A genetic polymorphism evolving in parallel in two cell compartments and in two clades

BMC Evolutionary Biology

Research Article

Baiqing Wang¹  Eddie Wang²  Ward B Watt³  Richard R Hudson⁴ 

[1] Department of Biology, Stanford University, 94305-5020, Stanford, CA, USA;Department of Biology, Stanford University, 94305-5020, Stanford, CA, USA;Department of Molecular and Cellular Biology, Harvard University, 0213, Cambridge, MA, USA;Department of Biology, Stanford University, 94305-5020, Stanford, CA, USA;Rocky Mountain Biological Laboratory, 81224, Crested Butte, CO, USA;Department of Ecology and Evolution, University of Chicago, 60637, Chicago, IL, USA;

关键词: Amino acid polymorphism;    Coalescent simulation;    Glycolysis;    Intramolecular bond variation;    Neutral null hypothesis;    Parallel evolution;    Phosphoenolpyruvate carboxykinase;    Selection hypothesis;    Splice variation;   

DOI  :  10.1186/1471-2148-13-9

 received in 2012-07-24, accepted in 2012-12-12,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundThe enzyme phosphoenolpyruvate carboxykinase, PEPCK, occurs in its guanosine-nucleotide-using form in animals and a few prokaryotes. We study its natural genetic variation in Colias (Lepidoptera, Pieridae). PEPCK offers a route, alternative to pyruvate kinase, for carbon skeletons to move between cytosolic glycolysis and mitochondrial Krebs cycle reactions.ResultsPEPCK is expressed in both cytosol and mitochondrion, but differently in diverse animal clades. In vertebrates and independently in Drosophila, compartment-specific paralogous genes occur. In a contrasting expression strategy, compartment-specific PEPCKs of Colias and of the silkmoth, Bombyx, differ only in their first, 5′, exons; these are alternatively spliced onto a common series of following exons. In two Colias species from distinct clades, PEPCK sequence is highly variable at nonsynonymous and synonymous sites, mainly in its common exons. Three major amino acid polymorphisms, Gly 335 ↔ Ser, Asp 503 ↔ Glu, and Ile 629 ↔ Val occur in both species, and in the first two cases are similar in frequency between species. Homology-based structural modelling shows that the variants can alter hydrogen bonding, salt bridging, or van der Waals interactions of amino acid side chains, locally or at one another’s sites which are distant in PEPCK’s structure, and thus may affect its enzyme function. We ask, using coalescent simulations, if these polymorphisms’ cross-species similarities are compatible with neutral evolution by genetic drift, but find the probability of this null hypothesis is 0.001 ≤ P ≤ 0.006 under differing scenarios.ConclusionOur results make the null hypothesis of neutrality of these PEPCK polymorphisms quite unlikely, but support an alternative hypothesis that they are maintained by natural selection in parallel in the two species. This alternative can now be justifiably tested further via studies of PEPCK genotypes’ effects on function, organismal performance, and fitness. This case emphasizes the importance, for evolutionary insight, of studying gene-specific mechanisms affected by natural genetic variation as an essential complement to surveys of such variation.

【 授权许可】

CC BY   
© Watt et al.; licensee BioMed Central Ltd. 2013