Genetic modification technology is a new molecular tool for targeted genome modification. It includes zinc finger nucleases (ZFN) technology, transcription activator-like effector nucleases (TALEN) technology and clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) (CRISPR-Cas) nucleases technology. All of these nucleases create DNA double-strand breaks (DSB) at chromosomal targeted sites and induce cell endogenous mechanisms that are primarily repaired by the non-homologous end joining (NHEJ) or homologous recombination (HR) pathway, resulting in targeted endogenous gene knock-out or exogenous gene insertion. In recent years, genetic modification technologies have been successfully applied to bacteria, yeast, human cells, fruit fly, zebra fish, mouse, rat, livestock, cynomolgus monkey, Arabidopsis, rice, tobacco, maize, sorghum, wheat, barley and other organisms, showing its enormous advantage in gene editing field. Especially, the newly developed CRISPR-Cas9 system arose more attention because of its low cost, high effectiveness, simplicity and easiness. We reviewed the principles and the latest research progress of these three technologies, as well as prospect of future research and applications.
Animals ; CRISPR-Cas Systems ; DNA Breaks, Double-Stranded ; Endonucleases ; Genetic Engineering ; methods ; Humans ; Mutagenesis, Insertional ; Mutagenesis, Site-Directed ; Plants ; Zinc Fingers

We first cloned the dsz operon of Pseudomonas delafieldii R-8 into the expressing plasmid (pPR9TT) to construct the recombinant plasmid pPR-dsz, and then reintroduced it into strain R-8 to obtain a muti-copy dsz operon engineering strain R-8-1. Compared with the wild-type, strain R-8-1 showed a higher desulfurization activity for dibenzothiophene (DBT). Initial rates of DBT removal by strain R-8-1 were 6.25 micromol/g dry cell/h, about 2-fold higher than that for wild-type strain. The recombinant cells were also applied in the desulfurization of diesel. It resulted in a 68% reduction of total sulfur from 310.8 mg/L to 100.1 mg/L, whereas only 53% of sulfur was removed by strain R-8. The stability of pPR-dsz in strain R-8-1 was studied. The results revealed the first obtain a muti-copy dsz operon engineering strain are helpful for further development in biodesulfurization.
Bacterial Proteins ; genetics ; metabolism ; Biodegradation, Environmental ; Genetic Engineering ; Genetic Enhancement ; methods ; Operon ; Oxygenases ; genetics ; Protein Engineering ; methods ; Pseudomonas ; genetics ; metabolism ; Sulfur ; metabolism ; Thiophenes ; metabolism

With the progess in studying gene structure and function of foot and mouth disease virus (FMDV), FMDV can express exogenous genes in different sites. Through transforming and modifying FMDV can achieve different application purposes such as improving virus titer, introducing tag, improving immune responses, and reducing pathogenicity. From the perspective of FMDV receiving inserted exogenous gene, this paper mainly describes the latest relevant developments of FMDV's expression to exogenous gene.
Foot-and-Mouth Disease Virus ; genetics ; Genetic Engineering ; Mutagenesis, Insertional

Genome editing is a useful research tool essentially applicable to gene therapy in the field of biotechnology, pharmaceutics and medicine. Scientists have developed three types of programmable nucleases for genome editing, and these include: Zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated) system particularly derived from bacterial adaptive immune system. Programmable nucleaseses occur double strand breaks (DSBs) on target strand, and a repair mechanism of DSBs introduces either non-homologous end joining (NHEJ) or homology directed repair (HDR), where the pathway is determined by presence of donor DNA template. In this sense, we can generate gene insertion, gene correction, point mutagenesis and chromosomal translocations via endogenous repair mechanism. However, these nucleases exhibit several discrepancies in the aspects of their compositions, targetable sites, efficiency and other characteristics. Here, we discuss on various characteristics of three programmable nucleases and potential outcomes of DSBs. Acknowledging the distinctions among these programmable nucleases will help scientists to select appropriate tools in genome engineering.
Biotechnology ; Clustered Regularly Interspaced Short Palindromic Repeats ; Deoxyribonuclease I ; DNA ; Genetic Engineering ; Genetic Therapy ; Genome* ; Humans ; Immune System ; Mutagenesis ; Mutagenesis, Insertional ; Tissue Donors ; Translocation, Genetic

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, 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

Genome shuffling methods were explored for Bacillus subtilis strain molecular breeding. Recycling protoplast fusion, recycling transformation and recycling universal transduction were used for genome shuffling in B. subtilis. Four strains with different nutrition-deficiency markers were used as initial strains. After five rounds protoplast fusion, transformation or transduction, the descendant with 4 markers had not been detected, and the rate of descendant with 3 markers were 4.53 x 10(-4), 1.64 x 10(-4), 4.47 x 10(-3), respectively. A computer program was made to simulate the recycling fusion process. Based on simulation result and comparing the genome shuffling result of B. subtilis in this experiment and that of Streptomyces coelicolor reported in references, effective genome shuffling needs a high recombination rate of at least between 10(-3) and 10(-2).
Bacillus subtilis ; classification ; genetics ; DNA Shuffling ; Genetic Techniques ; Genome, Bacterial ; genetics ; Protein Engineering ; Transformation, Bacterial

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

Transposons are the mobile and autonomic replication DNA fragments in genomes. With more understanding of the structure and function of transposons, numerous transposons have been developed to the genetics tool for gene function analysis, gene transformation and gene therapy. The low transpositional activity of the natural transposons is the main obstacles to the utilization of transposons. Recently, with the progress in bioinformatics and protein engineering methods, researchers have reconstructed and optimized natural transposases to create hyperactive transposases that catalyze the transposition with high efficiency. The resulted hyperactive transposons have been applied to gene-modification and gene-tagging. Meanwhile, transposase chimeras were created by protein fusion technology. The insertion characteristic of transposons were artificially regulated which could be utilized in gene therapy.
DNA Transposable Elements ; Gene Targeting ; Genetic Therapy ; Protein Engineering ; Transposases ; chemistry

The experiment was conducted by directed evolution strategy (error-prone PCR) to improve the activity of aflatoxin detoxifzyme with the high-throughput horse radish peroxidas and recessive brilliant green (HRP-RBG) screening system. We built up a mutant library to the order of 10(4). Two rounds of EP-PCR and HRP-RBG screening were used to obtain three optimum mutant strains A1773, A1476 and A2863. We found that mutant A1773 had upper temperature tolerance of 70 degrees C and that its enzyme activity was 6.5 times higher than that of the parent strain. Mutant strains A1476 worked well at pH 4.0 and its enzyme activity was 21 times higher than that of the parent strain. Mutant A2863 worked well at pH 4.0 and pH 7.5, and its enzyme activity was 12.6 times higher than that of the parent strain. With DNA sequencing we found that mutant A1773 revealed two amino acid substitutions, Glu127Lys and Gln613Arg. Mutant A1476 revealed four amino acid substitutions: Ser46Pro, Lys221Gln, Ile307Leu and Asn471lle. Mutant A2863 revealed four amino acid substitutions: Gly73Ser, Ile307Leu, Va1596Ala and Gln613Arg. The results provided a useful illustration for the deep understanding of the relationship between the function and structure of aflatoxin detoxifzyme.
Aflatoxin B1 ; antagonists & inhibitors ; chemistry ; Amino Acid Substitution ; Directed Molecular Evolution ; Enzyme Activation ; Enzyme Stability ; Multienzyme Complexes ; genetics ; metabolism ; Mutant Proteins ; genetics ; metabolism ; Point Mutation ; Polymerase Chain Reaction ; methods ; Protein Engineering