Rational design of S-adenosylmethionine decarboxylase SpeD and spermidine synthase SpeE for green synthesis of spermidine

Abstract

Spermidine, a natural polyamine, possesses multiple biological activities and holds excellent application value. However, the low-activity enzymes in spermidine synthesis pathway limits spermidine production, including S-adenosylmethionine decarboxylase (SpeD) and spermidine synthase (SpeE). In Bacillus amyloliquefaciens PM1 with xylose as substrate, this study performed the alanine scanning mutagenesis to screen the beneficial mutants of SpeD and SpeE by rational design. Therein, the spermidine titers of mutants PM1/speD^I39A/D22A and PM1/speE^I108A/T54A were improved by 53 % and 44 % compared to the control strain, respectively, and the enzyme activities of the SpeD^I39A/D22A and SpeE^I108A/T54A increased by 58 % and 44 % accordingly. The mechanism of the enhanced enzymatic activity was further explained by molecular dynamics simulations. Moreover, the optimal engineering strain PM1::D/E was constructed by combination of speD^I39A/D22A and speE^I108A/T54A to enhance spermidine pathway. Through fed-batch fermentation, the maximum spermidine titer reached 683.14 mg/L, representing a 16.38-fold increase in spermidine production compared with the unmodified strain PM1. This study provides a novel strategy for green synthesis of spermidine from xylose, which will promote the clean and efficient production of spermidine.