High-resolution mapping of plasmid transcriptomes in different host bacteria.
High-resolution mapping of plasmid transcriptomes in different host bacteria.
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DOI：
10.1186/1471-2164-10-12
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发表时间：
2009-01-09
期刊：
影响因子：
4.4
通讯作者：
Nojiri H
中科院分区：
文献类型：
--
作者：
Miyakoshi M;Nishida H;Shintani M;Yamane H;Nojiri H
质粒是自主复制的染色体外元件，并且许多质粒可以通过接合在细菌细胞之间传递。虽然质粒上基因的转录模式可以通过宿主背景的改变而改变，但是将导致表型变异的质粒基因的表达范围尚未被定量研究。使用具有密度为9 bp的均匀平铺探针的微阵列，我们绘制并定量了咔唑分解代谢质粒pCAR 1在其原始宿主食脂假单胞菌CA 10和接合子恶臭假单胞菌KT 2440（pCAR 1）中在咔唑或琥珀酸作为唯一碳源的生长期间的转录物。我们鉴定了pCAR 1中的操纵子，其由几乎相同的转录单位组成，尽管在相同碳源上生长期间宿主背景不同。根据以前的研究，咔唑降解的分解代谢操纵子在两种宿主的咔唑生长过程中上调。然而，我们的平铺阵列的结果也表明，几个操纵子侧翼的转移基因簇转录在显着更高的水平比在原始主机的transconjugant。转录本的数量和转录起始位点的位置与我们的定量RT-PCR和引物延伸结果一致。我们的平铺阵列结果表明，质粒上操纵子的转录水平可以因宿主背景而异。使用无偏平铺阵列的高分辨率映射是用于同时鉴定和定量原核转录组（包括多顺反子操纵子和非编码RNA）的有价值的工具。
Plasmids are extrachromosomal elements that replicate autonomously, and many can be transmitted between bacterial cells through conjugation. Although the transcription pattern of genes on a plasmid can be altered by a change in host background, the expression range of plasmid genes that will result in phenotypic variation has not been quantitatively investigated. Using a microarray with evenly tiled probes at a density of 9 bp, we mapped and quantified the transcripts of the carbazole catabolic plasmid pCAR1 in its original host Pseudomonas resinovorans CA10 and the transconjugant P. putida KT2440(pCAR1) during growth on either carbazole or succinate as the sole carbon source. We identified the operons in pCAR1, which consisted of nearly identical transcription units despite the difference in host background during growth on the same carbon source. In accordance with previous studies, the catabolic operons for carbazole degradation were upregulated during growth on carbazole in both hosts. However, our tiling array results also showed that several operons flanking the transfer gene cluster were transcribed at significantly higher levels in the transconjugant than in the original host. The number of transcripts and the positions of the transcription start sites agreed with our quantitative RT-PCR and primer extension results. Our tiling array results indicate that the levels of transcription for the operons on a plasmid can vary by host background. High-resolution mapping using an unbiased tiling array is a valuable tool for the simultaneous identification and quantification of prokaryotic transcriptomes including polycistronic operons and non-coding RNAs.
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