Functional Interrogation Of Ribosomal Biology Using Continuous Evolution

利用连续进化对核糖体生物学进行功能探究

基本信息

  • 批准号:
    10459135
  • 负责人:
  • 金额:
    $ 44.38万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
  • 财政年份:
    2021
  • 资助国家:
    美国
  • 起止时间:
    2021-09-01 至 2022-11-30
  • 项目状态:
    已结题

项目摘要

FUNCTIONAL INTERROGATION OF RIBOSOMAL BIOLOGY USING CONTINUOUS EVOLUTION PROJECT SUMMARY/ABSTRACT: In nature, fundamental biological phenomena that are central to cellular life are inherently hindered from probing and interrogation, as these dynamic systems cannot be easily decoupled from immediate artifactual disruptions throughout the living cell. One such case is the ribosome, a colossal multi-component protein factory that functions as the nexus for cellular information and signaling events, integrating nutrient availability with growth dynamics and resource allocation. Despite decades of research, this biomolecular assembly remains superficially understood and underexplored, owing to the difficulty associated with decoupling the translational apparatus from cellular viability. In fact, there is currently no generalizable experimental tool-kit for unbiased high-throughput interrogation of the structure-activity and functional relationships of the ribosome, the prediction of ribosome-small molecule interactions, or the identification of disruptive resistance mechanisms. The work proposed herein seeks to overcome the challenges associated with ribosomal manipulation in vivo, to illuminate the relationship between the rRNA and the effective translation initiation/elongation rates as they relate to growth fitness, and to provide an innovative framework for the interrogation of ribosome-small molecule interactions. The proposed work focuses on the development of a fully orthogonal ribosomal system for the real-time monitoring of ribosome activity in living cells through engineered transcription-translation networks based on independently tunable genetic components at all stages. The designed orthogonal sensor ribosomes will be subjected to directed evolution yielding novel variants with enhanced or diminished kinetic properties. To achieve this, the orthogonal ribosome circuit will be interfaced with an emergent technique based on a continuous culturing methodology called Phage-Assisted Continuous Evolution (PACE), facilitating hundreds of rounds of directed evolution in just a few days with minimal researcher intervention. Finally, to demonstrate the utility of the newly developed ribosomal sensors and the evolutionary platform, this technology will be leveraged to inform antibiotic-ribosome interactions, and to generate actionable drug resistance profiles for delaying or evading microbial resistance. This platform will be extended to high-throughput screening campaigns for novel chemical scaffolds capable of modulating ribosomal translation through potentially undiscovered modes of action. Broadly, our ability to harness bacteria for biomedical and biomaterial applications in the future will hinge on the detailed understanding of the mechanistic control and optimization of ribosomal output parameters enabled by these studies. The technological advances proposed herein have the potential to extend our understanding of key factors governing ribosomal function and dynamics, and will pave the way towards the development of novel mechanisms that will illuminate and enhance new approaches in biomedical research and targeted antimicrobial therapeutics.
基于连续进化的核糖体生物学功能查询 项目总结/摘要: 在自然界中,作为细胞生命中心的基本生物现象固有地受到阻碍, 探测和询问,因为这些动态系统不能轻易地与直接的人为因素脱钩。 整个活细胞的破坏。其中一个例子是核糖体,一种巨大的多组分蛋白质 作为细胞信息和信号事件的联系的工厂,整合营养物质的可用性 增长动力和资源分配。尽管经过了几十年的研究, 由于与经济和社会脱钩的困难, 细胞活力的翻译装置。事实上,目前还没有可推广的实验工具包, 无偏见的高通量审讯的结构活性和功能的关系的核糖体, 核糖体-小分子相互作用的预测,或破坏性抗性机制的鉴定。 本文提出的工作试图克服与体内核糖体操作相关的挑战, 阐明rRNA与有效翻译起始/延伸速率之间的关系,因为它们 与生长适应性有关,并为小核糖体的询问提供了一个创新的框架。 分子相互作用拟议的工作重点是发展一个完全正交的核糖体系统 用于通过工程化转录-翻译实时监测活细胞中的核糖体活性 网络的基础上独立可调的遗传组件在所有阶段。所设计的正交传感器 核糖体将进行定向进化,产生具有增强或减弱的动力学的新变体。 特性.为了实现这一点,正交核糖体电路将与一种新兴技术相结合 基于称为噬菌体辅助连续进化(PACE)的连续培养方法, 数百轮的定向进化在短短几天内,研究人员的干预最少。最后为 展示了新开发的核糖体传感器和进化平台的实用性,这项技术 将被用来告知抗生素-核糖体相互作用,并产生可操作的耐药谱, 来延缓或避免微生物的抗药性。该平台将扩展到高通量筛选 能够通过潜在的调节核糖体翻译的新型化学支架的活动 未被发现的行为模式。从广义上讲,我们利用细菌用于生物医学和生物材料的能力 未来的应用将取决于对机械控制和优化的详细理解, 核糖体输出参数使这些研究。本文提出的技术进步具有 有可能扩大我们对控制核糖体功能和动力学的关键因素的理解,并将铺平道路。 发展新机制的方式,将阐明和加强新的方法, 生物医学研究和有针对性的抗菌治疗。

项目成果

期刊论文数量(7)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
Orthogonal translation enables heterologous ribosome engineering in E. coli.
  • DOI:
    10.1038/s41467-020-20759-z
  • 发表时间:
    2021-01-26
  • 期刊:
  • 影响因子:
    16.6
  • 作者:
    Kolber NS;Fattal R;Bratulic S;Carver GD;Badran AH
  • 通讯作者:
    Badran AH
Directed evolution of rRNA improves translation kinetics and recombinant protein yield.
  • DOI:
    10.1038/s41467-021-25852-5
  • 发表时间:
    2021-09-24
  • 期刊:
  • 影响因子:
    16.6
  • 作者:
    Liu F;Bratulić S;Costello A;Miettinen TP;Badran AH
  • 通讯作者:
    Badran AH
Modern methods for laboratory diversification of biomolecules.
实验室多样化生物分子的现代方法。
A Deep Learning Approach to Antibiotic Discovery.
  • DOI:
    10.1016/j.cell.2020.01.021
  • 发表时间:
    2020-02-20
  • 期刊:
  • 影响因子:
    64.5
  • 作者:
    Stokes JM;Yang K;Swanson K;Jin W;Cubillos-Ruiz A;Donghia NM;MacNair CR;French S;Carfrae LA;Bloom-Ackermann Z;Tran VM;Chiappino-Pepe A;Badran AH;Andrews IW;Chory EJ;Church GM;Brown ED;Jaakkola TS;Barzilay R;Collins JJ
  • 通讯作者:
    Collins JJ
Synthetic Biological Circuits within an Orthogonal Central Dogma.
正交中央教条中的合成生物回路。
  • DOI:
    10.1016/j.tibtech.2020.05.013
  • 发表时间:
    2021-01
  • 期刊:
  • 影响因子:
    17.3
  • 作者:
    Costello A;Badran AH
  • 通讯作者:
    Badran AH
{{ item.title }}
{{ item.translation_title }}
  • DOI:
    {{ item.doi }}
  • 发表时间:
    {{ item.publish_year }}
  • 期刊:
  • 影响因子:
    {{ item.factor }}
  • 作者:
    {{ item.authors }}
  • 通讯作者:
    {{ item.author }}

数据更新时间:{{ journalArticles.updateTime }}

{{ item.title }}
  • 作者:
    {{ item.author }}

数据更新时间:{{ monograph.updateTime }}

{{ item.title }}
  • 作者:
    {{ item.author }}

数据更新时间:{{ sciAawards.updateTime }}

{{ item.title }}
  • 作者:
    {{ item.author }}

数据更新时间:{{ conferencePapers.updateTime }}

{{ item.title }}
  • 作者:
    {{ item.author }}

数据更新时间:{{ patent.updateTime }}

Ahmed Hussein Badran其他文献

Ahmed Hussein Badran的其他文献

{{ item.title }}
{{ item.translation_title }}
  • DOI:
    {{ item.doi }}
  • 发表时间:
    {{ item.publish_year }}
  • 期刊:
  • 影响因子:
    {{ item.factor }}
  • 作者:
    {{ item.authors }}
  • 通讯作者:
    {{ item.author }}

{{ truncateString('Ahmed Hussein Badran', 18)}}的其他基金

Functional Interrogation Of Ribosomal Biology Using Continuous Evolution
利用连续进化对核糖体生物学进行功能探究
  • 批准号:
    9553875
  • 财政年份:
    2017
  • 资助金额:
    $ 44.38万
  • 项目类别:
Functional Interrogation Of Ribosomal Biology Using Continuous Evolution
利用连续进化对核糖体生物学进行功能探究
  • 批准号:
    9593383
  • 财政年份:
    2017
  • 资助金额:
    $ 44.38万
  • 项目类别:

相似海外基金

How Does Particle Material Properties Insoluble and Partially Soluble Affect Sensory Perception Of Fat based Products
不溶性和部分可溶的颗粒材料特性如何影响脂肪基产品的感官知觉
  • 批准号:
    BB/Z514391/1
  • 财政年份:
    2024
  • 资助金额:
    $ 44.38万
  • 项目类别:
    Training Grant
BRC-BIO: Establishing Astrangia poculata as a study system to understand how multi-partner symbiotic interactions affect pathogen response in cnidarians
BRC-BIO:建立 Astrangia poculata 作为研究系统,以了解多伙伴共生相互作用如何影响刺胞动物的病原体反应
  • 批准号:
    2312555
  • 财政年份:
    2024
  • 资助金额:
    $ 44.38万
  • 项目类别:
    Standard Grant
RII Track-4:NSF: From the Ground Up to the Air Above Coastal Dunes: How Groundwater and Evaporation Affect the Mechanism of Wind Erosion
RII Track-4:NSF:从地面到沿海沙丘上方的空气:地下水和蒸发如何影响风蚀机制
  • 批准号:
    2327346
  • 财政年份:
    2024
  • 资助金额:
    $ 44.38万
  • 项目类别:
    Standard Grant
Graduating in Austerity: Do Welfare Cuts Affect the Career Path of University Students?
紧缩毕业:福利削减会影响大学生的职业道路吗?
  • 批准号:
    ES/Z502595/1
  • 财政年份:
    2024
  • 资助金额:
    $ 44.38万
  • 项目类别:
    Fellowship
感性個人差指標 Affect-X の構築とビスポークAIサービスの基盤確立
建立个人敏感度指数 Affect-X 并为定制人工智能服务奠定基础
  • 批准号:
    23K24936
  • 财政年份:
    2024
  • 资助金额:
    $ 44.38万
  • 项目类别:
    Grant-in-Aid for Scientific Research (B)
Insecure lives and the policy disconnect: How multiple insecurities affect Levelling Up and what joined-up policy can do to help
不安全的生活和政策脱节:多种不安全因素如何影响升级以及联合政策可以提供哪些帮助
  • 批准号:
    ES/Z000149/1
  • 财政年份:
    2024
  • 资助金额:
    $ 44.38万
  • 项目类别:
    Research Grant
How does metal binding affect the function of proteins targeted by a devastating pathogen of cereal crops?
金属结合如何影响谷类作物毁灭性病原体靶向的蛋白质的功能?
  • 批准号:
    2901648
  • 财政年份:
    2024
  • 资助金额:
    $ 44.38万
  • 项目类别:
    Studentship
Investigating how double-negative T cells affect anti-leukemic and GvHD-inducing activities of conventional T cells
研究双阴性 T 细胞如何影响传统 T 细胞的抗白血病和 GvHD 诱导活性
  • 批准号:
    488039
  • 财政年份:
    2023
  • 资助金额:
    $ 44.38万
  • 项目类别:
    Operating Grants
New Tendencies of French Film Theory: Representation, Body, Affect
法国电影理论新动向:再现、身体、情感
  • 批准号:
    23K00129
  • 财政年份:
    2023
  • 资助金额:
    $ 44.38万
  • 项目类别:
    Grant-in-Aid for Scientific Research (C)
The Protruding Void: Mystical Affect in Samuel Beckett's Prose
突出的虚空:塞缪尔·贝克特散文中的神秘影响
  • 批准号:
    2883985
  • 财政年份:
    2023
  • 资助金额:
    $ 44.38万
  • 项目类别:
    Studentship
{{ showInfoDetail.title }}

作者:{{ showInfoDetail.author }}

知道了