Saito Shinichi, Kakeshita Hiroshi, Nakamura Kouji
Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki, Japan.
Gene. 2009 Jan 1;428(1-2):2-8. doi: 10.1016/j.gene.2008.09.024. Epub 2008 Oct 2.
Small, non-coding RNAs (ncRNAs) perform diverse functions in a variety of organisms, but few ncRNAs have been identified in Bacillus subtilis. To search the B. subtilis genome for genes encoding ncRNAs, we focused on 123 intergenic regions (IGRs) over 500 bp in length and analyzed expression from these regions. Seven IGRs termed bsrC, bsrD, bsrE, bsrF, bsrG, bsrH and bsrI expressed RNAs smaller than 380 nt. All small RNAs except BsrD RNA were expressed in transformed Escherichia coli cells harboring a plasmid with PCR-amplified IGRs of B. subtilis, indicating that their own promoters independently express small RNAs. Under the non-stressed condition, depletion of the genes for the small RNAs did not affect growth. Although their functions are unknown, gene expression profiles at several time points showed that most of the genes except for bsrD were expressed during the vegetative phase (4-6 h), but undetectable during the stationary phase (8 h). Mapping the 5' ends of the 6 small RNAs revealed that the genes for BsrE, BsrF, BsrG, BsrH, and BsrI RNAs are preceded by a recognition site for RNA polymerase sigma factor sigma(A). These small RNAs might lack an SD sequence and exert their actions as ncRNAs.
小的非编码RNA（ncRNAs）在多种生物体中发挥着多样的功能，但在枯草芽孢杆菌中鉴定出的ncRNAs却很少。为了在枯草芽孢杆菌基因组中搜索编码ncRNAs的基因，我们聚焦于123个长度超过500 bp的基因间隔区（IGRs），并分析了这些区域的表达情况。7个IGRs，分别命名为bsrC、bsrD、bsrE、bsrF、bsrG、bsrH和bsrI，表达小于380 nt的RNA。除BsrD RNA外，所有小RNA在携带枯草芽孢杆菌PCR扩增IGRs质粒的转化大肠杆菌细胞中均有表达，这表明它们自身的启动子可独立表达小RNA。在非应激条件下，小RNA基因的缺失不影响生长。尽管它们的功能尚不清楚，但在几个时间点的基因表达谱显示，除bsrD外，大多数基因在营养期（4 - 6小时）表达，但在稳定期（8小时）检测不到。对6个小RNA的5'端进行定位发现，BsrE、BsrF、BsrG、BsrH和BsrI RNA的基因之前有一个RNA聚合酶σ因子σ(A)的识别位点。这些小RNA可能缺乏SD序列，并作为ncRNAs发挥作用。
