| 链霉菌基因组中放线菌型整合性接合元件的识别 |
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| 引用本文： | 徐珍,毕德玺,李鹏,谭之磊,邓子新,欧竑宇,贾士儒. 链霉菌基因组中放线菌型整合性接合元件的识别[J]. 微生物学通报, 2013, 40(12): 2259-2270 |
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| 作者姓名： | 徐珍 毕德玺 李鹏 谭之磊 邓子新 欧竑宇 贾士儒 |
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| 作者单位： | 1. 天津科技大学 工业微生物教育部重点实验室 天津 300457;2. 上海交通大学 微生物代谢国家重点实验室 上海 200030;2. 上海交通大学 微生物代谢国家重点实验室 上海 200030;1. 天津科技大学 工业微生物教育部重点实验室 天津 300457;2. 上海交通大学 微生物代谢国家重点实验室 上海 200030;2. 上海交通大学 微生物代谢国家重点实验室 上海 200030;1. 天津科技大学 工业微生物教育部重点实验室 天津 300457 |
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| 基金项目： | 国家自然科学基金项目(No. 31170082, 21276197); 国家973计划项目(No. 2012CB721002) |
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| 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。
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| 关 键 词： | 链霉菌基因组 放线菌型整合性接合元件 隐马尔科夫模型 |
In silico identification of actinomycete integrative and conjugative elements in completely sequenced Streptomyces genomes |
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| XU Zhen,BI De-Xi,LI Peng,TAN Zhi-Lei,DENG Zi-Xin,OU Hong-Yu and JIA Shi-Ru. In silico identification of actinomycete integrative and conjugative elements in completely sequenced Streptomyces genomes[J]. Microbiology China, 2013, 40(12): 2259-2270 |
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| Authors: | XU Zhen BI De-Xi LI Peng TAN Zhi-Lei DENG Zi-Xin OU Hong-Yu JIA Shi-Ru |
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| Affiliation: | 1. Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China;2. State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200030, China;2. State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200030, China;1. Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China;2. State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200030, China;2. State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200030, China;1. Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China |
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| 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. |
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| Keywords: | Streptomyces genome Actinomycete integrative and conjugative elements Profile Hidden Markov Model |
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