链霉菌基因组中放线菌型整合性接合元件的识别

In silico identification of actinomycete integrative and conjugative elements in completely sequenced Streptomyces genomes

摘要:

【目的】链霉菌染色体重组和外源DNA片段插入是影响其遗传多样性的主要因素。旨在考察放线菌型整合性接合元件(AICE)在链霉菌遗传多样性中所发挥的作用。【方法】基于AICE的特征性模块, 采用隐马尔科夫模型预测链霉菌基因组序列中的AICEs。【结果】在已全测序的12条链霉菌染色体和35个质粒中, 共识别出29个AICEs, 其中12个为首次报道。Streptomyces coelicolor基因组中发现了4个AICEs, 而其近缘的Streptomyces lividans却没有。【结论】AICEs都整合在链霉菌染色体的核心区, 且都具有典型的整合环出、复制和接合转移等核心模块, 这些可自行转移的元件在链霉菌基因组可塑性中扮演了重要角色。

Abstract:

[Objective] Chromosomal rearrangements and integration of alien DNA fragments contribute to the genome-wide genetic diversity of Streptomyces. This paper aims to study the role of actinomycete integrative and conjugative elements (AICEs) in Streptomyces genetic diversity. [Methods] AICEs were identified in the completely sequenced Streptomyces genomes using a profile Hidden Markov Model approach, based on their characteristic modules. [Results] Twenty-nine AICEs were found from 12 chromosome sequences and 35 plasmid sequences of Streptomyces, 12 of which were firstly reported. Four AICEs were identified in S. coelicolor, but none in the closely related S. lividans. [Conclusion] AICEs were found to be inserted into the core regions of the Streptomyces chromosomes. They typically comprised three core genetic modules, implementing chromosomal integration/excision, self-transfer by conjugation and replication, suggesting that they promote the plasticity of Streptomyces genomes.