Associated Faculty, Chemical and Biological Engineering and the Andlinger Center for Energy and the Environment

Contact

javalos@princeton.edu
609-258-9881
Hoyt Chemical Laboratory, 101
Avalos Lab

Research Area

Biochemistry, Biophysics & Structural Biology

Research Focus

Metabolic engineering, organelle engineering, synthetic biology, structural biology, and protein engineering



Research
Selected Publications
We engineer organisms with new desirable traits to address challenging problems in human health, sustainable energy, industry, and the environment. Our research interests span metabolic engineering, organelle engineering, synthetic biology, structural biology, and protein engineering.? We take a two-pronged approach to our research. On one hand, we engineer cells forging established methods with new technologies developed in the lab. On the other, we address fundamental questions of protein structure and function, cellular physiology, and metabolism that either currently limit our capabilities in cellular engineering, or that offer opportunities for new technologies. These two facets of the lab complement and fuel each other, as technological developments give rise to new fundamental questions, and basic research opens avenues for new technologies.

Metabolic Engineering

Metabolic engineering is the application of genetic engineering to modify and optimize the metabolism and regulatory systems of an organism to produce or degrade a desired compound. We are currently focused on engineering microorganisms (mostly yeasts) for two possible goals: 1) to produce molecules of commercial value, such as biofuels, bioplastics, commodity chemicals, or specialty chemicals (drugs, pigments, flavorants, etc.) from renewable sources, including cellulosic biomass; or 2) to degrade or remove contaminants from the environment (bioremediation).

Organelle Engineering

Subcellular engineering is a fast-growing field in bioengineering, in which metabolic pathways or other synthetic functions are targeted to specific cellular organelles to take advantage of their unique environments, metabolites, and enzymes, as well as their physical separation from the cytosol. We are particularly interested in mitochondrial engineering, where we have shown that targeting metabolic pathways to yeast mitochondria is an effective way to enhance the productivity of engineered pathways. In addition, we are interested in engineering the mitochondrial physiology to enhance metabolic pathways targeted to this highly dynamic, and versatile organelle.

Synthetic Biology

Synthetic biology combines molecular biology, genetic engineering (including genome editing), directed evolution, biophysics, computational biology, and protein engineering, aiming to generate synthetic phenotypes (analogous to synthetic chemistry aiming to generate synthetic molecules by designing series of chemical reactions). We are particularly interested in developing biosensors and regulatory genetic circuits applicable to metabolic engineering. Biosensors are useful to measure, monitor, screen, or select for desired functions (either natural or engineered). Genetic circuits are useful to control engineered metabolisms and other engineered functions in the cell.

Structural Biology and Protein Engineering

Our efforts in synthetic biology and metabolic engineering are complemented by fundamental studies on the molecular structure and function of the proteins involved, such as enzymes, transmembrane transporters, receptors, and transcription factors. To study these proteins in molecular detail, we use different biophysical and biochemical methods, including X-ray crystallography. Understanding the relationship between the structure and function of these proteins significantly enhances our ability to engineer them with new functions relevant to metabolic engineering or synthetic biology.




Hoffman SM, Tang AY, Avalos JL. Optogenetics Illuminates Applications in Microbial Engineering. Annu Rev Chem Biomol Eng. 2022 ;13:373-403. PubMed
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Hoffman SM, Lalwani MA, Avalos JL. Light-Controlled Fermentations for Microbial Chemical and Protein Production. J Vis Exp. 2022 ;(181). PubMed
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Zhang Y, Cortez JD, Hammer SK, Carrasco-López C, Echauri SáGarcía, Wiggins JB, et al.. Biosensor for branched-chain amino acid metabolism in yeast and applications in isobutanol and isopentanol production. Nat Commun. 2022 ;13(1):270. PubMed
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López JMonta?o, Duran L, Avalos JL. Physiological limitations and opportunities in microbial metabolic engineering. Nat Rev Microbiol. 2022 ;20(1):35-48. PubMed
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Hoffman SM, Alvarez M, Alfassi G, Rein DM, Garcia-Echauri S, Cohen Y, et al. Cellulosic biofuel production using emulsified simultaneous saccharification and fermentation (eSSF) with conventional and thermotolerant yeasts. Biotechnol Biofuels. 2021 ;14(1):157. PubMed
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Kichuk TC, Carrasco-López C, Avalos JL. Lights up on organelles: Optogenetic tools to control subcellular structure and organization. WIREs Mech Dis. 2021 ;13(1):e1500. PubMed
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Wegner SA, Chen J-M, Ip SS, Zhang Y, Dugar D, Avalos JL. Engineering acetyl-CoA supply and ERG9 repression to enhance mevalonate production in Saccharomyces cerevisiae. J Ind Microbiol Biotechnol. 2021 ;48(9-10). PubMed
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Lalwani MA, Zhao EM, Wegner SA, Avalos JL. 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. PubMed
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Lalwani MA, Kawabe H, Mays RL, Hoffman SM, Avalos JL. Optogenetic Control of Microbial Consortia Populations for Chemical Production. ACS Synth Biol. 2021 ;10(8):2015-2029. PubMed
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Zhao EM, Lalwani MA, Chen J-M, Orillac P, Toettcher JE, Avalos JL. Optogenetic Amplification Circuits for Light-Induced Metabolic Control. ACS Synth Biol. 2021 ;10(5):1143-1154. PubMed
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Lovelett RJ, Zhao EM, Lalwani MA, Toettcher JE, Kevrekidis IG, Avalos JL. Dynamical Modeling of Optogenetic Circuits in Yeast for Metabolic Engineering Applications. ACS Synth Biol. 2021 ;10(2):219-227. PubMed
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Lalwani MA, Ip SS, Carrasco-López C, Day C, Zhao EM, Kawabe H, et al.. Optogenetic control of the lac operon for bacterial chemical and protein production. Nat Chem Biol. 2021 ;17(1):71-79. PubMed
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Zhao EM, Lalwani MA, Lovelett RJ, García-Echauri SA, Hoffman SM, Gonzalez CL, et al.. Design and Characterization of Rapid Optogenetic Circuits for Dynamic Control in Yeast Metabolic Engineering. ACS Synth Biol. 2020 ;9(12):3254-3266. PubMed
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Carrasco-López C, García-Echauri SA, Kichuk T, Avalos JL. Optogenetics and biosensors set the stage for metabolic cybergenetics. Curr Opin Biotechnol. 2020 ;65:296-309. PubMed
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Duran L, López JMonta?o, Avalos JL. ?Viva la mitochondria!: harnessing yeast mitochondria for chemical production. FEMS Yeast Res. 2020 ;20(6). PubMed
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Hammer SK, Avalos JL. Corrigendum to "Uncovering the role of branched-chain amino acid transaminases in Saccharomyces cerevisiae isobutanol biosynthesis" [Metab. Eng. 44 (2017) 302-312]. Metab Eng. 2020 ;61:438. PubMed
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Gil AA, Carrasco-López C, Zhu L, Zhao EM, Ravindran PT, Wilson MZ, et al.. Optogenetic control of protein binding using light-switchable nanobodies. Nat Commun. 2020 ;11(1):4044. PubMed
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Carrasco-López C, Zhao EM, Gil AA, Alam N, Toettcher JE, Avalos JL. Development of light-responsive protein binding in the monobody non-immunoglobulin scaffold. Nat Commun. 2020 ;11(1):4045. PubMed
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Kapheim KM, Jones BM, Pan H, Li C, Harpur BA, Kent CF, et al. Developmental plasticity shapes social traits and selection in a facultatively eusocial bee. Proc Natl Acad Sci U S A. 2020 ;117(24):13615-13625. PubMed
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Doane MP, Morris MM, Papudeshi B, Allen L, Pande D, Haggerty JM, et al. The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge. Microbiome. 2020 ;8(1):93. PubMed
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Hammer SK, Zhang Y, Avalos JL. Mitochondrial Compartmentalization Confers Specificity to the 2-Ketoacid Recursive Pathway: Increasing Isopentanol Production in . ACS Synth Biol. 2020 ;9(3):546-555. PubMed
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Lane S, Zhang Y, Yun EJu, Ziolkowski L, Zhang G, Jin Y-S, et al. Xylose assimilation enhances the production of isobutanol in engineered Saccharomyces cerevisiae. Biotechnol Bioeng. 2020 ;117(2):372-381. PubMed
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Kuroda K, Hammer SK, Watanabe Y, López JMonta?o, Fink GR, Stephanopoulos G, et al.. Critical Roles of the Pentose Phosphate Pathway and GLN3 in Isobutanol-Specific Tolerance in Yeast. Cell Syst. 2019 ;9(6):534-547.e5. PubMed
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Zhao EM, Suek N, Wilson MZ, Dine E, Pannucci NL, Gitai Z, et al. Light-based control of metabolic flux through assembly of synthetic organelles. Nat Chem Biol. 2019 ;15(6):589-597. PubMed
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Lognonné P, Banerdt WB, Giardini D, Pike WT, Christensen U, Laudet P, et al.. SEIS: Insight's Seismic Experiment for Internal Structure of Mars. Space Sci Rev. 2019 ;215(1):12. PubMed
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Zhang Y, Lane S, Chen J-M, Hammer SK, Luttinger J, Yang L, et al. Xylose utilization stimulates mitochondrial production of isobutanol and 2-methyl-1-butanol in . Biotechnol Biofuels. 2019 ;12:223. PubMed
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Alper HS, Avalos JL. Metabolic pathway engineering. Synth Syst Biotechnol. 2018 ;3(1):1-2. PubMed
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Bracha D, Walls MT, Wei M-T, Zhu L, Kurian M, Avalos JL, et al. Mapping Local and Global Liquid Phase Behavior in Living Cells Using Photo-Oligomerizable Seeds. Cell. 2018 ;175(6):1467-1480.e13. PubMed
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Lalwani MA, Zhao EM, Avalos JL. Current and future modalities of dynamic control in metabolic engineering. Curr Opin Biotechnol. 2018 ;52:56-65. PubMed
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Zhao EM, Zhang Y, Mehl J, Park H, Lalwani MA, Toettcher JE, et al. Optogenetic regulation of engineered cellular metabolism for microbial chemical production. Nature. 2018 ;555(7698):683-687. PubMed
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Hammer SK, Avalos JL. Harnessing yeast organelles for metabolic engineering. Nat Chem Biol. 2017 ;13(8):823-832. PubMed
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Hammer SK, Avalos JL. Uncovering the role of branched-chain amino acid transaminases in Saccharomyces cerevisiae isobutanol biosynthesis. Metab Eng. 2017 ;44:302-312. PubMed
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Zhang Y, Avalos JL. Traditional and novel tools to probe the mitochondrial metabolism in health and disease. Wiley Interdiscip Rev Syst Biol Med. 2017 ;9(2). PubMed
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Hammer SK, Avalos JL. Metabolic engineering: Biosensors get the green light. Nat Chem Biol. 2016 ;12(11):894-895. PubMed
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Avalos JL, Fink GR, Stephanopoulos G. Compartmentalization of metabolic pathways in yeast mitochondria improves the production of branched-chain alcohols. Nat Biotechnol. 2013 ;31(4):335-41. PubMed
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Tao X, Avalos JL, Chen J, MacKinnon R. Crystal structure of the eukaryotic strong inward-rectifier K+ channel Kir2.2 at 3.1 A resolution. Science. 2009 ;326(5960):1668-74. PubMed
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Cosgrove MS, Bever K, Avalos JL, Muhammad S, Zhang X, Wolberger C. The structural basis of sirtuin substrate affinity. Biochemistry. 2006 ;45(24):7511-21. PubMed
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Hoff KG, Avalos JL, Sens K, Wolberger C. Insights into the sirtuin mechanism from ternary complexes containing NAD+ and acetylated peptide. Structure. 2006 ;14(8):1231-40. PubMed
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Avalos JL, Bever KM, Wolberger C. Mechanism of sirtuin inhibition by nicotinamide: altering the NAD(+) cosubstrate specificity of a Sir2 enzyme. Mol Cell. 2005 ;17(6):855-68. PubMed
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