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

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.