The evolution of transcription initiation mechanisms and its genetic basis

转录起始机制的进化及其遗传基础

• 批准号: 1951332
• 负责人: Zhenguo Lin
• 金额: $ 73.09万
• 依托单位: Saint Louis University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-03-15 至 2025-02-28
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1951332&HistoricalAwards=false
• 关键词: evolution; transcription; initiation; mechanisms; its

The DNA sequence of a gene needs to be copied into mRNA molecules to carry out its function, a process called transcription. Cells are highly selective in where they begin (initiate) transcription of their genes. The mechanism of locating the starting positions of transcription is shared by most eukaryotic organisms such as humans, plants, and fungi. Yet, a distinct way of transcription initiation has been found in a few fungal species including Baker’s yeast. This project aims to determine when and how the mechanisms of transcription initiation have diverged. Success of this project will advance basic understandings of the evolution and genetic mechanisms of transcription initiation, a first step in harnessing the power of biology for the bioeconomy. This project also develops new software and generates a large collection of mRNA sequences, which will benefit the research community. In addition, this project will build a user-friendly database that can serve as a portal for improving public literacy in genomics and facilitate teaching in K-12 schools and colleges. This project also contributes to the development of a globally competitive STEM workforce by training a postdoctoral scholar, graduate, undergraduate, and high school students.In most eukaryotes, transcription is initiated by a large enzyme preinitiation complex at about 30 nucleotides downstream of a short sequence element known as the TATA box, where the preinitiation complex is assembled. In contrast, the preinitiation complex scans DNA sequences further downstream of the TATA box for favorable transcription start sites in Saccharomyces cerevisiae. This project aims to elucidate when the transcription initiation mechanisms have diverged and to identify key genetic changes associated with this process. This project applies a combination of computational and experimental approaches to determine the initiation mechanism of 68 fungal species. Aim 1 of this project will develop novel bioinformatics tools for accurate mapping of transcription start sites based on high throughput sequencing data. In Aim 2, this project will capture the first nucleotide of RNA molecules and sequence these transcripts to generate transcription start site maps for 68 species representing all major fungal lineages. The initiation mechanism for each species will be determined based on the distribution of the TATA box relative to the transcription start site on a genomic scale. A detailed evolutionary history of initiation mechanisms will be depicted to pinpoint the occurrence of divergence. The third project aim will identify the key genes associated with the divergence of transcription initiation mechanisms based on their evolutionary history and expression profiles. Important genetic changes in these genes are also expected to be determined through comparative sequence analyses. These results will lay a solid foundation for future interrogation of the specific functions of preinitiation complex components in transcription initiation.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

基因的DNA序列需要被复制到mRNA分子中以执行其功能，这一过程称为转录。细胞在它们开始（起始）其基因转录的地方是高度选择性的。 定位转录起始位置的机制是大多数真核生物如人类、植物和真菌所共有的。然而，在包括面包酵母在内的一些真菌物种中发现了一种独特的转录起始方式。该项目旨在确定转录起始机制何时以及如何分化。该项目的成功将促进对转录起始的进化和遗传机制的基本理解，这是利用生物学力量促进生物经济的第一步。 该项目还开发了新的软件，并产生了大量的mRNA序列，这将有利于研究界。此外，该项目将建立一个用户友好的数据库，作为提高公众基因组学知识的门户，并促进K-12学校和学院的教学。该项目还通过培养博士后学者、研究生、本科生和高中生，为培养具有全球竞争力的STEM人才做出贡献。在大多数真核生物中，转录是由一个大的酶预起始复合物启动的，该复合物位于一个短序列元件TATA盒下游约30个核苷酸处，该元件被称为TATA盒，在那里组装预起始复合物。相比之下，preinitiation复合物扫描DNA序列进一步下游的TATA框有利的转录起始位点在酿酒酵母。 该项目旨在阐明转录起始机制何时出现分歧，并确定与此过程相关的关键遗传变化。该项目采用计算和实验相结合的方法来确定68种真菌的启动机制。本项目的目标1将开发新的生物信息学工具，用于基于高通量测序数据精确定位转录起始位点。在目标2中，该项目将捕获RNA分子的第一个核苷酸，并对这些转录本进行测序，以生成代表所有主要真菌谱系的68个物种的转录起始位点图。将基于TATA盒相对于转录起始位点在基因组规模上的分布来确定每个种属的起始机制。详细的演化历史的启动机制将被描绘，以查明发生的分歧。第三个项目的目标是根据它们的进化历史和表达谱来鉴定与转录起始机制分歧相关的关键基因。预计这些基因中的重要遗传变化也将通过比较序列分析来确定。这些结果将奠定坚实的基础，为未来审讯的具体功能preinitiation复杂的组件在transcriptioninitiation.This奖项反映了NSF的法定使命，并已被认为是值得通过使用基金会的智力价值和更广泛的影响审查标准进行评估的支持。

项目成果

Decapping factor Dcp2 controls mRNA abundance and translation to adjust metabolism and filamentation to nutrient availability.

• DOI: 10.7554/elife.85545
• 发表时间: 2023-06-02
• 期刊: eLife
• 影响因子: 7.7
• 作者: Vijjamarri AK;Niu X;Vandermeulen MD;Onu C;Zhang F;Qiu H;Gupta N;Gaikwad S;Greenberg ML;Cullen PJ;Lin Z;Hinnebusch AG
• 通讯作者: Hinnebusch AG

mRNA decapping activators Pat1 and Dhh1 regulate transcript abundance and translation to tune cellular responses to nutrient availability.

mRNA 脱帽激活剂 Pat1 和 Dhh1 调节转录丰度和翻译，以调节细胞对营养可用性的反应。

• DOI: 10.1093/nar/gkad584
• 发表时间: 2023
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Vijjamarri,AnilKumar;Gupta,Neha;Onu,Chisom;Niu,Xiao;Zhang,Fan;Kumar,Rakesh;Lin,Zhenguo;Greenberg,MiriamL;Hinnebusch,AlanG
• 通讯作者: Hinnebusch,AlanG