Engineering of methionine-auxotroph Escherichia coli via parallel evolution of two enzymes from Corynebacterium glutamicum's direct-sulfurylation pathway enables its recovery in minimal medium

Matan Gabay, Inbar Stern, Nadya Gruzdev, Adi Cohen, Lucia Adriana-Lifshits, Tamar Ansbacher, Itamar Yadid*, Maayan Gal*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Methionine biosynthesis relies on the sequential catalysis of multiple enzymes. Escherichia coli, the main bacteria used in research and industry for protein production and engineering, utilizes the three-step trans-sulfurylation pathway catalyzed by L-homoserine O-succinyl transferase, cystathionine gamma synthase and cystathionine beta lyase to convert L-homoserine to L-homocysteine. However, most bacteria employ the two-step direct-sulfurylation pathway involving L-homoserine O-acetyltransferases and O-acetyl homoserine sulfhydrylase. We previously showed that a methionine-auxotroph Escherichia coli strain (MG1655) with deletion of metA, encoding for L-homoserine O-succinyl transferase, and metB, encoding for cystathionine gamma synthase, could be complemented by introducing the genes metX, encoding for L-homoserine O-acetyltransferases and metY, encoding for O-acetyl homoserine sulfhydrylase, from various sources, thus altering the Escherichia coli methionine biosynthesis metabolic pathway to direct-sulfurylation. However, introducing metX and metY from Corynebacterium glutamicum failed to complement methionine auxotrophy. Herein, we generated a randomized genetic library based on the metX and metY of Corynebacterium glutamicum and transformed it into a methionine-auxotrophic Escherichia coli strain lacking the metA and metB genes. Through multiple enrichment cycles, we successfully isolated active clones capable of growing in M9 minimal media. The dominant metX mutations in the evolved methionine-autotrophs Escherichia coli were L315P and H46R. Interestingly, we found that a metY gene encoding only the N-terminus 106 out of 438 amino acids of the wild-type MetY enzyme is functional and supports the growth of the methionine auxotroph. Recloning the new genes into the original plasmid and transforming them to methionine auxotroph Escherichia coli validated their functionality. These results show that directed enzyme-evolution enables fast and simultaneous engineering of new active variants within the Escherichia coli methionine direct-sulfurylation pathway, leading to efficient complementation.

Original languageEnglish
Article numbere00236
JournalMetabolic Engineering Communications
Volume18
DOIs
StatePublished - Jun 2024

Funding

FundersFunder number
Gertner Institute for the Medical Nano System
Gertner Institute for Medical Nano System
Gertner Institute for the Medical Nano System in Tel Aviv University
Tel Aviv University
ADAMA Center for Novel Delivery Systems
Ministry of Agriculture and Rural Development21-36-0003
Ministry of Agriculture and Rural Development
Ministry of Science and Technology, Israel0005749
Ministry of Science and Technology, Israel

    Keywords

    • Direct-sulfurylation
    • Directed enzyme evolution
    • Escherichia coli
    • L-homoserine O-Acetyltransferases
    • Methionine biosynthesis
    • O-acetyl homoserine sulfhydrylase

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