Recent advances in genetic engineering tools based on synthetic biology

Jun Ren,Jingyu Lee,Dokyun Na 한국미생물학회 2020 The journal of microbiology Vol.58 No.1

Genome-scale engineering is a crucial methodology to rationally regulate microbiological system operations, leading to expected biological behaviors or enhanced bioproduct yields. Over the past decade, innovative genome modification technologies have been developed for effectively regulating and manipulating genes at the genome level. Here, we discuss the current genome-scale engineering technologies used for microbial engineering. Recently developed strategies, such as clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9, multiplex automated genome engineering (MAGE), promoter engineering, CRISPR-based regulations, and synthetic small regulatory RNA (sRNA)-based knockdown, are considered as powerful tools for genome-scale engineering in microbiological systems. MAGE, which modifies specific nucleotides of the genome sequence, is utilized as a genome-editing tool. Contrastingly, synthetic sRNA, CRISPRi, and CRISPRa are mainly used to regulate gene expression without modifying the genome sequence. This review introduces the recent genome-scale editing and regulating technologies and their applications in metabolic engineering.

A New Chemico-physical Method for Effective Bacterial Transformation

Jun REN,Phuong N.L VO,Yong Sung PARK,Dokyun NA,Seung Min YOO 한국생물공학회 2019 한국생물공학회 학술대회 Vol.2019 No.4

Evaluation of Various Escherichia coli Strains for Enhanced Lycopene Production

( Jun Ren ),( Junhao Shen ),( Thi Duc Thai ),( Min-gyun Kim ),( Seung Ho Lee ),( Wonseop Lim ),( Dokyun Na ) 한국미생물생명공학회 2023 Journal of microbiology and biotechnology Vol.33 No.7

Lycopene is a carotenoid widely used as a food and feed supplement due to its antioxidant, anti-inflammatory, and anti-cancer functions. Various metabolic engineering strategies have been implemented for high lycopene production in Escherichia coli, and for this purpose it was essential to select and develop an E. coli strain with the highest potency. In this study, we evaluated 16 E. coli strains to determine the best lycopene production host by introducing a lycopene biosynthetic pathway (crtE, crtB, and crtI genes cloned from Deinococcus wulumuqiensis R12 and dxs, dxr, ispA, and idi genes cloned from E. coli). The 16 lycopene strain titers diverged from 0 to 0.141 g/l, with MG1655 demonstrating the highest titer (0.141 g/l), while the SURE and W strains expressed the lowest (0 g/l) in an LB medium. When a 2 × YTg medium replaced the MG1655 culture medium, the titer further escalated to 1.595 g/l. These results substantiate that strain selection is vital in metabolic engineering, and further, that MG1655 is a potent host for producing lycopene and other carotenoids with the same lycopene biosynthetic pathway.

Experimental Investigation on Energy Mechanism of Freezing-Thawing Treated Sandstone under Uniaxial Static Compression

Hongwei Deng,Songtao Yu,Junren Deng,Bo Ke,Feng Bin 대한토목학회 2019 KSCE JOURNAL OF CIVIL ENGINEERING Vol.23 No.5

To gain a further understanding of Freeze-Thaw weathering effect on the damage of sandstone from the perspective of energy analysis, uniaxial static compression tests were conducted on sandstone samples that suffered 0, 20, 60, 100 and 140 freezingthawing cycles. Then total input strain energy, releasable elastic strain energy, dissipated energy and freezing-thawing induced damage of samples under uniaxial static compression tests were calculated and analyzed. In the mean time, the energy absorption of sandstone under dynamic loading tests (SHPB (Split-Hopkinson pressure bar) experiments) were cited and made a contrast with the dissipated energy of samples under uniaxial static compression tests. The results show that the tangent modulus, total input strain energy, releasable elastic strain energy and dissipated energy of samples decrease with Freezing-Thawing cycles go on, while the freezing-thawing induced damage grow with freezing-thawing cycles increase. In term of energy used for destroying rock samples in different test modes, less energy is needed for destroying samples in uniaxial static compression tests and it decreases with F-T cycles increase, while more energy is needed for destroying samples in dynamic impact loading and it increases with F-T cycles increase. In addition, the number of fragments of broken sample increase with the F-T cycles both in uniaxial static compression tests and dynamic loading tests, and sample under dynamic loading tests is more broken than sample under uniaxial static compression tests.

Nanoarchitectured air-stable supported lipid bilayer incorporating sucrose–bicelle complex system

Tae Hyunhyuk,Park Soohyun,Ma Gamaliel Junren,Cho Nam-Joon 나노기술연구협의회 2022 Nano Convergence Vol.9 No.3

Cell-membrane-mimicking supported lipid bilayers (SLBs) provide an ultrathin, self-assembled layer that forms on solid supports and can exhibit antifouling, signaling, and transport properties among various possible functions. While recent material innovations have increased the number of practically useful SLB fabrication methods, typical SLB platforms only work in aqueous environments and are prone to fluidity loss and lipid-bilayer collapse upon air exposure, which limits industrial applicability. To address this issue, herein, we developed sucrose–bicelle complex system to fabricate air-stable SLBs that were laterally mobile upon rehydration. SLBs were fabricated from bicelles in the presence of up to 40 wt% sucrose, which was verified by quartz crystal microbalance-dissipation (QCM-D) and fluorescence recovery after photobleaching (FRAP) experiments. The sucrose fraction in the system was an important factor; while 40 wt% sucrose induced lipid aggregation and defects on SLBs after the dehydration–rehydration process, 20 wt% sucrose yielded SLBs that exhibited fully recovered lateral mobility after these processes. Taken together, these findings demonstrate that sucrose–bicelle complex system can facilitate one-step fabrication of air-stable SLBs that can be useful for a wide range of biointerfacial science applications.

Temperature-Induced Denaturation of BSA Protein Molecules for Improved Surface Passivation Coatings

Park, Jae Hyeon,Jackman, Joshua A.,Ferhan, Abdul Rahim,Ma, Gamaliel Junren,Yoon, Bo Kyeong,Cho, Nam-Joon American Chemical Society 2018 ACS APPLIED MATERIALS & INTERFACES Vol.10 No.38

<P>Bovine serum albumin (BSA) is the most widely used protein for surface passivation applications, although it has relatively weak, nonsticky interactions with hydrophilic surfaces such as silica-based materials. Herein, we report a simple and versatile method to increase the stickiness of BSA protein molecules adsorbing onto silica surfaces, resulting in up to a 10-fold improvement in blocking efficiency against serum biofouling. Circular dichroism spectroscopy, dynamic light scattering, and nanoparticle tracking analysis showed that temperature-induced denaturation of BSA proteins in bulk solution resulted in irreversible unfolding and protein oligomerization, thereby converting weakly adhesive protein monomers into a more adhesive oligomeric form. The heat-treated, denatured BSA oligomers remained stable after cooling. Room-temperature quartz crystal microbalance-dissipation and localized surface plasmon resonance experiments revealed that denatured BSA oligomers adsorbed more quickly and in larger mass quantities onto silica surfaces than native BSA monomers. We also determined that the larger surface contact area of denatured BSA oligomers is an important factor contributing to their more adhesive character. Importantly, denatured BSA oligomers were a superior passivating agent to inhibit biofouling on silica surfaces and also improved Western blot application performance. Taken together, the findings demonstrate how temperature-induced denaturation of BSA protein molecules can lead to improved protein-based coatings for surface passivation applications.</P> [FIG OMISSION]</BR>