title: Principal component analysis of proteomics (PCAP) as a tool to direct metabolic engineering.
abstract: Targeted proteomics is a convenient method determining enzyme expression levels, but a quantitative analysis of these proteomic data has not been fully explored yet. Here, we present and demonstrate a computational tool (principal component analysis of proteomics, PCAP) that uses quantitative targeted proteomics data to guide metabolic engineering and achieve higher production of target molecules from heterologous pathways. The method is based on the application of principal component analysis to a collection of proteomics and target molecule production data to pinpoint specific enzymes that need to have their expression level adjusted to maximize production. We illustrated the method on the heterologous mevalonate pathway in Escherichia coli that produces a wide range of isoprenoids and requires balanced pathway gene expression for high yields and titers. PCAP-guided engineering resulted in over a 40% improvement in the production of two valuable terpenes. PCAP could potentially be productively applied to other heterologous pathways as well.
authors.affiliation: Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Jorge
authors.initials: J
authors.lastname: Alonso-Gutierrez
authors.affiliation: Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Eun-Mi
authors.initials: EM
authors.lastname: Kim
authors.affiliation: Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Tanveer S
authors.initials: TS
authors.lastname: Batth
authors.affiliation: Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA.
authors.forename: Nathan
authors.initials: N
authors.lastname: Cho
authors.affiliation: Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, CA 94720, USA.
authors.forename: Qijun
authors.initials: Q
authors.lastname: Hu
authors.affiliation: Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Leanne Jade G
authors.initials: LJG
authors.lastname: Chan
authors.affiliation: Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Petzold
authors.affiliation: Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Nathan J
authors.initials: NJ
authors.lastname: Hillson
authors.affiliation: Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, CA 94720, USA.
authors.forename: Paul D
authors.initials: PD
authors.lastname: Adams
authors.affiliation: Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, CA 94720, USA; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA.
authors.forename: Jay D
authors.initials: JD
authors.lastname: Keasling
authors.affiliation: Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: hgmartin@lbl.gov.
authors.forename: Hector
authors.initials: H
authors.lastname: Garcia Martin
authors.affiliation: Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: tslee@lbl.gov.
authors.forename: Taek Soon
authors.initials: TS
authors.lastname: Lee
mesh_terms: D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000096:biosynthesis / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D060847:Metabolic Engineering / Q000379:methods*; D040901:Proteomics; D013729:Terpenes / Q000378:metabolism*
chemical_list: D029968:Escherichia coli Proteins; D013729:Terpenes
keywords: Escherichia coli; Heterologous pathway; Metabolic engineering; Mevalonate pathway; Principal component analysis (PCA); Targeted proteomics