Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
BMC Genomics. 2009 Nov 16;10:528. doi: 10.1186/1471-2164-10-528.
U3 snoRNA is a box C/D small nucleolar RNA (snoRNA) involved in the processing events that liberate 18S rRNA from the ribosomal RNA precursor (pre-rRNA). Although U3 snoRNA is present in all eukaryotic organisms, most investigations of it have focused on fungi (particularly yeasts), animals and plants. Relatively little is known about U3 snoRNA and its gene(s) in the phylogenetically broad assemblage of protists (mostly unicellular eukaryotes). In the euglenozoon Euglena gracilis, a distant relative of the kinetoplastid protozoa, Southern analysis had previously revealed at least 13 bands hybridizing with U3 snoRNA, suggesting the existence of multiple copies of U3 snoRNA genes.
Through screening of a lambda genomic library and PCR amplification, we recovered 14 U3 snoRNA gene variants, defined by sequence heterogeneities that are mostly located in the U3 3'-stem-loop domain. We identified three different genomic arrangements of Euglena U3 snoRNA genes: i) stand-alone, ii) linked to tRNAArg genes, and iii) linked to a U5 snRNA gene. In arrangement ii), the U3 snoRNA gene is positioned upstream of two identical tRNAArg genes that are convergently transcribed relative to the U3 gene. This scenario is reminiscent of a U3 snoRNA-tRNA gene linkage previously described in trypanosomatids. We document here twelve different U3 snoRNA-U5 snRNA gene arrangements in Euglena; in each case, the U3 gene is linked to a downstream and convergently oriented U5 gene, with the intergenic region differing in length and sequence among the variants.
The multiple U3 snoRNA-U5 snRNA gene linkages, which cluster into distinct families based on sequence similarities within the intergenic spacer, presumably arose by genome, chromosome, and/or locus duplications. We discuss possible reasons for the existence of the unusually large number of U3 snoRNA genes in the Euglena genome. Variability in the signal intensities of the multiple Southern hybridization bands raises the possibility that Euglena contains a naturally aneuploid chromosome complement.
U3 snoRNA 是一种 box C/D 小核仁 RNA（snoRNA），参与从核糖体 RNA 前体（pre-rRNA）中释放 18S rRNA 的加工事件。尽管 U3 snoRNA 存在于所有真核生物中，但对其的大多数研究都集中在真菌（特别是酵母）、动物和植物上。相对而言，人们对在原生生物（主要是单细胞真核生物）这一广泛的系统发育集合体中的 U3 snoRNA 及其基因知之甚少。在 Euglenozoon Euglena gracilis 中，动基体原生动物的远亲，Southern 分析先前显示至少有 13 个与 U3 snoRNA 杂交的条带，表明存在多个 U3 snoRNA 基因的拷贝。
通过筛选 lambda 基因组文库和 PCR 扩增，我们回收了 14 种 U3 snoRNA 基因变体，这些变体的序列异质性主要位于 U3 3'-茎环结构域。我们确定了 Euglena U3 snoRNA 基因的三种不同基因组排列：i）独立，ii）与 tRNAArg 基因相连，和 iii）与 U5 snRNA 基因相连。在排列 ii）中，U3 snoRNA 基因位于两个相同的 tRNAArg 基因的上游，相对于 U3 基因，这两个 tRNAArg 基因是趋同转录的。这种情况让人联想到先前在动基体原生动物中描述的 U3 snoRNA-tRNA 基因连接。我们在这里记录了 Euglena 中 12 种不同的 U3 snoRNA-U5 snRNA 基因排列；在每种情况下，U3 基因与下游和趋同取向的 U5 基因相连，基因间区域在变体之间的长度和序列上存在差异。
基于基因间间隔区的序列相似性，多个 U3 snoRNA-U5 snRNA 基因连接簇形成了不同的家族，推测是通过基因组、染色体和/或基因座的复制而产生的。我们讨论了 Euglena 基因组中存在大量 U3 snoRNA 基因的可能原因。多个 Southern 杂交带信号强度的可变性提出了 Euglena 可能含有自然非整倍体染色体组成的可能性。
