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Published on: September 20, 2016
Decoding critical CAZyme genes and transcription factors for pathogen-suppressing lignocellulosic biomass
Peng Ren1, Tianjie Yang1, Xinlan Mei1
1Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing 210095, PR China.
Abstract:
Carbohydrate-active enzyme (CAZyme) genes and their transcription factors (TFs) are crucial for the fermentation of lignocellulosic biomass to inhibit pathogen. However, the diversity of CAZyme genes and the complexity of TFs identification limit the efficient biovalorization of bio-resources. This study aimed to inhibit the pathogen Ralstonia solanacearum by fermenting two substrates (chrysanthemum and peanut stems) with Bacillus amyloliquefaciens, while employing multi-omics and machine learning to analyze key CAZyme genes as well as their TFs. The results showed that the water-soluble extracts (WSEs) from fermented chrysanthemum stem (days 6-7) exhibited strong antimicrobial activity. Glycosyl transferase (GT) and polysaccharide lyase (PL) gene sets were enriched significantly during chrysanthemum stem fermentation. Genes, encoding a UDP-glycosyltransferase (GT1) and a pectin lyase (PL1), were identified as key and correlated with the inhibition rate significantly. Through computational prediction, we further revealed the sigma factor RpoE as an indirect positive regulator of PL1 gene expression. Our study provides valuable insights into the identification of key CAZyme genes and the rapid discovery of their TFs, offering a foundation and promising direction for future optimization of fermentation technology.
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