Rational design and structure-based engineering of alkaline pectate lyase from Paenibacillus sp. 0602 to improve thermostability

Zhanping Zhou,Xiao Wang

doi:10.1186/s12896-021-00693-8

Abstract

BackgroundRamie degumming is often carried out at high temperatures; therefore, thermostable alkaline pectate lyase (PL) is beneficial for ramie degumming for industrial applications. Thermostable PLs are usually obtained by exploring new enzymes or reconstructing existing enzyme by rational design. Here, we improved the thermostability of an alkaline pectate lyase (PelN) from Paenibacillus sp. 0602 with rational design and structure-based engineering.ResultsFrom 26 mutants, two mutants of G241A and G241V showed a higher thermostability compared with the wild-type PL. The mutant K93I showed increasing specific activity at 45 °C. Subsequently, we obtained combinational mutations (K93I/G241A) and found that their thermostability and specific activity improved simultaneously. The K93I/G241A mutant showed a half-life time of 15.9 min longer at 60 °C and a melting temperature of 1.6 °C higher than those of the wild PL. The optimum temperature decreased remarkably from 67.5 °C to 60 °C, accompanied by a 57% decrease in Km compared with the Km value of the wild-type strain. Finally, we found that the intramolecular interaction in PelN was the source in the improvements of molecular properties by comparing the model structures. Rational design of PelN was performed by stabilizing the α-helices with high conservation and increasing the stability of the overall structure of the protein. Two engineering strategies were applied by decreasing the mutation energy calculated by Discovery Studio and predicting the free energy in the process of protein folding by the PoPMuSiC algorithm.ConclusionsThe results demonstrated that the K93I/G241A mutant was more suitable for industrial production than the wild-type enzyme. Furthermore, the two forementioned strategies could be extended to reveal engineering of other kinds of industrial enzymes.

Highlights

Ramie degumming is often carried out at high temperatures; thermostable alkaline pectate lyase (PL) is beneficial for ramie degumming for industrial applications
The combined mutant K93I/G241A displayed the Conclusions In conclusion, the alkaline PelN from the Paenibacillus sp. 0602 was successfully engineered by the PoPMuSiC algorithm and conformational analysis for increasing the protein thermostability in this study
The variant K93I/G241A should be more efficient in industrial applications with a higher specific activity at moderate temperature that could significantly reduce energy consumption

Summary

Introduction

Ramie degumming is often carried out at high temperatures; thermostable alkaline pectate lyase (PL) is beneficial for ramie degumming for industrial applications. We improved the thermostability of an alkaline pectate lyase (PelN) from Paenibacillus sp. Bio-scouring is one of the most important industrial applications of alkaline Pels [2, 4, 5]. Bio-scouring shows obvious advantages than conventional chemical degumming [6,7,8,9]. In textile industry, degumming process is usually executed at the temperature from 40 °C to 70 °C and in alkaline condition of pH (8–11) [10]. It is desirable for Pels to keep stable and active under the corresponding thermal and alkaline conditions for industrial application. Thermostability is a major obstacle on PelN application in industrial degumming

Methods

Results

Discussion

Conclusion