微小杆菌属(Exiguobacterium)细菌的能量代谢途径分析

Energy metabolism pathways in Exiguobacterium

摘要:

【目的】微小杆菌属(Exiguobacterium)细菌广泛分布于海洋及非海洋环境中，具有多种代谢途径以适应复杂多样的生境。本研究从能量代谢途径角度出发，探究该属菌株对不同生境的适应能力。【方法】从美国国家生物科技数据中心(National Center for Biotechnology Information, NCBI)数据库中获取146个Exiguobacterium属菌株的基因组，查找并统计光营养、厌氧呼吸和底物代谢等多种能量代谢途径的关键蛋白或关键酶基因在各菌株基因组中的分布，包括光营养型的视紫红质基因、厌氧呼吸营养型的钼辅因子合成蛋白基因，以及底物代谢营养型中乙醛酸分流途径的异柠檬酸裂解酶及苹果酸合酶基因等。根据对应的氨基酸序列构建视紫红质、MoaC和异柠檬酸裂解酶的系统发育树，分析不同能量代谢途径在该属菌株进化过程中的保守性，推测其对于该属菌株的重要性。【结果】Exiguobacterium属中50%的种具有视紫红质基因，其中分离自非海洋生境的菌株更趋向于含有视紫红质基因。本研究所统计的全部非海洋生境菌株中，含有视紫红质基因的菌株占比约为70%，而在海洋生境菌株中该比例仅为19%。Exiguobacterium属约27%的种存在钼辅因子合成蛋白基因，分离自海洋环境的菌株有该类蛋白的可能性更高(32%:21%)，具有完整钼辅因子合成途径的菌株集中于进化树同一分支上的少数种。该属约61%的种存在乙醛酸分流途径相关酶基因，这些种隶属进化树的同一分支，且种内所有菌株都具备相关基因，表明乙醛酸分流途径在Exiguobacterium属的分布具有种特异性。【结论】Exiguobacterium属细菌具有多种能量代谢途径相关基因，包括基于视紫红质的光营养型能量代谢途径、基于钼酶的厌氧呼吸型能量代谢途径和底物代谢营养型能量代谢途径中的乙醛酸分流途径。能量代谢途径多样性可能是Exiguobacterium属细菌适应复杂多样生境的机制之一。此外，本研究发现Exiguobacterium属中不同种、同种不同菌株间存在能量代谢途径差异，且能量代谢途径在该属内的分布多不具备种特异性，表明仅通过16S rRNA基因种属鉴定来预测目标菌株的代谢类型可能有较大偏差和局限性。

Abstract:

[Objective] Bacteria of Exiguobacterium are ubiquitous in marine and non-marine environments and display versatile metabolism pathways to adapt to complex and diverse habitats. In this study, we explored the adaptability of Exiguobacterium to different habitats from the perspective of energy metabolism pathways. [Methods] The genomes of a total 146 Exiguobacterium strains available at National Center for Biotechnology Information (NCBI) database were downloaded for the mining of the genes encoding key enzymes of multiple energy metabolism pathways. The encoded enzymes mainly included rhodopsin for phototrophy, molybdenum cofactor synthesis protein for anaerobic respiration, and isocitrate lyase and malate synthase for glyoxylate shunt. We then built the phylogenetic trees based on the amino acid sequences of rhodopsin, MoaC, and isocitrate lyase to analyze the conservation of different energy metabolism pathways. [Results] Fifty percent of Exiguobacterium species possessed rhodopsin gene. The strains isolated from non-marine habitats tended to carry rhodopsin gene, accounting for about 70%, while the strains carrying rhodopsin gene from marine habitats accounted for only 19%. Approximately 27% of species possessed the gene encoding molybdenum cofactor synthesis protein, and the strains isolated from marine habitats (32%) carrying this gene were more than those from non-marine habitats (21%). The strains with complete molybdenum cofactor synthesis pathway concentrated in several species, sharing the same branch on the phylogenetic tree. The glyoxylate shunt existed in approximately 61% of the species, which clustered in the same branch of the phylogenetic tree. All the strains of such species possessed related genes, which indicated that this pathway had species specificity in Exiguobacterium. [Conclusion] The key genes for energy metabolism vary in different species or different strains of Exiguobacterium. The diversity of energy metabolism pathways may, to some extent, facilitate the adaptation of these bacteria to complex habitats. Furthermore, the distribution of most energy metabolism pathways is not species-specific for this genus. This finding suggests that the prediction of metabolic types of targeted strains by 16S rRNA gene-based species identification alone may be biased and limited.