Enhanced Thermostability and Catalytic Activity of Streptomyces mobaraenesis Transglutaminase by Rationally Engineering Its Flexible Regions.

Streptomyces mobaraenesis transglutaminase can catalyze the cross-linking of proteins, which has been widely used in food processing. In this study, we rationally modified flexible regions to further improve the thermostability of FRAPD-TGm2 (S2P-S23V-Y24N-E28T-S199A-A265P-A287P-K294L), a stable mutant of the transglutaminase constructed in our previous study. First, five flexible regions of FRAPD-TGm2 were identified by molecular dynamics simulations at 330 and 360 K. Second, a script based on Rosetta Cartesian_ddg was developed for virtual saturation mutagenesis within the flexible regions far from the substrate binding pocket, generating the top 18 mutants with remarkable decreases in folding free energy. Third, from the top 18 mutants, we identified two mutants (S116A and S179L) with increased thermostability and activity. Finally, the above favorable mutations were combined to obtain FRAPD-TGm2-S116A-S179L (FRAPD-TGm2A), exhibiting a half-life of 132.38 min at 60 °C (t1/2(60 °C)) and a specific activity of 79.15 U/mg, 84 and 21% higher than those of FRAPD-TGm2, respectively. Therefore, the current result may benefit the application of S. mobaraenesis transglutaminase at high temperatures.

[1]  Qiuhua Wu,et al.  Improved thermostability, acid tolerance as well as catalytic efficiency of Streptomyces rameus L2001 GH11 xylanase by N-terminal replacement. , 2022, Enzyme and microbial technology.

[2]  F. Ahmad,et al.  Thermal stability enhancement: Fundamental concepts of protein engineering strategies to manipulate the flexible structure. , 2022, International journal of biological macromolecules.

[3]  Jianghua Li,et al.  Significantly Enhanced Thermostability of Aspergillus niger Xylanase by Modifying Its Highly Flexible Regions. , 2022, Journal of agricultural and food chemistry.

[4]  Jian Chen,et al.  Significantly Improving the Thermostability and Catalytic Efficiency of Streptomyces mobaraenesis Transglutaminase through Combined Rational Design. , 2021, Journal of agricultural and food chemistry.

[5]  Lian Xu,et al.  Design of a PL18 alginate lyase with flexible loops and broader entrance to enhance the activity and thermostability. , 2021, Enzyme and microbial technology.

[6]  D. Ivankov,et al.  Best templates outperform homology models in predicting the impact of mutations on protein stability , 2021, bioRxiv.

[7]  H. Fuchsbauer Approaching transglutaminase from Streptomyces bacteria over three decades , 2021, The FEBS journal.

[8]  S. Razavi,et al.  Recent advances in microbial transglutaminase biosynthesis and its application in the food industry , 2021 .

[9]  E. Suzuki,et al.  Effect of introducing a disulfide bridge on the thermostability of microbial transglutaminase from Streptomyces mobaraensis , 2021, Applied Microbiology and Biotechnology.

[10]  Jian Chen,et al.  Enhanced Production of Transglutaminase in Streptomyces mobaraensis through Random Mutagenesis and Site-Directed Genetic Modification. , 2021, Journal of agricultural and food chemistry.

[11]  Yan Xu,et al.  Computational design of noncanonical amino acid-based thioether staples at N/C-terminal domains of multi-modular pullulanase for thermostabilization in enzyme catalysis , 2021, Computational and structural biotechnology journal.

[12]  B. Moritz,et al.  Enzymatic activity and thermoresistance of improved microbial transglutaminase variants , 2019, Amino Acids.

[13]  Martin Fechner,et al.  More bang for your buck: Improved use of GPU nodes for GROMACS 2018 , 2019, J. Comput. Chem..

[14]  S. Knapp,et al.  Structure of a glutamine donor mimicking inhibitory peptide shaped by the catalytic cleft of microbial transglutaminase , 2018, The FEBS journal.

[15]  Bian Wu,et al.  Engineering improved thermostability of the GH11 xylanase from Neocallimastix patriciarum via computational library design , 2018, Applied Microbiology and Biotechnology.

[16]  Jens Rudat,et al.  FoldX as Protein Engineering Tool: Better Than Random Based Approaches? , 2018, Computational and structural biotechnology journal.

[17]  Shaotong Jiang,et al.  Improvement of the activity and thermostability of microbial transglutaminase by multiple-site mutagenesis , 2018, Bioscience, biotechnology, and biochemistry.

[18]  Jaroslav Bendl,et al.  FireProt: web server for automated design of thermostable proteins , 2017, Nucleic Acids Res..

[19]  Paul A. Dalby,et al.  Two strategies to engineer flexible loops for improved enzyme thermostability , 2017, Scientific Reports.

[20]  David E. Kim,et al.  Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules. , 2016, Journal of chemical theory and computation.

[21]  Berk Hess,et al.  GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers , 2015 .

[22]  C. Simmerling,et al.  ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. , 2015, Journal of chemical theory and computation.

[23]  Yang Zhang,et al.  I-TASSER server: new development for protein structure and function predictions , 2015, Nucleic Acids Res..

[24]  Yang Zhang,et al.  The I-TASSER Suite: protein structure and function prediction , 2014, Nature Methods.

[25]  D. Baker,et al.  Relaxation of backbone bond geometry improves protein energy landscape modeling , 2014, Protein science : a publication of the Protein Society.

[26]  Jian Chen,et al.  Enhanced thermal stability of Pseudomonas aeruginosa lipoxygenase through modification of two highly flexible regions , 2014, Applied Microbiology and Biotechnology.

[27]  M. Kieliszek,et al.  Microbial transglutaminase and its application in the food industry. A review , 2013, Folia Microbiologica.

[28]  Ross C. Walker,et al.  An overview of the Amber biomolecular simulation package , 2013 .

[29]  Richard A. Goldstein,et al.  Assessing Predictors of Changes in Protein Stability upon Mutation Using Self-Consistency , 2012, PloS one.

[30]  M. Pietzsch,et al.  Increased thermostability of microbial transglutaminase by combination of several hot spots evolved by random and saturation mutagenesis , 2012, Amino Acids.

[31]  N. Shimba,et al.  Screening for improved activity of a transglutaminase from Streptomyces mobaraensis created by a novel rational mutagenesis and random mutagenesis , 2010, Applied Microbiology and Biotechnology.

[32]  J. Buchert,et al.  Cross-linking of β-casein by Trichoderma reesei tyrosinase and Streptoverticillium mobaraense transglutaminase followed by SEC-MALLS. , 2009 .

[33]  Thomas Henle,et al.  Affinity of microbial transglutaminase to αs1-, β-, and acid casein under atmospheric and high pressure conditions. , 2009, Journal of agricultural and food chemistry.

[34]  K. Ohta,et al.  Dependence of microbial transglutaminase on meat type in myofibrillar proteins cross-linking , 2009 .

[35]  M. Pietzsch,et al.  Random mutagenesis of a recombinant microbial transglutaminase for the generation of thermostable and heat-sensitive variants. , 2008, Journal of biotechnology.

[36]  E. Curotto,et al.  Transglutaminase effects on gelation capacity of thermally induced beef protein gels , 2006 .

[37]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[38]  A. Matsuura,et al.  Purification and Characteristics of a Novel Transglutaminase Derived from Microorganisms , 1989 .