Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing

Applied and Environmental Microbiology, vol. 88, pp. e0243021

Abstract

Understanding the genetic basis of P. putida's diverse metabolism is imperative for us to reach its full potential as a host for metabolic engineering. Many target molecules of the bioeconomy and their precursors contain nitrogen. This study provides functional evidence linking hundreds of genes to their roles in the metabolism of nitrogenous compounds, and provides an interactive tool for visualizing these data. We further characterize several aminotransferases, lactamases, and regulators, which are of particular interest for metabolic engineering.

Authors 11

1. Matthias Schmidt Aachen Institute of Applied Microbiology

   Lawrence Berkeley National Laboratory · Joint BioEnergy Institute · RWTH Aachen University

   Affiliation as printed

   Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

   Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany

   Joint BioEnergy Institute, Emeryville, California, USA

2. Allison N. Pearson

   Lawrence Berkeley National Laboratory · Joint BioEnergy Institute · University of California, Berkeley

   Affiliation as printed

   Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

   Department of Plant and Microbial Biology, University of California, Berkeley, California, USA

   Joint BioEnergy Institute, Emeryville, California, USA

3. Matthew R. Incha

   Lawrence Berkeley National Laboratory · Joint BioEnergy Institute · University of California, Berkeley

   Affiliation as printed

   Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

   Department of Plant and Microbial Biology, University of California, Berkeley, California, USA

   Joint BioEnergy Institute, Emeryville, California, USA

4. Mitchell G. Thompson

   Lawrence Berkeley National Laboratory · Joint BioEnergy Institute

   Affiliation as printed

   Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

   Joint BioEnergy Institute, Emeryville, California, USA

5. Edward E. K. Baidoo

   Lawrence Berkeley National Laboratory · Joint BioEnergy Institute

   Affiliation as printed

   Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

   Joint BioEnergy Institute, Emeryville, California, USA

6. Ramu D. Kakumanu

   Lawrence Berkeley National Laboratory · Joint BioEnergy Institute

   Affiliation as printed

   Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

   Joint BioEnergy Institute, Emeryville, California, USA

7. Aindrila Mukhopadhyay

   Lawrence Berkeley National Laboratory · Joint BioEnergy Institute

   Affiliation as printed

   Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

   Joint BioEnergy Institute, Emeryville, California, USA

8. Patrick M. Shih

   Lawrence Berkeley National Laboratory · Joint BioEnergy Institute · University of California, Berkeley

   Affiliation as printed

   Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

   Department of Plant and Microbial Biology, University of California, Berkeley, California, USA

   Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

   Joint BioEnergy Institute, Emeryville, California, USA

9. Adam M. Deutschbauer

   Lawrence Berkeley National Laboratory · University of California, Berkeley

   Affiliation as printed

   Department of Plant and Microbial Biology, University of California, Berkeley, California, USA

   Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

10. Lars M. Blank Aachen Institute of Applied Microbiology

    RWTH Aachen University

    Affiliation as printed

    Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany

11. Jay D. Keasling corresponding

    Lawrence Berkeley National Laboratory · Novo Nordisk Foundation · Shenzhen Institutes of Advanced Technology · Joint BioEnergy Institute · University of California, Berkeley · Technical University of Denmark

    Affiliation as printed

    Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

    Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA

    Institute for Quantitative Biosciences, University of California, Berkeley, California, USA

    Joint BioEnergy Institute, Emeryville, California, USA

    Joint Program in Bioengineering, University of California, Berkeley, California, USA

    Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China

    The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark