BII: Mechanisms of Cellular Evolution

BII：细胞进化机制

• 批准号: 2119963
• 负责人: Michael Lynch
• 金额: $ 1250万
• 依托单位: Arizona State University
• 依托单位国家: 美国
• 项目类别: Cooperative Agreement
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-01 至 2026-08-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2119963&HistoricalAwards=false
• 关键词: BII; Mechanisms; Cellular; Evolution

By integrating across disparate fields in the life, physical, and mathematical sciences, this institute is designed to yield a mechanistic understanding of evolutionary processes. The broad goal is to decipher the general rules by which evolution proceeds at the cellular level, while simultaneously engaging in research and educational activities to help build a formal field of evolutionary cell biology. An immediate goal is to determine how aspects of cellular evolution across the Tree of Life are governed by: internal cellular constraints, the laws of biophysics and bioenergetics, and the genetic features of populations. Specific projects include: a quantitative survey of how cells apportion their energy budgets into a range of structures and functions; the development of theory to understand the paths that are open vs. closed to evolutionary modification in various lineages; comparative analyses of the structures and functional capacities of the major molecular machines in cells; and the use experimental laboratory populations of microbes to determine how cells respond evolutionarily and developmentally to temperature and nutritional challenges. By identifying key details at the cellular level, the institute will greatly expand our understanding of mechanisms underlying evolutionary processes, while also revealing rational strategies for engineering microbes with novel beneficial functions and for eradicating harmful pathogens. A range of activities, including student-exchange programs with collaborators, annual workshops, development of educational materials, and establishment of an atlas of cellular information will expand the reach of the institute to national and international levels. Over its duration, the institute is expected to connect with a wide range of integrative research and educational foci, with a common goal of bringing a new dimension of evolutionary biology to cell biology and vice versa. The research starts with several multifaceted projects, the first using comparative genomics, spatial intracellular proteomics, ultramicroscopy, and bioenergetic analyses to provide a broad phylogenetic overview of cellular features and the relative costs of constructing and operating them. The second project draws from empirical observations to build quantitative theory for the mechanisms by which cell-biological features evolve, in particular how the paths open to evolutionary exploitation vary phylogenetically. This project also takes a structural-biology approach to explore how major cellular complexes with essential and highly conserved functions, e.g., ATP synthase and ribosomes, are nonetheless free to diverge evolutionarily. The third project capitalizes and expands upon established long-term evolution experiments with microbes to evaluate the genomic changes that arise in response to selection on cell size and growth rate over gradients of nutrient, temperature, and population-genetic conditions, and seeks to understand why the phylogenetic scalings of growth rates and cell sizes have opposite directionality in prokaryotes and eukaryotes. The integration of these projects will reveal the Rules of Life at the cellular level and establish mechanistic explanations for them from first principles. Involving work from scientists from diverse backgrounds, the collaborative projects build outwardly from the local to the national/international level.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.

通过在生活，物理和数学科学中跨越不同领域的整合，该研究所旨在对进化过程产生机械理解。广泛的目标是破译演化在细胞水平上进行的一般规则，同时从事研究和教育活动，以帮助建立正式的进化细胞生物学领域。一个直接的目标是确定整个生命树的细胞进化的各个方面如何受到：内部细胞约束，生物物理学和生物能学的定律以及人群的遗传特征。特定项目包括：对细胞如何将其能源预算分配为一系列结构和功能的定量调查；理论的发展是了解开放的路径与在各种谱系中的进化修饰的开放式途径；细胞中主要分子机器的结构和功能能力的比较分析；以及微生物的实验实验室种群，以确定细胞如何在温度和营养挑战上进化和发展。通过在细胞水平上确定关键细节，该研究所将大大扩展我们对进化过程基础机制的理解，同时还揭示了具有新型有益功能和消除有害病原体的工程微生物的理性策略。一系列活动，包括与合作者的学生交往计划，年度研讨会，教育材料的开发以及建立蜂窝信息地图集的活动，将扩大研究所的影响力到国家和国际级别。在其持续时间内，该研究所有望与广泛的综合研究和教育焦点建立联系，其共同目标是将进化生物学的新维度带入细胞生物学，反之亦然。该研究始于几个多面项目，首次使用比较基因组学，空间内蛋白质组学，超显微镜和生物能分析，以提供细胞特征的广泛系统发育概述及其构建和操作的相对成本。第二个项目从经验观察中得出，以建立定量理论，以构建细胞生物特征进化的机制，尤其是通向进化剥削的路径如何变化的系统发育。该项目还采用了一种结构生物学方法来探索具有必不可少和高度保守功能的主要细胞复合物，例如ATP合酶和核糖体如何自由地进化。第三个项目在用微生物进行了既定的长期演化实验中大写和扩展，以评估响应于养分，温度和人口遗传条件梯度的细胞大小和生长速率而产生的基因组变化，并试图理解为什么生长速率和细胞尺寸的系统发育量表和细胞尺寸的方向相反。这些项目的整合将揭示细胞层面的生命规则，并根据第一原则为其建立机械解释。涉及来自不同背景的科学家的工作，合作项目从本地/国际层面向外发展。该奖项反映了NSF的法定任务，并被认为是值得通过基金会的知识分子和更广泛影响的评估评估来获得支持的。

项目成果

EukProt: a database of genome-scale predicted proteins across the diversity of eukaryotes

• DOI: 10.1101/2020.06.30.180687
• 发表时间: 2020-07
• 期刊: bioRxiv
• 作者: D. Richter;C. Berney;Jürgen F. H. Strassert;Y. Poh;Emily K. Herman;Sergio A. Muñoz-Gómez;Jeremy G. Wideman;Fabien Burki;C. de Vargas

Evolutionary bioenergetics of ciliates

• DOI: 10.1111/jeu.12934
• 发表时间: 2022-07-28
• 期刊: JOURNAL OF EUKARYOTIC MICROBIOLOGY
• 影响因子: 2.2
• 作者: Lynch，Michael;Schavemaker，Paul E.;Pezzano，Arianna
• 通讯作者: Pezzano，Arianna

Challenges and potential solutions for studying the genetic and phenotypic architecture of adaptation in microbes

• DOI: 10.1016/j.gde.2022.101951
• 发表时间: 2022-07-04
• 期刊: CURRENT OPINION IN GENETICS & DEVELOPMENT
• 影响因子: 4
• 作者: Brettner, Leandra;Ho, Wei-Chin;Geiler-Samerotte, Kerry
• 通讯作者: Geiler-Samerotte, Kerry

Recommendations for improving statistical inference in population genomics

• DOI: 10.1101/2021.10.27.466171
• 发表时间: 2022-05-06
• 期刊: bioRxiv
• 作者: Johri，P.;Aquadro，C. F.;Jensen，J. D.
• 通讯作者: Jensen，J. D.

The fidelity of transcription in human cells.

• DOI: 10.1073/pnas.2210038120
• 发表时间: 2023-01-31
• 期刊: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• 影响因子: 11.1
• 作者: Chung, Claire;Verheijen, Bert M.;Zhang, Xinmin;Huang, Biao;Coakley, Aeowynn;McGann, Eric;Wade, Emily;Dinep-Schneider, Olivia;LaGosh, Jessica;Anagnostou, Maria-Eleni;Simpson, Stephen;Thomas, Kelly;Ernst, Mimi;Rattray, Allison;Lynch, Michael;Kashlev, Mikhail;Benayoun, Berenice A.;Li, Zhongwei;Strathern, Jeffrey;Gout, Jean-Francois;Vermulst, Marc
• 通讯作者: Vermulst, Marc