Wong Mabel T, Wang Weijun, Couturier Marie, Razeq Fakhria M, Lombard Vincent, Lapebie Pascal, Edwards Elizabeth A, Terrapon Nicolas, Henrissat Bernard, Master Emma R
Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada.
Centre de Recherches sur les Macromolécules Végétales - Université Grenoble Alpes, Grenoble, France.
Front Microbiol. 2017 Dec 20;8:2504. doi: 10.3389/fmicb.2017.02504. eCollection 2017.
To identify carbohydrate-active enzymes (CAZymes) that might be particularly relevant for wood fiber processing, we performed a comparative metagenomic analysis of digestive systems from Canadian beaver () and North American moose () following 3 years of enrichment on either microcrystalline cellulose or poplar hydrolysate. In total, 9,386 genes encoding CAZymes and carbohydrate-binding modules (CBMs) were identified, with up to half predicted to originate from , and phyla, and up to 17% from unknown phyla. Both PCA and hierarchical cluster analysis distinguished the annotated glycoside hydrolase (GH) distributions identified herein, from those previously reported for grass-feeding mammals and herbivorous foragers. The CAZyme profile of moose rumen enrichments also differed from a recently reported moose rumen metagenome, most notably by the absence of GH13-appended dockerins. Consistent with substrate-driven convergence, CAZyme profiles from both poplar hydrolysate-fed cultures differed from cellulose-fed cultures, most notably by increased numbers of unique sequences belonging to families GH3, GH5, GH43, GH53, and CE1. Moreover, pairwise comparisons of moose rumen enrichments further revealed higher counts of GH127 and CE15 families in cultures fed with poplar hydrolysate. To expand our scope to lesser known carbohydrate-active proteins, we identified and compared multi-domain proteins comprising both a CBM and domain of unknown function (DUF) as well as proteins with unknown function within the 416 predicted polysaccharide utilization loci (PULs). Interestingly, DUF362, identified in iron-sulfur proteins, was consistently appended to CBM9; on the other hand, proteins with unknown function from PULs shared little identity unless from identical PULs. Overall, this study sheds new light on the lignocellulose degrading capabilities of microbes originating from digestive systems of mammals known for fiber-rich diets, and highlights the value of enrichment to select new CAZymes from metagenome sequences for future biochemical characterization.
为了鉴定可能与木纤维加工特别相关的碳水化合物活性酶（CAZymes），我们对以微晶纤维素或杨树水解产物富集培养3年后的加拿大海狸（Castor canadensis）和北美驼鹿（Alces americanus）的消化系统进行了比较宏基因组分析。总共鉴定出9386个编码CAZymes和碳水化合物结合模块（CBMs）的基因，其中多达一半预计来自拟杆菌门（Bacteroidetes）和厚壁菌门（Firmicutes），高达17%来自未知门。主成分分析（PCA）和层次聚类分析均将本文鉴定的注释糖苷水解酶（GH）分布与先前报道的食草哺乳动物和食草觅食者的分布区分开来。驼鹿瘤胃富集培养物的CAZyme谱也与最近报道的驼鹿瘤胃宏基因组不同，最显著的是缺少与GH13相连的dockerins。与底物驱动的趋同一致，两种以杨树水解产物为食的培养物的CAZyme谱与以纤维素为食的培养物不同，最显著的是属于GH3、GH5、GH43、GH53和CE1家族的独特序列数量增加。此外，驼鹿瘤胃富集培养物的成对比较进一步显示，以杨树水解产物为食的培养物中GH127和CE15家族的数量更多。为了将研究范围扩展到鲜为人知的碳水化合物活性蛋白，我们鉴定并比较了包含一个CBM和未知功能结构域（DUF）的多结构域蛋白，以及416个预测的多糖利用位点（PULs）内功能未知的蛋白。有趣的是，在铁硫蛋白中鉴定出的DUF362始终与CBM9相连；另一方面，除非来自相同的PULs，PULs中功能未知的蛋白几乎没有同源性。总体而言，本研究揭示了源自以富含纤维饮食著称的哺乳动物消化系统的微生物降解木质纤维素的能力，并强调了富集培养从宏基因组序列中选择新的CAZymes用于未来生化表征的价值。
