Bridging the gap between in vitro and in vivo RNA folding.
Bridging the gap between in vitro and in vivo RNA folding.
复制标题
弥合体外和体内RNA折叠之间的间隙。
DOI：
10.1017/s003358351600007x
复制
发表时间：
2016-01
影响因子：
6.1
通讯作者：
Bevilacqua PC
中科院分区：
文献类型：
--
作者：
Leamy KA;Assmann SM;Mathews DH;Bevilacqua PC
破译折叠途径和预测复杂的三维生物分子的结构是阐明生物功能的核心。RNA是单链的，这使它能够自由折叠成复杂的二级和三级结构。这些结构赋予RNA执行从酶活性到基因调控的复杂化学和功能的能力。鉴于RNA参与许多重要的细胞过程，了解它在体内如何折叠和发挥作用至关重要。在过去的几年中，已经开发了在体内和全基因组范围内探测RNA结构的方法。这些研究揭示了RNA在体内和体外经常采用非常不同的结构，并为RNA生物学提供了深刻的见解。尽管如此，体外和体内方法都有局限性：在复杂和不受控制的细胞环境中进行的研究很难深入了解RNA折叠途径和热力学，体外研究通常缺乏直接的细胞相关性，这使得我们对RNA体内折叠的了解存在空白。这一差距正在弥合的RNA结构和功能的生物物理和机制的研究条件下，模拟细胞环境。迄今为止，大多数人工细胞培养物使用各种聚合物作为分子拥挤剂和一系列小分子作为共溶质。在这种类似体内的条件下进行的研究正在产生新的见解，例如功能RNA的合作折叠和核酶活性的增加。这些观察结果部分是由分子拥挤效应和与其他分子的相互作用引起的。在这篇综述中，我们报告了体外和体内RNA折叠的里程碑，并讨论了正在进行的实验和计算工作，以弥合这两种情况之间的差距，以了解RNA如何在细胞中折叠。
Deciphering the folding pathways and predicting the structures of complex three-dimensional biomolecules is central to elucidating biological function. RNA is single-stranded, which gives it the freedom to fold into complex secondary and tertiary structures. These structures endow RNA with the ability to perform complex chemistries and functions ranging from enzymatic activity to gene regulation. Given that RNA is involved in many essential cellular processes, it is critical to understand how it folds and functions in vivo. Within the last few years, methods have been developed to probe RNA structures in vivo and genome-wide. These studies reveal that RNA often adopts very different structures in vivo and in vitro, and provide profound insights into RNA biology. Nonetheless, both in vitro and in vivo approaches have limitations: studies in the complex and uncontrolled cellular environment make it difficult to obtain insight into RNA folding pathways and thermodynamics, and studies in vitro often lack direct cellular relevance, leaving a gap in our knowledge of RNA folding in vivo. This gap is being bridged by biophysical and mechanistic studies of RNA structure and function under conditions that mimic the cellular environment. To date, most artificial cytoplasms have used various polymers as molecular crowding agents and a series of small molecules as cosolutes. Studies under such in vivo-like conditions are yielding fresh insights, such as cooperative folding of functional RNAs and increased activity of ribozymes. These observations are accounted for in part by molecular crowding effects and interactions with other molecules. In this review, we report milestones in RNA folding in vitro and in vivo and discuss ongoing experimental and computational efforts to bridge the gap between these two conditions in order to understand how RNA folds in the cell.