• Biotechnology and Bioprocess Engineering:BBE
• /
• v.7 no.3
• /
• pp.121-129
• /
• 2002

Existing methods for optimization of sequences by random mutagenesis generate libraries with a small number of mostly deleterious mutations, resulting in libraries containing a large fraction of non-functional clones that explore only a small part of sequence space. Large numbers of clones need to be screened to find the rare mutants with improvements. Library display formats are useful to screen very large libraries but impose screening limitations that limit the value of this approach for most commercial applications. By contrast, in both classical breeding and in DNA shuffling, natural diversity is permutated by homologous recombination, generating libraries of very high quality, from which improved clones can be identified with a small number of complex screens. Given that this small number of screens can be performed under the conditions of actual use of the product, commercially relevant improvements can be reliably obtained.

• Journal of Microbiology and Biotechnology
• /
• v.16 no.12
• /
• pp.2004-2007
• /
• 2006

An efficient method for the in vitro reassembly of homologous DNA sequences is presented. The proposed method involves obtaining single strands of homologous genes and hybridizing them to obtain partially hybridized heteroduplex DNA; cleaving the single-stranded regions of the heteroduplex DNA using S1 nuclease to generate double-strand DNA fragments; denaturing the double-strand DNA fragments to generate single-strand DNA fragments; conducting a series of polymerase chain reactions (PCR) using the single-strand DNA fragments as internal primers and a mixture of homologous DNA as templates to obtain elongated reassembled DNA; and finally, amplifying the reassembled DNA by a PCR using terminal primers. As a result, DNA reassembly could be achieved between homologous genes with a sequence similarity as low as 78%.

• Korean Journal of Microbiology
• /
• v.39 no.2
• /
• pp.76-82
• /
• 2003

To prepare evolved PHB depolymerase with increased activity for PHB or P(3HB-co-3HV) compared to the activity of the original PHB depolymerase from Alcaligenes faecalis T1, random mutation of the cloned PHB depolymerase gene was performed by using a DNA shuffling method. A library of mutated PHB depolymerase genes from A. faecalis T1 was fused to the ice nucleation protein (INP) gene from Pseudomonas syringae in pJHCl 1 and approximately 7,000 transformants were isolated. Using M9 minimal medium containing PHB or P(3HB-co-3HV) as the carbon source, mutants showing alteration in PHB depolymerase activity were selected from the transformants. The PHB depolymease activity of the transformants was confirmed by the formation of halo around colony and the turbidity decrease tests using culture supermatants. The catalytic activity of PHB depolymerase of the best mutant II-4 for PHB or P(3HB-co-13 mol% 3HV) was approximately 1.8-fold and 3.2-fold, respectively, higher than that of the original PHB depolymerase. DNA sequence analysis revealed that three amino acid residues (Ala209Val, Leu258Phe, and Asp263Thr) were substituted in II-4. From the mutational analysis, it was presumed that the substitution of amino acids near catalytic triad to more hydrophobic amino acids enhance the catalytic activity of PHB depolymerase from A. faecalis T1.

• Journal of Microbiology and Biotechnology
• /
• v.32 no.6
• /
• pp.800-807
• /
• 2022

Four aprE genes encoding alkaline serine proteases from B. subtilis strains were used as template genes for family gene shuffling. Shuffled genes obtained by DNase I digestion followed by consecutive primerless and regular PCR reactions were ligated with pHY300PLK, an E. coli-Bacillus shuttle vector. The ligation mixture was introduced into B. subtilis WB600 and one transformant (FSM4) showed higher fibrinolytic activity. DNA sequencing confirmed that the shuffled gene (aprEFSM4) consisted of DNA mostly originated from either aprEJS2 or aprE176 in addition to some DNA from either aprE3-5 or aprESJ4. Mature AprEFSM4 (275 amino acids) was different from mature AprEJS2 in 4 amino acids and mature AprE176 in 2 amino acids. aprEFSM4 was overexpressed in E. coli BL21 (DE3) by using pET26b(+) and recombinant AprEFSM4 was purified. The optimal temperature and pH of AprEFSM4 were similar to those of parental enzymes. However, AprEFM4 showed better thermostability and fibrinogen hydrolytic activity than the parental enzymes. The results indicated that DNA shuffling could be used to improve fibrinolytic enzymes from Bacillus sp. for industrial applications.

• BMB Reports
• /
• v.40 no.3
• /
• pp.419-425
• /
• 2007

In vitro directed evolution through DNA shuffling is a powerful molecular tool for creation of new biological phenotypes. E. coli $\beta$-galactosidase and $\beta$-glucuronidase are widely used, and their biological function, catalytic mechanism, and molecular structures are well characterized. We applied an in vitro directed evolution strategy through DNA shuffling and obtained five mutants named YG6764, YG6768, YG6769, YG6770 and YG6771 after two rounds of DNA shuffling and screening, which exhibited more $\beta$-glucuronidase activity than wild-type $\beta$-galactosidase. These variants had mutations at fourteen nucleic acid sites, resulting in changes in ten amino acids: S193N, T266A, Q267R, V411A, D448G, G466A, L527I, M543I, Q626R and Q951R. We expressed and purified those mutant proteins. Compared to the wild-type protein, five mutant proteins exhibited high $\beta$-glucuronidase activity. The comparison of molecular models of the mutated and wildtype enzymes revealed the relationship between protein function and structural modification.

• Journal of Microbiology and Biotechnology
• /
• v.19 no.12
• /
• pp.1536-1541
• /
• 2009

The DNA shuffling technique has been used to generate libraries of evolved enzymes in thermostability. We have shuffled two thermostable cytidine deaminases (CDAs) from Bacillus caldolyticus DSM405 (T53) and B. stearothermophilus IFO12550 (T101). The shuffled CDA library (SH1067 and SH1077 from the first round and SH2426 and SH2429 from the second round) showed various patterns in thermostability. The CDAs of SH1067 and SH1077 were more thermostable than that of T53. SH2426 showed 150% increased halftime than that of T53 at $70^{\circ}C$. The CDA of SH2429 showed about 200% decreased thermostability than that of T53 at $70^{\circ}C$. A single amino acid residue replacement that presented between SH1077 and SH2429 contributed to dramatic changes in specific activity and thermostability. On SDS-PAGE, the purified CDA of SH1077 tetramerized, whereas that of SH2429 denatured and became almost monomeric at $80^{\circ}C$. A simulated three-dimensional structure for the mutant CDA was used to interpret the mutational effect.

• Journal of Microbiology and Biotechnology
• /
• v.14 no.1
• /
• pp.153-157
• /
• 2004

Tyrosine phenol-lyase (TPL) is a useful enzyme for the synthesis of pharmaceutical aromatic amino acids. In the current study, sequential DNA shuffling and screening were used to enhance the stability of TPL. Twenty-thousand mutants were screened, and several improved variants were isolated. One variant named A13V, in which the $13^{th}$ amino acid alanine was substituted by valine, exhibited a higher temperature and denaturant stability than the wild-type TPL. The purified mutant TPL, A13V, retained about 60% of its activity at $76^\circ{C}$, whereas the activity of the wild-type TPL decreased to less than 20% at the same temperature. Plus, A13V exhibited about 50% activity with 3 M urea, while the wild-type TPL lost almost all its catalytic activity, indicating an increased denaturant tolerance in the mutant A13V. It is speculated that the substitution of Val for the Ala in the $\beta$-strand of the N-terminal arm was responsible for the heightened stabilization, and that the current results will contribute to further research on the structural stability of TPL.

• Korean Journal of Microbiology
• /
• v.46 no.4
• /
• pp.383-388
• /
• 2010

Alkaline protease-overproducing strains of Vibrio metschnikovii were developed by using the molecular evolution from the classical mutants V. metschnikovii L12-23, N4-8, and KS1. Each vapK (Vibrio alkaline protease K) was obtained from the genomic DNAs of mutants by PCR to carry out the DNA shuffling. The modified vapK-1 obtained by DNA shuffling was used again as a template for the error-prone PCR to make the vapK-2. Both genes were cloned in the plasmid pKF3 to construct the recombinant plasmids which have one or two copies of the modified genes. The recombinant plasmids were back-transformed to V. metschnikovii KS1 to construct recombinant V. metschnikovii that expresses the alkaline protease. About 3.9-fold more protease activity was measured in the strain which has the plasmid containing two copies of vapK-2 when compared to strain KS1. When compared to wild type V. metschnikovii RH530, 43-fold more activity was achieved. Comparison of amino acids among vapK, vapK-1, and vapK-2 revealed that the active sites was highly conserved and not changed. However, many amino acids except the active sites were changed. These results suggested that the changes in amino acids might play an important role in the increase of protease activity by allowing the easy access of substrate to active sites of the protease. The fermentation of alkaline protease from the V. metschnikovii KS1 harboring the plasmid that contains two copies of vapK-1 showed the possibility of this strain to be used as industrial producer.

• 한국생물공학회:학술대회논문집
• /
• 2002.04a
• /
• pp.52-52
• /
• 2002

• Proceedings of the Korean Society for Applied Microbiology Conference
• /
• 2001.06a
• /
• pp.47-57
• /
• 2001