Collaborative Research: Functional and evolutionary bases of substrate-specificity in wood-decaying basidiomycetes

木材(木质纤维素)是陆地生态系统中最丰富的碳库之一。木材的真菌分解是碳循环的关键组成部分，影响土壤生产力，并有可能被开发用于生产生物燃料和其他“绿色”技术。主要的木材腐烂真菌是形成蘑菇的真菌(蘑菇菌)。木材的物理特性和化学成分因植物种类不同而不同，大多数腐木真菌具有独特的木材基质范围。然而，为什么个别种类的木材腐烂真菌往往出现在特定的植物寄主上，目前还不清楚。这个项目将结合对腐烂过程中表达的基因的分析，以及腐烂过程的物理和化学特征，来研究木材腐烂蘑菇中底物专一性和底物转换的机制。参与木材腐烂或降解的真菌酶在新兴的生物过程中具有潜在的应用，例如与能源有关的生物转化，包括生物燃料生产和生物修复。加强对允许不同种类的真菌利用特定木材基质的机制的了解，有助于指导可用于此类应用目的的遗传资源的开发。该项目将支持一名博士后研究员和两名研究生，并将为美国三个合作学术机构的本科生提供培训。为了将有关真菌和木材分解的信息带给广大观众，该项目将在伍斯特生态博物馆(http://www.ecotarium.org/)，)创建互动展品并开发配套的公共节目，这是一个科学和自然博物馆，每年接待超过140,000名游客，其中包括大量来自地区公立学校的学生。展品将展示真菌的多样性、腐烂过程和真菌在碳循环中的作用。拟议的研究将集中在具有可用基因组序列的四种真菌(具有不同的底物偏好)上。这些真菌将在四种不同树种(两种针叶树和两种硬木)的固体晶片上培养。转录组分析将使用Illumina HiSeq 2000平台进行，重点是编码已知或怀疑与木材腐烂有关的酶的基因，以及功能未知的共表达基因。系统基因组分析将利用木材腐烂真菌的所有可用基因组，重点放在可能在腐烂过程中发挥作用的基因家族，如表达谱所知。腐烂的物理和化学特征将使用显微镜、质谱学和定植底物的化学分析来解决。这项拟议的研究是拥有真菌系统学和分子进化、木材腐烂和林产品病理学、真菌基因组学以及腐烂系统的遗传学和生物化学专业知识的研究人员之间的合作。该项目将利用木材腐烂担子菌基因组学的最新进展。它将提供对森林生态系统中真菌的功能和进化的洞察，并为未来的研究创造一个框架，旨在了解影响特定真菌基因表达的特定植物衍生化合物。

Wood (lignocellulose) is one of the most abundant carbon pools in terrestrial ecosystems. Fungal decomposition of wood is a critical component of the carbon cycle, impacts soil productivity, and has the potential to be exploited in the production of biofuels and other 'green' technologies. The major wood-decaying fungi are mushroom-forming (Agaricomycetes). The physical characteristics and chemical composition of wood vary among plant species, and most wood-decaying Agaricomycetes have characteristic wood substrate ranges. However, it is not understood why individual species of wood decaying fungi tend to occur on specific plant hosts. This project will investigate the mechanisms of substrate specificity and substrate switching in wood-decaying Agaricomycetes using a combination of analyses of genes expressed during decay, and physical and chemical characterization of the decay process. Fungal enzymes that are involved in wood decay or degradation have potential applications in emerging bioprocesses, such as energy-related bioconversions, including biofuel production, and bioremediation. Enhanced understanding of the mechanisms that allow different species of fungi to exploit particular wood substrates could help guide development of genetic resources that could be used for such applied purposes. This project will support one Postdoctoral Fellow and two graduate students, and will provide training to undergraduates at three collaborating academic institutions in the US. To bring information about fungi and wood decomposition to a wide audience, this project will create interactive exhibits and develop accompanying public programs at the Worcester EcoTarium (http://www.ecotarium.org/), a science and nature museum which serves over 140,000 visitors annually including large numbers of students from regional public schools. Exhibits will illustrate fungal diversity, the decay process, and the role of fungi in the carbon cycle.The proposed research will focus on four species of Agaricomycetes (with distinct substrate preferences) with available genome sequences. The fungi will be cultured on solid wafers of four different tree species (two conifers and two hardwoods). Transcriptome profiling will be performed with the Illumina HiSeq 2000 platform, focusing on genes encoding enzymes known or suspected to be involved in wood decay, as well as co-expressed genes of unknown function. Phylogenomic analyses will make use of all available genomes of wood-decaying Agaricomycetes, focusing on gene families that are likely to play a role in decay, as informed by expression profiles. Physical and chemical characteristics of decay will be addressed using microscopy, mass spectrometry, and chemical analyses of colonized substrates. The proposed research is a collaboration between researchers with expertise in fungal systematics and molecular evolution, wood decay and forest products pathology, fungal genomics, and genetics and biochemistry of decay systems. This project will capitalize on recent advances in genomics of wood-decaying basidiomycetes. It will provide insight into the functioning and evolution of fungi in forest ecosystems, and create a framework for future studies aimed at understanding the specific plant-derived compounds that affect expression of particular fungal genes.