title: Co-occurrence of analogous enzymes determines evolution of a novel (βα)8-isomerase sub-family after non-conserved mutations in flexible loop.
abstract: We investigate the evolution of co-occurring analogous enzymes involved in L-tryptophan and L-histidine biosynthesis in Actinobacteria Phylogenetic analysis of trpF homologues, a missing gene in certain clades of this lineage whose absence is complemented by a dual-substrate HisA homologue, termed PriA, found that they fall into three categories: (i) trpF-1, an L-tryptophan biosynthetic gene horizontally acquired by certain Corynebacterium species; (ii) trpF-2, a paralogue known to be involved in synthesizing a pyrrolopyrrole moiety and (iii) trpF-3, a variable non-conserved orthologue of trpF-1 We previously investigated the effect of trpF-1 upon the evolution of PriA substrate specificity, but nothing is known about the relationship between trpF-3 and priA After in vitro steady-state enzyme kinetics we found that trpF-3 encodes a phosphoribosyl anthranilate isomerase. However, mutation of this gene in Streptomyces sviceus did not lead to auxothrophy, as expected from the biosynthetic role of trpF-1 Biochemical characterization of a dozen co-occurring TrpF-2 or TrpF-3, with PriA homologues, explained the prototrophic phenotype, and unveiled an enzyme activity trade-off between TrpF and PriA. X-ray structural analysis suggests that the function of these PriA homologues is mediated by non-conserved mutations in the flexible L5 loop, which may be responsible for different substrate affinities. Thus, the PriA homologues that co-occur with TrpF-3 represent a novel enzyme family, termed PriB, which evolved in response to PRA isomerase activity. The characterization of co-occurring enzymes provides insights into the influence of functional redundancy on the evolution of enzyme function, which could be useful for enzyme functional annotation.
authors.affiliation: Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, CP36821, México.
authors.forename: Ernesto A
authors.initials: EA
authors.lastname: Verduzco-Castro
authors.affiliation: Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, U.S.A. Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, U.S.A.
authors.forename: Karolina
authors.initials: K
authors.lastname: Michalska
authors.affiliation: Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, U.S.A.
authors.forename: Michael
authors.initials: M
authors.lastname: Endres
authors.affiliation: Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, CP36821, México.
authors.forename: Ana L
authors.initials: AL
authors.lastname: Juárez-Vazquez
authors.affiliation: Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, CP36821, México.
authors.forename: Lianet
authors.initials: L
authors.lastname: Noda-García
authors.affiliation: Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, U.S.A. Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, U.S.A.
authors.forename: Changsoo
authors.initials: C
authors.lastname: Chang
authors.affiliation: Mathematics and Computer Science, Argonne National Laboratory, Argonne, Illinois 60439, U.S.A.
authors.forename: Christopher S
authors.initials: CS
authors.lastname: Henry
authors.affiliation: Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, U.S.A.
authors.forename: Gyorgy
authors.initials: G
authors.lastname: Babnigg
authors.affiliation: Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, U.S.A. Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, U.S.A. Department of Biochemistry and Molecular Biology, University of Chicago, Illinois 60637, U.S.A.
authors.forename: Andrzej
authors.initials: A
authors.lastname: Joachimiak
authors.affiliation: Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, CP36821, México fbarona@langebio.cinvestav.mx.
authors.forename: Francisco
authors.initials: F
authors.lastname: Barona-Gómez
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D019143:Evolution, Molecular; D007535:Isomerases / Q000235:genetics*; D017433:Protein Structure, Secondary; D013302:Streptomyces / Q000201:enzymology / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D007535:Isomerases
keywords: (βα)8-barrel; PriA; Streptomyces; TrpF; analogous enzymes; substrate specificity