基于转录组与翻译组的海洋食烷菌(Alcanivorax)烷烃代谢调控研究

Regulation of alkane metabolism in Alcanivorax based on transcriptome and translatome

摘要:

【目的】食烷菌是海洋烃类降解优势菌，其烷烃代谢调控机制有待深入研究。本研究拟从食烷菌转录和翻译水平上认识烷烃降解的调控过程。【方法】分别以乙酸和正十六烷(C16)为唯一碳源与能源，获取柴油食烷菌(Alcanivorax dieselolei) B5菌株的转录组和翻译组数据，并整合数据计算得到该菌在2种碳源培养条件下基因的翻译效率。采用基因本体论(gene ontology, GO)和京都基因和基因组百科全书(Kyoto encyclopedia of genes and genomes, KEGG)对差异翻译和翻译效率基因进行功能和代谢通路注释。【结果】当以C16为唯一碳源与能源时，B5菌株烷烃代谢途径的关键基因在转录与翻译水平均大量提升，包括烷烃单加氧酶、细胞色素P450氧化酶、醇脱氢酶和醛脱氢酶等。KEGG富集结果表明，翻译水平显著上调基因参与了肽聚糖生物合成、脂肪酸降解、氯代烷烃降解、氧化磷酸化和生物膜形成等通路；翻译效率差异基因主要富集在铁载体非核糖体肽的生物合成、氧化磷酸化和不饱和脂肪酸的生物合成等途径。通过转录组和翻译组学的联合分析显示，为了适应烷烃氧化，B5有效地协调了转录与翻译过程；B5在2种碳源培养条件下基因表达水平与翻译效率均呈现负相关性；全局蛋白调节因子CsrA和sRNAs参与的转录后调控可能导致了烷烃代谢相关基因的翻译效率差异。【结论】转录组和翻译组数据的联合分析表明转录后调控参与了食烷菌的烷烃代谢过程，本研究为进一步探究食烷菌烷烃代谢的转录后调控机制奠定了基础。

Abstract:

[Objective] Alcanivorax is a genus of dominant hydrocarbon-degrading bacteria in the marine environment, and the knowledge about the regulation mechanism of its alkane metabolism is limited. This study aims to decipher the regulation mechanism of alkane degradation by Alcanivorax at both transcriptional and translational levels. [Methods] The transcriptome and translatome data of A. dieselolei B5 grown in the medium with n-hexadecane as the sole carbon and energy source were obtained. The changes in the gene translation efficiency were calculated with sodium acetate as the control. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment was performed for the differentially translated genes (DTGs) and differential translation efficiency genes (DTEGs). [Results] Both the transcriptional and translational levels of the key genes involved in alkane metabolism were significantly up-regulated when A. dieselolei was grown on n-hexadecane. These key genes mainly encoded alkane monooxygenase, cytochrome P450 oxidase, alcohol dehydrogenase, and aldehyde dehydrogenase. KEGG enrichment analysis revealed that the up-regulated DTGs were involved in peptidoglycan biosynthesis, fatty acid degradation, chloroalkane degradation, oxidative phosphorylation, biofilm formation, etc. DTEGs were mainly involved in the biosynthesis of siderophore non-ribosomal peptides, oxidative phosphorylation, biosynthesis of unsaturated fatty acids, etc. The combined analysis of transcriptome and proteome data showed that A. dieselolei efficiently coordinated the transcription and translation processes to adapt to alkane oxidation. The gene expression level and translational efficiency showed a negative correlation under both culture conditions. The global protein regulators CsrA and sRNAs may be involved in post-transcriptional regulation of genes involved in alkane metabolism, leading to differences in the translational efficiency. [Conclusion] The combined analysis of transcriptome and translatome data suggested that post-transcriptional regulation was involved in the alkane metabolism of A. dieselolei. This study underpins further exploration of the post-transcriptional regulatory mechanisms controlling alkane metabolism.