Phylogenetic Distribution of Potential Cellulases in Bacteria
Phylogenetic Distribution of Potential Cellulases in Bacteria
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DOI：
10.1128/aem.03305-12
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发表时间：
2013-03-01
影响因子：
4.4
通讯作者：
Martiny, Adam C.
中科院分区：
文献类型：
--
作者：
Berlemont, Renaud;Martiny, Adam C.
许多微生物含有纤维素酶，对植物细胞壁降解和整个土壤生态系统功能都很重要。目前，我们对纤维素酶有广泛的生物化学知识，但对这些酶的系统发育分布知之甚少。为了解决这个问题，我们分析了5123个测序的细菌基因组中编码纤维素利用相关蛋白质的21,985个基因的分布。首先，我们确定了参与纤维素利用和合成的糖苷水解酶在不同分类水平上的分布，从门到菌株。纤维素降解/利用能力出现在几乎所有主要类群中，导致菌株表现出不同的酶基因组合。同时具有纤维素酶和-葡萄糖苷酶的潜在纤维素降解菌占所有基因组的24%，而仅具有-葡萄糖苷酶的潜在机会菌株占56%。最后，20%的细菌没有相关的酶，不依赖于纤维素的利用。后一组主要与特定的细菌生活方式有关，如自养和寄生。纤维素降解者和机会主义者一样，都有多种具有类似功能的酶。然而，潜在的降解物系统地比它们潜在的机会性亲戚多携带大约两倍的β -葡萄糖苷酶。虽然分散，功能类型的分布，在细菌谱系，不是随机的，但大多遵循布朗运动进化模型。降解者在种水平上形成亲缘群，而机会主义者在属水平上聚集。这些信息可以为微生物群落组成变化与土壤生态系统过程的联系提供机制基础。
Many microorganisms contain cellulases that are important for plant cell wall degradation and overall soil ecosystem functioning. At present, we have extensive biochemical knowledge of cellulases but little is known about the phylogenetic distribution of these enzymes. To address this, we analyzed the distribution of 21,985 genes encoding proteins related to cellulose utilization in 5,123 sequenced bacterial genomes. First, we identified the distribution of glycoside hydrolases involved in cellulose utilization and synthesis at different taxonomic levels, from the phylum to the strain. Cellulose degradation/utilization capabilities appeared in nearly all major groups and resulted in strains displaying various enzyme gene combinations. Potential cellulose degraders, having both cellulases and beta-glucosidases, constituted 24% of all genomes whereas potential opportunistic strains, having beta-glucosidases only, accounted for 56%. Finally, 20% of the bacteria have no relevant enzymes and do not rely on cellulose utilization. The latter group was primarily connected to specific bacterial lifestyles like autotrophy and parasitism. Cellulose degraders, as well as opportunists, have multiple enzymes with similar functions. However, the potential degraders systematically harbor about twice more beta-glucosidases than their potential opportunistic relatives. Although scattered, the distribution of functional types, in bacterial lineages, is not random but mostly follows a Brownian motion evolution model. Degraders form clusters of relatives at the species level, whereas opportunists are clustered at the genus level. This information can form a mechanistic basis for the linking of changes in microbial community composition to soil ecosystem processes.