Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, UK.
School of Life Sciences and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, NT, Hong Kong.
Nucleic Acids Res. 2021 Dec 2;49(21):12486-12501. doi: 10.1093/nar/gkab1095.
G-quadruplexes are non-helical secondary structures that can fold in vivo in both DNA and RNA. In human cells, they can influence replication, transcription and telomere maintenance in DNA, or translation, transcript processing and stability of RNA. We have previously showed that G-quadruplexes are detectable in the DNA of the malaria parasite Plasmodium falciparum, despite a very highly A/T-biased genome with unusually few guanine-rich sequences. Here, we show that RNA G-quadruplexes can also form in P. falciparum RNA, using rG4-seq for transcriptome-wide structure-specific RNA probing. Many of the motifs, detected here via the rG4seeker pipeline, have non-canonical forms and would not be predicted by standard in silico algorithms. However, in vitro biophysical assays verified formation of non-canonical motifs. The G-quadruplexes in the P. falciparum transcriptome are frequently clustered in certain genes and associated with regions encoding low-complexity peptide repeats. They are overrepresented in particular classes of genes, notably those that encode PfEMP1 virulence factors, stress response genes and DNA binding proteins. In vitro translation experiments and in vivo measures of translation efficiency showed that G-quadruplexes can influence the translation of P. falciparum mRNAs. Thus, the G-quadruplex is a novel player in post-transcriptional regulation of gene expression in this major human pathogen.
G-四链体是一种非螺旋的二级结构，可在体内的 DNA 和 RNA 中折叠。在人类细胞中，它们可以影响 DNA 中的复制、转录和端粒维持，或影响 RNA 的翻译、转录加工和稳定性。我们之前已经表明，疟原虫 Plasmodium falciparum 的 DNA 中可以检测到 G-四链体，尽管其基因组 A/T 偏倚非常高，且很少有富含鸟嘌呤的序列。在这里，我们使用 rG4-seq 进行全转录组结构特异性 RNA 探测，表明 P. falciparum RNA 中也可以形成 RNA G-四链体。通过 rG4seeker 管道检测到的许多基序具有非典型形式，无法通过标准的计算算法预测。然而，体外生物物理测定验证了非典型基序的形成。疟原虫转录组中的 G-四链体经常在某些基因中聚集，并与编码低复杂度肽重复的区域相关。它们在特定的基因类别中过表达，特别是编码 PfEMP1 毒力因子、应激反应基因和 DNA 结合蛋白的基因。体外翻译实验和体内翻译效率测量表明，G-四链体可以影响疟原虫 mRNA 的翻译。因此，G-四链体是这种主要人类病原体中基因表达转录后调控的新参与者。
