Presentation Information
[P03-406]Integrative and Conjugative Elements (ICEs) from Stutzerimonas and Their Ubiquitous Distribution and Potential Application to Bioremediation
○JUN HIROSE1, Ayako Okumura1, Hiroto Fujinami1 (1. Faculty of Engineering, University of Miyazaki (Japan))
Keywords:
bioremediation,BTEX,evolution,integrative and conjugative elements,Stutzerimonas
[Objective] The environmental bacterium Stutzerimonas was recently proposed as a new genus within the Pseudomonadaceae family and was reclassified from the former systematic group of the genus Pseudomonas. The genome of Stutzerimonas contains numerous mobile genetic elements that enable horizontal gene transfer, and the acquisition of these elements is recognized as a source of environmental adaptation. This study focused on the integrative and conjugative elements (ICEs) carried by bacterial strains belonging to the genus Stutzerimonas and conducted screening and comparative analysis using genome databases.
[Methods] Partial sequences containing "marker genes" characteristic of ICEs, such as integrases, Type IV secretion system (T4SS), and relaxases, were searched for in the genome sequences of Stutzerimonas registered in public databases. Genes homologous to known Stutzerimonas-derived ICE integrases, T4SS, and relaxases were searched using BLASTp, where genes with an E-value of 10-5 were considered to have significant homology. Localized regions within 150 kb in which all three genes were detected were considered candidate ICEs. Furthermore, the boundary regions of the ICEs were identified by 18–20-bp direct repeat sequences.
[Results] We identified and analyzed ICEs from 21 strains using genome sequences available in public databases. The majority belonged to the same ICE group and contained highly conserved core regions essential for conjugative transfer to other bacteria. However, these ICEs originated from bacteria isolated in different countries, and the non-core regions showed diversity among them. They also contained cargo regions associated with environmental adaptation, such as aromatic compound degradation and heavy metal resistance. Interestingly, the 10 ICEs in this group encoded a highly conserved xylene/toluene or naphthalene meta-cleavage pathway. This pathway was homologous to that of ICEbph-salKF716, which was derived from the known PCB/biphenyl-degrading bacterium S. stutzeri KF716. Although ICEs from this group were also identified in the genomes of strains belonging to the genus Pseudomonas, it was confirmed that most of them are members of Stutzerimonas.
[Discussion] From the Stutzerimonas genomes, we were able to identify ICEs containing aromatic compound degradation genes as cargo genes without screening under selective pressure. Because many of these Stutzerimonas-specific ICEs contain genes involved in the degradation of BTEX found in petroleum as cargo genes, this finding suggests the potential application of ICE-mediated horizontal gene transfer among environmental bacteria for bioremediation.
[Conclusion] Stutzerimonas genomes include a particularly large number of ICEs compared with those of other bacterial species, and the majority are similar and belong to the same family. Thus, we confirmed the presence and characteristics of ICEs that are ubiquitously distributed in Stutzerimonas. These ICEs are suggested to play a significant role in the environmental adaptation and genome evolution of Stutzerimonas.
[Methods] Partial sequences containing "marker genes" characteristic of ICEs, such as integrases, Type IV secretion system (T4SS), and relaxases, were searched for in the genome sequences of Stutzerimonas registered in public databases. Genes homologous to known Stutzerimonas-derived ICE integrases, T4SS, and relaxases were searched using BLASTp, where genes with an E-value of 10-5 were considered to have significant homology. Localized regions within 150 kb in which all three genes were detected were considered candidate ICEs. Furthermore, the boundary regions of the ICEs were identified by 18–20-bp direct repeat sequences.
[Results] We identified and analyzed ICEs from 21 strains using genome sequences available in public databases. The majority belonged to the same ICE group and contained highly conserved core regions essential for conjugative transfer to other bacteria. However, these ICEs originated from bacteria isolated in different countries, and the non-core regions showed diversity among them. They also contained cargo regions associated with environmental adaptation, such as aromatic compound degradation and heavy metal resistance. Interestingly, the 10 ICEs in this group encoded a highly conserved xylene/toluene or naphthalene meta-cleavage pathway. This pathway was homologous to that of ICEbph-salKF716, which was derived from the known PCB/biphenyl-degrading bacterium S. stutzeri KF716. Although ICEs from this group were also identified in the genomes of strains belonging to the genus Pseudomonas, it was confirmed that most of them are members of Stutzerimonas.
[Discussion] From the Stutzerimonas genomes, we were able to identify ICEs containing aromatic compound degradation genes as cargo genes without screening under selective pressure. Because many of these Stutzerimonas-specific ICEs contain genes involved in the degradation of BTEX found in petroleum as cargo genes, this finding suggests the potential application of ICE-mediated horizontal gene transfer among environmental bacteria for bioremediation.
[Conclusion] Stutzerimonas genomes include a particularly large number of ICEs compared with those of other bacterial species, and the majority are similar and belong to the same family. Thus, we confirmed the presence and characteristics of ICEs that are ubiquitously distributed in Stutzerimonas. These ICEs are suggested to play a significant role in the environmental adaptation and genome evolution of Stutzerimonas.
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