NSF PRFB FY 2023: Deciphering the Structural Evolution of Alternative-End Joining

这项行动资助了2023财年的NSF生物学博士后研究奖学金，综合研究调查了基因组，环境和表型之间的生命管理相互作用的规则。该研究金支持研究员的研究和培训，以创新的方式为生活规则领域做出贡献。DNA是地球上所有细胞生命的基本遗传储存分子，但它很容易受到各种细胞和环境过程的破坏，这可能会损害细胞的存活。因此，细胞已经进化出专门的DNA修复途径，统称为DNA损伤反应（DDR），以识别和纠正基因组中的错误。当DNA双螺旋的两条链断裂时，这会产生双链断裂（DSB），并通过称为交替末端连接（alt-EJ）的机制进行修复，这是一种将两个DNA末端缝合在一起的途径。这一过程的结构基础尚不清楚，但它对地球上所有复杂生命的进化都很重要。这项研究将探索alt-EJ通路中蛋白质和DNA的三维结构，并将为生物体如何保护和修复其基因组免受损伤提供更深入的了解。这项研究还将支持教学，指导和推广的研究员，以改善科学交流和参与的代表性不足的群体。交替末端连接（alt-EJ）途径是一个多步骤的途径，是由DNA解旋酶/聚合酶，Pol θ（Polθ）进行。Alt-EJ是介于非同源末端连接（NHEJ）和同源重组（HR）之间的一条中间DSB修复途径，本研究将有助于对途径选择的理解。在结构上，在其天然环境中尚未观察到全长Polθ，并且Polθ向DNA的募集以及与其他修复途径的协调尚未阐明。该提案的研究目标涉及耦合高分辨率低温电子显微镜（cryo-EM）和生物化学/系统发育学技术，以揭示两个目标：（i）人类替代末端连接的Polθ的结构基础和（ii）Polθ和alt-EJ的进化机制，使用生物化学测定和分子生物学。Alt-EJ复合物将在磁性DNA珠上组装，以构建特定的大分子组装体，用于原子分辨率的可视化。拟议的研究将为研究员提供结构生物学，生物化学/生物物理学和科学交流（出版物，会议，研讨会）方面的培训和发展机会。该研究员还将继续获得本科生和研究生的教学和指导经验，并通过参与DEI和隐性偏见培训，努力提高STEM领域的多样性和包容性。该奖项反映了NSF的法定使命，并通过使用基金会的智力优点和更广泛的影响力审查标准进行评估，被认为值得支持。

This action funds an NSF Postdoctoral Research Fellowship in Biology for FY 2023, Integrative Research Investigating the Rules of Life Governing Interactions Between Genomes, Environment, and Phenotypes. The fellowship supports research and training of the fellow that will contribute to the area of Rules of Life in innovative ways. DNA is the fundamental genetic storage molecule for all cellular life on Earth, yet it is susceptiple to damage by various cellular and environmental processes, which can impair cell survival. Consequently, cells have evolved dedicated DNA repair pathways, collectively known as the DNA damage response (DDR) to recognize and correct mistakes in the genome. When both strands of the DNA double helix are broken, this creates a double-strand break (DSB), and is repaired by a mechanisms called alternative-end joining (alt-EJ), a pathway that stitches two DNA ends back together. The structural basis for how this process works is unknown, but it is important for the evolution of all complex life on Earth. This research will explore the 3-dimensional architecture of proteins and DNAs within the alt-EJ pathway, and will provide a deeper understanding for how organisms protect and repair their genome from damage. This research will also support teaching, mentoring, and outreach by the fellow to improve scientific communication and participation of underrepresented groups.The alternative-end joining (alt-EJ) pathway is a multi-step pathway that is conducted by the DNA helicase/polymerase, Pol theta (Polθ). Alt-EJ is an intermediate DSB repair pathway between non-homologous end-joining (NHEJ) and homologous recombination (HR), and this research will contribute to the understanding of pathway choice. Structurally, full-length Polθ has not been observed in its native context, and the recruitment of Polθ to DNA and coordination with other repair pathways has not been elucidated. The research goals of this proposal involve coupling high-resolution cryogenic-electron microscopy (cryo-EM) and biochemical/phylogenetic techniques to uncover two objectives: (i) the structural basis for human alternative-end joining by Polθ and (ii) the mechanistic evolution of Polθ and alt-EJ using biochemical assays and molecular phylogeny. Alt-EJ complexes will be assembled on magnetic DNA-beads to construct specific macromolecular assemblies for visualization at atomic resolution. The proposed research will provide the fellow with training and development opportunities in structural biology, biochemistry/biophysics, and scientific communication (publications, conferences, seminars). The fellow will also continue to gain experience in teaching and mentoring undergraduate and graduate students, and work to improve diversity and inclusivity in the STEM fields by participation in DEI and implicit bias training.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.