假单胞菌NyZ12基因组的可塑多变特征

Plasticity and variability of Pseudomonas plecoglossicida NyZ12 genome

摘要:

【背景】假单胞菌是广泛存在于土壤、水体环境的微生物，其中Pseudomonas plecoglossicida NyZ12是一株能够以环己胺为唯一碳源和氮源生长的革兰氏阴性菌，其基因组达到7.0 Mb左右。【目的】研究假单胞菌NyZ12的基因组是否具有可塑性和多变特征。【方法】以环己胺为唯一碳源和氮源生长的P. plecoglossicida NyZ12为研究对象，以琥珀酸或者代谢中间产物环己酮为碳源连续传代让其自然发生突变，然后筛选在以环己胺为唯一碳源和氮源的无机盐培养基上不能生长的突变体。将获得的突变体进行全基因组测序，并与野生型假单胞菌NyZ12的全基因组进行比对。【结果】以琥珀酸和环己酮为碳源分别筛选到一株突变体T₁和T₂，测序比对后发现假单胞菌突变体T₁、T₂的基因组发生大量的缺失和突变。对基因丢失的原因进行了分析，丢失的2个大片段中存在大量的重复序列、转座酶、转座子和原噬菌体。【结论】假单胞菌NyZ12的基因组具有可塑多变的特征。其可能的机制为进一步揭示微生物的适应和进化提供了参考。

Abstract:

[Background] Pseudomonas is genus of bacteria ubiquitous in soil and water environments, among which Pseudomonas plecoglossicida NyZ12 is a Gram-negative bacterium that can grow on cyclohexylamine as the sole carbon and nitrogen source, with the genome up to 7.0 Mb. [Objective] To investigate whether the genome of P. plecoglossicida NyZ12 has plasticity and variability. [Methods] P. plecoglossicida NyZ12 was continuously cultured with succinic acid or the intermediate cyclohexanone as the carbon source for natural mutation, and then the mutants incapable of growing on cyclohexylamine as the sole carbon and nitrogen source were isolated. The whole genomes of the mutants T₁ and T₂ were sequenced and compared with that of the wild-type P. plecoglossicida NyZ12. [Results] The genomes of mutants T₁ and T₂ presented a large number of deletions and mutations compared with the wild type. A large number of repeats, transposons, and prophages were present in the two missing large gene fragments. [Conclusion] The genome of P. plecoglossicida NyZ12 is characterized with plasticity and variability. This study explores the possible mechanism and gives insight into the adaptation and evolution of microorganisms.