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
AUTHORS (15)
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.
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CITATIONS (23)
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