Zhang Jiwei, Meng Markillie Lye, Mitchell Hugh D, Gaffrey Matthew J, Orr Galya, Schilling Jonathan S
Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN, United States.
Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States.
Fungal Genet Biol. 2022 Apr;159:103673. doi: 10.1016/j.fgb.2022.103673. Epub 2022 Feb 9.
Brown rot fungi dominate the carbon degradation of northern terrestrial conifers. These fungi adapted unique genetic inventories to degrade lignocellulose and to rapidly release a large quantity of carbohydrates for fungal catabolism. We know that brown rot involves "two-step" gene regulation to delay most hydrolytic enzyme expression until after harsh oxidative pretreatments. This implies the crucial role of concise gene regulation to brown rot efficacy, but the underlying regulatory mechanisms remain uncharacterized. Here, using the combined transcriptomic and enzyme analyses we investigated the roles of carbon catabolites in controlling gene expression in model brown rot fungus Rhodonia placenta. We identified co-regulated gene regulons as shared transcriptional responses to no-carbon controls, glucose, cellobiose, or aspen wood (Populus sp.). We found that cellobiose, a common inducing catabolite for fungi, induced expression of main chain-cleaving cellulases in GH5 and GH12 families (cellobiose vs. no-carbon > 4-fold, P < 0.05), whereas complex aspen was a universal inducer for Carbohydrate Active Enzymes (CAZymes) expression. Importantly, we observed the attenuated glucose-mediated repression effects on cellulases expression, but not on hemicellulases and lignin oxidoreductases, suggesting fungi might have adapted diverged regulatory routes to boost cellulase production for the fast carbohydrate release. Using carbon regulons, we further predicted the cis- and trans-regulatory elements and assembled a network model of the distinctive regulatory machinery of brown rot. These results offer mechanistic insights into the energy efficiency traits of a common group of decomposer fungi with enormous influence on the carbon cycle.
褐腐真菌主导着北半球陆地针叶树的碳降解过程。这些真菌拥有独特的基因库，用于降解木质纤维素并迅速释放大量碳水化合物以供真菌分解代谢。我们知道，褐腐涉及“两步”基因调控，即延迟大多数水解酶的表达，直到经过严苛的氧化预处理之后。这意味着精确的基因调控对褐腐功效起着关键作用，但其潜在的调控机制仍未明确。在此，我们结合转录组学和酶分析方法，研究了碳分解代谢物在控制模式褐腐真菌——红褐肉座菌（Rhodonia placenta）基因表达中的作用。我们鉴定出了共同调控的基因调控子，它们是对无碳对照、葡萄糖、纤维二糖或白杨木（Populus sp.）的共同转录反应。我们发现，纤维二糖作为真菌常见的诱导性分解代谢物，可诱导GH5和GH12家族中主要的主链切割纤维素酶的表达（纤维二糖与无碳对照相比，>4倍，P<0.05），而复杂的白杨木是碳水化合物活性酶（CAZymes）表达的通用诱导剂。重要的是，我们观察到葡萄糖介导的对纤维素酶表达的抑制作用减弱，但对半纤维素酶和木质素氧化还原酶的抑制作用未减弱，这表明真菌可能已经采用了不同的调控途径来促进纤维素酶的产生，以便快速释放碳水化合物。利用碳调控子，我们进一步预测了顺式和反式调控元件，并构建了褐腐独特调控机制的网络模型。这些结果为一类对碳循环有巨大影响的常见分解真菌的能量效率特性提供了机制上的见解。
