Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom.
PLoS One. 2010 Aug 30;5(8):e12476. doi: 10.1371/journal.pone.0012476.
The cellulosome is a multi-enzyme machine, which plays a key role in the breakdown of plant cell walls in many anaerobic cellulose-degrading microorganisms. Ruminococcus flavefaciens FD-1, a major fiber-degrading bacterium present in the gut of herbivores, has the most intricate cellulosomal organization thus far described. Cellulosome complexes are assembled through high-affinity cohesin-dockerin interactions. More than two-hundred dockerin-containing proteins have been identified in the R. flavefaciens genome, yet the reason for the expansion of these crucial cellulosomal components is yet unknown.
METHODOLOGY/PRINCIPAL FINDINGS: We have explored the full spectrum of 222 dockerin-containing proteins potentially involved in the assembly of cellulosome-like complexes of R. flavefaciens. Bioinformatic analysis of the various dockerin modules showed distinctive conservation patterns within their two Ca(2+)-binding repeats and their flanking regions. Thus, we established the conceptual framework for six major groups of dockerin types, according to their unique sequence features. Within this framework, the modular architecture of the parent proteins, some of which are multi-functional proteins, was evaluated together with their gene expression levels. Specific dockerin types were found to be associated with selected groups of functional components, such as carbohydrate-binding modules, numerous peptidases, and/or carbohydrate-active enzymes. In addition, members of other dockerin groups were linked to structural proteins, e.g., cohesin-containing proteins, belonging to the scaffoldins.
CONCLUSIONS/SIGNIFICANCE: This report profiles the abundance and sequence diversity of the R. flavefaciens FD-1 dockerins, and provides the molecular basis for future understanding of the potential for a wide array of cohesin-dockerin specificities. Conserved differences between dockerins may be reflected in their stability, function or expression within the context of the parent protein, in response to their role in the rumen environment.
细胞体是一种多酶机器，在许多厌氧纤维素降解微生物中对植物细胞壁的分解起着关键作用。反刍兽胃中的主要纤维降解菌 Ruminococcus flavefaciens FD-1 具有迄今为止描述的最复杂的细胞体组织。细胞体复合物通过高亲和力的粘着蛋白-衔接蛋白相互作用组装。在 R. flavefaciens 基因组中已经鉴定出超过 200 种含有衔接蛋白的蛋白质，但这些关键细胞体成分扩展的原因尚不清楚。
方法/主要发现：我们探索了可能涉及 R. flavefaciens 组装细胞体样复合物的 222 种含有衔接蛋白的蛋白质的全部范围。对各种衔接蛋白模块的生物信息学分析显示，其两个 Ca（2+）结合重复及其侧翼区域内具有独特的保守模式。因此，根据其独特的序列特征，我们建立了六个主要类型的衔接蛋白类型的概念框架。在此框架内，评估了具有多功能蛋白质的亲本蛋白的模块化结构及其基因表达水平。发现特定的衔接蛋白类型与选定的功能组件群相关，例如碳水化合物结合模块、许多肽酶和/或碳水化合物活性酶。此外，其他衔接蛋白组的成员与结构蛋白（例如属于支架蛋白的粘着蛋白）相关联。
结论/意义：本报告描绘了 R. flavefaciens FD-1 衔接蛋白的丰度和序列多样性，并为未来理解广泛的粘着蛋白-衔接蛋白特异性的潜力提供了分子基础。衔接蛋白之间的保守差异可能反映在其稳定性、功能或在亲本蛋白中的表达，以响应它们在瘤胃环境中的作用。
