Department of Cell and Molecular Biology, Uppsala University, Uppsala S-75124, Sweden.
Department of Molecular Biology, Biomedical Center, Swedish University of Agricultural Sciences, Uppsala S-75124, Sweden.
Genome Res. 2021 Mar;31(3):436-447. doi: 10.1101/gr.272856.120. Epub 2021 Jan 21.
Aggregative multicellularity has evolved multiple times in diverse groups of eukaryotes, exemplified by the well-studied development of dictyostelid social amoebas, for example, However, it is still poorly understood why multicellularity emerged in these amoebas while the majority of other members of Amoebozoa are unicellular. Previously, a novel type of noncoding RNA, Class I RNAs, was identified in and shown to be important for normal multicellular development. Here, we investigated Class I RNA evolution and its connection to multicellular development. We identified a large number of new Class I RNA genes by constructing a covariance model combined with a scoring system based on conserved upstream sequences. Multiple genes were predicted in representatives of each major group of Dictyostelia and expression analysis confirmed that our search approach identifies expressed Class I RNA genes with high accuracy and sensitivity and that the RNAs are developmentally regulated. Further studies showed that Class I RNAs are ubiquitous in Dictyostelia and share highly conserved structure and sequence motifs. In addition, Class I RNA genes appear to be unique to dictyostelid social amoebas because they could not be identified in outgroup genomes, including their closest known relatives. Our results show that Class I RNA is an ancient class of ncRNAs, likely to have been present in the last common ancestor of Dictyostelia dating back at least 600 million years. Based on previous functional analyses and the presented evolutionary investigation, we hypothesize that Class I RNAs were involved in evolution of multicellularity in Dictyostelia.
聚集性多细胞化在不同的真核生物群体中多次进化，例如研究充分的盘基网柄菌社会性阿米巴的发育，然而，为什么多细胞化出现在这些阿米巴中，而阿米巴动物门的大多数其他成员是单细胞，这仍然知之甚少。以前，在 中发现了一种新型非编码 RNA，即 I 类 RNA，并证明其对正常的多细胞发育很重要。在这里，我们研究了 I 类 RNA 的进化及其与多细胞发育的关系。我们通过构建基于保守上游序列的评分系统的协方差模型，鉴定了大量新的 I 类 RNA 基因。在盘基网柄菌的每个主要群体的代表中预测了多个基因，表达分析证实了我们的搜索方法能够以高精度和高灵敏度识别表达的 I 类 RNA 基因，并且这些 RNA 是发育调节的。进一步的研究表明，I 类 RNA 在盘基网柄菌中是普遍存在的，它们具有高度保守的结构和序列基序。此外，I 类 RNA 基因似乎是盘基网柄菌社会性阿米巴所特有的，因为在包括其最接近的已知亲缘关系的外群基因组中无法识别它们。我们的结果表明，I 类 RNA 是一类古老的 ncRNAs，可能存在于至少 6 亿年前的盘基网柄菌最后共同祖先中。基于以前的功能分析和提出的进化研究，我们假设 I 类 RNA 参与了盘基网柄菌多细胞化的进化。
