Molecular engineering of cellulases can improve enzymatic activity and efficiency. Recently, the Carbohydrate-Active enZYmes Database (CAZy), including glycoside hydrolase (GH) families, has been established with the development of Omics and structural measurement technologies. Molecular engineering based on GH families can obviously decrease the probing space of target sequences and structures, and increase the odds of experimental success. Besides, the study of cellulase active-site architecture paves the way toward the explanation of catalytic mechanism. This review focuses on the main GH families and the latest progresses in molecular engineering of catalytic domain. Based on the combination of analysis of a large amount of data in the same GH family and their conservative active-site architecture information, rational design will be an important direction for molecular engineering and promote the rapid development of the conversion of biomass.
Catalytic Domain ; genetics ; Cellulase ; chemistry ; genetics ; Directed Molecular Evolution ; methods ; Evolution, Molecular ; Glycoside Hydrolases ; chemistry ; genetics ; Protein Engineering ; methods

As an efficient and promising protein engineering strategy, directed evolution includes the construction of mutant libraries and screening of desirable mutants. A rapid and high-throughput screening method has played a critical role in the successful application of directed evolution strategy. We reviewed several high-throughput screening tools which have great potential to be applied in directed evolution. The development of powerful high-throughput screening tools will make great contributions to the advancement of protein engineering.
Directed Molecular Evolution ; methods ; High-Throughput Screening Assays ; methods ; Mutagenesis, Site-Directed ; methods ; Mutant Proteins ; genetics ; Protein Engineering ; methods

The application of in vitro selection method to isolate nucleic acids, peptides and proteins according to their functions has been studied intensively in recent years. In vitro display technologies are not limited by cellular transformation efficiencies; thus, very large libraries of up to 10(13)-10(14) members can be built. The most popular in vitro display technologies are ribosome display and mRNA display; ribosome display achieves the mRNA-ribosome-nascent peptide complexes by stalling the translating ribosome in an in vitro translation reaction. In mRNA display, the mRNA-protein complex is achieved by binding the two macromolecules through a small adaptor molecule, typically puromycin; these mRNA-peptide fusions can then be purified and subjected to in vitro selection. In vitro display technologies provide a different approach to the in vitro selection and directed evolution of peptides and proteins. This review focuses on the principle and method of ribosome display and mRNA display technologies, and discusses their applications.
Animals ; Directed Molecular Evolution ; Gene Library ; Humans ; Peptide Library ; Protein Interaction Mapping ; methods ; RNA, Messenger ; chemistry ; genetics ; Ribosomes ; chemistry ; genetics

Directed evolution, which is also called molecular evolution, or artificial evolution, combines random mutagenesis and directed selection. In previous studies, it has been extensively applied for the improvement of enzyme catalytic properties and stability, as well as the expanding of substrate specificity. In recent years, directed evolution was also employed in metabolic engineering of promoters for improving their strength and function, and the engineering of global transcription machinery. These techniques contribute to breeding more tolerant strains against environmental stress, as well as strains with improved fermentation efficiency. In this article, we reviewed the applications of directed evolution in the metabolic engineering of promoters and global transcription machinery. These techniques enabled fine-tuning of gene expression and simultaneous alternation of multiple gene transcription inside the cells, and thus are powerful new tools for metabolic engineering.
Directed Molecular Evolution ; Genetic Engineering ; Industrial Microbiology ; methods ; Metabolism ; Promoter Regions, Genetic ; genetics ; Saccharomyces cerevisiae ; genetics ; Transcription, Genetic ; genetics

Random mutagenesis on Bacillus pumilus lipase YZ02 gene was conducted by using error-prone PCR strategy. Through two cycles of directed evolution, two optimum mutants BpL1-7 and BpL2-1369 with lipase activity improved 2 folds and 6 folds respectively were screened. The sequence of BpL2-1369 lipase gene showed that four nucleotides substitution, T61C, C147T, A334G and T371A have occurred, and three of them caused amino acid changes. Thus, amine acid Ser21 was changed into Pro21, Arg112 to Gly112, and Leu124 to His124. According to the 3D structure of Bacillus pumilus lipase mimicked by SWISS-MODEL Repository, three mutated amino acids were located at the third amino acid of the first alpha-helix, the turn between the fourth and fifth beta fold, and the first amino acid of the fifth beta fold, respectively. The BpL and BpL2-1369 genes were ligated into pET28a vector, and transferred into E. coli BL21 (DE3). After induced by IPTG the lipases were purified and characterized. The results showed that the specific activity of the evolved lipase was 1.31-fold than that of the wild lipase, and the Km decreased from 8.24 mmol/L to 7.17 mmol/L. The pH stability of the evolved lipase was better than wild lipase when pH>8.0.
Bacillus ; enzymology ; genetics ; Directed Molecular Evolution ; Lipase ; chemistry ; genetics ; metabolism ; Point Mutation ; Polymerase Chain Reaction ; methods ; Protein Engineering ; Sequence Analysis, Protein

D-lactonohydrolase is useful in the procedure of resolution of racemic pantolactone to produce D-pantolactone, but the activity and stability under low pH of the wild type enzyme is not satisfactory enough to be applied to industrial production. The expected properties of wild type enzyme were enhanced by directed evolution. According to the formation of products and pH indicators, a screening system was designed. After three sequential error prone PCR and one round DNA shuffling followed by screening, Mut E-861, the best mutant with improved activity and stability under low pH situation was obtained. Gene analysis of the Mut E-861 mutant indicated that the mutant enzyme had A352C, G721A mutations and a silent mutation of position 1038. Moreover, the activity and stability of Mut E-861 were determined. The results showed that the activity of this mutant was 5.5-fold higher than that of wild type, and the stability under low pH was improved at no expense of D-lactonohydrolase activity. After incubated at pH 6.0 and pH 5.0 the activity of D-lactonohydrolase could be retained 75% to 50%, however, compared with 40% to 20% for wild type.
Carboxylic Ester Hydrolases ; biosynthesis ; genetics ; DNA Shuffling ; Directed Molecular Evolution ; Enzyme Stability ; Escherichia coli ; enzymology ; genetics ; Mutagenesis, Site-Directed ; Mutant Proteins ; genetics ; metabolism ; Polymerase Chain Reaction ; methods ; Protein Engineering ; Saccharomyces cerevisiae ; enzymology ; genetics

Directed evolution was conducted to improve the thermostability of lipase from Rhizopus chinensis CCTCC M201021. Mutations were introduced by two rounds of error-prone PCR and mutant lipase was selected by fast-blue RR top agar screening. Two positive variants were selected in the first-round and four in the second-round screening process. Ep2-4 was proved as the most thermostable lipase and its DNA sequencing revealed three amino acid substitutions: A129S, P168L and V329A. Compared with the parent, its half-life at 60 degrees C was 5.4- times longer and T50 was 7.8 degrees higher. Purified lipase of Ep2-4 was characterized and the result shows that its thermostability improved without compromising enzyme activity. According to the mimicked protein structure, mutation A129S formed a hydrogen bond with Gln133 and improved the thermostability by increasing the hydrophilicity and polarity of protein; mutation P168L by forming a hydrophobic bond with the nearby Leu164.
Cloning, Molecular ; Directed Molecular Evolution ; methods ; Enzyme Stability ; genetics ; Hot Temperature ; Industrial Microbiology ; Lipase ; chemistry ; genetics ; Mutation ; Pichia ; genetics ; metabolism ; Polymerase Chain Reaction ; methods ; Protein Engineering ; methods ; Rhizopus ; enzymology

Directed evolution of transcription factors can be employed to effectively improve the phenotypes which are controlled by multiple genetic loci. In this study, we used error-prone PCR for the directed evolution of SPT3, which is the component of yeast Spt-Ada-Gcn5-acetyltransferase (SAGA) complex responsible for the transcription of stress-related genes, and studied its effect on the improvement of ethanol tolerance. Mutant library was constructed by ligating the error-prone PCR products with a modified pYES2.0 plasmid, and the expression plasmids were subsequently transformed to yeast industrial strain Saccharomyces cerevisiae 4126. One mutant strain M25 showing superior growth in presence of 10% ethanol was selected. M25 produced 11.7% more ethanol than the control strain harboring the empty vector when 125 g/L glucose was used as substrate. This study revealed that SPT3 is an important transcription factor for the metabolic engineering of yeast ethanol tolerance.
Directed Molecular Evolution ; methods ; Drug Resistance, Fungal ; Drug Tolerance ; Ethanol ; metabolism ; pharmacology ; Industrial Microbiology ; methods ; Saccharomyces cerevisiae ; drug effects ; genetics ; metabolism ; Saccharomyces cerevisiae Proteins ; genetics ; Trans-Activators ; genetics ; Transcription Factors ; genetics

Directed evolution was used to improve the performance of beta-1,3-1,4-glucanase (designated as PtLicl6A) from Paecilomyces thermophila J18 under acidic condition. A mutant library was constructed by error-prone PCR and DNA shuffling, and positive clones were screened by Congo red staining. More than 1 500 mutants were selected. One mutant (PtLic16AM1) exhibited an optimal activity at pH 5.5, while the optimal pH of the wild-type enzyme was 7.0. The mutant PtLic16AM1 kept the high specific activity and thermotolerence of the wild-type enzyme. Sequence analysis revealed that the mutant enzyme has four sense substitutions which caused four amino acid substitutions - namely T58S, Y110N, G195E and D221G.. Homology modeling showed that among the four amino acid substitutions, Y110N was near the active site of the enzyme, while the other three was distant. T58S and G195E may play key roles in the change of optimal pH. This study provided a new perspective of obtaining applicable 3-1,3-1,4-glucanase for industrial use.
Catalysis ; Directed Molecular Evolution ; methods ; Endo-1,3(4)-beta-Glucanase ; biosynthesis ; genetics ; metabolism ; Enzyme Stability ; Hot Temperature ; Hydrogen-Ion Concentration ; Mutant Proteins ; metabolism ; Mutation ; Paecilomyces ; classification ; enzymology ; genetics ; Protein Engineering ; methods

Firstly, We used error-prone PCR to induce mutations on Armillariella tabescens MAN47 beta-mannanase gene, Secondly, we cloned the mutated fragments into secreted expression vector pYCalpha, Then the recombinant plasmids were transformed into Saccharomyces cerevisiae BJ5465 after amplified and extracted in DH5alpha cells. Through three cycles of error-prone PCR we built a mutant database, Then we screened one optimum (named M262) from about 104 mutants. The evoluted MAN47 beta-mannanase displayed both higher thermal stability and activity than wide type. The evoluted enzyme M262 retained high activity after treatment at 80 degrees C for 30 min, whereas, the wild type nearly lost activity under this condition. Meanwhile, the activity of M262 can reach to 25 U/mL, which is 4.3 times as wide type under optimum temperature. In addition, pH stability and pH range of evoluted enzyme M262 were both improved compared with wild-type enzyme. The optimum pH was estimated to be similar to that of wild-type enzyme. The sequence comparison illustrated that there were three nucleotide substitutions (T343A/C827T/T1139C) which carried corresponding amino acid changes (Ser115Thr/Thr276Met/Val380Ala). According to homologous modeling by SWISS-MODEL Repository, three mutated amino acids located at the sixth amino acid of the fourth beta-sheet, the first amino acid of the sixth alpha-helix, the turn between the tenth and eleventh beta-sheet, respectively.
Armillaria ; classification ; enzymology ; genetics ; Directed Molecular Evolution ; Enzyme Stability ; Escherichia coli ; enzymology ; genetics ; Hot Temperature ; Mutant Proteins ; genetics ; metabolism ; Point Mutation ; Polymerase Chain Reaction ; methods ; Protein Engineering ; Recombinant Proteins ; genetics ; metabolism ; Saccharomyces cerevisiae ; enzymology ; genetics ; beta-Mannosidase ; chemistry ; genetics ; metabolism