细菌萜类合成酶的生物信息学分析

【目的】目前对于萜类合成酶(Terpenoid synthase，TPS)的研究主要集中在植物和真菌中，而对细菌TPS的系统研究尚少。建立在大量已经被测序的细菌基因组基础上，利用生物信息学方法，对细菌TPS在全基因组范围内进行识别、分类和功能分析。【方法】利用TPS的隐马尔科夫模型(Pfam编号为PF03936)搜索自建的细菌蛋白质组数据库，预测出细菌TPS。对这些候选TPS的蛋白序列用MAFFT 7.130b进行多序列比对，并利用MEGA 6.0对多序列比对结果进行进化分析。利用MEME和PredictProtein分别进行细菌TPS的基序(Motifs)和点突变分析。【结果】建立在生物信息学分析的基础上，1 423条细菌TPS被识别，它们分布在8个门中，即放线菌门(Actinobacteria)、变形菌门(Proteobacteria)、蓝藻门(Cyanobacteria)、拟杆菌门(Bacteroidetes)、厚壁菌门(Firmicutes)、绿弯菌门(Chloroflexi)、酸杆菌门(Acidobacteria)和衣原体门(Chlamydiae)。进化分析表明细菌TPS可分为4大类，Motifs分析表明除了各类之间保守的基序(Motifs)外，还有特异的Motifs，这暗示着细菌TPS在不同类别之间的功能分化。点突变分析表明，细菌TPS不同位点的氨基酸突变对TPS功能的影响不同。【结论】细菌TPS主要分布于8个门中，其中在2个门中细菌TPS尚未见报道，即厚壁菌门(Firmicutes)与酸杆菌门(Acidobacteria)。基于进化分析，可以把细菌TPS分为4类，各类之间的差异可能是由类特异的Motifs决定的，另外细菌TPS不同氨基酸位点的突变分析为今后验证TPS的功能提供了很好的理论基础。

Analysis of bacterial terpenoid synthase by bioinformatics

Objective] At present, studies on terpenoid synthase mainly focus on plants and fungi. The systematic study of bacterial terpenoid synthase is still rare. Based on a large number of bacterial genomes, we identified bacterial terpenoid synthase in genome-wide and predicted their function by bioinformatics. Methods] Local bacterial proteome database was first built based on the bacterial protein sequences, and hidden markov model (HMM) of PF03936 in Pfam was used to predict bacterial terpenoid synthase. Then multiple sequence alignment for candidate terpenoid synthase was aligned by the tool of MAFFT 7.130b, and phylogenetic tree was constructed by MEGA 6.0. Finally, analysis of motifs was conducted by MEME and point mutation of TPS by PredictProtein. Results] In total 1 423 terpenoid synthases were identified; they are distributed in 8 phylum, including: Actinobacteria, Proteobacteria, Cyanobacteria, Bacteroidetes, Firmicutes, Chloroflexi, Acidobacteria and Chlamydiae. Phylogenetic analysis revealed that bacterial terpenoid synthases can be divided into 4 groups. Motifs analysis of each group by MEME showed that in addition to conserved motifs among groups, there were some specific motifs within each group, which implies functional differentiation among different groups. Point mutations analysis showed that mutations of amino acid sites in different positions of terpenoid synthase could have different effect on TPS function. Conclusion] Bacterial terpenoid synthases are mainly distributed in 8 phylum, of which 2 phylum have not been reported before; they are Firmicutes and Acidobacteria. Phylogenetic analysis showed that the difference among 4 groups of terpenoid synthase is mainly caused by group-specific motifs. In addition, mutation analysis of amino acids in different positions of terpenoid synthase provides a fundament for further verification of bacterial terpenoid synthase function.