Comprehensive Transcriptome Analysis of the Periodontopathogenic Bacterium Porphyromonas gingivalis W83
Comprehensive Transcriptome Analysis of the Periodontopathogenic Bacterium Porphyromonas gingivalis W83
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DOI：
10.1128/jb.06385-11
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发表时间：
2012-01-01
影响因子：
3.2
通讯作者：
Chen, Tsute
中科院分区：
文献类型：
--
作者：
Hovik, Hedda;Yu, Wen-Han;Chen, Tsute
采用高密度贴片芯片技术和RNA测序技术对牙周病病原菌牙龈卟啉单胞菌的转录组进行分析。编译的牙龈卟啉卟啉转录组图谱基于三种不同实验室培养条件下分离的总RNA样本，生成的链特异性转录图谱覆盖整个基因组，包括蛋白质编码区和非编码区。转录谱揭示了不同的操纵子结构，5‘端和3’端非翻译区（utr），差异表达模式，以及在基因间和反义区域内许多新的，尚未注释的转录本。进一步的转录组分析发现，大多数基因在操纵子内表达，大多数5‘和3’端是突出的utr，其中几个3' utr延伸到相反/反义链上携带的重叠基因。在大多数插入序列（IS）元件的反面检测到广泛的反义rna。对三种培养条件下的转录组谱进行两两比较分析，鉴定出差异表达的基因和代谢途径。随着人们越来越认识到非编码rna发挥重要的生物学功能，本研究发现的新rna和编制的全面转录组谱可能为进一步了解牙龈假单胞菌的基因调控和毒力机制提供基础。转录组档案可以在微生物转录组数据库网站http://bioinformatics.forsyth.org/mtd上查看和下载。
High-density tiling microarray and RNA sequencing technologies were used to analyze the transcriptome of the periodontopathogenic bacterium Porphyromonas gingivalis. The compiled P. gingivalis transcriptome profiles were based on total RNA samples isolated from three different laboratory culturing conditions, and the strand-specific transcription profiles generated covered the entire genome, including both protein coding and noncoding regions. The transcription profiles revealed various operon structures, 5'- and 3'-end untranslated regions (UTRs), differential expression patterns, and many novel, not-yet-annotated transcripts within intergenic and antisense regions. Further transcriptome analysis identified the majority of the genes as being expressed within operons and most 5' and 3' ends to be protruding UTRs, of which several 3' UTRs were extended to overlap genes carried on the opposite/antisense strand. Extensive antisense RNAs were detected opposite most insertion sequence (IS) elements. Pairwise comparative analyses were also performed among transcriptome profiles of the three culture conditions, and differentially expressed genes and metabolic pathways were identified. With the growing realization that noncoding RNAs play important biological functions, the discovery of novel RNAs and the comprehensive transcriptome profiles compiled in this study may provide a foundation to further understand the gene regulation and virulence mechanisms in P. gingivalis. The transcriptome profiles can be viewed at and downloaded from the Microbial Transcriptome Database website, http://bioinformatics.forsyth.org/mtd.