Non-canonical gene expression: Investigating a novel stimulator and a novel function for ribosomal frameshifting

弗朗西斯·克里克在1958年提出了分子生物学的中心“教条”，描述了三种主要的携带信息的生物聚合物之间的信息传递：遗传信息通过DNA的复制从一代传递到下一代，在生物体内，DNA中编码的基因被转录成“信使”RNA，RNA被翻译成蛋白质。DNA到DNA或DNA到RNA的简单复制是由称为聚合酶的分子“机器”介导的。从信使RNA翻译蛋白质的过程要复杂得多，它是由一种称为核糖体的复杂分子机器介导的。核糖体是所有生物体的重要组成部分。事实上，核糖体的存在可以被视为我们所知的生命的定义：即使是最简单的细菌也会制造自己的核糖体;相反，即使是最复杂的病毒也会“劫持”宿主的核糖体。DNA和RNA分子包含四种类型的核苷酸的长串，为了方便起见，用字母A、C、G和T（对于DNA）和A、C、G和U（对于RNA）表示。整个人类基因组由约30亿个核苷酸组成，其中包含构建约25000种不同蛋白质的“指令”。蛋白质由一串氨基酸组成，其中有20种标准类型。为了从信使RNA产生蛋白质，核糖体读取连续的三个核苷酸组，并根据“遗传密码”将三联体翻译成氨基酸。然而，在可能所有生物体中的一部分基因中，信使RNA中的特定基序可以刺激一部分核糖体偏离标准翻译。一种类型的例外被称为“-1核糖体移码”。在这里，在信使RNA内的特定位点，一部分核糖体通过单个核苷酸的“向后滑动”而偏离了连续的核苷酸阅读三联体。然后这些核糖体继续翻译一系列三联体，这些三联体相对于其他不滑动的核糖体偏移-1个核苷酸。因此，一个信使RNA可以编码两种完全不同的蛋白质。核糖体移码被许多病毒使用，如HIV、SARS、西尼罗河病毒、日本脑炎病毒和猪生殖与呼吸综合征病毒等。这些病毒的基因组非常小（约10000至25000个核苷酸），核糖体移码在允许它们将尽可能多的遗传信息包装到可用空间中方面起着核心作用。因此，核糖体移码在许多病毒的生物学和毒力中起着至关重要的作用。我们的研究涉及我们最近在一组称为心脏病毒的病毒中发现的一种新的核糖体移码。虽然这些病毒不是可怕的末日的预兆，但它们已被广泛用于医学和基础生物学研究（包括为多发性硬化症提供模型）。因此，表征这些病毒中以前未检测到的特征将提供可能有助于重新解释以前研究的数据，并允许对未来结果进行更清晰的解释。然而，我们提出的研究的主要重点是更广泛的意义，了解这种特殊的情况下，移码。这是因为我们以前的研究表明，心脏病毒中的核糖体移码涉及一些根本上新的机制，并且很可能具有一些根本上新的功能方面。对这些新特征的研究和表征将使我们对以下问题有新的认识：（a）核糖体可能被诱导偏离信使RNA到蛋白质的标准三联体解码的机制，（B）其他病毒中核糖体移码的潜在新方面和功能，包括一些对公共卫生有重要意义的病毒（艾滋病毒，SARS病毒，西尼罗河等），以及（c）目前对人类基因中移码的作用知之甚少，但显然很重要。

The central 'dogma' of molecular biology, articulated by Francis Crick in 1958, describes the transfer of information between the three major classes of information-carrying biopolymers: genetic information passes from one generation to the next via the replication of DNA and, within an organism, genes encoded within the DNA are transcribed into 'messenger' RNAs which are translated into proteins. Simple copying of DNA to DNA or DNA to RNA is mediated by molecular 'machines' known as polymerases. The far more complex process of translating proteins from messenger RNAs is mediated by a complex molecular machine known as the ribosome. Ribosomes are an essential component of all living organisms. Indeed the presence of ribosomes could be taken as a definition of life as we know it: even the simplest bacteria make their own ribosomes; in contrast, even the most complex viruses 'hijack' the ribosomes of their hosts. DNA and RNA molecules comprise long strings of fours types of nucleotides which, for convenience, are denoted by the letters A, C, G and T (for DNA) and A, C, G and U (for RNA). The entire human genomes comprises ~3 billion nucleotides, within which are the 'instructions' to build ~25000 different proteins. Proteins comprise strings of amino acids, of which there are 20 standard types. To produce a protein from a messenger RNA, a ribosome reads consecutive groups of three nucleotides and translates the triplet into an amino acid, according to the 'genetic code'. However, in a proportion of genes in probably all organisms, specific motifs within messenger RNAs can stimulate a portion of ribosomes to deviate from standard translation. One type of exception is known as '-1 ribosomal frameshifting'. Here, at a specific site within a messenger RNA, a proportion of ribosomes deviate from reading consecutive triplets of nucleotides by 'slipping backward' by a single nucleotide. These ribosomes then continue to translate a series of triplets that are offset -1 nucleotide relative to other ribosomes that do not slip. Thus one messenger RNA can encode two completely different proteins. Ribosomal frameshifting is used by many viruses, such as HIV, SARS, West Nile, Japanese encephalitis and Porcine reproductive and respiratory syndrome viruses, and many more. Such viruses have very small genomes (~10000 to 25000 nucleotides) and ribosomal frameshifting plays a central role in allowing them to pack as much genetic information as possible into the available space. As such, ribosomal frameshifting plays a crucial role in the biology and virulence of many viruses.Our research concerns a new case of ribosomal frameshifting that we recently discovered in a group of viruses known as the cardioviruses. Although not harbingers of dreadful doom, these viruses have been used extensively for medical and fundamental biological research (including to provide a model for multiple sclerosis). Thus, characterizing this previously undetected feature in these viruses will provide data that will likely aid reinterpretation of previous studies and allow for clearer interpretation of future results. However the main focus of our proposed research concerns the broader implications of understanding this particular case of frameshifting. This is because our previous research indicates that ribosomal frameshifting in the cardioviruses involves some fundamentally new mechanisms and very likely has some fundamentally new functional aspects. Investigating and characterizing these new features should shed new light on (a) mechanisms by which the ribosome may be induced to deviate from standard triplet decoding of messenger RNA to protein, (b) potential new aspects and functions of ribosomal frameshifting in other viruses including some of great public health import (HIV, SARS virus, West Nile, etc), and (c) the currently overall poorly understood, but clearly important, role of frameshifting in human genes.