Co-occurrence of analogous enzymes determines evolution of a novel (βα)8 -isomerase sub-family after non-conserved mutations in flexible loop

Ernesto A. Verduzco-Castro, Karolina Michalska, Michael Endres, Ana L. Juárez-Vazquez, Lianet Noda-García, Changsoo Chang, Christopher S. Henry, Gyorgy Babnigg, Andrzej Joachimiak, Francisco Barona-Gómez*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

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.

Original languageAmerican English
Pages (from-to)1141-1152
Number of pages12
JournalBiochemical Journal
Volume473
Issue number9
DOIs
StatePublished - 1 May 2016
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2016 Authors; published by Portland Press Limited.

Keywords

  • (βα) -barrel
  • Analogous enzymes
  • PriA
  • Streptomyces
  • Substrate specificity
  • TrpF.

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