Puggioni Vincenzo, Dondi Ambra, Folli Claudia, Shin Inchul, Rhee Sangkee, Percudani Riccardo
Laboratory of Biochemistry, Molecular Biology, and Bioinformatics, Department of Life Sciences, University of Parma , Italy.
Biochemistry. 2014 Feb 4;53(4):735-45. doi: 10.1021/bi4010107. Epub 2014 Jan 23.
A major problem of genome annotation is the assignment of a function to a large number of genes of known sequences through comparison with a relatively small number of experimentally characterized genes. Because functional divergence is a widespread phenomenon in gene evolution, the transfer of a function to homologous genes is not a trivial exercise. Here, we show that a family of homologous genes which are found in purine catabolism clusters and have hypothetically equivalent functions can be divided into two distinct groups based on the genomic distribution of functionally related genes. One group (UGLYAH) encodes proteins that are able to release ammonia from (S)-ureidoglycine, the enzymatic product of allantoate amidohydrolase (AAH), but are unable to degrade allantoate. The presence of a gene encoding UGLYAH implies the presence of AAH in the same genome. The other group (UGLYAH2) encodes proteins that are able to release ammonia from (S)-ureidoglycine as well as urea from allantoate. The presence of a gene encoding UGLYAH2 implies the absence of AAH in the same genome. Because (S)-ureidoglycine is an unstable compound that is only formed by the AAH reaction, the in vivo function of this group of enzymes must be the release of urea from allantoate (allantoicase activity), while ammonia release from (S)-ureidoglycine is an accessory activity that evolved as a specialized function in a group of genes in which the coexistence with AAH was established. Insights on the active site modifications leading to a change in the enzyme activity were provided by comparison of three-dimensional structures of proteins belonging to the two different groups and by site-directed mutagenesis. Our results indicate that when the neighborhood of uncharacterized genes suggests a role in the same process or pathway of a characterized homologue, a detailed analysis of the gene context is required for the transfer of functional annotations.
基因组注释的一个主要问题是，通过与相对较少的经过实验表征的基因进行比较，为大量已知序列的基因赋予功能。由于功能分化是基因进化中的普遍现象，将功能转移到同源基因并非易事。在这里，我们表明，在嘌呤分解代谢簇中发现的、假设具有等效功能的一组同源基因，可根据功能相关基因的基因组分布分为两个不同的组。一组（UGLYAH）编码的蛋白质能够从尿囊酸酰胺水解酶（AAH）的酶促产物（S）-脲基甘氨酸中释放氨，但不能降解尿囊酸。编码UGLYAH的基因的存在意味着同一基因组中存在AAH。另一组（UGLYAH2）编码的蛋白质既能从（S）-脲基甘氨酸中释放氨，又能从尿囊酸中释放尿素。编码UGLYAH2的基因的存在意味着同一基因组中不存在AAH。由于（S）-脲基甘氨酸是一种不稳定的化合物，仅由AAH反应形成，这组酶在体内的功能必定是从尿囊酸中释放尿素（尿囊酸酶活性），而从（S）-脲基甘氨酸中释放氨是一种附属活性，它在一组与AAH共存的基因中作为一种特殊功能进化而来。通过比较属于两个不同组的蛋白质的三维结构以及定点诱变，提供了导致酶活性变化的活性位点修饰的见解。我们的结果表明，当未表征基因的邻域暗示其在已表征同源物的相同过程或途径中起作用时，为了进行功能注释的转移，需要对基因背景进行详细分析。
