Evolution of substrate specificity in a retained enzyme driven by gene loss

0301 basic medicine 570 Biomedical and clinical sciences Evolution QH301-705.5 Science Bioinformatics and Computational Biology evolution by gene loss Adaptation, Biological Histidine and tryprophan biosynthesis Biochemistry Substrate Specificity Evolution, Molecular 03 medical and health sciences Genetics genomics biochemistry genome decay enzyme substrate specificity Actinomyces human Adaptation Biology (General) Aldose-Ketose Isomerases 0303 health sciences Human Genome evolutionary biology Q R Molecular Health sciences Biological Sciences Biological 3. Good health Biological sciences phosphoribosyl isomerase A Actinomycetaceae Mutation Medicine Biochemistry and Cell Biology Gene Deletion Biotechnology
DOI: 10.7554/elife.22679 Publication Date: 2017-03-31T12:08:58Z
ABSTRACT
The connection between gene loss and the functional adaptation of retained proteins is still poorly understood. We apply phylogenomics and metabolic modeling to detect bacterial species that are evolving by gene loss, with the finding that Actinomycetaceae genomes from human cavities are undergoing sizable reductions, including loss of L-histidine and L-tryptophan biosynthesis. We observe that the dual-substrate phosphoribosyl isomerase A or priA gene, at which these pathways converge, appears to coevolve with the occurrence of trp and his genes. Characterization of a dozen PriA homologs shows that these enzymes adapt from bifunctionality in the largest genomes, to a monofunctional, yet not necessarily specialized, inefficient form in genomes undergoing reduction. These functional changes are accomplished via mutations, which result from relaxation of purifying selection, in residues structurally mapped after sequence and X-ray structural analyses. Our results show how gene loss can drive the evolution of substrate specificity from retained enzymes.
SUPPLEMENTAL MATERIAL
Coming soon ....
REFERENCES (50)
CITATIONS (23)
EXTERNAL LINKS
PlumX Metrics
RECOMMENDATIONS
FAIR ASSESSMENT
Coming soon ....
JUPYTER LAB
Coming soon ....