title: Mapping of amino acid substitutions conferring herbicide resistance in wheat glutathione transferase.
abstract: We have used design of experiments (DOE) and systematic variance to efficiently explore glutathione transferase substrate specificities caused by amino acid substitutions. Amino acid substitutions selected using phylogenetic analysis were synthetically combined using a DOE design to create an information-rich set of gene variants, termed infologs. We used machine learning to identify and quantify protein sequence-function relationships against 14 different substrates. The resulting models were quantitative and predictive, serving as a guide for engineering of glutathione transferase activity toward a diverse set of herbicides. Predictive quantitative models like those presented here have broad applicability for bioengineering.
authors.affiliation: †DNA2.0, Inc., 1140 O'Brien Drive, Suite A, Menlo Park, California 94025, United States.
authors.forename: Sridhar
authors.initials: S
authors.lastname: Govindarajan
authors.affiliation: ‡Department of Neurochemistry, Stockholm University, SE-10691 Stockholm, Sweden.
authors.forename: Bengt
authors.initials: B
authors.lastname: Mannervik
authors.affiliation: §Calysta, 1140 O'Brien Drive, Suite B, Menlo Park, California 94025, United States.
authors.forename: Joshua A
authors.initials: JA
authors.lastname: Silverman
authors.affiliation: †DNA2.0, Inc., 1140 O'Brien Drive, Suite A, Menlo Park, California 94025, United States.
authors.forename: Kathy
authors.initials: K
authors.lastname: Wright
authors.affiliation: §Calysta, 1140 O'Brien Drive, Suite B, Menlo Park, California 94025, United States.
authors.forename: Drew
authors.initials: D
authors.lastname: Regitsky
authors.affiliation: ∥National Research Centre, Dokki, Cairo 12311, Egypt.
authors.forename: Usama
authors.initials: U
authors.lastname: Hegazy
authors.affiliation: †DNA2.0, Inc., 1140 O'Brien Drive, Suite A, Menlo Park, California 94025, United States.
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Purcell
authors.affiliation: †DNA2.0, Inc., 1140 O'Brien Drive, Suite A, Menlo Park, California 94025, United States.
authors.forename: Mark
authors.initials: M
authors.lastname: Welch
authors.affiliation: †DNA2.0, Inc., 1140 O'Brien Drive, Suite A, Menlo Park, California 94025, United States.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Minshull
authors.affiliation: †DNA2.0, Inc., 1140 O'Brien Drive, Suite A, Menlo Park, California 94025, United States.
authors.forename: Claes
authors.initials: C
authors.lastname: Gustafsson
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution / Q000235:genetics*; D005982:Glutathione Transferase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D053209:Herbicide Resistance / Q000235:genetics*; D000069550:Machine Learning; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012107:Research Design; D020539:Sequence Analysis, Protein; D058615:Synthetic Biology / Q000379:methods*; D014908:Triticum / Q000235:genetics*
chemical_list: D010940:Plant Proteins; D005982:Glutathione Transferase
keywords: bioengineering; design of experiment; enzymes; herbicide resistance; machine learning; optimization; sequence space; synthetic biology