Journal of Microbiology

Jun Ren

2 Articles

Enhancement of the solubility of recombinant proteins by fusion with a short-disordered peptide: Jun Ren , Suhee Hwang , Junhao Shen , Hyeongwoo Kim , Hyunjoo Kim , Jieun Kim , Soyoung Ahn , Min-gyun Kim , Seung Ho Lee , Dokyun Na; J. Microbiol. 2022;60(9):960-967. Published online July 14, 2022; DOI: https://doi.org/10.1007/s12275-022-2122-z

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In protein biotechnology, large soluble fusion partners are widely utilized for increased yield and solubility of recombinant proteins. However, the production of additional large fusion partners poses an additional burden to the host, leading to a decreased protein yield. In this study, we identified two highly disordered short peptides that were able to increase the solubility of an artificially engineered aggregationprone protein, GFP-GFIL4, from 0.6% to 61% (D3-DP00592) and 46% (D4-DP01038) selected from DisProt database. For further confirmation, the peptides were applied to two insoluble E. coli proteins (YagA and YdiU). The peptides also enhanced solubility from 52% to 90% (YagA) and from 27% to 93% (YdiU). Their ability to solubilize recombinant proteins was comparable with strong solubilizing tags, maltosebinding protein (40 kDa) and TrxA (12 kDa), but much smaller (< 7 kDa) in size. For practical application, the two peptides were fused with a restriction enzyme, I-SceI, and they increased I-SceI solubility from 24% up to 75%. The highly disordered peptides did not affect the activity of I-SceI while I-SceI fused with MBP or TrxA displayed no restriction activity. Despite the small size, the highly disordered peptides were able to solubilize recombinant proteins as efficiently as conventional fusion tags and did not interfere with the function of recombinant proteins. Consequently, the identified two highly disordered peptides would have practical utility in protein biotechnology and industry.

Citations

Citations to this article as recorded by

A review on computational models for predicting protein solubility
Teerapat Pimtawong, Jun Ren, Jingyu Lee, Hyang-Mi Lee, Dokyun Na
Journal of Microbiology.2025; 63(1): e:2408001. CrossRef
Synthetic intrinsically disordered protein fusion tags that enhance protein solubility
Nicholas C. Tang, Jonathan C. Su, Yulia Shmidov, Garrett Kelly, Sonal Deshpande, Parul Sirohi, Nikhil Peterson, Ashutosh Chilkoti
Nature Communications.2024;[Epub] CrossRef
Biosynthesis of Indigo Dyes and Their Application in Green Chemical and Visual Biosensing for Heavy Metals
Yan Guo, Shun-Yu Hu, Can Wu, Chao-Xian Gao, Chang-Ye Hui
ACS Omega.2024; 9(31): 33868. CrossRef
Functional small peptides for enhanced protein delivery, solubility, and secretion in microbial biotechnology
Hyang-Mi Lee, Thi Duc Thai, Wonseop Lim, Jun Ren, Dokyun Na
Journal of Biotechnology.2023; 375: 40. CrossRef
Directed Evolution of Soluble α-1,2-Fucosyltransferase Using Kanamycin Resistance Protein as a Phenotypic Reporter for Efficient Production of 2'-Fucosyllactose
Jonghyeok Shin, Seungjoo Kim, Wonbeom Park, Kyoung Chan Jin, Sun-Ki Kim, Dae-Hyuk Kweon
Journal of Microbiology and Biotechnology.2022; 32(11): 1471. CrossRef
Effects of spray drying, freeze drying, and vacuum drying on physicochemical and nutritional properties of protein peptide powder from salted duck egg white
Tianyin Du, Jicheng Xu, Shengnan Zhu, Xinjun Yao, Jun Guo, Weiqiao Lv
Frontiers in Nutrition.2022;[Epub] CrossRef

[Minireview]Recent advances in genetic engineering tools based on synthetic biology: Jun Ren , Jingyu Lee , Dokyun Na; J. Microbiol. 2020;58(1):1-10. Published online January 2, 2020; DOI: https://doi.org/10.1007/s12275-020-9334-x

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Abstract

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.

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Critical Reviews in Biotechnology.2024; 44(4): 660. CrossRef
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ACS Synthetic Biology.2024; 13(10): 3256. CrossRef
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3 Biotech.2024;[Epub] CrossRef
Synthetic bacteria for the detection and bioremediation of heavy metals
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An Account of Models of Molecular Circuits for Associative Learning with Reinforcement Effect and Forced Dissociation
Zonglun Li, Alya Fattah, Peter Timashev, Alexey Zaikin
Sensors.2022; 22(15): 5907. CrossRef
CRISPR-Cas9 based stress tolerance: New hope for abiotic stress tolerance in chickpea (Cicer arietinum)
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Molecular Biology Reports.2022; 49(9): 8977. CrossRef
Microbes of traditional fermentation processes as synthetic biology chassis to tackle future food challenges
Adán Andrés Ramírez Rojas, Razan Swidah, Daniel Schindler
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In silico genome mining of potential novel biosynthetic gene clusters for drug discovery from Burkholderia bacteria
Khorshed Alam, Md Mahmudul Islam, Kai Gong, Muhammad Nazeer Abbasi, Ruijuan Li, Youming Zhang, Aiying Li
Computers in Biology and Medicine.2022; 140: 105046. CrossRef
Developing of specific monoclonal recombinant antibody fused to alkaline phosphatase (AP) for one-step detection of fig mosaic virus
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3 Biotech.2022;[Epub] CrossRef
Identification of efficient prokaryotic cell-penetrating peptides with applications in bacterial biotechnology
Hyang-Mi Lee, Jun Ren, Kha Mong Tran, Byeong-Min Jeon, Won-Ung Park, Hyunjoo Kim, Kyung Eun Lee, Yuna Oh, Myungback Choi, Dae-Sung Kim, Dokyun Na
Communications Biology.2021;[Epub] CrossRef
Flapjack: Data Management and Analysis for Genetic Circuit Characterization
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ACS Synthetic Biology.2021; 10(1): 183. CrossRef
Synthetic small regulatory RNAs in microbial metabolic engineering
Wen-Hai Xie, Hong-Kuan Deng, Jie Hou, Li-Juan Wang
Applied Microbiology and Biotechnology.2021; 105(1): 1. CrossRef
Combinatorial metabolic pathway assembly approaches and toolkits for modular assembly
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Metabolic Engineering.2021; 63: 81. CrossRef
Fourth generation biofuel from genetically modified algal biomass: Challenges and future directions
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Chemosphere.2021; 285: 131535. CrossRef
Construction of a tunable promoter library to optimize gene expression in Methylomonas sp. DH-1, a methanotroph, and its application to cadaverine production
Hyang-Mi Lee, Jun Ren, Myeong-Sang Yu, Hyunjoo Kim, Woo Young Kim, Junhao Shen, Seung Min Yoo, Seong-il Eyun, Dokyun Na
Biotechnology for Biofuels.2021;[Epub] CrossRef
Trans-acting regulators of ribonuclease activity
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International Journal of Molecular Sciences.2020; 21(5): 1627. CrossRef
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Nachweismethoden von SARS‐CoV‐2
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Chemie in unserer Zeit.2020; 54(6): 368. CrossRef

Jun Ren

2 Articles

Untranslated region engineering strategies for gene overexpression, fine-tuning, and dynamic regulation: Jun Ren, So Hee Oh, Dokyun Na; J. Microbiol. 2025;63(3):e2501033. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2501033

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Abstract PDF

Precise and tunable gene expression is crucial for various biotechnological applications, including protein overexpression, fine-tuned metabolic pathway engineering, and dynamic gene regulation. Untranslated regions (UTRs) of mRNAs have emerged as key regulatory elements that modulate transcription and translation. In this review, we explore recent advances in UTR engineering strategies for bacterial gene expression optimization. We discuss approaches for enhancing protein expression through AU-rich elements, RG4 structures, and synthetic dual UTRs, as well as ProQC systems that improve translation fidelity. Additionally, we examine strategies for fine-tuning gene expression using UTR libraries and synthetic terminators that balance metabolic flux. Finally, we highlight riboswitches and toehold switches, which enable dynamic gene regulation in response to environmental or metabolic cues. The integration of these UTR-based regulatory tools provides a versatile and modular framework for optimizing bacterial gene expression, enhancing metabolic engineering, and advancing synthetic biology applications.

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Citations to this article as recorded by

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

A review on computational models for predicting protein solubility: Teerapat Pimtawong, Jun Ren, Jingyu Lee, Hyang-Mi Lee, Dokyun Na; J. Microbiol. 2025;63(1):e.2408001. Published online January 24, 2025; DOI: https://doi.org/10.71150/jm.2408001

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143 Download

Abstract PDF: Protein solubility is a critical factor in the production of recombinant proteins, which are widely used in various industries, including pharmaceuticals, diagnostics, and biotechnology. Predicting protein solubility remains a challenging task due to the complexity of protein structures and the multitude of factors influencing solubility. Recent advances in computational methods, particularly those based on machine learning, have provided powerful tools for predicting protein solubility, thereby reducing the need for extensive experimental trials. This review provides an overview of current computational approaches to predict protein solubility. We discuss the datasets, features, and algorithms employed in these models. The review aims to bridge the gap between computational predictions and experimental validations, fostering the development of more accurate and reliable solubility prediction models that can significantly enhance recombinant protein production.

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