# Evolution of lysine and arginine biosynthesis revealed by substrate specificity of lysine biosynthetic enzymes in Thermus thermophilus

## TL;DR

This study shows that two enzymes in Thermus thermophilus can work on both lysine and arginine pathways, suggesting a shared evolutionary origin for these amino acid synthesis routes.

## Contribution

The study reveals substrate promiscuity in lysine biosynthetic enzymes and suggests a shared evolutionary origin with arginine biosynthesis.

## Key findings

- LysZ and LysY enzymes can act on intermediates from the arginine biosynthetic pathway.
- LysZ activity on arginine intermediates is about 60% of its activity on lysine intermediates.
- Phylogenetic analysis suggests a shared ancestral pathway for lysine and arginine biosynthesis.

## Abstract

Metabolic pathways are considered to originate from broad‐specificity ancestors that later diverged into specialized routes. Thermus thermophilus possesses an unusual amino group carrier protein (AmCP)‐mediated lysine biosynthetic pathway alongside a canonical arginine biosynthetic pathway. Although each route is considered specific to its cognate amino acid, several lysine biosynthetic enzymes have been shown to accept arginine intermediates. We herein investigated [LysW]‐aminoadipate kinase (LysZ; EC:2.7.2.17) and [LysW]‐L‐2‐aminoadipate 6‐phosphate reductase (LysY; EC:1.2.1.103), which catalyze the second and third steps, respectively, in the conversion of α‐aminoadipate (AAA) to lysine using amino group carrier protein LysW (AmCP), to define their specificity and evolutionary origin. To examine the potential promiscuity, we engineered LysX variants capable of synthesizing LysW‐Glu, an artificial LysW‐bound analogue that mimics an arginine pathway intermediate. LysZ exhibited activity for LysW‐Glu that was approximately 60% of the original activity for LysW‐AAA. The activity of LysY for LysW‐Glu phosphate was estimated to be approximately 15–20% of that observed with LysW‐AAA phosphate. The present study revealed that both enzymes can also act on an arginine biosynthetic intermediate, but with distinct degrees of efficiency. Phylogenetic reconstructions further suggested that an AmCP‐mediated biosynthetic pathway represents a primitive route for the synthesis of lysine and arginine in a primordial cell. More generally, the results obtained herein will contribute to a more detailed understanding of the evolutionary strategies employed by nature to specialize and expand metabolic pathways and adjust enzyme promiscuity.

Two enzymes from the Thermus thermophilus lysine biosynthetic pathway, LysZ and LysY, unexpectedly exhibit substrate promiscuity. They are able to recognize the LysW intermediates utilized by the ArgW‐mediated arginine route, even though the bacterium already possesses the canonical arginine biosynthetic pathway. This promiscuity suggests an evolutionary link between lysine and arginine biosynthesis, shedding new light on the evolution of essential amino acid pathways.