TY - JOUR
T1 - Evolution of substrate specificity in a retained enzyme driven by gene loss
AU - Juárez-Vázquez, Ana Lilia
AU - Edirisinghe, Janaka N.
AU - Verduzco-Castro, Ernesto A.
AU - Michalska, Karolina
AU - Wu, Chenggang
AU - Noda-García, Lianet
AU - Babnigg, Gyorgy
AU - Endres, Michael
AU - Medina-Ruíz, Sofía
AU - Santoyo-Flores, Julián
AU - Carrillo-Tripp, Mauricio
AU - Ton-That, Hung
AU - Joachimiak, Andrzej
AU - Henry, Christopher S.
AU - Barona-Gómez, Francisco
N1 - Publisher Copyright:
© Juárez-Vázquez et al.
PY - 2017/3/31
Y1 - 2017/3/31
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85019265919&partnerID=8YFLogxK
U2 - 10.7554/eLife.22679
DO - 10.7554/eLife.22679
M3 - Article
C2 - 28362260
AN - SCOPUS:85019265919
SN - 2050-084X
VL - 6
JO - eLife
JF - eLife
M1 - e22679
ER -