Engineering of the Lrp/AsnC-type transcriptional regulator DecR as a genetically encoded biosensor for multilevel optimization of L-cysteine biosynthesis pathway in Escherichia coli

L-cysteine is an important sulfur-containing amino acid being difficult to produce by microbial fermentation. Due to the lack of high-throughput screening methods, existing genetically engineered bacteria have been developed by simply optimizing the expression of L-cysteine-related genes one by one. To overcome this limitation, in this study, a biosensor-based approach for multilevel biosynthetic pathway optimization of L-cysteine from the DecR regulator variant of Escherichia coli was applied. Through protein engineering, we obtained the DecRN29Y/C81E/M90Q/M99E variant-based biosensor with improved specificity and an 8.71-fold increase in dynamic range. Using the developed biosensor, we performed high-throughput screening of the constructed promoter and RBS combination library, and successfully obtained the optimized strain, which resulted in a 6.29-fold increase in L-cysteine production. Molecular dynamics (MD) simulations and electrophoretic mobility shift analysis (EMSA) showed that the N29Y/C81E/M90Q/M99E variant had enhanced induction activity. This enhancement may be due to the increased binding of the variant to DNA in the presence of L-cysteine, which enhances transcriptional activation. Overall, our biosensor-based strategy provides a promising approach for optimizing biosynthetic pathways at multiple levels. The successful implementation of this strategy demonstrates its potential for screening improved recombinant strains.

Escherichia coli Uses a Dedicated Importer and Desulfidase To Ferment Cysteine

CyuA of Escherichia coli is an inducible desulfidase that degrades cysteine to pyruvate, ammonium, and hydrogen sulfide. Workers have conjectured that its role may be to defend bacteria against the toxic effects of cysteine. However, cyuA sits in an operon alongside cyuP, which encodes a cysteine importer that seems ill suited to protecting the cell from environmental cysteine. In this study, transport measurements established that CyuP is a cysteine-specific, high-flux importer. The concerted action of CyuP and CyuA allowed anaerobic E. coli to employ cysteine as either the sole nitrogen or the sole carbon/energy source. CyuA was essential for this function, and although other transporters can slowly bring cysteine into the cell, CyuP-proficient cells outcompeted cyuP mutants. Cells immediately consumed the ammonia and pyruvate that CyuA generated, with little or none escaping from the cell. The expression of the cyuPA operon depended upon both CyuR, a cysteine-activated transcriptional activator, and Crp. This control is consistent with its catabolic function. In fact, the cyuPA operon sits immediately downstream of the thrABCDEFG operon, which allows the analogous fermentation of serine and threonine; this arrangement suggests that this gene cluster may have moved jointly through the anaerobic biota, providing E. coli with the ability to ferment a limited set of amino acids. Interestingly, both the cyu- and thr-encoded pathways depend upon oxygen-sensitive enzymes and cannot contribute to amino acid catabolism in oxic environments.