Department of Biochemistry and Molecular Biology, Dalhousie University, Nova Scotia, Canada.
Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden.
Genome Biol Evol. 2019 Apr 1;11(4):1117-1134. doi: 10.1093/gbe/evz064.
The regulation of gene expression and RNA maturation underlies fundamental processes such as cell homeostasis, development, and stress acclimation. The biogenesis and modification of RNA is tightly controlled by an array of regulatory RNAs and nucleic acid-binding proteins. While the role of small RNAs (sRNAs) in gene expression has been studied in-depth in select model organisms, little is known about sRNA biology across the eukaryotic tree of life. We used deep sequencing to explore the repertoires of sRNAs encoded by the miniaturized, endosymbiotically derived "nucleomorph" genomes of two single-celled algae, the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. A total of 32.3 and 35.3 million reads were generated from G. theta and B. natans, respectively. In G. theta, we identified nucleomorph U1, U2, and U4 spliceosomal small nuclear RNAs (snRNAs) as well as 11 C/D box small nucleolar RNAs (snoRNAs), five of which have potential plant and animal homologs. The snoRNAs are predicted to perform 2'-O methylation of rRNA (but not snRNA). In B. natans, we found the previously undetected 5S rRNA as well as six orphan sRNAs. Analysis of chlorarachniophyte snRNAs shed light on the removal of the miniature 18-21 nt introns found in B. natans nucleomorph genes. Neither of the nucleomorph genomes appears to encode RNA pseudouridylation machinery, and U5 snRNA cannot be found in the cryptophyte G. theta. Considering the central roles of U5 snRNA and RNA modifications in other organisms, cytoplasm-to-nucleomorph RNA shuttling in cryptophyte algae is a distinct possibility.
基因表达和 RNA 成熟的调控是细胞内稳态、发育和应激适应等基本过程的基础。RNA 的生物发生和修饰受到一系列调节 RNA 和核酸结合蛋白的严格控制。虽然在一些模式生物中已经深入研究了小分子 RNA（sRNA）在基因表达中的作用，但对于真核生物树中的 sRNA 生物学知之甚少。我们使用深度测序来探索两种单细胞藻类——隐藻 Guillardia theta 和绿藻 Bigelowiella natans 的小型内共生衍生“核质体”基因组编码的 sRNA 谱。分别从 G. theta 和 B. natans 生成了 3230 万和 3530 万个读数。在 G. theta 中，我们鉴定了核质体 U1、U2 和 U4 剪接体小核 RNA（snRNA）以及 11 个 C/D 盒小核仁 RNA（snoRNA），其中 5 个具有潜在的植物和动物同源物。这些 snoRNA 被预测能够对 rRNA（而不是 snRNA）进行 2'-O 甲基化。在 B. natans 中，我们发现了以前未检测到的 5S rRNA 以及六个孤儿 sRNA。对绿藻 snoRNA 的分析揭示了在 B. natans 核质体基因中发现的小型 18-21nt 内含子的去除。这两个核质体基因组似乎都不编码 RNA 假尿嘧啶化机制，并且在隐藻 G. theta 中找不到 U5 snRNA。考虑到 U5 snRNA 和 RNA 修饰在其他生物中的核心作用，隐藻藻类中的细胞质到核质体 RNA 穿梭是一种可能性。
