哺乳动物细胞中蛋白质编码RNA到RNA的信息传递:RNA依赖性mRNA扩增。嵌合RNA中间体和假定RNA终产物的鉴定。
Protein-Encoding RNA to RNA Information Transfer in Mammalian Cells: RNA-dependent mRNA Amplification. Identification of Chimeric RNA Intermediates and Putative RNA End Products.
作者信息
Rits Sophia, Olsen Bjorn R, Volloch Vladimir
机构信息
Division of Molecular Medicine, Children's Hospital, Boston, USA.
Deptartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, USA.
出版信息
Ann Integr Mol Med. 2019;1(1):23-47. Epub 2019 Aug 22.
Our initial unidirectional understanding of the flow of protein-encoding genetic information, DNA to RNA to protein, a process defined as the "Central Dogma of Molecular Biology" and usually depicted as a downward arrow, was eventually amended to account for the "vertical" information back-flow from RNA to DNA, reverse transcription, and for its "horizontal" side-flow from RNA to RNA, RNA-dependent RNA synthesis, RdRs. These processes, both potentially leading to protein production, were assumed to be strictly virus-specific. However, whereas this presumption might be true for the former, it became apparent that the cellular enzymatic machinery for the later, a conventional RNA-dependent RNA polymerase activity, RdRp, is ubiquitously present and RdRs regularly occurs in eukaryotes. The strongest evidence for the occurrence and functionality of RdRp activity in mammalian cells comes from viruses, such as hepatitis delta virus, HDV, that do not encode RdRp yet undergo a robust RNA replication once inside the host. Eventually, it became clear that RdRp activity, apparently in a non-conventional form, is constitutively present in most, if not in all, mammalian cells. Because such activity was shown to produce short transcripts, because of its apparent involvement in RNA interference phenomena, and because double-stranded RNA is known to trigger cellular responses leading to its degradation, it was generally assumed that its role in mammalian cells is restricted to a regulatory function. However, at the same time, an enzymatic activity capable of generating complete antisense RNA complements of mRNAs was discovered in mammalian cells undergoing terminal differentiation. Moreover, observations of widespread synthesis of antisense RNA initiating at the 3'poly(A) of mRNAs in human cells suggested an extensive cellular utilization of mammalian RdRp. These results led to the development of a model of RdRp-facilitated and antisense RNA-mediated amplification of mammalian mRNA. Here, we report the detection in cells undergoing terminal erythroid differentiation of the major model-predicted identifiers of such a process, a chimeric double-stranded/pinhead-structured intermediates containing both sense and antisense RNA strands covalently joined in a rigorously predicted and uniquely defined manner. We also report the identification of the putative chimeric RNA end product of mRNA amplification. It is heavily modified, uniformly truncated, yet retains the intact coding region, and terminates with the OH group at both ends; its massive cellular amount is unprecedented for a conventional mRNA transcription product and it translates into polypeptides indistinguishable from the translation product of conventional mRNA. Moreover, we describe the occurrence of the second Tier of mammalian RNA-dependent mRNA amplification, a physiologically occurring, RdRp-driven intracellular PCR process, "iPCR", and report the detection of its distinct RNA end products. Whether mammalian mRNA amplification is a specialized occurrence limited to extreme circumstances of terminal differentiation in cells programmed for only a short survival span or a general physiological phenomenon was answered in the companion article Volloch et al. Ann Integr Mol Med. 2019;1(1):1004. by the detection of major identifiers of this process for mRNA encoding α1, β1, and γ1 chains of laminin, a major extracellular matrix protein abundantly produced throughout the tissue and organ development and homeostasis and an exceptionally revealing indicator of the range and scope of this phenomenon. The results obtained introduce the occurrence of RNA-dependent mRNA amplification as a new mode of genomic protein-encoding information transfer in mammalian cells and establish it as a general physiological phenomenon.
我们最初对蛋白质编码遗传信息流动的单向理解,即从DNA到RNA再到蛋白质,这一过程被定义为“分子生物学的中心法则”,通常被描绘为一个向下的箭头,最终被修正以解释从RNA到DNA的“垂直”信息回流,即逆转录,以及从RNA到RNA的“水平”侧流,即RNA依赖性RNA合成(RdRs)。这些过程都有可能导致蛋白质产生,曾被认为是严格病毒特异性的。然而,虽然前一种情况可能确实如此,但后来发现,用于后一种情况的细胞酶机制,即一种传统的RNA依赖性RNA聚合酶活性(RdRp),普遍存在,并且RdRs在真核生物中经常发生。哺乳动物细胞中RdRp活性存在及功能的最有力证据来自病毒,如丁型肝炎病毒(HDV),它不编码RdRp,但一旦进入宿主细胞就能进行强大的RNA复制。最终,很明显RdRp活性,显然以一种非传统形式,在大多数(如果不是所有)哺乳动物细胞中持续存在。由于这种活性被证明能产生短转录本,因其明显参与RNA干扰现象,且已知双链RNA会引发导致其降解的细胞反应,所以一般认为它在哺乳动物细胞中的作用仅限于调节功能。然而,与此同时,在经历终末分化的哺乳动物细胞中发现了一种能够产生mRNA完整反义RNA互补物的酶活性。此外,在人类细胞中观察到从mRNA的3'聚腺苷酸起始广泛合成反义RNA,这表明哺乳动物RdRp在细胞中有广泛利用。这些结果促成了一个RdRp促进和反义RNA介导的哺乳动物mRNA扩增模型的发展。在此,我们报告在经历终末红细胞分化的细胞中检测到该过程主要模型预测的标志物,即一种嵌合双链/针头状结构中间体,其包含以严格预测和独特定义方式共价连接的有义链和反义链RNA。我们还报告了mRNA扩增假定嵌合RNA终产物的鉴定。它经过大量修饰,均匀截短,但保留完整编码区,两端均以羟基终止;其在细胞中的大量存在对于传统mRNA转录产物来说是前所未有的,并且它能翻译成与传统mRNA翻译产物无法区分的多肽。此外,我们描述了哺乳动物RNA依赖性mRNA扩增的第二层情况的发生,即一种生理上发生的、RdRp驱动的细胞内PCR过程,“iPCR”,并报告了其独特RNA终产物的检测。哺乳动物mRNA扩增是仅限于仅编程短暂存活期的细胞终末分化极端情况的特殊现象,还是一般生理现象,在配套文章Volloch等人的《Ann Integr Mol Med. 2019;1(1):1004》中通过检测层粘连蛋白α1、β1和γ1链mRNA编码该过程的主要标志物得到了回答,层粘连蛋白是一种在整个组织和器官发育及稳态过程中大量产生的主要细胞外基质蛋白,是该现象范围和规模的一个特别有揭示性的指标。所获得的结果引入了RNA依赖性mRNA扩增作为哺乳动物细胞中基因组蛋白质编码信息传递的一种新模式,并将其确立为一种一般生理现象。