Pathways and Enzymes from Fungal Genomes for Degradation of Aromatic Compounds

近年来，许多国家，特别是美国，对真菌基因组测序产生了相当大的兴趣。目前，基因组测序相对容易和便宜，公共数据库中有超过150个真菌基因组序列，而且数量还在快速增长。真菌是生物圈的主要降解者和回收者，它们有能力将几乎任何物质首先转化为其组成部分，然后转化为二氧化碳和水。它们这样做是为了获得生长所需的碳和能量，利用一种叫做酶的蛋白质催化剂来驱动降解过程的每一步。对真菌基因组测序的兴趣很大程度上在于鉴定每种真菌参与这些降解活动的全部酶的编码基因的可能性。一旦确定，人们相信这些酶的降解能力可以用来将复杂的植物材料降解成有用的产品，如乙醇和精细化学品，或破坏污染物。事实上，许多商业过程，从烘焙到生物燃料生产，已经依赖于真菌酶。然而，这些都来自少数真菌，而世界上有超过一百万种真菌生活在各种各样的栖息地，有一个巨大的潜在有用的酶库尚未开发。真菌可以降解的一类化学物质是芳香族化合物，它是由一个或多个苯环的存在来定义的，但除此之外，这些苯环上附着的物质是非常多样化的。植物会产生各种各样的芳香族化合物，我们在饮食中会接触到这些化合物，但我们在制造和工业过程中也会使用大量芳香族化合物。虽然人体对这些化合物的代谢通常是为了解毒和消除，但真菌和细菌利用它们作为生长所需的碳和能量的唯一来源。虽然真菌基因组中的许多基因在芳香化合物的降解中被指定了功能，但通常很少有实验证据支持这些指定。本提案的目的是将真菌基因组序列数据与用于降解芳香化合物的代谢途径中基因及其编码酶功能的实验证据联系起来。最初，我们专注于少数已知能够降解一系列这些化合物的物种，为降解途径中涉及的基因和相应的酶提供定义良好且完整的数据集。从这些定义明确的例子开始，我们将扩展到真菌生命树中的其他物种，以及更广泛的化合物。预计这项工作将在许多方面具有重要意义。首先，它将允许真菌基因组中的一大群基因，这些基因目前很少或不正确地理解，与功能特性牢固地联系起来。许多使用基因组信息的实验研究只能用我们将要生成的信息来正确地解释。其次，它将揭示真菌用于降解大量具有环境意义并可能与人类健康有关的化合物的策略，这些策略目前尚未得到很好的理解。这将有助于更好地预测芳香化合物在环境中的命运和真菌的代谢能力。第三，预计所鉴定的一些酶将具有新的催化特性，这将有助于新的生化知识，并有助于作为催化剂的特定应用，例如在化学废物的降解或将植物废物转化为生物柴油。

In recent years there has been considerable interest in many countries, especially the US, in sequencing the genomes of fungi. Sequencing a genome nowadays is relatively easy and inexpensive, and there are over 150 fungal genome sequences available in public databases, with the number growing fast. Fungi are the master degraders and recyclers of the biosphere, and have the ability to transform almost any material, first into its constituent parts and then carbon dioxide and water. They do so in order to obtain carbon and energy to grow, using protein catalysts called enzymes to drive each step in the degradation process. Much of the interest in sequencing fungal genomes lies in the possibility of identifying genes encoding the complete repertoire of enzymes that each fungus has to contribute to these degradation activities. Once identified, it is believed that the degradative power of these enzymes can be harnessed to degrade complex plant materials to useful products, such as ethanol and fine chemicals, or to destroy pollutants. Indeed, many commercial processes, from baking to biofuel production already rely on fungal enzymes. However these come from a handful of fungi, and with well over a million fungal species in the world living in a wide variety of habitats, there is a huge reservoir of potentially useful enzymes that remains untapped. One group of chemicals that fungi can degrade are the aromatic compounds, which are defined by the presence of one or more benzene rings, but otherwise are very diverse in terms of what is attached to those rings. A large variety of aromatic compounds is made by plants, and we are exposed to those in our diets, but we also use large quantities of aromatics for manufacturing and in industrial processes. Although human metabolism of such compounds is generally directed towards detoxification and elimination, fungi and bacteria utilize them as sole sources of carbon and energy to grow. While many genes in fungal genomes have been assigned functions in the degradation of aromatic compounds, there is often very little experimental evidence that supports these assignments. The aim of this proposal is to connect fungal genome sequence data to experimental evidence for the functions of genes and their encoded enzymes in metabolic pathways used for the degradation of aromatic compounds. Initially, we are focusing on a few species, with known abilities to degrade a range of these compounds, to produce well-defined and complete sets of data for the genes and corresponding enzymes involved in the degradation pathways. From these well-defined examples we will expand to other species across the fungal tree of life, and to a broader range of compounds. This work is expected to be significant in a number of ways. First, it will allow a large group of genes in fungal genomes, which currently are poorly or incorrectly understood, to be solidly linked to functional properties. Many experimental studies that use the genome information can only be interpreted properly with the information that we will be generating. Second, it will reveal strategies, currently not well understood, used by fungi for the degradation of a large group of compounds of environmental significance and potentially related to human health. This will allow better prediction of the fate of aromatic compounds in the environment and the metabolic capabilities of fungi. Third, it is anticipated that some of the enzymes identified will have novel catalytic properties that will contribute to new biochemical knowledge and be useful for specific applications as catalysts, for example in the degradation of chemical wastes or conversion or plant waste to biodiesel.