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Saccharomyces cerevisiae

  • 1.
    Hu M, Dinh H, Shen Y, Suthers P, Foster C, Call C, Ye X, Pratas J, Fatma Z, Zhao H, Rabinowitz J, Maranas C. Comparative study of two Saccharomyces cerevisiae strains with kinetic models at genome-scale. Metab Eng. 2023;76:1–17. PMID: 36603705
    Reference Link
  • 1.
    Xiao T, Khan A, Shen Y, Chen L, Rabinowitz J. Glucose feeds the tricarboxylic acid cycle via excreted ethanol in fermenting yeast. Nat Chem Biol. 2022;18(12):1380–1387. PMCID: 1082793
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  • 1.
    Hoffman S, Lalwani M, Avalos J. Light-Controlled Fermentations for Microbial Chemical and Protein Production. J Vis Exp. 2022;(181). PMID: 35404352
    Reference Link
  • 1.
    Zhang Y, Cortez J, Hammer S, Carrasco-López C, Echauri S, Wiggins J, Wang W, Avalos J. Biosensor for branched-chain amino acid metabolism in yeast and applications in isobutanol and isopentanol production. Nat Commun. 2022;13(1):270. PMCID: PMC8755756
    Reference Link
  • 1.
    Chen L, Lu W, Wang L, Xing X, Chen Z, Teng X, Zeng X, Muscarella A, Shen Y, Cowan A, McReynolds M, Kennedy B, Lato A, Campagna S, Singh M, Rabinowitz J. Metabolite discovery through global annotation of untargeted metabolomics data. Nat Methods. 2021;18(11):1377–1385. PMCID: PMC8733904
    Reference Link
  • 1.
    Nofal M, Wang T, Yang L, Jankowski C, Li S, Han S, Parsons L, Frese A, Gitai Z, Anthony T, Wühr M, Sabatini D, Rabinowitz J. GCN2 adapts protein synthesis to scavenging-dependent growth. Cell Syst. 2022;13(2):158–172.e9. PMCID: PMC8961722
    Reference Link
  • 1.
    Wegner S, Chen J-M, Ip S, Zhang Y, Dugar D, Avalos J. Engineering acetyl-CoA supply and ERG9 repression to enhance mevalonate production in Saccharomyces cerevisiae. J Ind Microbiol Biotechnol. 2021;48(9-10). PMCID: PMC8788843
    Reference Link
  • 1.
    Lalwani M, Kawabe H, Mays R, Hoffman S, Avalos J. Optogenetic Control of Microbial Consortia Populations for Chemical Production. ACS Synth Biol. 2021;10(8):2015–2029. PMID: 34351122
    Reference Link
  • 1.
    Lalwani M, Zhao E, Wegner S, Avalos J. The Inducible Q System Enables Simultaneous Optogenetic Amplification and Inversion in for Bidirectional Control of Gene Expression. ACS Synth Biol. 2021;10(8):2060–2075. PMID: 34346207
    Reference Link
  • 1.
    Arita Y, Kim G, Li Z, Friesen H, Turco G, Wang R, Climie D, Usaj M, Hotz M, Stoops E, Baryshnikova A, Boone C, Botstein D, Andrews B, McIsaac S. A genome-scale yeast library with inducible expression of individual genes. Mol Syst Biol. 2021;17(6):e10207. PMCID: PMC8182650
    Reference Link
  • 1.
    Zhao E, Lalwani M, Chen J-M, Orillac P, Toettcher J, Avalos J. Optogenetic Amplification Circuits for Light-Induced Metabolic Control. ACS Synth Biol. 2021;10(5):1143–1154. PMCID: PMC8721662
    Reference Link
  • 1.
    Valastyan J, Kraml C, Pelczer I, Ferrante T, Bassler B. Saccharomyces cerevisiae Requires To Produce 4-Hydroxy-5-Methylfuran-3(2H)-One, a Mimic of the Bacterial Quorum-Sensing Autoinducer AI-2. mBio. 2021;12(2). PMCID: PMC8092285
    Reference Link
  • 1.
    Lovelett R, Zhao E, Lalwani M, Toettcher J, Kevrekidis I, Avalos J. Dynamical Modeling of Optogenetic Circuits in Yeast for Metabolic Engineering Applications. ACS Synth Biol. 2021;10(2):219–227. PMID: 33492138
    Reference Link
  • 1.
    Zhao E, Lalwani M, Lovelett R, García-Echauri S, Hoffman S, Gonzalez C, Toettcher J, Kevrekidis I, Avalos J. Design and Characterization of Rapid Optogenetic Circuits for Dynamic Control in Yeast Metabolic Engineering. ACS Synth Biol. 2020;9(12):3254–3266. PMID: 33232598
    Reference Link
  • 1.
    Wong S, Hepowit N, Port S, Yau R, Peng Y, Azad N, Habib A, Harpaz N, Schuldiner M, Hughson F, MacGurn J, Weisman L. Cargo Release from Myosin V Requires the Convergence of Parallel Pathways that Phosphorylate and Ubiquitylate the Cargo Adaptor. Curr Biol. 2020;30(22):4399–4412.e7. PMCID: PMC8025699
    Reference Link
  • 1.
    Luongo T, Eller J, Lu M-J, Niere M, Raith F, Perry C, Bornstein M, Oliphint P, Wang L, McReynolds M, Migaud M, Rabinowitz J, Johnson B, Johnsson K, Ziegler M, Cambronne X, Baur J. SLC25A51 is a mammalian mitochondrial NAD transporter. Nature. 2020;588(7836):174–179. PMCID: PMC7718333
    Reference Link
  • 1.
    Green R, Wang L, Hart S, Lu W, Skelding D, Burton J, Mi H, Capel A, Chen H, Lin A, Subramaniam A, Rabinowitz J, Shou W. Metabolic excretion associated with nutrient-growth dysregulation promotes the rapid evolution of an overt metabolic defect. PLoS Biol. 2020;18(8):e3000757. PMCID: PMC7470746
    Reference Link
  • 1.
    Duran L, López J, Avalos J. ¡Viva la mitochondria!: harnessing yeast mitochondria for chemical production. FEMS Yeast Res. 2020;20(6). PMID: 32592388
    Reference Link
  • 1.
    Murawska M, Schauer T, Matsuda A, Wilson M, Pysik T, Wojcik F, Muir T, Hiraoka Y, Straub T, Ladurner A. The Chaperone FACT and Histone H2B Ubiquitination Maintain S. pombe Genome Architecture through Genic and Subtelomeric Functions. Mol Cell. 2020;77(3):501–513.e7. PMCID: PMC7007867
    Reference Link
  • 1.
    Gibney P, Chen A, Schieler A, Chen J, Xu Y, Hendrickson D, McIsaac S, Rabinowitz J, Botstein D. A tps1Δ persister-like state in Saccharomyces cerevisiae is regulated by MKT1. PLoS One. 2020;15(5):e0233779. PMCID: PMC7259636
    Reference Link
  • 1.
    Travis S, DAmico K, Yu I-M, McMahon C, Hamid S, Ramirez-Arellano G, Jeffrey P, Hughson F. Structural basis for the binding of SNAREs to the multisubunit tethering complex Dsl1. J Biol Chem. 2020;295(30):10125–10135. PMCID: PMC7383367
    Reference Link
  • 1.
    Dao H, Dul B, Dann G, Liszczak G, Muir T. A basic motif anchoring ISWI to nucleosome acidic patch regulates nucleosome spacing. Nat Chem Biol. 2020;16(2):134–142. PMCID: PMC6982587
    Reference Link
  • 1.
    Garcia D, Leach R, Wadsworth G, Choudhary K, Li H, Aviran S, Kim H, Zakian V. Stability and nuclear localization of yeast telomerase depend on protein components of RNase P/MRP. Nat Commun. 2020;11(1):2173. PMCID: PMC7195438
    Reference Link
  • 1.
    Hammer S, Zhang Y, Avalos J. Mitochondrial Compartmentalization Confers Specificity to the 2-Ketoacid Recursive Pathway: Increasing Isopentanol Production in . ACS Synth Biol. 2020;9(3):546–555. PMID: 32049515
    Reference Link
  • 1.
    Park J-D, Moon K, Miller C, Rose J, Xu F, Ebmeier C, Jacobsen J, Mao D, Old W, DeShazer D, Seyedsayamdost M. Thailandenes, Cryptic Polyene Natural Products Isolated from Using Phenotype-Guided Transposon Mutagenesis. ACS Chem Biol. 2020;15(5):1195–1203. PMCID: PMC9106368
    Reference Link
  • 1.
    Travis S, Kokona B, Fairman R, Hughson F. Roles of singleton tryptophan motifs in COPI coat stability and vesicle tethering. Proc Natl Acad Sci U S A. 2019;116(48):24031–24040. PMCID: PMC6883825
    Reference Link
  • 1.
    Lane S, Zhang Y, Yun E, Ziolkowski L, Zhang G, Jin Y-S, Avalos J. Xylose assimilation enhances the production of isobutanol in engineered Saccharomyces cerevisiae. Biotechnol Bioeng. 2020;117(2):372–381. PMID: 31631318
    Reference Link
  • 1.
    Kuroda K, Hammer S, Watanabe Y, López J, Fink G, Stephanopoulos G, Ueda M, Avalos J. Critical Roles of the Pentose Phosphate Pathway and GLN3 in Isobutanol-Specific Tolerance in Yeast. Cell Syst. 2019;9(6):534–547.e5. PMID: 31734159
    Reference Link
  • 1.
    Chen C-F, Pohl T, Chan A, Slocum J, Zakian V. Centromere RNA Is Negatively Regulated by Cbf1 and Its Unscheduled Synthesis Impacts CenH3 Binding. Genetics. 2019;213(2):465–479. PMCID: PMC6781895
    Reference Link
  • 1.
    Chen X, Robinson D, Storey J. The functional false discovery rate with applications to genomics. Biostatistics. 2021;22(1):68–81. PMCID: PMC7846131
    Reference Link
  • 1.
    Pohl T, Zakian V. Pif1 family DNA helicases: A helpmate to RNase H?. DNA Repair (Amst). 2019;84:102633. PMCID: PMC6901714
    Reference Link
  • 1.
    Zhao E, Suek N, Wilson M, Dine E, Pannucci N, Gitai Z, Avalos J, Toettcher J. Light-based control of metabolic flux through assembly of synthetic organelles. Nat Chem Biol. 2019;15(6):589–597. PMCID: PMC6755918
    Reference Link
  • 1.
    Hall A, Rose M. Cell fusion in yeast is negatively regulated by components of the cell wall integrity pathway. Mol Biol Cell. 2019;30(4):441–452. PMCID: PMC6594448
    Reference Link
  • 1.
    Allard C, Decker F, Weiner O, Toettcher J, Graziano B. A size-invariant bud-duration timer enables robustness in yeast cell size control. PLoS One. 2018;13(12):e0209301. PMCID: PMC6303054
    Reference Link
  • 1.
    Tye B, Commins N, Ryazanova L, Wühr M, Springer M, Pincus D, Churchman S. Proteotoxicity from aberrant ribosome biogenesis compromises cell fitness. Elife. 2019;8. PMCID: PMC6453566
    Reference Link
  • 1.
    Chen C-F, Pohl T, Pott S, Zakian V. Two Pif1 Family DNA Helicases Cooperate in Centromere Replication and Segregation in . Genetics. 2019;211(1):105–119. PMCID: PMC6325707
    Reference Link
  • 1.
    Jeon J, McGinty R, Muir T, Kim J-A, Kim J. Crosstalk among Set1 complex subunits involved in H2B ubiquitylation-dependent H3K4 methylation. Nucleic Acids Res. 2018;46(21):11129–11143. PMCID: PMC6265457
    Reference Link
  • 1.
    Xu Y-F, Lu W, Chen J, Johnson S, Gibney P, Thomas D, Brown G, May A, Campagna S, Yakunin A, Botstein D, Rabinowitz J. Discovery and Functional Characterization of a Yeast Sugar Alcohol Phosphatase. ACS Chem Biol. 2018;13(10):3011–3020. PMCID: PMC6466636
    Reference Link
  • 1.
    Geronimo C, Singh S, Galletto R, Zakian V. The signature motif of the Saccharomyces cerevisiae Pif1 DNA helicase is essential in vivo for mitochondrial and nuclear functions and in vitro for ATPase activity. Nucleic Acids Res. 2018;46(16):8357–8370. PMCID: PMC6144861
    Reference Link
  • 1.
    Hammer S, Avalos J. Harnessing yeast organelles for metabolic engineering. Nat Chem Biol. 2017;13(8):823–832. PMID: 28853733
    Reference Link
  • 1.
    Hammer S, Avalos J. Uncovering the role of branched-chain amino acid transaminases in Saccharomyces cerevisiae isobutanol biosynthesis. Metab Eng. 2017;44:302–312. PMID: 29037781
    Reference Link
  • 1.
    Zhao E, Zhang Y, Mehl J, Park H, Lalwani M, Toettcher J, Avalos J. Optogenetic regulation of engineered cellular metabolism for microbial chemical production. Nature. 2018;555(7698):683–687. PMCID: PMC5876151
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  • 1.
    Lalwani M, Zhao E, Avalos J. Current and future modalities of dynamic control in metabolic engineering. Curr Opin Biotechnol. 2018;52:56–65. PMID: 29574344
    Reference Link
  • 1.
    Gibney P, Schieler A, Chen J, Bacha-Hummel J, Botstein M, Volpe M, Silverman S, Xu Y, Bennett B, Rabinowitz J, Botstein D. Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast. Mol Biol Cell. 2018;29(8):897–910. PMCID: PMC5896929
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  • 1.
    Smith J, Hall A, Rose M. Membrane curvature directs the localization of Cdc42p to novel foci required for cell-cell fusion. J Cell Biol. 2017;216(12):3971–3980. PMCID: PMC5716282
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  • 1.
    Melloy P, Rose M. Influence of the bud neck on nuclear envelope fission in Saccharomyces cerevisiae. Exp Cell Res. 2017;358(2):390–396. PMCID: PMC6067115
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  • 1.
    Choi J, Rajagopal A, Xu Y-F, Rabinowitz J, O’Shea E. A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae. PLoS One. 2017;12(5):e0176085. PMCID: PMC5435139
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  • 1.
    Geronimo C, Zakian V. Getting it done at the ends: Pif1 family DNA helicases and telomeres. DNA Repair (Amst). 2016;44:151–158. PMCID: PMC5441554
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  • 1.
    Tran P, Pohl T, Chen C-F, Chan A, Pott S, Zakian V. PIF1 family DNA helicases suppress R-loop mediated genome instability at tRNA genes. Nat Commun. 2017;8:15025. PMCID: PMC5413955
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  • 1.
    Park J, Rubin S, Xu Y-F, Amador-Noguez D, Fan J, Shlomi T, Rabinowitz J. Metabolite concentrations, fluxes and free energies imply efficient enzyme usage. Nat Chem Biol. 2016;12(7):482–9. PMCID: PMC4912430
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