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!

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.

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