Gradual neofunctionalization in the convergent evolution of trichomonad lactate and malate dehydrogenases.
Gradual neofunctionalization in the convergent evolution of trichomonad lactate and malate dehydrogenases.
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DOI：
10.1002/pro.2904
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发表时间：
2016-07
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影响因子：
--
通讯作者：
Theobald DL
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文献类型：
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作者：
Steindel PA;Chen EH;Wirth JD;Theobald DL
乳酸脱氢酶和苹果酸脱氢酶（LDH和MDH）是几乎所有生物体共同的同源核心代谢酶。LDH至少从MDH进化了四次，每次通过不同的机制实现改变的底物特异性。例如，厌氧滴虫寄生虫的LDH最近通过基因复制独立地从祖先滴虫MDH进化而来。LDH通过催化丙酮酸还原为乳酸，从而再生糖酵解所需的NAD+，在滴虫代谢中发挥核心作用。使用祖先重建的方法，我们确定了生化和进化机制负责这一收敛事件。这些酶的最后共同祖先是高度特异性的MDH，类似于现代毛滴虫MDH。相比之下，LDH谱系通过在新功能化的逐渐过程中放松特异性而进化出混杂活性，所述新功能化涉及在“特异性残基”（R91 L）处的一个高度有害的取代和许多小作用的额外突变。L91在LDH和MDH中具有不同的功能后果，表明上位性的突出作用。现代和祖先酶的晶体结构表明，底物特异性的演变导致二聚化和α-螺旋取向的结构变化。毛滴虫LDH的相对小的“特异性残基”可以适应一系列底物大小，并且可以允许溶剂进入活性位点，这两者都促进底物混杂。毛滴虫LDHs与其他生物中LDHs的独立进化存在多方面的对应关系，并说明了蛋白质功能，结构和稳定性共同进化的多种机制。PDB代码：4UUL; 4UUM; 4UUN; 4UUO; 4UUP; 5A 1 T
Lactate and malate dehydrogenases (LDH and MDH) are homologous, core metabolic enzymes common to nearly all living organisms. LDHs have evolved convergently from MDHs at least four times, achieving altered substrate specificity by a different mechanism each time. For instance, the LDH of anaerobic trichomonad parasites recently evolved independently from an ancestral trichomonad MDH by gene duplication. LDH plays a central role in trichomonad metabolism by catalyzing the reduction of pyruvate to lactate, thereby regenerating the NAD+ required for glycolysis. Using ancestral reconstruction methods, we identified the biochemical and evolutionary mechanisms responsible for this convergent event. The last common ancestor of these enzymes was a highly specific MDH, similar to modern trichomonad MDHs. In contrast, the LDH lineage evolved promiscuous activity by relaxing specificity in a gradual process of neofunctionalization involving one highly detrimental substitution at the “specificity residue” (R91L) and many additional mutations of small effect. L91 has different functional consequences in LDHs and in MDHs, indicating a prominent role for epistasis. Crystal structures of modern‐day and ancestral enzymes show that the evolution of substrate specificity paralleled structural changes in dimerization and α‐helix orientation. The relatively small “specificity residue” of the trichomonad LDHs can accommodate a range of substrate sizes and may permit solvent to access the active site, both of which promote substrate promiscuity. The trichomonad LDHs present a multi‐faceted counterpoint to the independent evolution of LDHs in other organisms and illustrate the diverse mechanisms by which protein function, structure, and stability coevolve. PDB Code(s): 4UUL; 4UUM; 4UUN; 4UUO; 4UUP; 5A1T