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Genomic and experimental evidence for multiple metabolic functions in the RidA/YjgF/YER057c/UK114 (Rid) protein
Thomas D Niehaus1, Svetlana Gerdes2, Kelsey Hodge-Hanson3
1Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA. tomniehaus@ufl.edu.
BMC Genomics
|May 16, 2015
Summary
RidA proteins and related subfamilies protect against metabolite damage by hydrolyzing reactive imines. Some Rid family members also play roles in carbamoyl phosphate metabolism, while others remain uncharacterized.
Area of Science:
- Biochemistry
- Molecular Biology
- Evolutionary Biology
Background:
- Metabolic side-reactions can produce toxic byproducts.
- Enzymes like RidA protect against such damage by hydrolyzing reactive imines.
- The Rid family, including RidA, is widespread, but functions of most members are unknown.
Purpose of the Study:
- To investigate the functional diversity within the Rid protein family.
- To determine the enzymatic activities and biological roles of different Rid subfamilies.
- To understand the evolutionary relationships and functional conservation within the Rid family.
Main Methods:
- Phylogenetic analysis to classify Rid family members.
- Biochemical assays to test imine-hydrolyzing activity.
- Genetic analysis and metabolomic profiling in Salmonella enterica.
Main Results:
- The Rid family was divided into RidA and seven other subfamilies (Rid1-Rid7).
- RidA, Rid1, Rid2, and Rid3 subfamilies possess conserved residues for imine hydrolysis.
- RidA and Rid2 hydrolyze imines from amino acid oxidases; RidA is also involved in carbamoyl phosphate metabolism.
- Rid4-Rid7 subfamilies lack imine-hydrolyzing activity.
Conclusions:
- RidA, Rid1, Rid2, and Rid3 subfamilies likely share imine-hydrolyzing functions, protecting against damage from various enzymes.
- RidA has an additional, yet undefined, role in carbamoyl phosphate metabolism.
- The functions of the Rid4-Rid7 subfamilies remain elusive.
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