DNA与RNA谁是主角?

DNA与RNA相伴而生,是一对孪生分子。生命起源最早出现可能是“核酸世界”,DNA与RNA是后来分化产生的。在当今生命系统中,DNA、RNA和蛋白质起着决定的作用,成为生命系统中的三驾马车。RNA干扰的发现表明,生物基因表型的变化是受RNA控制的。RNA转录后复杂的加工过程反映了RNA的进化历程。因此,重新认识RNA已成为当前生命科学亟待解决的问题。     

The antiquity of RNA-based evolution

All life that is known to exist on Earth today and all life for which there is evidence in the geological record seems to be of the same form--one based on DNA genomes and protein enzymes. Yet there are strong reasons to conclude that DNA- and protein-based life was preceded by a simpler life form based primarily on RNA. This earlier era is referred to as the 'RNA world', during which the genetic information resided in the sequence of RNA molecules and the phenotype derived from the catalytic properties of RNA.     

A ribozyme that lacks cytidine

The RNA-world hypothesis proposes that, before the advent of DNA and protein, life was based on RNA, with RNA serving as both the repository of genetic information and the chief agent of catalytic function. An argument against an RNA world is that the components of RNA lack the chemical diversity necessary to sustain life. Unlike proteins, which contain 20 different amino-acid subunits, nucleic acids are composed of only four subunits which have very similar chemical properties. Yet RNA is capable of a broad range of catalytic functions. Here we show that even three nucleic-acid subunits are sufficient to provide a substantial increase in the catalytic rate. Starting from a molecule that contained roughly equal proportions of all four nucleosides, we used in vitro evolution to obtain an RNA ligase ribozyme that lacks cytidine. This ribozyme folds into a defined structure and has a catalytic rate that is about 10(5)-fold faster than the uncatalysed rate of template-directed RNA ligation.     

The chemical repertoire of natural ribozymes

Although RNA is generally thought to be a passive genetic blueprint, some RNA molecules, called ribozymes, have intrinsic enzyme-like activity--they can catalyse chemical reactions in the complete absence of protein cofactors. In addition to the well-known small ribozymes that cleave phosphodiester bonds, we now know that RNA catalysts probably effect a number of key cellular reactions. This versatility has lent credence to the idea that RNA molecules may have been central to the early stages of life on Earth.     

日新月异的RNA

８０年代以来,科学家们揭示了许多有关ＲＮＡ的功能,并使传统分类学、生物定律以及中心法则产生了动摇。从国外报到来看,象Ｓｃｉｅｎｃｅ、Ｎａｔｕｒｅ、Ｃｅｌｌ、Ｂｉｏｃｈｅｍｉｓｔｒｙ等刊物对ＲＮＡ的报道都特别多,ＲＮＡ研究确实是世界的一个研究热点。人们惊奇地发现了ＲＮＡ许多鲜为人知的事实,这不仅是对分子生物学、结构生物学的重大贡献和有益补充,而且使整个生命科学的研究更具科学性和客观性,使历史上许多悬     

具有催化活性的RNA

本文简要介绍了具有催化活性ＲＮＡ的发现过程、作用机理及研究进展。这一发现对于人们重新认识生物催化剂的本质，追溯基因的演化，进一步研究ＲＮＡ的功能、深入理解生命的起源等重大理论问题，都具有十分重要的意义。     

Functional complexity and regulation through RNA dynamics

Changes to the conformation of coding and non-coding RNAs form the basis of elements of genetic regulation and provide an important source of complexity, which drives many of the fundamental processes of life. Although the structure of RNA is highly flexible, the underlying dynamics of RNA are robust and are limited to transitions between the few conformations that preserve favourable base-pairing and stacking interactions. The mechanisms by which cellular processes harness the intrinsic dynamic behaviour of RNA and use it within functionally productive pathways are complex. The versatile functions and ease by which it is integrated into a wide variety of genetic circuits and biochemical pathways suggests there is a general and fundamental role for RNA dynamics in cellular processes.     

RNAi及其在生命科学研究中的应用

RNAi即RNA干扰(RNA interfering),是近几年才发现的一种由双链RNA引起的基因沉默的现象,是目前分子生物学领域研究的热点。介绍RNAi的发现,并对RNAi在生命科学研究领域的最新应用进行综述。     

Crystal structure of the RNA component of bacterial ribonuclease P

Transfer RNA (tRNA) is produced as a precursor molecule that needs to be processed at its 3' and 5' ends. Ribonuclease P is the sole endonuclease responsible for processing the 5' end of tRNA by cleaving the precursor and leading to tRNA maturation. It was one of the first catalytic RNA molecules identified and consists of a single RNA component in all organisms and only one protein component in bacteria. It is a true multi-turnover ribozyme and one of only two ribozymes (the other being the ribosome) that are conserved in all kingdoms of life. Here we show the crystal structure at 3.85 A resolution of the RNA component of Thermotoga maritima ribonuclease P. The entire RNA catalytic component is revealed, as well as the arrangement of the two structural domains. The structure shows the general architecture of the RNA molecule, the inter- and intra-domain interactions, the location of the universally conserved regions, the regions involved in pre-tRNA recognition and the location of the active site. A model with bound tRNA is in agreement with all existing data and suggests the general basis for RNA-RNA recognition by this ribozyme.     

Unravelling the dynamics of RNA degradation by ribonuclease II and its RNA-bound complex

RNA degradation is a determining factor in the control of gene expression. The maturation, turnover and quality control of RNA is performed by many different classes of ribonucleases. Ribonuclease II (RNase II) is a major exoribonuclease that intervenes in all of these fundamental processes; it can act independently or as a component of the exosome, an essential RNA-degrading multiprotein complex. RNase II-like enzymes are found in all three kingdoms of life, but there are no structural data for any of the proteins of this family. Here we report the X-ray crystallographic structures of both the ligand-free (at 2.44 A resolution) and RNA-bound (at 2.74 A resolution) forms of Escherichia coli RNase II. In contrast to sequence predictions, the structures show that RNase II is organized into four domains: two cold-shock domains, one RNB catalytic domain, which has an unprecedented alphabeta-fold, and one S1 domain. The enzyme establishes contacts with RNA in two distinct regions, the 'anchor' and the 'catalytic' regions, which act synergistically to provide catalysis. The active site is buried within the RNB catalytic domain, in a pocket formed by four conserved sequence motifs. The structure shows that the catalytic pocket is only accessible to single-stranded RNA, and explains the specificity for RNA versus DNA cleavage. It also explains the dynamic mechanism of RNA degradation by providing the structural basis for RNA translocation and enzyme processivity. We propose a reaction mechanism for exonucleolytic RNA degradation involving key conserved residues. Our three-dimensional model corroborates all existing biochemical data for RNase II, and elucidates the general basis for RNA degradation. Moreover, it reveals important structural features that can be extrapolated to other members of this family.     

Crystal structure of the specificity domain of ribonuclease P

RNase P is the only endonuclease responsible for processing the 5' end of transfer RNA by cleaving a precursor and leading to tRNA maturation. It contains an RNA component and a protein component and has been identified in all organisms. It was one of the first catalytic RNAs identified and the first that acts as a multiple-turnover enzyme in vivo. RNase P and the ribosome are so far the only two ribozymes known to be conserved in all kingdoms of life. The RNA component of bacterial RNase P can catalyse pre-tRNA cleavage in the absence of the RNase P protein in vitro and consists of two domains: a specificity domain and a catalytic domain. Here we report a 3.15-A resolution crystal structure of the 154-nucleotide specificity domain of Bacillus subtilis RNase P. The structure reveals the architecture of this domain, the interactions that maintain the overall fold of the molecule, a large non-helical but well-structured module that is conserved in all RNase P RNA, and the regions that are involved in interactions with the substrate.     

几种内源性小RNA的比较

RNA干涉是近年来的研究热点,广泛参与生物发育、细胞分化、细胞凋亡等多种生物学过程。本文综述了近年来对转录后靶基因调控的几种小RNA：siRNA、microRNA、piRNA和endo-siRNA,从特点、生物发生过程和生物学功能方面进行了综述性地比较,以期为进一步深入研究提供参考。     

原核生物中心法则形成过程的逻辑分析

对生命早期原核细胞内遗传信息传递法则的形成过程进行推演是一项值得探索的工作. 基于地球诞生初期所可能存在的理化条件及演化,提出了生物小分子产生的化学必然性以及籍此促使生物大分子产生并呈现生命端倪的逻辑必然性. 在提出不同原始反应之间维持相对平衡观点的基础上,分析了产生结构相对稳定、对体系危害程度小的生物大分子以及大分子聚集体的成因及重要意义,阐释了囊泡（类细胞结构）的形成机制与意义;基于模板反应,提出了“软模板”（即mRNA）与“硬合成装置”（即核糖体）进行蛋白质合成时的相互筛选（即柔-刚对接模型）以及多种RNA参与蛋白质生物合成的成因,籍此提出了囊泡内因长期演化所导致的“弱遗传关系”的模型. 同时,也从逻辑学的视角分析了DNA与RNA形成先后的问题、蛋白质与核酸形成先后问题、病毒进化与细胞进化之关系等关乎生命起源与进化的重要科学问题. 最后,对生命起源的逻辑、生命现象的重新定义等问题进行了讨论.      

Selection in vitro of single-stranded DNA molecules that fold into specific ligand-binding structures.

We have isolated a set of ligand-binding DNA sequences from a large pool of random sequence DNAs by selection and amplification in vitro, using similar methods to those described for the isolation of ligand-binding RNAs. The ligand-DNA interactions are both sequence- and ligand-specific, and are dependent on proper folding of the single-stranded DNA. Some ligands led to the isolation of more DNA sequences than RNA sequences, and vice versa. Analysis of individual sequences reveals that ligand binding is DNA-specific; RNAs of identical sequence could not interact with the same ligands. Ligand-binding DNAs might be more suitable than RNAs as potential pharmacological reagents because of the greater stability of DNA. The apparent primacy of RNA in the early evolution of life may have been due to its availability rather than to its functional superiority.     

In silico simulations reveal that replicators with limited dispersal evolve towards higher efficiency and fidelity

The emergence of functional replicases, acting quickly and with high accuracy, was crucial to the origin of life. Although where the first RNA molecules came from is still unknown, it is nevertheless assumed that catalytic RNA enzymes (ribozymes) with replicase function emerged at some early stage of evolution. The fidelity of copying is especially important because the mutation load limits the length of replicating templates that can be maintained by natural selection. An increase in template length is disadvantageous for a fixed digit copying fidelity, however, longer molecules are expected to be better replicases. An iteration for longer molecules with better replicase function has been suggested and analysed mathematically. Here we show that more efficient replicases can spread, provided they are adsorbed to a prebiotic mineral surface. A cellular automaton simulation reveals that copying fidelity, replicase speed and template efficiency all increase with evolution, despite the presence of molecular parasites, essentially because of reciprocal atruism ('within-species mutualism') on the surface, thus making a gradual improvement of replicase function more plausible.