1-phosphatse assay developed by LBMS
April 2017 Ptc7p dephosphorylates select mitochondrial proteins to enhance metabolic function.

Guo X*, Niemi NM*, Hutchins PD, Condon SGF, Jochem A, Ulbrich A, Higbee AJ, Russell JD, Senes A, Coon JJ, and Pagliarini DJ,
Cell Reports, 2017 18: 1–7

This publication reveals that disruption of the poorly characterized mitochondrial phosphatase, Ptc7p, perturbs mitochondrial phosphorylation of ~20 matrix proteins, partially inactivates citrate synthase, and decreases mitochondrial respiratory function.

  • LC-MS/MS-based phosphoproteomics
  • Recombinant protein purification, including site-specific phospho-incorporation
  • Citrate synthase assays
  • Blue native PAGE
  • Yeast liquid culture and plate-based assays
  • Molecular modeling of point mutations
April 2017 Dietary Conjugated Linoleic Acid-c9t11 Prevents Collagen-Induced Arthritis, Whereas Conjugated Linoleic Acid-t10c12 Increases Arthritic Severity.

Muhlenbeck JA, Butz DE, Olson JM, Uribe-Cano D, Cook ME.
Lipids. 2017 Mar 15. doi: 10.1007/s11745-017-4241-6. [Epub ahead of print] PubMed PMID: 28299528.]

This publication shows slight alteration in the positioning and geometric configuration of double bonds in isomers of linoleic acid have substantial effects on the onset of arthritis. Tissue fatty acids and joint cytokines are also presented.

  • GC fatty acid analysis conducted in ME Cook lab
  • Lumines Systems Cytokine array analysis conducted in the shared Pharmacokinetics, Pharmacodynamics, Pharmacogenetics Laboratory (3Plab)
  • Arthritic mouse experiment conducted in Animal Sciences Vivarium

Measuring the molecules of life – Q&A with Josh Coon

Proteins are the workhorse molecules that perform all the functions in the cell and the body. Being able to detect and measure proteins is critical to figuring out basic biology, and the signature of diseases such as Alzheimer’s, cancer and diabetes. Josh Coon is creating technologies to do exactly that.

Regulating iron in the blood for optimal health – Q&A with Rick Eisenstein

Iron is an essential nutrient to human life, the element by which we regenerate red blood cells. Too little iron can cause serious problems such as anemia. But too much can be toxic, potentially causing blood clotting. Rick Eisenstein studies iron metabolism, with the goal of helping humans achieve the optimal balance for health.

Creating the blueprints for new biofuels – Q&A with Tim Donohue

Earlier this month, the Great Lakes Bioenergy Research Center (GLBRC) received another major boost from the U.S. Department of Energy, receiving more than $250 million to conduct another five years of groundbreaking work on alternative fuels.

What we can learn from hibernation – Q&A with Hannah Carey

Hannah Carey, a UW-Madison professor of comparative biosciences, uses hibernating mammals as models to study extreme changes in physiology and nutrition that occur on a seasonal basis. Carey discusses this remarkable process and its potential to impact human health by improving trauma care.