Journal of Microbiology

Review

Expanding the genetic code: In vivo approaches for incorporating non-proteinogenic monomers: Dongheon Lee, Suk Min Yun, Jong-il Choi; J. Microbiol. 2025;63(3):e2501005. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2501005

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The application of genetic code expansion has enabled the incorporation of non-canonical amino acids (ncAAs) into proteins, introducing novel functional groups and significantly broadening the scope of protein engineering. Over the past decade, this approach has extended beyond ncAAs to include non-proteinogenic monomers (npMs), such as β-amino acids and hydroxy acids. In vivo incorporation of these monomers requires maintaining orthogonality between endogenous and engineered aminoacyl-tRNA synthetase (aaRS)/tRNA pairs while optimizing the use of the translational machinery. This review introduces the fundamental principles of genetic code expansion and highlights the development of orthogonal aaRS/tRNA pairs and ribosomal engineering to incorporate npMs. Despite these advancements, challenges remain in engineering aaRS/tRNA pairs to accommodate npMs, especially monomers that differ significantly from L-α-amino acids due to their incompatibility with existing translational machinery. This review also introduces recent methodologies that allow aaRSs to recognize and aminoacylate npMs without reliance on the ribosomal translation system, thereby unlocking new possibilities for synthesizing biopolymers with chemically diverse monomers.

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Advancing microbial engineering through synthetic biology
Ki Jun Jeong
Journal of Microbiology.2025; 63(3): e2503100. CrossRef

Journal Articles

Improved tolerance of recombinant Chlamydomonas rainhardtii with putative 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase from Pyropia yezoensis to nitrogen starvation: Seo-jeong Park , Joon Woo Ahn , Jong-il Choi; J. Microbiol. 2022;60(1):63-69. Published online December 29, 2021; DOI: https://doi.org/10.1007/s12275-022-1491-7

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Abstract

In a previous study, a putative 2-amino-3-carboxymuconate- 6-semialdehyde decarboxylase (ACMSD) was highly expressed in a mutant strain of Pyropia yezoensis, which exhibited an improved growth rate compared to its wild strain. To investigate the functional role of the putative ACMSD (Pyacmsd) of P. yezoensis, the putative Pyacmsd was cloned and expressed in Chlamydomonas reinhardtii. Recombinant C. reinhardtii cells with Pyacmsd (Cr_Pyacmsd) exhibited enhanced tolerance compared to control C. reinhardtii cells (Cr_control) under nitrogen starvation. Notably, Cr_Pyacmsd cells showed accumulation of lipids in nitrogen-enriched conditions. These
results
demonstrate the role of Pyacmsd in the generation of acetyl-coenzyme A. Thus, it can be used to enhance the production of biofuel using microalgae such as C. reinhardtii and increase the tolerance of other biological systems to nitrogendeficient conditions.

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Characteristics of Recombinant Chlamydomonas reinhardtii Expressing Putative Germin-Like Protein from Neopyropia yezoensis
Jiae Kim, Jong-il Choi
Journal of Microbiology and Biotechnology.2024; 34(10): 2132. CrossRef
Overexpression of putative glutathione peroxidase from Neopyropia-associated microorganisms in Chlamydomonas to respond to abiotic stress
Jeong Hyeon Kim, Eun-Jeong Park, Jong-il Choi
Archives of Microbiology.2023;[Epub] CrossRef
Overexpression of S-Adenosylmethionine Synthetase in Recombinant Chlamydomonas for Enhanced Lipid Production
Jeong Hyeon Kim, Joon Woo Ahn, Eun-Jeong Park, Jong-il Choi
Journal of Microbiology and Biotechnology.2023; 33(3): 310. CrossRef

Improved tolerance of Escherichia coli to oxidative stress by expressing putative response regulator homologs from Antarctic bacteria: Seo-jeong Park , Sangyong Lim , Jong-il Choi; J. Microbiol. 2020;58(2):131-141. Published online December 23, 2019; DOI: https://doi.org/10.1007/s12275-020-9290-5

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Abstract

Response regulator (RR) is known a protein that mediates cell’s response to environmental changes. The effect of RR from extremophiles was still under investigation. In this study, response regulator homologs were mined from NGS data of Antarctic bacteria and overexpressed in Escherichia coli. Sixteen amino acid sequences were annotated corresponding to response regulators related to the two-component regulatory systems; of these, 3 amino acid sequences (DRH632, DRH1601 and DRH577) with high homology were selected. These genes were cloned in pRadGro and expressed in E. coli. The transformant strains were subjected to various abiotic stresses including oxidative, osmotic, thermal stress, and acidic stress. There was found that the robustness of E. coli to abiotic stress was increased in the presence of these response regulator homologs. Especially, recombinant E. coli overexpressing drh632 had the highest survival rate in oxidative, hypothermic, osmotic, and acidic conditions. Recombinant E. coli overexpressing drh1601 showed the highest tolerance level to osmotic stress. These results will be applicable for development of recombinant strains with high tolerance to abiotic stress.

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Deionococcus proteotlycius Genomic Library Exploration Enhances Oxidative Stress Resistance and Poly-3-hydroxybutyrate Production in Recombinant Escherichia coli
Seul-Ki Yang, Soyoung Jeong, Inwoo Baek, Jong-il Choi, Sangyong Lim, Jong-Hyun Jung
Microorganisms.2023; 11(9): 2135. CrossRef
Bacterial redox response factors in the management of environmental oxidative stress
Sudharsan M, Rajendra Prasad N, Saravanan Rajendrasozhan
World Journal of Microbiology and Biotechnology.2023;[Epub] CrossRef
Bacteriophages as Antimicrobial Agents? Proteomic Insights on Three Novel Lytic Bacteriophages Infecting ESBL-Producing Escherichia coli
Sadika Dkhili, Miguel Ribeiro, Salma Ghariani, Houssem Ben Yahia, Mélanie Hillion, Patricia Poeta, Karim Ben Slama, Michel Hébraud, Gilberto Igrejas
OMICS: A Journal of Integrative Biology.2021; 25(10): 626. CrossRef
Regulator of ribonuclease activity modulates the pathogenicity of Vibrio vulnificus
Jaejin Lee, Eunkyoung Shin, Jaeyeong Park, Minho Lee, Kangseok Lee
Journal of Microbiology.2021; 59(12): 1133. CrossRef

PprM is necessary for up-regulation of katE1, encoding the major catalase of Deinococcus radiodurans, under unstressed culture conditions: Sun-Wook Jeong , Ho Seong Seo , Min-Kyu Kim , Jong-Il Choi , Heon-Man Lim , Sangyong Lim; J. Microbiol. 2016;54(6):426-431. Published online May 27, 2016; DOI: https://doi.org/10.1007/s12275-016-6175-8

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Abstract

Deinococcus radiodurans is a poly-extremophilic organism, capable of tolerating a wide variety of different stresses, such as gamma/ultraviolet radiation, desiccation, and oxidative stress. PprM, a cold shock protein homolog, is involved in the radiation resistance of D. radiodurans, but its role in the oxidative stress response has not been investigated. In this study, we investigated the effect of pprM mutation on catalase gene expression. pprM disruption decreased the mRNA and protein levels of KatE1, which is the major catalase in D. radiodurans, under normal culture conditions. A pprM mutant strain (pprMMT) exhibited decreased catalase activity, and its resistance to hydrogen peroxide (H2O2) decreased accordingly compared with that of the wild-type strain. We confirmed that RecG helicase negatively regulates katE1 under normal culture conditions. Among katE1 transcriptional regulators, the positive regulator drRRA was not altered in pprM-, while the negative regulators perR, dtxR, and recG were activated more than 2.5-fold in pprMMT. These findings suggest that PprM is necessary for KatE1 production under normal culture conditions by down-regulation of katE1 negative regulators.

Citations

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Antioxidant defense of Deinococcus radiodurans : how does it contribute to extreme radiation resistance?
Izabela Sadowska-Bartosz, Grzegorz Bartosz
International Journal of Radiation Biology.2023; 99(12): 1803. CrossRef
Development and Regulation of the Extreme Biofilm Formation of Deinococcus radiodurans R1 under Extreme Environmental Conditions
Qiannan Guo, Yuhua Zhan, Wei Zhang, Jin Wang, Yongliang Yan, Wenxiu Wang, Min Lin
International Journal of Molecular Sciences.2023; 25(1): 421. CrossRef
A small RNA regulates pprM, a modulator of pleiotropic proteins promoting DNA repair, in Deinococcus radiodurans under ionizing radiation
Jordan K. Villa, Runhua Han, Chen-Hsun Tsai, Angela Chen, Philip Sweet, Gabriela Franco, Respina Vaezian, Rok Tkavc, Michael J. Daly, Lydia M. Contreras
Scientific Reports.2021;[Epub] CrossRef
Lack of the Bacterial Phytochrome Protein Decreases Deinococcus radiodurans Resistance to Mitomycin C
Jong-Hyun Jung, Soyoung Jeong, Seonghun Im, Min-Kyu Kim, Ho Seong Seo, Sangyong Lim
Frontiers in Microbiology.2021;[Epub] CrossRef
Effects of Conserved Wedge Domain Residues on DNA Binding Activity of Deinococcus radiodurans RecG Helicase
Sun-Wook Jeong, Min-Kyu Kim, Lei Zhao, Seul-Ki Yang, Jong-Hyun Jung, Heon-Man Lim, Sangyong Lim
Frontiers in Genetics.2021;[Epub] CrossRef
The Novel ncRNA OsiR Positively Regulates Expression of katE2 and is Required for Oxidative Stress Tolerance in Deinococcus radiodurans
Lihua Gao, Xiaonan Chen, Ye Tian, Yongliang Yan, Yuhua Zhan, Zhengfu Zhou, Wei Zhang, Min Lin, Ming Chen
International Journal of Molecular Sciences.2020; 21(9): 3200. CrossRef
Conservation and diversity of radiation and oxidative stress resistance mechanisms inDeinococcusspecies
Sangyong Lim, Jong-Hyun Jung, Laurence Blanchard, Arjan de Groot
FEMS Microbiology Reviews.2019; 43(1): 19. CrossRef
Gene regulation for the extreme resistance to ionizing radiation of Deinococcus radiodurans
Wuzhou Wang, Yun Ma, Junyan He, Huizhou Qi, Fangzhu Xiao, Shuya He
Gene.2019; 715: 144008. CrossRef
PprM, a Cold Shock Domain-Containing Protein from Deinococcus radiodurans, Confers Oxidative Stress Tolerance to Escherichia coli
Sun-Ha Park, Harinder Singh, Deepti Appukuttan, Sunwook Jeong, Yong Jun Choi, Jong-Hyun Jung, Issay Narumi, Sangyong Lim
Frontiers in Microbiology.2017;[Epub] CrossRef
Knockout of pprM Decreases Resistance to Desiccation and Oxidation in Deinococcus radiodurans
Yang Zeng, Yun Ma, Fangzhu Xiao, Wuzhou Wang, Shuya He
Indian Journal of Microbiology.2017; 57(3): 316. CrossRef
RNA-Binding Domain is Necessary for PprM Function in Response to the Extreme Environmental Stress in Deinococcus radiodurans
Wei Li, Yun Ma, Jie Yang, Fangzhu Xiao, Wuzhou Wang, Shuya He
Indian Journal of Microbiology.2017; 57(4): 492. CrossRef

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