Directed Evolution of a Selective and Sensitive Serotonin Sensor via Machine Learning.

Journal: Cell
PMID: 33333022

Abstract

Serotonin plays a central role in cognition and is the target of most pharmaceuticals for psychiatric disorders. Existing drugs have limited efficacy; creation of improved versions will require better understanding of serotonergic circuitry, which has been hampered by our inability to monitor serotonin release and transport with high spatial and temporal resolution. We developed and applied a binding-pocket redesign strategy, guided by machine learning, to create a high-performance, soluble, fluorescent serotonin sensor (iSeroSnFR), enabling optical detection of millisecond-scale serotonin transients. We demonstrate that iSeroSnFR can be used to detect serotonin release in freely behaving mice during fear conditioning, social interaction, and sleep/wake transitions. We also developed a robust assay of serotonin transporter function and modulation by drugs. We expect that both machine-learning-guided binding-pocket redesign and iSeroSnFR will have broad utility for the development of other sensors and in vitro and in vivo serotonin detection, respectively.

Authors

  • Elizabeth K Unger
    Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA.
  • Jacob P Keller
    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20174, USA.
  • Michael Altermatt
    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
  • Ruqiang Liang
    Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA.
  • Aya Matsui
    Laboratory on Neurobiology of Compulsive Behaviors, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 20892, USA.
  • Chunyang Dong
    Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA.
  • Olivia J Hon
    Bowles Center for Alcohol Studies, Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
  • Zi Yao
    Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA.
  • Junqing Sun
    Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA.
  • Samba Banala
    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20174, USA.
  • Meghan E Flanigan
    Bowles Center for Alcohol Studies, Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
  • David A Jaffe
    Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA.
  • Samantha Hartanto
    Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA.
  • Jane Carlen
    Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA.
  • Grace O Mizuno
    Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA.
  • Phillip M Borden
    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20174, USA.
  • Amol V Shivange
    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
  • Lindsay P Cameron
    Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA.
  • Steffen Sinning
    Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.
  • Suzanne M Underhill
    Laboratory of Molecular and Cellular Neurobiology, National Institute on Mental Health, NIH, Bethesda, MD 20892, USA.
  • David E Olson
    Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA.
  • Susan G Amara
    Laboratory of Molecular and Cellular Neurobiology, National Institute on Mental Health, NIH, Bethesda, MD 20892, USA.
  • Duncan Temple Lang
    Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA.
  • Gary Rudnick
    Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.
  • Jonathan S Marvin
    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20174, USA.
  • Luke D Lavis
    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20174, USA.
  • Henry A Lester
    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
  • Veronica A Alvarez
    Laboratory on Neurobiology of Compulsive Behaviors, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 20892, USA.
  • Andrew J Fisher
    Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA.
  • Jennifer A Prescher
    Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA.
  • Thomas L Kash
    Bowles Center for Alcohol Studies, Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
  • Vladimir Yarov-Yarovoy
    Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA.
  • Viviana Gradinaru
    Division of Biology and Biological Engineering; California Institute of Technology; Pasadena, California; United States of America.
  • Loren L Looger
    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20174, USA. Electronic address: loogerl@hhmi.org.
  • Lin Tian
    The Affiliated Mental Health Center of Jiangnan University, Wuxi Central Rehabilitation Hospital, Wuxi, Jiangsu, China.

Keywords

External Resources

Popular Topics
Recent Journals