Yang Dong-Dong, de Billerbeck Gustavo M, Zhang Jin-Jing, Rosenzweig Frank, Francois Jean-Marie
LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
School of Agriculture and Food Sciences, Zhejiang A & F University, Lin'an, China.
Appl Environ Microbiol. 2017 Dec 15;84(1). doi: 10.1128/AEM.01553-17. Print 2018 Jan 1.
Homology searches indicate that strain BY4741 contains seven redundant genes that encode putative aryl-alcohol dehydrogenases (AAD). Yeast genes are located in subtelomeric regions of different chromosomes, and their functional role(s) remain enigmatic. Here, we show that two of these genes, and , encode functional enzymes that reduce aliphatic and aryl-aldehydes concomitant with the oxidation of cofactor NADPH, and that Aad4p and Aad14p exhibit different substrate preference patterns. Other yeast genes are undergoing pseudogenization. The 5' sequence of has been deleted from the genome. Repair of an missense mutation at the catalytically essential Tyr residue did not result in a functional enzyme. However, ancestral-state reconstruction by fusing Aad6 with Aad16 and by N-terminal repair of Aad10 restores NADPH-dependent aryl-alcohol dehydrogenase activities. Phylogenetic analysis indicates that genes are narrowly distributed in wood-saprophyte fungi and in yeast that occupy lignocellulosic niches. Because yeast genes exhibit activity on veratraldehyde, cinnamaldehyde, and vanillin, they could serve to detoxify aryl-aldehydes released during lignin degradation. However, none of these compounds induce yeast gene expression, and Aad activities do not relieve aryl-aldehyde growth inhibition. Our data suggest an ancestral role for genes in lignin degradation that is degenerating as a result of yeast's domestication and use in brewing, baking, and other industrial applications. Functional characterization of hypothetical genes remains one of the chief tasks of the postgenomic era. Although the first genome sequence was published over 20 years ago, 22% of its estimated 6,603 open reading frames (ORFs) remain unverified. One outstanding example of this category of genes is the enigmatic seven-member family. Here, we demonstrate that proteins encoded by two members of this family exhibit aliphatic and aryl-aldehyde reductase activity, and further that such activity can be recovered from pseudogenized genes via ancestral-state reconstruction. The phylogeny of yeast genes suggests that these proteins may have played an important ancestral role in detoxifying aromatic aldehydes in ligninolytic fungi. However, in yeast adapted to niches rich in sugars, genes become subject to mutational erosion. Our findings shed new light on the selective pressures and molecular mechanisms by which genes undergo pseudogenization.
同源性搜索表明，BY4741菌株包含七个冗余基因，这些基因编码假定的芳基醇脱氢酶（AAD）。酵母基因位于不同染色体的亚端粒区域，其功能仍然不明。在这里，我们表明其中两个基因，即 和 ，编码功能性酶，它们在辅因子NADPH氧化的同时还原脂肪族和芳基醛，并且Aad4p和Aad14p表现出不同的底物偏好模式。其他酵母基因正在经历假基因化。 的5'序列已从基因组中删除。修复催化必需的Tyr残基处的 错义突变并未产生功能性酶。然而，通过将Aad6与Aad16融合以及对Aad10进行N端修复来重建祖先状态可恢复NADPH依赖性芳基醇脱氢酶活性。系统发育分析表明， 基因在木腐生真菌和占据木质纤维素生态位的酵母中分布狭窄。由于酵母 基因对藜芦醛、肉桂醛和香草醛具有活性，它们可能用于解毒木质素降解过程中释放的芳基醛。然而，这些化合物均未诱导酵母 基因表达，并且AAD活性不能缓解芳基醛对生长的抑制作用。我们的数据表明 基因在木质素降解中具有祖先作用，但由于酵母在酿造、烘焙和其他工业应用中的驯化和使用，该作用正在退化。对假设基因的功能表征仍然是后基因组时代的主要任务之一。尽管第一个酵母基因组序列在20多年前就已发表，但其估计的6603个开放阅读框（ORF）中有22%仍未得到验证。这类基因的一个突出例子是神秘的七成员 家族。在这里，我们证明该家族两个成员编码的蛋白质具有脂肪族和芳基醛还原酶活性，并且进一步证明通过祖先状态重建可以从假基因化的 基因中恢复这种活性。酵母 基因的系统发育表明，这些蛋白质可能在木质素分解真菌中对芳香醛解毒方面发挥了重要的祖先作用。然而，在适应富含糖的生态位的酵母中， 基因会受到突变侵蚀。我们的发现为基因经历假基因化的选择压力和分子机制提供了新的线索。
