Smit A, Mushegian A
Institute for Systems Biology, Seattle, Washington 98195, USA.
Genome Res. 2000 Oct;10(10):1468-84. doi: 10.1101/gr.145600.
Isoprenoid compounds are ubiquitous in living species and diverse in biological function. Isoprenoid side chains of the membrane lipids are biochemical markers distinguishing archaea from the rest of living forms. The mevalonate pathway of isoprenoid biosynthesis has been defined completely in yeast, while the alternative, deoxy-D-xylulose phosphate synthase pathway is found in many bacteria. In archaea, some enzymes of the mevalonate pathway are found, but the orthologs of three yeast proteins, accounting for the route from phosphomevalonate to geranyl pyrophosphate, are missing, as are the enzymes from the alternative pathway. To understand the evolution of isoprenoid biosynthesis, as well as the mechanism of lipid biosynthesis in archaea, sequence motifs in the known enzymes of the two pathways of isoprenoid biosynthesis were analyzed. New sequence relationships were detected, including similarities between diphosphomevalonate decarboxylase and kinases of the galactokinase superfamily, between the metazoan phosphomevalonate kinase and the nucleoside monophosphate kinase superfamily, and between isopentenyl pyrophosphate isomerases and MutT pyrophosphohydrolases. Based on these findings, orphan members of the galactokinase, nucleoside monophosphate kinase, and pyrophosphohydrolase families in archaeal genomes were evaluated as candidate enzymes for the three missing steps. Alternative methods of finding these missing links were explored, including physical linkage of open reading frames and patterns of ortholog distribution in different species. Combining these approaches resulted in the generation of a short list of 13 candidate genes for the three missing functions in archaea, whose participation in isoprenoid biosynthesis is amenable to biochemical and genetic investigation.
类异戊二烯化合物在生物物种中普遍存在，且生物功能多样。膜脂的类异戊二烯侧链是区分古菌与其他生物形式的生化标记。类异戊二烯生物合成的甲羟戊酸途径已在酵母中完全明确，而另一条途径，即脱氧-D-木酮糖磷酸合酶途径则存在于许多细菌中。在古菌中，发现了甲羟戊酸途径的一些酶，但负责从磷酸甲羟戊酸到香叶基焦磷酸这一路径的三种酵母蛋白的直系同源物缺失，替代途径的酶也同样缺失。为了解类异戊二烯生物合成的进化以及古菌类脂生物合成的机制，对类异戊二烯生物合成两条途径中已知酶的序列基序进行了分析。检测到了新的序列关系，包括二磷酸甲羟戊酸脱羧酶与半乳糖激酶超家族激酶之间的相似性、后生动物磷酸甲羟戊酸激酶与核苷单磷酸激酶超家族之间的相似性，以及异戊烯基焦磷酸异构酶与MutT焦磷酸水解酶之间的相似性。基于这些发现，对古菌基因组中半乳糖激酶、核苷单磷酸激酶和焦磷酸水解酶家族的孤儿成员进行了评估，将其作为三个缺失步骤的候选酶。探索了寻找这些缺失环节的替代方法，包括开放阅读框的物理连接和不同物种中直系同源物分布模式。综合这些方法，生成了一份包含13个候选基因的简短列表，用于古菌中三个缺失功能，其参与类异戊二烯生物合成的情况适合进行生化和遗传研究。
