Project Information

deep-learning, genomics, hpc-tools, NSF ACCESS Resources
Project Status: In Progress
Project Region: CAREERS
Submitted By: Anita Schwartz
Project Email: milton.x.muldrow@wilmu.edu
Project Institution: Wilmington University
Anchor Institution: CR-University of Delaware
Project Address: Wilmington, Delaware

Mentors: Daniel Chauss
Students: Samantha Kidwell

Project Description

We would like to further understand the structure and function of Sirtuins and functionally related proteins expressed by Aiptasia and evolutionarily compare across eukaryotic organisms. We plan to implement deep-learning methods as well as integrative genomic methods to further understand and map the interactively complex regulatory nature of Sirtuins during homeostasis and bleaching.

One of our initial goals of our research program are to study Aiptasia protein interactions in silico via alphafold generated models using the colabfold implementation. In the future we hope to evolve these methods to consider physiological conditions such as those during various Aiptasia disease-states.
Related: https://www.nature.com/articles/s41592-022-01488-1

Project goals include:

Compare protein functional sites across taxa (ex: active and binding sites) to develop hypotheses regarding function
Examine potential protein interactions (ex: NAD+)
Predict evolutionary conservation and divergence
Inform small molecule coral drug design if pathology is linked
Mutations?
How will DARWIN contribute?
How We Will Leverage Former CAREERS progress:

Student Natalie Vazques did a great job assisting in the establishment of the evaluation of coral/aiptasia proteins in our lab. Her work with BLAST will be leveraged as a starting point to further investigate attributes of coral sirtuin proteins. Natalie found there was significant similarity among coral/human/aiptasia sirtuin proteins, indicating overlapping function and potentially wide-ranging influence of these proteins. In this project, we will look to gain further insight into protein structure and potential function.

Skills Students will gain:

Structural Biology Research
Deep Learning Applications
Genomic Data Analysis
Evolutionary Comparative Analysis
High Performance Computing
Research Skills Development
Debugging
Understanding Model organisms
Teamwork and Collaboration
Communication Skills
Critical Thinking and Problem-Solving

Symbiodinium microadriaticum strain:CCMP2467 (ID 292355) - BioProject - NCBI (nih.gov)


Introduction:
Sirtuins are a class of NAD+-dependent deacetylases that regulate a diverse set of biological processes including stress response, aging and metabolism. Sirtuins are found in every organismal kingdom, and are highly conserved throughout evolutionary time. Sirtuins are also found in the Aiptasia, an established animal model for corals. In this project, we seek to understand what influence sirtuins play in the complex bleaching process. This area of research is virtually unexplored given the likely importance sirtuins play in coral stress response. Also, there is a significant gap in knowledge regarding structural and function difference of sirtuins across diverse taxa. This research seeks to address this gap in knowledge by harnessing deep learning methodologies and integrative genomic techniques.
Research Objectives and Methodology:
Structural Analysis and Comparative Study of Functional Sites across Taxa: We will utilize AlphaFold software, via the ColabFold implementation, to generate high-resolution structural models of Sirtuins from Aiptasia and other species of interest. The computing power of DARWIN will enable us to run these programs and generate large data sets. This approach will enable us to investigate the structural conservation and divergence of these proteins and locate critical functional sites, such as active and binding sites. Comparative analysis of these sites across various taxa will inform hypotheses regarding the functional adaptations of Sirtuins.
Protein-Protein Interaction and Metabolic Pathway Analysis: We aim to examine and identify partners of Sirtuins. This would include known partners, such as NAD+, but there is also the potential to identify new relationships. Integrating this knowledge with our structural data may facilitate the mapping of complex regulatory networks centered on Sirtuins.
Investigation of Evolutionary Conservation and Divergence: By analyzing the sequence and structural data from various organisms, we will identify site changes in sirtuins over evolutionary time.
Implications for Drug Design and Therapeutics: If our studies link Sirtuin-associated pathology to coral bleaching or other coral disease, this new will guide the rational design of small-molecule modulators targeting these proteins. There is potential for therapeutic interventions to combat coral bleaching.
Assessment of the Impact of Mutations: By using both in silico models and potentially CRISPR/Cas9 gene editing in the future, we will study the effects of specific mutations on the structure, function, and interactions of Sirtuins.
Sequencing: Our goal is to also run whole-genome experiments to best utilize DARWIN as well. This will be useful for population-level genetics.
Conclusion:
In accordance, the Darwin software will be utilized for the integrative analysis of structural, functional, and evolutionary data. As a cutting-edge tool for genomic data interpretation, Darwin will enhance our ability to gain insights from the immense amount of data generated in this project and facilitate the illumination of complex regulatory mechanisms.

Our comprehensive and integrative approach will not only develop our understanding of Sirtuins in Aiptasia and across diverse animal taxa but also pioneer a new frontier in coral biology and conservation. Our findings could have profound implications for clarifying the mechanisms of coral bleaching and fostering innovations in coral reef restoration strategies.