Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1
Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1
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DOI：
10.1128/jb.00684-07
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发表时间：
2007-10-01
影响因子：
3.2
通讯作者：
Nojiri, Hideaki
中科院分区：
文献类型：
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作者：
Miyakoshi, Masatoshi;Shintani, Masaki;Nojiri, Hideaki
树脂假单胞菌CA10的IncP-7质粒pCAR1在转移到恶臭假单胞菌KT2440中时具有降解咔唑的能力。我们设计了一种定制的全基因组寡核苷酸芯片来研究pCAR1与染色体在转接菌株KT2440(PCAR1)中的协调表达。首先，比较了KT2440(PCAR1)在咔唑为唯一碳源和以琥珀酸为唯一碳源生长过程中的转录组。诱导了咔唑分解代谢CAR和蚂蚁操纵子，以及与β-酮基己二酸途径的儿茶酚分支有关的染色体CAT和豌豆基因。此外，编码针对CAR和ANT操纵子的AraC/XylS家族转录激活因子的调控基因AntR也上调了。对AntR启动子的鉴定表明，AntR是从RpoN依赖的启动子转录而来的，这表明咔唑分解代谢操纵子的成功表达取决于染色体是否含有特定的RpoN依赖的激活子。接下来，为了分析水平转移是否改变了宿主染色体的转录网络，我们比较了KT2440(PCAR1)和KT2440在相同生长条件下的染色体转录本。PCAR1的转移只引起了微小的变化，除了显著诱导了假想基因PP3700，命名为parI，它编码了一个N-末端具有XRE-型DNA结合基序的类类ATPase。进一步的转录分析表明，PARI启动子受PARI本身和pCAR1编码蛋白PARA的正调控。
The IncP-7 plasmid pCAR1 of Pseudomonas resinovorans CA10 confers the ability to degrade carbazole upon transfer to the recipient strain P. putida KT2440. We designed a customized whole-genome oligonucleotide microarray to study the coordinated expression of pCAR1 and the chromosome in the transconjugant strain KT2440(pCAR1). First, the transcriptome of KT2440(pCAR1) during growth with carbazole as the sole carbon source was compared to that during growth with succinate. The carbazole catabolic car and ant operons were induced, along with the chromosomal cat and pea genes involved in the catechol branch of the beta-ketoadipate pathway. Additionally, the regulatory gene antR encoding the AraC/XylS family transcriptional activator specific for car and ant operons was upregulated. The characterization of the antR promoter revealed that antR is transcribed from an RpoN-dependent promoter, suggesting that the successful expression of the carbazole catabolic operons depends on whether the chromosome contains the specific RpoN-dependent activator. Next, to analyze whether the horizontal transfer of a plasmid alters the transcription network of its host chromosome, we compared the chromosomal transcriptomes of KT2440(pCAR1) and KT2440 under the same growth conditions. Only subtle changes were caused by the transfer of pCAR1, except for the significant induction of the hypothetical gene PP3700, designated parI, which encodes a putative ParA-like ATPase with an N-terminal Xre-type DNA-binding motif. Further transcriptional analyses showed that the parI promoter was positively regulated by ParI itself and the pCAR1-encoded protein ParA.