Bringing to light the molecular evolution of GUX genes in plants

Abstract Hemicellulose and cellulose are essential polysaccharides for plant development and major components of cell wall. They are also an important energy source for the production of ethanol from plant biomass, but their conversion to fermentable sugars is hindered by the complex structure of cell walls. The glucuronic acid substitution of xylan (GUX) enzymes attach glucuronic acid to xylan, a major component of hemicellulose, decreasing the efficiency of enzymes used for ethanol production. Since loss-of-function gux mutants of Arabidopsis thaliana enhance enzyme accessibility and cell wall digestion without adverse phenotypes, GUX genes are potential targets for genetically improving energy crops. However, comprehensive identification of GUX in important species and their evolutionary history are largely lacking. Here, we identified putative GUX proteins using hidden Markov model searches with the GT8 domain and a GUX-specific motif, and inferred the phylogenetic relationship of 18 species with Maximum likelihood and Bayesian approaches. Each species presented a variable number of GUX, and their evolution can be explained by a mixture of divergent, concerted and birth-and-death evolutionary models. This is the first broad insight into the evolution of GUX gene family in plants and will potentially guide genetic and functional studies in species used for biofuel production.

摘要 半纤维素（hemicellulose）与纤维素（cellulose）是植物生长发育不可或缺的多糖类物质，同时也是植物细胞壁的主要组成成分。二者亦是利用植物生物质制备乙醇的重要能量来源，但细胞壁的复杂结构阻碍了它们向可发酵糖的转化。木聚糖葡萄糖醛酸取代酶（GUX）可将葡萄糖醛酸连接至半纤维素的主要组分木聚糖，此举会降低乙醇生产所用酶制剂的催化效率。由于拟南芥（Arabidopsis thaliana）的功能缺失型gux突变体能够提升酶的可及性与细胞壁消化效率且无不良表型，GUX基因遂成为能源作物遗传改良的潜在靶点。然而，目前学界对重要物种中GUX基因的全面鉴定及其进化历程的研究仍较为匮乏。本研究通过基于GT8结构域与GUX特异性基序的隐马尔可夫模型检索，鉴定得到潜在GUX蛋白，并采用最大似然法与贝叶斯法推断了18个物种的系统发育关系。各物种所含GUX基因的数量存在差异，其进化过程可通过趋异进化、协同进化与生死进化的混合模型加以解释。本研究首次为植物GUX基因家族的进化提供了全局性视角，有望为生物燃料生产相关物种的遗传与功能研究提供指导。