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

非规范基因表达：研究核糖体移码的新型刺激物和新功能

• 批准号: BB/J007072/1
• 负责人: Andrew Firth
• 金额: $ 42万
• 依托单位: University of Cambridge
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2012
• 资助国家: 英国
• 起止时间: 2012 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FJ007072%2F1
• 关键词: Non; canonical; gene; expression; Investigating

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.

由Francis Crick在1958年提出的分子生物学的中心“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转移：遗传信息通过DNA的复制从一代传到下一代，在生物体内，DNA中编码的基因被转录成“信使”RNA，再翻译成蛋白质。DNA到DNA或DNA到RNA的简单复制是由被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，这一过程是由一种名为核糖体的复杂分子机器介导的。核糖体是所有生物的重要组成部分。事实上，核糖体的存在可以被认为是我们所知的生命的一种定义：即使是最简单的细菌也会产生自己的核糖体；相比之下，即使是最复杂的病毒也会“劫持”它们宿主的核糖体。DNA和RNA分子由四种类型的核苷酸组成的长串，为方便起见，用字母A、C、G和T(代表DNA)和A、C、G和U(代表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中产生蛋白质，核糖体读取连续的三组核苷酸，并根据“遗传密码”将三联体翻译成氨基酸。然而，在可能所有生物体的一定比例的基因中，信使RNA中的特定基序可以刺激部分核糖体偏离标准翻译。一种例外情况被称为“-1核糖体移码”。在这里，在信使RNA的特定位置，一定比例的核糖体通过向后滑动单核苷酸来偏离连续的三联核苷酸的读数。然后，这些核糖体继续翻译一系列的三联体，这些三联体相对于其他不会滑动的核糖体来说是偏置-1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、日本脑炎和猪繁殖与呼吸综合征病毒等。这类病毒的基因组非常小(约10000到25000个核苷酸)，核糖体移码在使它们能够将尽可能多的遗传信息装入可用的空间中发挥着核心作用。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。我们的研究涉及最近在一组被称为心脏病毒的病毒中发现的核糖体移码的新病例。尽管这些病毒不是可怕厄运的预兆，但它们已被广泛用于医学和基础生物学研究(包括提供多发性硬化症的模型)。因此，表征这些病毒以前未被检测到的特征将提供可能有助于重新解释先前研究的数据，并允许对未来结果进行更清晰的解释。然而，我们提议的研究的主要焦点涉及理解这一特殊的移码案例的更广泛的影响。这是因为我们之前的研究表明，心脏病毒中的核糖体移码涉及一些全新的机制，并且很可能具有一些全新的功能方面。对这些新特征的研究和表征将为以下方面提供新的线索：(A)可能导致核糖体偏离信使RNA到蛋白质的标准三联体解码的机制，(B)在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大影响的病毒(艾滋病毒、SARS病毒、西尼罗河病毒等)，以及(C)目前对移码在人类基因中的整体了解较少但显然很重要的作用。

项目成果

Characterization of Ribosomal Frameshifting in Theiler's Murine Encephalomyelitis Virus.

• DOI: 10.1128/jvi.01043-15
• 发表时间: 2015-08
• 期刊: Journal of virology
• 影响因子: 5.4
• 作者: Finch LK;Ling R;Napthine S;Olspert A;Michiels T;Lardinois C;Bell S;Loughran G;Brierley I;Firth AE
• 通讯作者: Firth AE

An analysis by metabolic labelling of the encephalomyocarditis virus ribosomal frameshifting efficiency and stimulators

脑心肌炎病毒核糖体移码效率和刺激物的代谢标记分析

• DOI: 10.17863/cam.11380
• 发表时间: 2017
• 作者: Firth A

Novel virus discovery and genome reconstruction from field RNA samples reveals highly divergent viruses in dipteran hosts.

• DOI: 10.1371/journal.pone.0080720
• 发表时间: 2013
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Cook S;Chung BY;Bass D;Moureau G;Tang S;McAlister E;Culverwell CL;Glücksman E;Wang H;Brown TD;Gould EA;Harbach RE;de Lamballerie X;Firth AE
• 通讯作者: Firth AE

Structural and molecular basis for Cardiovirus 2A protein as a viral gene expression switch.

• DOI: 10.1038/s41467-021-27400-7
• 发表时间: 2021-12-09
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Hill CH;Pekarek L;Napthine S;Kibe A;Firth AE;Graham SC;Caliskan N;Brierley I
• 通讯作者: Brierley I

Mapping overlapping functional elements embedded within the protein-coding regions of RNA viruses.

• DOI: 10.1093/nar/gku981
• 发表时间: 2014-11-10
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Firth AE