Temporal proteome dynamics of Clostridium cellulovorans cultured with major plant cell wall polysaccharides
Temporal proteome dynamics of Clostridium cellulovorans cultured with major plant cell wall polysaccharides
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DOI：
10.1186/s12866-019-1480-0
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发表时间：
2019-06-03
期刊：
影响因子：
4.2
通讯作者：
Ueda, Mitsuyoshi
中科院分区：
文献类型：
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作者：
Aburaya, Shunsuke;Aoki, Wataru;Ueda, Mitsuyoshi
食纤维梭菌（Clostridium cellulovorans）是一种嗜温、产纤维素酶体的细菌，含有57个编码纤维素酶体的基因。除纤维素体蛋白外，C.食纤维素菌还分泌非纤维素体蛋白以降解植物细胞壁多糖。与其他产生纤维素酶体的梭菌不同，C.食纤维素菌可以代谢所有主要的植物细胞壁多糖（纤维素、半纤维素和果胶）。在这项研究中，我们进行了时间蛋白质组分析的C。研究了食纤维菌降解植物细胞壁多糖的机制。用五种不同的碳源（葡萄糖、纤维素、木聚糖、半乳甘露聚糖和果胶）对食纤维素菌进行了蛋白质组学分析，并对细胞和分泌蛋白进行了蛋白质组学分析。我们总共鉴定了1895个细胞蛋白和875个分泌蛋白。对应于每种碳源的鉴定的独特碳水化合物降解酶被注释为对每种碳源具有特异性活性。然而，我们鉴定出果胶酸裂解酶是C.在木聚糖上培养的食纤维素菌，其先前与木聚糖降解无关。我们进行了k-均值聚类分析，以阐明每个碳源中细胞和分泌蛋白质的时间变化。我们发现大多数k-means聚类中的细胞蛋白质参与碳水化合物代谢、氨基酸代谢、翻译或膜转运。当木聚糖和果胶被用作碳源时，增加最多的k均值聚类包含参与辅因子和维生素代谢的蛋白质。C.在纤维素或木聚糖、半乳甘露聚糖和果胶上培养的食纤维素菌中，具有最大增加趋势的簇分别含有25种纤维素体蛋白和5种非纤维素体蛋白或8-19种纤维素体蛋白和9-16种非纤维素体蛋白。这些差异可能反映了其他碳源降解纤维素的机制。共丰度分析显示，蛋白酶和蛋白酶抑制剂的分泌蛋白协同积累。这一观察结果意味着分泌的蛋白酶抑制剂和蛋白酶保护碳水化合物降解酶免受植物的攻击。结论在这项研究中，我们首次阐明了C.食纤维菌。这些数据对于理解C.食纤维素菌降解主要植物细胞壁多糖。
BackgroundClostridium cellulovorans is a mesophilic, cellulosome-producing bacterium containing 57 genomic cellulosomal enzyme-encoding genes. In addition to cellulosomal proteins, C. cellulovorans also secretes non-cellulosomal proteins to degrade plant cell wall polysaccharides. Unlike other cellulosome-producing Clostridium species, C. cellulovorans can metabolize all major plant cell wall polysaccharides (cellulose, hemicelluloses, and pectins). In this study, we performed a temporal proteome analysis of C. cellulovorans to reveal strategies underlying plant cell wall polysaccharide degradation.ResultsWe cultured C. cellulovorans with five different carbon sources (glucose, cellulose, xylan, galactomannan, and pectin) and performed proteome analysis on cellular and secreted proteins. In total, we identified 1895 cellular proteins and 875 secreted proteins. The identified unique carbohydrate-degrading enzymes corresponding to each carbon source were annotated to have specific activity against each carbon source. However, we identified pectate lyase as a unique enzyme in C. cellulovorans cultivated on xylan, which was not previously associated with xylan degradation. We performed k-means clustering analysis for elucidation of temporal changes of the cellular and secreted proteins in each carbon sources. We found that cellular proteins in most of the k-means clusters are involved in carbohydrate metabolism, amino acid metabolism, translation, or membrane transport. When xylan and pectin were used as the carbon sources, the most increasing k-means cluster contained proteins involved in the metabolism of cofactors and vitamins. In case of secreted proteins of C. cellulovorans cultured either on cellulose or xylan, galactomannan, and pectin, the clusters with the most increasing trend contained either 25 cellulosomal proteins and five non-cellulosomal proteins or 8-19 cellulosomal proteins and 9-16 non-cellulosomal proteins, respectively. These differences might reflectmechanisms for degrading cellulose of other carbon source. Co-abundance analysis of the secreted proteins revealed that proteases and protease inhibitors accumulated coordinately. This observation implies that the secreted protease inhibitors and proteases protect carbohydrate-degrading enzymes from an attack from the plant.ConclusionIn this study, we clarified, for the first time, the temporal proteome dynamics of cellular and secreted proteins in C. cellulovorans. This data will be valuable in understanding strategies employed by C. cellulovorans for degrading major plant cell wall polysaccharides.