Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Washington Street, Blacksburg, VA 24061-0477, USA.
Microbiol Mol Biol Rev. 2010 Dec;74(4):479-503. doi: 10.1128/MMBR.00017-10.
Microbes form intimate relationships with hosts (symbioses) that range from mutualism to parasitism. Common microbial mechanisms involved in a successful host association include adhesion, entry of the microbe or its effector proteins into the host cell, mitigation of host defenses, and nutrient acquisition. Genes associated with these microbial mechanisms are known for a broad range of symbioses, revealing both divergent and convergent strategies. Effective comparisons among these symbioses, however, are hampered by inconsistent descriptive terms in the literature for functionally similar genes. Bioinformatic approaches that use homology-based tools are limited to identifying functionally similar genes based on similarities in their sequences. An effective solution to these limitations is provided by the Gene Ontology (GO), which provides a standardized language to describe gene products from all organisms. The GO comprises three ontologies that enable one to describe the molecular function(s) of gene products, the biological processes to which they contribute, and their cellular locations. Beginning in 2004, the Plant-Associated Microbe Gene Ontology (PAMGO) interest group collaborated with the GO consortium to extend the GO to accommodate terms for describing gene products associated with microbe-host interactions. Currently, over 900 terms that describe biological processes common to diverse plant- and animal-associated microbes are incorporated into the GO database. Here we review some unifying themes common to diverse host-microbe associations and illustrate how the new GO terms facilitate a standardized description of the gene products involved. We also highlight areas where new terms need to be developed, an ongoing process that should involve the whole community.
微生物与宿主（共生关系）形成亲密关系，从互利共生到寄生关系不等。微生物在成功与宿主关联中涉及的常见机制包括粘附、微生物或其效应蛋白进入宿主细胞、减轻宿主防御和获取营养。与这些微生物机制相关的基因在广泛的共生关系中是已知的，揭示了发散和趋同的策略。然而，由于文献中对功能相似基因的描述术语不一致，这些共生关系之间的有效比较受到阻碍。使用基于同源性工具的生物信息学方法仅限于根据其序列的相似性来识别功能相似的基因。基因本体论 (GO) 提供了一种有效的解决方案，它提供了一种标准化的语言来描述来自所有生物体的基因产物。GO 由三个本体组成，使人们能够描述基因产物的分子功能、它们所贡献的生物学过程以及它们的细胞位置。从 2004 年开始，植物相关微生物基因本体论 (PAMGO) 兴趣小组与 GO 联盟合作，将 GO 扩展到容纳描述与微生物-宿主相互作用相关的基因产物的术语。目前，超过 900 个描述与不同植物和动物相关微生物共有的生物学过程的术语已被纳入 GO 数据库。在这里，我们回顾了一些不同宿主-微生物关联共有的统一主题，并说明了新的 GO 术语如何促进所涉及基因产物的标准化描述。我们还强调了需要开发新术语的领域，这是一个应该涉及整个社区的持续过程。
