Liam M. Longo

Understanding the emergence and evolution of agency is one of the great challenges in both biological research and philosophy. Hiroki Kojima (University of Tokyo), Eran Agmon (University of Connecticut), and I will bring agential studies into the laboratory by constructing a real-time evolution platform in which populations of organic (B-life) and digital (A-life) organisms are under mutual control and poised to form mutualistic community structures. Will community structure promote the emergence of agential features in the A-life population? Stay tuned! Calls for two open positions in Tokyo (Longo Lab) and one open position in Connecticut (Agmon Lab with support mentorship from Co-I Kojima) will follow shortly.

After a brief stint at her home institution in Stockholm, Marina has returned to the Longo Lab to continue her research on the evolution of exon structure (and provide some much needed programming mentorship to all those around her). Welcome back, Marina!

Prof. Gruić Sovulj is an expert in the enzymology of amino-acyl tRNA synthetases, the enzymes that define the genetic code. During her 2-month visit to the Longo Lab at ELSI, she will use bioinformatic approaches to study the evolution of this most important enzyme class.

Tatsuya received a Bachelor's degree in Biological Chemistry from the University of Toronto. As a student in the ELSI Graduate Program, his research efforts will focus on the origin of life and the emergence of complex biopolymer structure. Welcome, Tatsuya!

My passion for science started with Science Fair, and so it was a great pleasure to be able to share my research on early protein evolution with these amazingly talented young scientists! Image credit: ELSI

Marina (left) is a Mathematics PhD student working in the laboratory of Lars Arvestad where she studies the evolution of exon duplication. At ELSI, she will explore the consequences of exon duplication from the perspective of protein structure evolution.

Sarah (right) is a Bioinformatics PhD student working in the laboratory of Peter Stadler where she develops methods for RNA structure prediction. At ELSI, she will study the forces that drive protein sequence convergence between distantly related species.

Nat/Ivy is a diverse and ubiquitous CoA-binding evolutionary lineage that catalyzes acyltransferase reactions, primarily converting thioesters into amides. At the heart of the Nat/Ivy fold is a phosphate-binding loop that bears a striking resemblance to that of P-loop NTPases – both are extended, glycine-rich loops situated between a β-strand and an α-helix. Nat/Ivy, therefore, represents an intriguing intersection between thioester chemistry, a putative primitive energy currency, and an ancient mode of phospho-ligand binding. Current evidence suggests that Nat/Ivy emerged independently of other cofactor-utilizing enzymes, and that the observed structural similarity – particularly of the cofactor binding site – is the product of shared constraints instead of shared ancestry. The reliance of Nat/Ivy on a β-α-β motif for CoA binding highlights the extent to which this simple structural motif may have been a fundamental evolutionary ‘nucleus’ around which modern cofactor-binding domains condensed, as has been suggested for HUP domains, Rossmanns, and P-loop NTPases. Finally, by dissecting the patterns of conserved interactions between Nat/Ivy families and CoA, the coevolution of the enzyme and the cofactor was analyzed. As with the Rossmann, it appears that the pyrophosphate moiety at the center of the cofactor predates the enzyme, suggesting that Nat/Ivy emerged sometime after the metabolite dephospho-CoA.