Yan Shaomin, Wu Guang
Bioscience and Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China.
J Appl Genet. 2017 Nov;58(4):545-563. doi: 10.1007/s13353-017-0402-9. Epub 2017 Jul 7.
Although polycyclic aromatic hydrocarbons (PAHs) are harmful to human health, their elimination from the environment is not easy. Biodegradation of PAHs is promising since many bacteria have the ability to use hydrocarbons as their sole carbon and energy sources for growth. Of various microorganisms that can degrade PAHs, Pseudomonas aeruginosa is particularly important, not only because it causes a series of diseases including infection in cystic fibrosis patients, but also because it is a model bacterium in various studies. The genes that are responsible for degrading PAHs have been identified in P. aeruginosa, however, no gene acts alone as various stresses often initiate different metabolic pathways, quorum sensing, biofilm formation, antibiotic tolerance, etc. Therefore, it is important to study how PAH degradation genes behave under different conditions. In this study, we apply network analysis to investigating how 46 PAH degradation genes reorganized among 5549 genes in P. aeruginosa PAO1 under nine different conditions using publicly available gene coexpression data from GEO. The results provide six aspects of novelties: (i) comparing the number of gene clusters before and after stresses, (ii) comparing the membership in each gene cluster before and after stresses, (iii) defining which gene changed its membership together with PAH degradation genes before and after stresses, (iv) classifying membership-changed-genes in terms of category in Pseudomonas Genome Database, (v) postulating unknown gene's function, and (vi) proposing new mechanisms for genes of interests. This study can shed light on understanding of cooperative mechanisms of PAH degradation from the level of entire genes in an organism, and paves the way to conduct the similar studies on other genes.
尽管多环芳烃（PAHs）对人类健康有害，但从环境中消除它们并非易事。PAHs的生物降解具有前景，因为许多细菌有能力将碳氢化合物作为其生长的唯一碳源和能源。在各种能够降解PAHs的微生物中，铜绿假单胞菌尤为重要，这不仅是因为它会引发一系列疾病，包括囊性纤维化患者的感染，还因为它是各种研究中的模式细菌。在铜绿假单胞菌中已经鉴定出负责降解PAHs的基因，然而，没有单个基因单独起作用，因为各种应激通常会启动不同的代谢途径、群体感应、生物膜形成、抗生素耐受性等。因此，研究PAH降解基因在不同条件下的行为很重要。在本研究中，我们应用网络分析来研究在九种不同条件下，铜绿假单胞菌PAO1中46个PAH降解基因如何在5549个基因中重新组织，使用来自GEO的公开可用基因共表达数据。结果提供了六个方面的新发现：（i）比较应激前后基因簇的数量，（ii）比较应激前后每个基因簇中的成员，（iii）确定哪些基因在应激前后与PAH降解基因一起改变了其成员身份，（iv）根据假单胞菌基因组数据库中的类别对成员身份改变的基因进行分类，（v）推测未知基因的功能，以及（vi）为感兴趣的基因提出新机制。本研究有助于从生物体中整个基因的层面理解PAH降解的协同机制，并为对其他基因进行类似研究铺平道路。
