Journal of Microbiology

Reviews

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

180 View
11 Download
1 Crossref

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.

Citations

Citations to this article as recorded by

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

Progress and challenges in CRISPR/Cas applications in microalgae: Quynh-Giao Tran, Trang Thi Le, Dong-Yun Choi, Dae-Hyun Cho, Jin-Ho Yun, Hong Il Choi, Hee-Sik Kim, Yong Jae Lee; J. Microbiol. 2025;63(3):e2501028. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2501028

168 View
12 Download
1 Crossref

Abstract PDF

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technologies have emerged as powerful tools for precise genome editing, leading to a revolution in genetic research and biotechnology across diverse organisms including microalgae. Since the 1950s, microalgal production has evolved from initial cultivation under controlled conditions to advanced metabolic engineering to meet industrial demands. However, effective genetic modification in microalgae has faced significant challenges, including issues with transformation efficiency, limited target selection, and genetic differences between species, as interspecies genetic variation limits the use of genetic tools from one species to another. This review summarized recent advancements in CRISPR systems applied to microalgae, with a focus on improving gene editing precision and efficiency, while addressing organism-specific challenges. We also discuss notable successes in utilizing the class 2 CRISPR-associated (Cas) proteins, including Cas9 and Cas12a, as well as emerging CRISPR-based approaches tailored to overcome microalgal cellular barriers. Additionally, we propose future perspectives for utilizing CRISPR/Cas strategies in microalgal biotechnology.

Citations

Citations to this article as recorded by

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

Synthetic biology strategies for sustainable bioplastic production by yeasts: Huong-Giang Le, Yongjae Lee, Sun-Mi Lee; J. Microbiol. 2025;63(3):e2501022. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2501022

143 View
3 Download
1 Crossref

Abstract PDF

The increasing environmental concerns regarding conventional plastics have led to a growing demand for sustainable alternatives, such as biodegradable plastics. Yeast cell factories, specifically Saccharomyces cerevisiae and Yarrowia lipolytica, have emerged as promising platforms for bioplastic production due to their scalability, robustness, and ease of manipulation. This review highlights synthetic biology approaches aimed at developing yeast cell factories to produce key biodegradable plastics, including polylactic acid (PLA), polyhydroxyalkanoates (PHAs), and poly (butylene adipate-co-terephthalate) (PBAT). We explore recent advancements in engineered yeast strains that utilize various synthetic biology strategies, such as the incorporation of new genetic elements at the gene, pathway, and cellular system levels. The combined efforts of metabolic engineering, protein engineering, and adaptive evolution have enhanced strain efficiency and maximized product yields. Additionally, this review addresses the importance of integrating computational tools and machine learning into the Design-Build-Test-Learn cycle for strain development. This integration aims to facilitate strain development while minimizing effort and maximizing performance. However, challenges remain in improving strain robustness and scaling up industrial production processes. By combining advanced synthetic biology techniques with computational approaches, yeast cell factories hold significant potential for the sustainable and scalable production of bioplastics, thus contributing to a greener bioeconomy.

Citations

Citations to this article as recorded by

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

Recent advances in targeted mutagenesis to expedite the evolution of biological systems: Seungjin Kim, Seungwon Lee, Hyun Gyu Lim; J. Microbiol. 2025;63(3):e2501008. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2501008

221 View
16 Download
1 Crossref

Abstract PDF

Evolution has been systematically exploited to engineer biological systems to obtain improved or novel functionalities by selecting beneficial mutations. Recent innovations in continuous targeted mutagenesis within living cells have emerged to generate large sequence diversities without requiring multiple steps. This review comprehensively introduces recent advancements in this field, categorizing them into three approaches depending on methods to create mutations: orthogonal error-prone DNA polymerases, site-specific base editors, and homologous recombination of mutagenic DNA fragments. Combined with high-throughput screening methods, these advances expedited evolution processes with significant reduction of labor and time. These approaches promise broader industrial and research applications, including enzyme improvement, metabolic engineering, and drug resistance studies.

Citations

Citations to this article as recorded by

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

Journal Articles

A mucin-responsive hybrid two-component system controls Bacteroides thetaiotaomicron colonization and gut homeostasis: Ju-Hyung Lee , Soo-Jeong Kwon , Ji-Yoon Han , Sang-Hyun Cho , Yong-Joon Cho , Joo-Hong Park; J. Microbiol. 2022;60(2):215-223. Published online February 1, 2022; DOI: https://doi.org/10.1007/s12275-022-1649-3

56 View
0 Download
5 Web of Science
5 Crossref

Abstract

The mammalian intestinal tract contains trillions of bacteria. However, the genetic factors that allow gut symbiotic bacteria to occupy intestinal niches remain poorly understood. Here, we identified genetic determinants required for Bacteroides thetaiotaomicron colonization in the gut using transposon sequencing analysis. Transposon insertion in BT2391, which encodes a hybrid two-component system, increased the competitive fitness of B. thetaiotaomicron. The BT2391 mutant showed a growth advantage in a mucin-dependent manner and had an increased ability to adhere to mucus-producing cell lines. The increased competitive advantage of the BT2391 mutant was dependent on the BT2392–2395 locus containing susCD homologs. Deletion of BT2391 led to changes in the expression levels of B. thetaiotaomicron genes during gut colonization. However, colonization of the BT2391 mutant promoted DSS colitis in low-fiber diet-fed mice. These results indicate that BT2391 contributes to a sustainable symbiotic relationship by maintaining a balance between mucosal colonization and gut homeostasis.

Citations

Citations to this article as recorded by

Effect of Lactobacillus plantarum BFS1243 on a female frailty model induced by fecal microbiota transplantation in germ-free mice
Sashuang Dong, Qi Zeng, Weimin He, Wei Cheng, Ling Zhang, Ruimin Zhong, Wen He, Xiang Fang, Hong Wei
Food & Function.2024; 15(8): 3993. CrossRef
A conserved inhibitory interdomain interaction regulates DNA-binding activities of hybrid two-component systems in Bacteroides
Rong Gao, Ti Wu, Ann M. Stock, Michael T. Laub
mBio.2024;[Epub] CrossRef
Polysaccharides from Polygonatum cyrtonema Hua prevent depression-like behaviors in mice with chronic unpredictable mild stress through refining gut microbiota-lipopolysaccharide-paraventricular nucleus signal axis
Xinya Wang, Xueqing Wang, Feng Gao, Shaojie Yang, Yilan Zhen, Xuncui Wang, Guoqi Zhu
Heliyon.2024; 10(19): e38554. CrossRef
Metal Messengers: Communication in the Bacterial World through Transition-Metal-Sensing Two-Component Systems
Alexander Paredes, Chioma Iheacho, Aaron T. Smith
Biochemistry.2023; 62(16): 2339. CrossRef
Tang-Ping-San Decoction Remodel Intestinal Flora and Barrier to Ameliorate Type 2 Diabetes Mellitus in Rodent Model
Wen Yin, Si-Qi Zhang, Wen-Lin Pang, Xiao-Jiao Chen, Jing Wen, Jiong Hou, Cui Wang, Li-Yun Song, Zhen-Ming Qiu, Peng-Tao Liang, Jia-Li Yuan, Zhong-Shan Yang, Yao Bian
Diabetes, Metabolic Syndrome and Obesity: Targets and Therapy.2022; Volume 15: 2563. CrossRef

Melatonin attenuates microbiota dysbiosis of jejunum in short-term sleep deprived mice: Ting Gao , Zixu Wang , Jing Cao , Yulan Dong , Yaoxing Chen; J. Microbiol. 2020;58(7):588-597. Published online May 18, 2020; DOI: https://doi.org/10.1007/s12275-020-0094-4

50 View
0 Download
22 Web of Science
22 Crossref

Abstract

Our study demonstrated that sleep deprivation resulted in homeostasis disorder of colon. Our study goes deeper into the positive effects of melatonin on small intestinal microbiota disorder caused by sleep deprivation. We successfully established a multiplatform 72 h sleep deprivation mouse model with or without melatonin supplementation, and analyzed the change of small intestinal microbiota using high-throughput sequencing of the 16S rRNA. We found melatonin supplementation suppressed the decrease of plasma melatonin level in sleep deprivation mice. Meanwhile, melatonin supplementation improved significantly the reduction in OTU numbers and the diversity and richness of jejunal microbiota and the abundance of Bacteroidaeae and Prevotellaceae, as well as an increase in the Firmicutes-to-Bacteroidetes ratio and the content of Moraxellaceae and Aeromonadaceae in the jejunum of sleep deprived-mice. Moreover, melatonin supplementation reversed the change of metabolic pathway in sleep deprived-mice, including metabolism, signal transduction mechanisms and transcription etc, which were related to intestinal health. Furthermore, melatonin supplementation inverted the sleep deprivation-induced a decline of anti-inflammatory cytokines (IL-22) and an increase of the ROS and proinflammatory cytokines (IL-17) in jejunum. These findings suggested that melatonin, similar to a probiotics agent, can reverse sleep deprivation-induced small intestinal microbiota disorder by suppressing oxidative stress and inflammation response.

Citations

Citations to this article as recorded by

Microbial melatonin metabolism in the human intestine as a therapeutic target for dysbiosis and rhythm disorders
Petra Zimmermann, Salome Kurth, Benoit Pugin, Nicholas A. Bokulich
npj Biofilms and Microbiomes.2024;[Epub] CrossRef
Melatonin and gut microbiome
N. E. Garashchenko, N. V. Semenova, L. I. Kolesnikova
Acta Biomedica Scientifica.2024; 9(2): 12. CrossRef
Mitochondrial dysfunction, a weakest link of network of aging, relation to innate intramitochondrial immunity of DNA recognition receptors
Dun-Xian Tan
Mitochondrion.2024; 76: 101886. CrossRef
Advances in molecular mechanisms and therapeutic strategies for central nervous system diseases based on gut microbiota imbalance
Wei Tao, Yanren Zhang, Bingbin Wang, Saiqun Nie, Li Fang, Jian Xiao, Yanqing Wu
Journal of Advanced Research.2024;[Epub] CrossRef
Polycystic Ovary Syndrome Pathophysiology: Integrating Systemic, CNS and Circadian Processes
George Anderson
Frontiers in Bioscience-Landmark.2024;[Epub] CrossRef
Melatonin: Both a Messenger of Darkness and a Participant in the Cellular Actions of Non-Visible Solar Radiation of Near Infrared Light
Dun-Xian Tan, Russel J. Reiter, Scott Zimmerman, Ruediger Hardeland
Biology.2023; 12(1): 89. CrossRef
Understanding the combined effects of sleep deprivation and acute social stress on cognitive performance using a comprehensive approach
Charelle Bottenheft, Koen Hogenelst, Ivo Stuldreher, Robert Kleemann, Eric Groen, Jan van Erp, Anne-Marie Brouwer
Brain, Behavior, & Immunity - Health.2023; 34: 100706. CrossRef
The relationship between sleep, gut microbiota, and metabolome in patients with depression and anxiety: A secondary analysis of the observational study
Arisa Tanaka, Kenji Sanada, Katsuma Miyaho, Tomoyuki Tachibana, Shunya Kurokawa, Chiharu Ishii, Yoshihiro Noda, Shinichiro Nakajima, Shinji Fukuda, Masaru Mimura, Taishiro Kishimoto, Akira Iwanami, Tanja Grubić Kezele
PLOS ONE.2023; 18(12): e0296047. CrossRef
Melatonin as a Mediator of the Gut Microbiota–Host Interaction: Implications for Health and Disease
María-Ángeles Bonmatí-Carrión, Maria-Angeles Rol
Antioxidants.2023; 13(1): 34. CrossRef
The orchestra of human bacteriome by hormones
Arif Luqman
Microbial Pathogenesis.2023; 180: 106125. CrossRef
Targeting microbiota to alleviate the harm caused by sleep deprivation
Hongyu Chen, Chen Wang, Junying Bai, Jiajia Song, Linli Bu, Ming Liang, Huayi Suo
Microbiological Research.2023; 275: 127467. CrossRef
Targeting the blood–brain barrier to delay aging-accompanied neurological diseases by modulating gut microbiota, circadian rhythms, and their interplays
Yanping Wang, Weihong Du, Xiaoyan Hu, Xin Yu, Chun Guo, Xinchun Jin, Wei Wang
Acta Pharmaceutica Sinica B.2023; 13(12): 4667. CrossRef
Melatonin, a natural antioxidant therapy in spinal cord injury
Lei Xie, Hang Wu, Xiaohong Huang, Tengbo Yu
Frontiers in Cell and Developmental Biology.2023;[Epub] CrossRef
Melatonin mitigates aflatoxin B1‐induced liver injury via modulation of gut microbiota/intestinal FXR/liver TLR4 signaling axis in mice
Shuiping Liu, Weili Kang, Xinru Mao, Lei Ge, Heng Du, Jinyan Li, Lili Hou, Dandan Liu, Yulong Yin, Yunhuan Liu, Kehe Huang
Journal of Pineal Research.2022;[Epub] CrossRef
Regulation of wheat bran feruloyl oligosaccharides in the intestinal antioxidative capacity of rats associated with the p38/JNK‐Nrf2 signaling pathway and gut microbiota
Wenwen Wang, Yuan Wang, Yuanxiao Duan, Ziqi Meng, Xiaoping An, Jingwei Qi
Journal of the Science of Food and Agriculture.2022; 102(15): 6992. CrossRef
Mechanism of interventional effect and targets of Zhuyu pill in regulating and suppressing colitis and cholestasis
Han Yu, Fenghua Zhang, Yueqiang Wen, Zhili Zheng, Gaoyang Chen, Yingying Pan, Peijie Wu, Qiaobo Ye, Jun Han, Xiaofeng Chen, Chao Liu, Tao Shen
Frontiers in Pharmacology.2022;[Epub] CrossRef
Intervention Effects of Okra Extract on Brain-Gut Peptides and Intestinal Microorganisms in Sleep Deprivation Rats
Jingru Wu, Mingxue Cao, Ming Hu, Yu Gong, Jianming Xue, Yilin Yang, Hairui Zhou, Duygu Ağagündüz
Evidence-Based Complementary and Alternative Medicine.2022; 2022: 1. CrossRef
Intestinal microbiota and melatonin in the treatment of secondary injury and complications after spinal cord injury
Yiwen Zhang, Rui Lang, Shunyu Guo, Xiaoqin Luo, Huiting Li, Cencen Liu, Wei Dong, Changshun Bao, Yang Yu
Frontiers in Neuroscience.2022;[Epub] CrossRef
Impact of the Gastrointestinal Tract Microbiota on Cardiovascular Health and Pathophysiology
Aysenur Gunaydin Akyildiz, Giuseppe Biondi-Zoccai, Daniela De Biase
Journal of Cardiovascular Pharmacology.2022; 80(1): 13. CrossRef
Melatonin–Microbiome Two-Sided Interaction in Dysbiosis-Associated Conditions
Mara Ioana Iesanu, Carmen Denise Mihaela Zahiu, Ioana-Alexandra Dogaru, Diana Maria Chitimus, Gratiela Gradisteanu Pircalabioru, Suzana Elena Voiculescu, Sebastian Isac, Felicia Galos, Bogdan Pavel, Siobhain M. O’Mahony, Ana-Maria Zagrean
Antioxidants.2022; 11(11): 2244. CrossRef
Melatonin and Cancer: A Polyhedral Network Where the Source Matters
Maria-Angeles Bonmati-Carrion, Antonia Tomas-Loba
Antioxidants.2021; 10(2): 210. CrossRef
Ziziphus jujuba Mill. var. spinosa (Bunge) Hu ex H. F. Chou Seed Ameliorates Insomnia in Rats by Regulating Metabolomics and Intestinal Flora Composition
Yue Hua, Sheng Guo, Hong Xie, Yue Zhu, Hui Yan, Wei-wei Tao, Er-xin Shang, Da-wei Qian, Jin-ao Duan
Frontiers in Pharmacology.2021;[Epub] CrossRef

Review

MINIREVIEW] Development of bacteria as diagnostics and therapeutics by genetic engineering: Daejin Lim , Miryoung Song; J. Microbiol. 2019;57(8):637-643. Published online May 11, 2019; DOI: https://doi.org/10.1007/s12275-019-9105-8

45 View
0 Download
15 Web of Science
13 Crossref

Abstract

Bacteria sense and respond to the environment, communicate, and continuously interact with their surroundings, including host bodies. For more than a century, engineers have been trying to harness the natural ability of bacteria as live biotherapeutics for the treatment of diseases. Recent advances in synthetic biology facilitate the enlargement of the repertoire of genetic parts, tools, and devices that serve as a framework for biotherapy. This review describes bacterial species developed for specific diseases shown in in vitro studies and clinical stages. Here, we focus on drug delivery by programing bacteria and discuss the challenges for safety and improvement.

Citations

Citations to this article as recorded by

Engineered Microorganisms for Advancing Tumor Therapy
Jinxuan Jia, Xiaocheng Wang, Xiang Lin, Yuanjin Zhao
Advanced Materials.2024;[Epub] CrossRef
Therapeutic bacteria and viruses to combat cancer: double-edged sword in cancer therapy: new insights for future
Aref Yarahmadi, Mitra Zare, Masoomeh Aghayari, Hamed Afkhami, Gholam Ali Jafari
Cell Communication and Signaling.2024;[Epub] CrossRef
Physiochemically and Genetically Engineered Bacteria: Instructive Design Principles and Diverse Applications
Xia Lin, Rong Jiao, Haowen Cui, Xuebing Yan, Kun Zhang
Advanced Science.2024;[Epub] CrossRef
Intestinal Delivery of Probiotics: Materials, Strategies, and Applications
Chengcheng Li, Zi‐Xi Wang, Huining Xiao, Fu‐Gen Wu
Advanced Materials.2024;[Epub] CrossRef
Research and application of intelligent diagnosis and treatment engineering bacteria
Na Zhao, Junwei Chen, Jingtian Shi, Yan Gao, Lijing Li, Liyun Dong
Frontiers in Bioengineering and Biotechnology.2024;[Epub] CrossRef
Gastrointestinal worms and bacteria: From association to intervention
James Rooney, Cinzia Cantacessi, Javier Sotillo, Alba Cortés
Parasite Immunology.2023;[Epub] CrossRef
Bacterial Therapy of Cancer: A Way to the Dustbin of History or to the Medicine of the Future?
Larisa N. Ikryannikova, Neonila V. Gorokhovets, Darya A. Belykh, Leonid K. Kurbatov, Andrey A. Zamyatnin
International Journal of Molecular Sciences.2023; 24(11): 9726. CrossRef
Derivation and elimination of uremic toxins from kidney-gut axis
Ying Xu, Wen-Di Bi, Yu-Xuan Shi, Xin-Rui Liang, Hai-Yan Wang, Xue-Li Lai, Xiao-Lu Bian, Zhi-Yong Guo
Frontiers in Physiology.2023;[Epub] CrossRef
Decorated bacteria and the application in drug delivery
Feng Wu, Jinyao Liu
Advanced Drug Delivery Reviews.2022; 188: 114443. CrossRef
Bakterie Modyfikowane Genetycznie – Perspektywy Zastosowania w Profilaktyce, Diagnostyce I Terapii
Barbara Macura, Aneta Kiecka, Marian Szczepanik
Postępy Mikrobiologii - Advancements of Microbiology.2022; 61(1): 21. CrossRef
Bacteria and cells as alternative nano-carriers for biomedical applications
Rafaela García-Álvarez, María Vallet-Regí
Expert Opinion on Drug Delivery.2022; 19(1): 103. CrossRef
Tabrizicola piscis sp. nov., isolated from the intestinal tract of a Korean indigenous freshwater fish, Acheilognathus koreensis
Jeong Eun Han, Woorim Kang, June-Young Lee, Hojun Sung, Dong-Wook Hyun, Hyun Sik Kim, Pil Soo Kim, Euon Jung Tak, Yun-Seok Jeong, Jae-Yun Lee, So-Yeon Lee, Ji-Hyun Yun, Mi-Ja Jung, Na-Ri Shin, Tae Woong Whon, Myung-Suk Kang, Ki-Eun Lee, Byoung-Hee Lee, Ji
International Journal of Systematic and Evolutionary Microbiology .2020; 70(4): 2305. CrossRef
Novel Strategies for Efficient Production and Delivery of Live Biotherapeutics and Biotechnological Uses of Lactococcus lactis: The Lactic Acid Bacterium Model
Laísa M. Tavares, Luís C. L. de Jesus, Tales F. da Silva, Fernanda A. L. Barroso, Viviane L. Batista, Nina D. Coelho-Rocha, Vasco Azevedo, Mariana M. Drumond, Pamela Mancha-Agresti
Frontiers in Bioengineering and Biotechnology.2020;[Epub] CrossRef

First
Prev
Page of 1
Next
Last

Search