State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China.
BMC Genomics. 2011 Aug 31;12:438. doi: 10.1186/1471-2164-12-438.
Our previously published reports have described an effective biocontrol agent named Pseudomonas sp. M18 as its 16S rDNA sequence and several regulator genes share homologous sequences with those of P. aeruginosa, but there are several unusual phenotypic features. This study aims to explore its strain specific genomic features and gene expression patterns at different temperatures.
The complete M18 genome is composed of a single chromosome of 6,327,754 base pairs containing 5684 open reading frames. Seven genomic islands, including two novel prophages and five specific non-phage islands were identified besides the conserved P. aeruginosa core genome. Each prophage contains a putative chitinase coding gene, and the prophage II contains a capB gene encoding a putative cold stress protein. The non-phage genomic islands contain genes responsible for pyoluteorin biosynthesis, environmental substance degradation and type I and III restriction-modification systems. Compared with other P. aeruginosa strains, the fewest number (3) of insertion sequences and the most number (3) of clustered regularly interspaced short palindromic repeats in M18 genome may contribute to the relative genome stability. Although the M18 genome is most closely related to that of P. aeruginosa strain LESB58, the strain M18 is more susceptible to several antimicrobial agents and easier to be erased in a mouse acute lung infection model than the strain LESB58. The whole M18 transcriptomic analysis indicated that 10.6% of the expressed genes are temperature-dependent, with 22 genes up-regulated at 28°C in three non-phage genomic islands and one prophage but none at 37°C.
The P. aeruginosa strain M18 has evolved its specific genomic structures and temperature dependent expression patterns to meet the requirement of its fitness and competitiveness under selective pressures imposed on the strain in rhizosphere niche.
我们之前的报告描述了一种有效的生物防治剂，命名为 Pseudomonas sp. M18，其 16S rDNA 序列和几个调节基因与铜绿假单胞菌的同源序列，但存在一些不寻常的表型特征。本研究旨在探索其菌株在不同温度下的特定基因组特征和基因表达模式。
M18 全基因组由一个 6327754 碱基对的单染色体组成，包含 5684 个开放阅读框。除了保守的铜绿假单胞菌核心基因组外，还鉴定了 7 个基因组岛，包括两个新的噬菌体和五个特定的非噬菌体岛。每个噬菌体都包含一个假定的几丁质酶编码基因，而噬菌体 II 包含一个编码假定冷应激蛋白的 capB 基因。非噬菌体基因组岛包含负责吡咯霉素生物合成、环境物质降解以及 I 型和 III 型限制修饰系统的基因。与其他铜绿假单胞菌菌株相比，M18 基因组中的插入序列最少（3 个），而串联重复短回文序列（CRISPRs）最多（3 个），这可能有助于其相对基因组的稳定性。尽管 M18 基因组与铜绿假单胞菌菌株 LESB58 最为密切相关，但与 LESB58 相比，M18 菌株对几种抗菌药物更敏感，在小鼠急性肺感染模型中更容易被清除。整个 M18 转录组分析表明，10.6%的表达基因是温度依赖的，在三个非噬菌体基因组岛和一个噬菌体中有 22 个基因在 28°C 时上调，但在 37°C 时没有基因上调。
铜绿假单胞菌 M18 株已进化出其特定的基因组结构和温度依赖性表达模式，以满足其在根际生态位选择性压力下适应和竞争力的要求。
