Using comparative genomics to uncover new kinds of protein-based metabolic organelles in bacteria
Using comparative genomics to uncover new kinds of protein-based metabolic organelles in bacteria
复制标题
DOI：
10.1002/pro.2196
复制
发表时间：
2013-02-01
期刊：
影响因子：
8
通讯作者：
Yeates, Todd O.
中科院分区：
文献类型：
--
作者：
Jorda, Julien;Lopez, David;Yeates, Todd O.
细菌微室 (MCP) 细胞器是胞质多面体结构，由薄薄的蛋白质壳和一系列封装的、顺序作用的酶组成。迄今为止，已经在各种细菌中对执行三种不同类型的代谢过程的不同微区室进行了实验表征。在目前的工作中，我们使用比较基因组学来探索尚未表征的微区室的存在，这些微区室封装了更广泛的代谢途径。使用聚类方法将酶分组在一起，这些酶显示出在染色体上彼此接近的编码倾向，同时也靠近微区室壳蛋白的基因。结果揭示了新型的推定微区室，其中一种似乎封装了不依赖 B12、基于甘氨酰自由基的 1,2-丙二醇降解，以及另一种可能参与分枝杆菌中氨基醇代谢的微区室。初步实验表明，在基于甘氨酰自由基的微区室中编码的一种不寻常的壳蛋白与铁硫簇结合，暗示了这个未知系统中的复杂机制。此外，对计算出的微区室簇的检查表明，某些类型的 MCP 中存在特定的功能变异，包括 α 羧基体和基于甘氨酰自由基的微区室。这些发现有助于更深入地了解细菌微区室及其隔离途径。
Bacterial microcompartment (MCP) organelles are cytosolic, polyhedral structures consisting of a thin protein shell and a series of encapsulated, sequentially acting enzymes. To date, different microcompartments carrying out three distinct types of metabolic processes have been characterized experimentally in various bacteria. In the present work, we use comparative genomics to explore the existence of yet uncharacterized microcompartments encapsulating a broader set of metabolic pathways. A clustering approach was used to group together enzymes that show a strong tendency to be encoded in chromosomal proximity to each other while also being near genes for microcompartment shell proteins. The results uncover new types of putative microcompartments, including one that appears to encapsulate B12-independent, glycyl radical-based degradation of 1,2-propanediol, and another potentially involved in amino alcohol metabolism in mycobacteria. Preliminary experiments show that an unusual shell protein encoded within the glycyl radical-based microcompartment binds an iron-sulfur cluster, hinting at complex mechanisms in this uncharacterized system. In addition, an examination of the computed microcompartment clusters suggests the existence of specific functional variations within certain types of MCPs, including the alpha carboxysome and the glycyl radical-based microcompartment. The findings lead to a deeper understanding of bacterial microcompartments and the pathways they sequester.