Comparative microarray analysis reveals that the core biofilm-associated transcriptome of Pseudomonas aeruginosa comprises relatively few genes.
Comparative microarray analysis reveals that the core biofilm-associated transcriptome of Pseudomonas aeruginosa comprises relatively few genes.
复制标题
DOI：
10.1111/j.1758-2229.2010.00158.x
复制
发表时间：
2010-06
影响因子：
3.3
通讯作者：
Sanaya Patell;M. Gu;P. Davenport;M. Givskov;Richard D. Waite;M. Welch
中科院分区：
文献类型：
--
作者：
Sanaya Patell;M. Gu;P. Davenport;M. Givskov;Richard D. Waite;M. Welch
铜绿假单胞菌是研究细胞间通讯和生物膜形成的模式生物。因此，铜绿假单胞菌已经成为几种微阵列分析的对象，比较了生物膜和浮游生物培养中的基因表达。在目前的工作中，我们对这些数据集进行了荟萃分析，试图识别在所有检查的条件下与生物膜形成一般相关的基因。尽管在个别研究中，生物膜中调节的转录本的总数很大，但数据集之间的重叠很小。事实上，在分析的三个数据集中，只有五个转录上调，六个转录下调了两倍以上。然而，当阈值调制放宽到不到两倍时，数据集之间的重叠增加，揭示了所有研究的一组共同的转录本。转录融合和定量实时聚合酶链式反应被用来独立地确认所观察到的调控的选择。值得注意的是，我们发现编码支链和芳香族氨基酸分解代谢途径的基因在生物膜中的表达谱发生了变化，并且这些变化与厌氧生长的开始相关。培养上清液的氨基酸定量分析证实了这一发现。在附着试验中，我们鉴定的其中一个基因的突变体显示生物膜形成减少。相对较少的常见生物膜特异终点转录本让人怀疑生物膜的形成是通过预先确定的发育途径进行的。
Pseudomonas aeruginosa is a model organism for the study of intercellular communication and biofilm formation. As such, P. aeruginosa has been the subject of several microarray analyses comparing gene expression in biofilms and planktonic cultures. In the current work, we carried out a meta-analysis of these data sets to try and identify genes that are generically associated with biofilm formation in all of the conditions examined. Although the total number of transcripts modulated in the biofilms was large within the individual studies, the overlap between the data sets was small. Indeed, only five transcripts were upregulated and six transcripts were downregulated by more than twofold in the three data sets analysed. However, when the threshold modulation was relaxed to less than twofold, the overlap between the data sets increased, revealing a set of transcripts common to all of the studies. Transcriptional fusions and quantitative real-time PCR were used to independently confirm a selection of the observed modulations. Notably, we found that the expression profile of genes encoding the catabolic pathways for branched chain and aromatic amino acids was altered in biofilms, and that these alterations correlated with the onset of anaerobic growth. These findings were confirmed by quantitative amino acid analysis of culture supernatants. A mutant in one of the genes that we identified showed diminished biofilm formation in an attachment assay. The relatively small number of common biofilm-specific endpoint transcripts throws doubt on the suggestion that biofim formation proceeds through a pre-determined developmental pathway.