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

被引:19
|
作者
Lilia Juarez-Vazquez, Ana [1 ]
Edirisinghe, Janaka N. [2 ,3 ]
Verduzco-Castro, Ernesto A. [1 ]
Michalska, Karolina [4 ,5 ]
Wu, Chenggang [6 ]
Noda-Garcia, Lianet [1 ,9 ]
Babnigg, Gyorgy [4 ]
Endres, Michael [4 ]
Medina-Ruiz, Sofia [1 ,10 ]
Santoyo-Flores, Julian [7 ]
Carrillo-Tripp, Mauricio [7 ,11 ]
Ton-That, Hung [6 ]
Joachimiak, Andrezej [4 ,6 ,8 ]
Henry, Christopher S. [2 ,3 ]
Barona-Gomez, Francisco [1 ]
机构
[1] Cinvestav IPN, Unidad Gen Avanzada Langebio, Evolut Metabol Divers Lab, Irapuato, Mexico
[2] Argonne Natl Lab, Comp Environm & Life Sci Directorate, Lemont, IL USA
[3] Univ Chicago, Computat Inst, Chicago, IL 60637 USA
[4] Argonne Natl Lab, Midwest Ctr Struct Gen, Biosci Div, Lemont, IL USA
[5] Argonne Natl Lab, Struct Biol Ctr, Biosci Div, Lemont, IL USA
[6] Univ Texas Hlth Sci Ctr Houston, Dept Microbiol & Mol Genet, Houston, TX 77030 USA
[7] Cinvestav IPN, Irapuato, Mexico
[8] Univ Chicago, Dept Biochem & Mol Biol, Chicago, IL 60637 USA
[9] Weizmann Inst Sci, Dept Biol Chem, Rehovot, Israel
[10] Univ Calif Berkeley, Dept Mol & Cell Biol, Berkeley, CA 94720 USA
[11] Ctr Invest Matemat, Ciencias Computac, Guanajuato, Mexico
来源
ELIFE | 2017年 / 6卷
基金
美国国家卫生研究院; 美国国家科学基金会;
关键词
PHYLOGENETIC ANALYSIS; ACTINOMYCES-ORIS; NATURAL-PRODUCTS; MODEL; OPTIMIZATION; ISOMERASE; ADAPTATION; REDUCTION; DISCOVERY; ALIGNMENT;
D O I
10.7554/eLife.22679
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
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.
引用
收藏
页数:21
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