Resurrecting Protein Ancestors that Predate the Last Universal Common Ancestor of Life

Project Title

Resurrecting Protein Ancestors that Predate the Last Universal Common Ancestor of Life

Faculty Mentor(s)

Project Description

Project Description: 

All life on Earth shares a Last Universal Common Ancestor (LUCA) that lived 3.5-4 billion years ago. The only method available to study evolution before the LUCA using standard evolutionary biology methods relies on protein families that underwent a duplication prior to the last universal common ancestor. These protein families, which are referred to as universal paralogs, have at least two members of the protein family present in the LUCA that resulted from a duplication (or multiple duplications) that took place prior to the LUCA. Here we describe the creation of a database of universal paralog families. We will use this database to reconstruct the amino acid sequences of the pre-LUCA and LUCA ancestral proteins within each of these families in order to better understand molecular evolution before the time of the LUCA.
 

Why is your research important?

Our research focuses on understanding molecular evolution before the emergence of the Last Universal Common Ancestor (LUCA) by studying universal paralog families, protein groups with duplicated members present in the LUCA. Through a comprehensive database, we reconstruct the amino acid sequences of ancestral proteins predating the LUCA within these families, shedding light on the ancient genetic landscape of life on Earth. By unraveling the evolutionary history encoded in these proteins, we aim to uncover pivotal insights into the origins and early diversification of life.
 

What does the process of doing your research look like?

Typically, we analyze different gene families within E. coli and Sulfolobus acidocaldarius through the program called BLAST, a tool that searches matches for match gene sequences from the Zhaxybayeva (2005) study. Afterwards, the data for each gene family is compiled and run through another program which then gives us the protein name and identifier, then we compile all of the results into a database. Typically, all of this takes place wherever I have my laptop, however, all data compiled is checked thoroughly by Professor Aaron Goldman for flaws.
 

What knowledge has your research contributed to your field?

We have found anciently duplicated proteins for 17 paralogue families in Sulfolobus acidocaldarius and E. coli.

 

How did you get involved in research? What drove you to seek out research experiences in college?

My childhood has been filled with memories of my parents conducting research and writing research papers on internal medicine, and this has greatly impacted my desire to conduct research. With the help of Professor Leslie Kwakye, I was able to get in contact with several professors and was fortunate enough to be able to conduct research with Professor Aaron Goldman.
 

What is your favorite aspect of the research process?

My personal favorite aspect was finding the unique protein names and identifiers given by the serial code from BLAST search sequences. It was an amusing task as not all serial numbers gave specific names, for example, one result turned out to be a "hypothetical protein."
 

How has working with your mentor impacted the development of your research project? How has it impacted you as a researcher?

Professor Goldman's expertise in the field of genomics and evolutionary biology has guided the direction of the project as a whole, ensuring that the methods used are sound and the results are meaningful/reasonable. His feedback has helped refine the research questions and improve the overall quality of the project. 

On a more personal level, my mentor has greatly impacted my growth as a researcher. Their guidance has improved my technical skills in bioinformatics and has taught me the importance of patience. If something goes wrong, just try again or try a new methodology.

 

How has the research you’ve conducted contributed to your professional or academic development?  

By working hands-on with bioinformatics tools such as BLAST, I have enhanced my technical skills in the genomics field. As a byproduct of this, I have deepened my knowledge of genomics and how they work through protein identifiers and serial numbers/codes. In terms of professional goals, if I were to receive the opportunity to present my findings at a conference, I would be able to fully explain not only the methodology, but also the results and what they could mean.
 

What advice would you give to a younger student wanting to get involved in research in your field?

For aspiring researchers in evolutionary biology, I recommend cultivating a strong foundation in molecular biology, genetics, and bioinformatics. Engage with current literature, seek out research opportunities such as internships or volunteer positions in labs, and don't hesitate to reach out to professors or researchers for mentorship and guidance. Persistence, curiosity, and a willingness to embrace interdisciplinary approaches will serve you well in exploring the fascinating complexities of evolutionary biology.