Institute for Biology (Genetics), Humboldt-University Berlin, D-10115 Berlin, Germany.
Plant Cell. 2012 Jan;24(1):123-36. doi: 10.1105/tpc.111.089441. Epub 2012 Jan 20.
Gene expression in plastids of higher plants is dependent on two different transcription machineries, a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. The division of labor between PEP and NEP during plastid development and in mature chloroplasts is unclear due to a lack of comprehensive information on promoter usage. Here, we present a thorough investigation into the distribution of PEP and NEP promoters within the plastid genome of barley (Hordeum vulgare). Using a novel differential RNA sequencing approach, which discriminates between primary and processed transcripts, we obtained a genome-wide map of transcription start sites in plastids of mature first leaves. PEP-lacking plastids of the albostrians mutant allowed for the unambiguous identification of NEP promoters. We observed that the chloroplast genome contains many more promoters than genes. According to our data, most genes (including genes coding for photosynthesis proteins) have both PEP and NEP promoters. We also detected numerous transcription start sites within operons, indicating transcriptional uncoupling of genes in polycistronic gene clusters. Moreover, we mapped many transcription start sites in intergenic regions and opposite to annotated genes, demonstrating the existence of numerous noncoding RNA candidates.
高等植物质体中的基因表达依赖于两种不同的转录机制，一种是质体编码的细菌型 RNA 聚合酶（PEP），另一种是核编码的噬菌体型 RNA 聚合酶（NEP），它们识别不同类型的启动子。由于缺乏关于启动子使用的综合信息，因此在质体发育和成熟叶绿体中 PEP 和 NEP 之间的分工尚不清楚。在这里，我们对大麦（Hordeum vulgare）质体基因组中 PEP 和 NEP 启动子的分布进行了全面研究。我们使用一种新颖的差异 RNA 测序方法，该方法可区分初级转录物和加工转录物，从而获得了成熟第一片叶子质体中转录起始位点的全基因组图谱。白化突变体中缺乏 PEP 的质体允许明确识别 NEP 启动子。我们观察到叶绿体基因组包含的启动子比基因多得多。根据我们的数据，大多数基因（包括编码光合作用蛋白的基因）都有 PEP 和 NEP 启动子。我们还在操纵子内和注释基因的反义检测到许多转录起始位点，表明多顺反子基因簇中的基因转录解偶联。此外，我们还在基因间区和对应于注释基因的位置映射了许多转录起始位点，表明存在许多非编码 RNA 候选物。
