Members of the Rid protein family have broad imine deaminase activity and can accelerate the Pseudomonas aeruginosa D-arginine dehydrogenase (DauA) reaction in vitro.

Kelsey M Hodge-Hanson,Diana M Downs,Roy Martin Roop

doi:10.1371/journal.pone.0185544

Abstract

The Rid (YjgF/YER057c/UK114) protein family is a group of small, sequence diverse proteins that consists of eight subfamilies. The archetypal RidA subfamily is found in all domains, while the Rid1-7 subfamilies are present only in prokaryotes. Bacterial genomes often encode multiple members of the Rid superfamily. The best characterized member of this protein family, RidA from Salmonella enterica, is a deaminase that quenches the reactive metabolite 2-aminoacrylate generated by pyridoxal 5’-phosphate-dependent enzymes and ultimately spares certain enzymes from damage. The accumulation of 2-aminoacrylate can damage enzymes and lead to growth defects in bacteria, plants, and yeast. While all subfamily members have been annotated as imine deaminases based on the RidA characterization, experimental evidence to support this annotation exists for a single protein outside the RidA subfamily. Here we report that six proteins, spanning Rid subfamilies 1–3, deaminate a variety of imine/enamine substrates with differing specific activities. Proteins from the Rid2 and Rid3 subfamilies, but not from the RidA and Rid1 subfamilies deaminated iminoarginine, generated in situ by the Pseudomonas aeruginosa D-arginine dehydrogenase DauA. These data biochemically distinguished the subfamilies and showed Rid proteins have activity on a metabolite that is physiologically relevant in Pseudomonas and other bacteria.

Highlights

The Rid family is a group of small, sequence diverse proteins that has been divided into eight subfamilies by phylogenetic and bioinformatics analyses [1, 2]
Primers used to generate plasmids are listed in Table 2. pDM1474 was synthesized by GenScript (Piscataway, NJ) and the coding sequence was codon optimized for expression in Escherichia coli
Members of Rid2 came from S. enterica, Pseudomonas aeruginosa, and Pseudomonas syringae, and members from Rid3 came from Pseudomonas syringae and Pseudomonas fluorescens

Summary

Introduction

The Rid family is a group of small, sequence diverse proteins that has been divided into eight subfamilies by phylogenetic and bioinformatics analyses [1, 2]. The archetypal RidA subfamily is highly conserved and present in all domains of life, where its importance is reflected by its broad conservation and the diverse consequences caused by its absence. RidA has been implicated in various processes in a number of organisms including bacteria [3,4,5,6,7], plants [8, 9], fungi [10,11,12], and humans [13,14,15].

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Conclusion