Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds
Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds
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DOI：
10.1111/1462-2920.12498
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发表时间：
2015-01-01
影响因子：
5.1
通讯作者：
van der Meer, Jan Roelof
中科院分区：
文献类型：
--
作者：
Miyazaki, Ryo;Bertelli, Claire;van der Meer, Jan Roelof
假单胞菌knackmussiiB13是1974年分离到的第一株能降解氯代芳烃的菌株。这一发现是随后表征许多细菌代谢途径的序幕，用于遗传和生物化学研究，并激发了污染物生物修复的想法。在这项研究中，我们确定了完整的基因组序列的B13使用下一代测序技术和光学定位。基因组注释表明B13具有多种降解单芳烃的代谢途径，包括氯苯甲酸、氨基酚、邻氨基苯甲酸和羟基喹啉，但不降解多环芳烃化合物。比较基因组分析表明，B13最接近于铜绿假单胞菌和铜绿假单胞菌。B13基因组包含至少8个基因组岛[原噬菌体和整合接合元件（ICE）]，这在密切相关的假单胞菌中不存在。我们确认，两个ICE是相同的副本的103kb的自我传递元件ICEclc进行氯儿茶酚代谢的基因。ICEclc基因由一个可变区和一个核心区组成，在变形菌基因组中非常保守，表明它是一个广泛分布的ICE家族。两个自发B13突变体的重测序揭示了一些单核苷酸取代，以及切除一个大的220kb区域和一个前噬菌体，大大改变了宿主的代谢能力和生存能力。
Pseudomonas knackmussiiB13 was the first strain to be isolated in 1974 that could degrade chlorinated aromatic hydrocarbons. This discovery was the prologue for subsequent characterization of numerous bacterial metabolic pathways, for genetic and biochemical studies, and which spurred ideas for pollutant bioremediation. In this study, we determined the complete genome sequence of B13 using next generation sequencing technologies and optical mapping. Genome annotation indicated that B13 has a variety of metabolic pathways for degrading monoaromatic hydrocarbons including chlorobenzoate, aminophenol, anthranilate and hydroxyquinol, but not polyaromatic compounds. Comparative genome analysis revealed that B13 is closest to Pseudomonas denitrificans and Pseudomonas aeruginosa. The B13 genome contains at least eight genomic islands [prophages and integrative conjugative elements (ICEs)], which were absent in closely related pseudomonads. We confirm that two ICEs are identical copies of the 103kb self-transmissible element ICEclc that carries the genes for chlorocatechol metabolism. Comparison of ICEclc showed that it is composed of a variable and a core' region, which is very conserved among proteobacterial genomes, suggesting a widely distributed family of so far uncharacterized ICE. Resequencing of two spontaneous B13 mutants revealed a number of single nucleotide substitutions, as well as excision of a large 220kb region and a prophage that drastically change the host metabolic capacity and survivability.