Journal of Microbiology

Reviews

Recent advances in the Design-Build-Test-Learn (DBTL) cycle for systems metabolic engineering of Corynebacterium glutamicum: Subeen Jeon, Yu Jung Sohn, Haeyoung Lee, Ji Young Park, Dojin Kim, Eun Seo Lee, Si Jae Park; J. Microbiol. 2025;63(3):e2501021. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2501021

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Existing microbial engineering strategies—encompassing metabolic engineering, systems biology, and systems metabolic engineering—have significantly enhanced the potential of microbial cell factories as sustainable alternatives to the petrochemical industry by optimizing metabolic pathways. Recently, systems metabolic engineering, which integrates tools from synthetic biology, enzyme engineering, omics technology, and evolutionary engineering, has been successfully developed. By leveraging modern engineering strategies within the Design-Build-Test-Learn (DBTL) cycle framework, these advancements have revolutionized the biosynthesis of valuable compounds. This review highlights recent progress in the metabolic engineering of Corynebacterium glutamicum, a versatile microbial platform, achieved through various approaches from traditional metabolic engineering to advanced systems metabolic engineering, all within the DBTL cycle. A particular focus is placed C5 platform chemicals derived from L-lysine, one of the key amino acid production pathways of C. glutamicum. The development of DBTL cycle-based metabolic engineering strategies for this process is discussed.

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

Harnessing organelle engineering to facilitate biofuels and biochemicals production in yeast: Phuong Hoang Nguyen Tran, Taek Soon Lee; J. Microbiol. 2025;63(3):e2501006. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2501006

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Abstract PDF

Microbial biosynthesis using yeast species offers numerous advantages to produce industrially relevant biofuels and biochemicals. Conventional metabolic engineering approaches in yeast focus on biosynthetic pathways in the cytoplasm, but these approaches are disturbed by various undesired factors including metabolic crosstalk, competing pathways and insufficient precursors. Given that eukaryotic cells contain subcellular organelles with distinct physicochemical properties, an emerging strategy to overcome cytosolic pathway engineering bottlenecks is through repurposing these organelles as specialized microbial cell factories for enhanced production of valuable chemicals. Here, we review recent progress and significant outcomes of harnessing organelle engineering for biofuels and biochemicals production in both conventional and non-conventional yeasts. We highlight key engineering strategies for the compartmentalization of biosynthetic pathways within specific organelles such as mitochondria, peroxisomes, and endoplasmic reticulum; involved in engineering of signal peptide, cofactor and energy enhancement, organelle biogenesis and dual subcellular engineering. Finally, we discuss the potential and challenges of organelle engineering for future studies and propose an automated pipeline to fully exploit this approach.

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

Journal Articles

Mst1/2-ALK promotes NLRP3 inflammasome activation and cell apoptosis during Listeria monocytogenes infection: Aijiao Gao , Huixin Tang , Qian Zhang , Ruiqing Liu , Lin Wang , Yashan Liu , Zhi Qi , Yanna Shen; J. Microbiol. 2021;59(7):681-692. Published online April 20, 2021; DOI: https://doi.org/10.1007/s12275-021-0638-2

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Abstract

Listeria monocytogenes (L. monocytogenes) is a Gram-positive intracellular foodborne pathogen that causes severe diseases, such as meningitis and sepsis. The NLR family pyrin domain-containing 3 (NLRP3) inflammasome has been reported to participate in host defense against pathogen infection. However, the exact molecular mechanisms underlying NLRP3 inflammasome activation remain to be fully elucidated. In the present study, the roles of mammalian Ste20- like kinases 1/2 (Mst1/2) and Anaplastic Lymphoma Kinase (ALK) in the activation of the NLRP3 inflammasome induced by L. monocytogenes infection were investigated. The expression levels of Mst1/2, phospho (p)-ALK, p-JNK, Nek7, and NLRP3 downstream molecules including activated caspase- 1 (p20) and mature interleukin (IL)-1β (p17), were upregulated in L. monocytogenes-infected macrophages. The ALK inhibitor significantly decreased the expression of p-JNK, Nek7, and NLRP3 downstream molecules in macrophages infected with L. monocytogenes. Furthermore, the Mst1/2 inhibitor markedly inhibited the L. monocytogenes-induced activation of ALK, subsequently downregulating the expression of p-JNK, Nek7, and NLRP3 downstream molecules. Therefore, our study demonstrated that Mst1/2-ALK mediated the activation of the NLRP3 inflammasome by promoting the interaction between Nek7 and NLRP3 via JNK during L. monocytogenes infection, which subsequently increased the maturation and release of proinflammatory cytokine to resist pathogen infection. Moreover, Listeriolysin O played a key role in the process. In addition, we also found that the L. monocytogenes-induced apoptosis of J774A.1 cells was reduced by the Mst1/2 or ALK inhibitor. The present study reported, for the first time, that the Mst1/2-ALK-JNK-NLRP3 signaling pathway plays a vital proinflammatory role during L. monocytogenes infection.

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IL-18 biology in severe asthma
Sarita Thawanaphong, Aswathi Nair, Emily Volfson, Parameswaran Nair, Manali Mukherjee
Frontiers in Medicine.2024;[Epub] CrossRef
TRAF6-TAK1-IKKβ pathway mediates TLR2 agonists activating “one-step” NLRP3 inflammasome in human monocytes
Mengdan Chen, Shi Yu, Yuhui Gao, Jiaxun Li, Xun Wang, Bin Wei, Guangxun Meng
Cytokine.2023; 169: 156302. CrossRef
ALK-JNK signaling promotes NLRP3 inflammasome activation and pyroptosis via NEK7 during Streptococcus pneumoniae infection
Xia Wang, Yan Zhao, Dan Wang, Chang Liu, Zhi Qi, Huixin Tang, Yashan Liu, Shiqi Zhang, Yali Cui, Yingying Li, Ruiqing Liu, Yanna Shen
Molecular Immunology.2023; 157: 78. CrossRef
Inflammasome activation by Gram-positive bacteria: Mechanisms of activation and regulation
A. Marijke Keestra-Gounder, Prescilla Emy Nagao
Frontiers in Immunology.2023;[Epub] CrossRef
Toxoplasma gondii profilin induces NLRP3 activation and IL-1β production/secretion in THP-1 cells
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Microbial Pathogenesis.2023; 180: 106120. CrossRef
The Critical Role of Potassium Efflux and Nek7 in Pasteurella multocida-Induced NLRP3 Inflammasome Activation
Yu Wang, Zheng Zeng, Jinrong Ran, Lianci Peng, Xingping Wu, Chao Ye, Chunxia Dong, Yuanyi Peng, Rendong Fang
Frontiers in Microbiology.2022;[Epub] CrossRef
Coral and it's symbionts responses to the typical global marine pollutant BaP by 4D-Proteomics approach
Yuebin Pei, Shuai Chen, Yuting Zhang, Volovych Olga, Yuanchao Li, Xiaoping Diao, Hailong Zhou
Environmental Pollution.2022; 307: 119440. CrossRef
NEK7-Mediated Activation of NLRP3 Inflammasome Is Coordinated by Potassium Efflux/Syk/JNK Signaling During Staphylococcus aureus Infection
Ruiqing Liu, Yashan Liu, Chang Liu, Aijiao Gao, Lin Wang, Huixin Tang, Qiang Wu, Xia Wang, Derun Tian, Zhi Qi, Yanna Shen
Frontiers in Immunology.2021;[Epub] CrossRef

Changes in the microbial community of Litopenaeus vannamei larvae and rearing water during different growth stages after disinfection treatment of hatchery water: Yafei Duan , Yapeng Tang , Jianhua Huang , Jiasong Zhang , Heizhao Lin , Shigui Jiang , Ruixuan Wang , Guofu Wang; J. Microbiol. 2020;58(9):741-749. Published online July 24, 2020; DOI: https://doi.org/10.1007/s12275-020-0053-0

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Abstract

Microbial communities greatly affect rearing water quality and the larvae health during shrimp hatchery periods. In this study, we investigated the microbial communities of rearing water and larvae of Litopenaeus vannamei after treating hatchery water with different kinds of chemical disinfectants: no disinfectants (Con), chlorine dioxide (ClO2), formaldehyde solution (HCHO), bleach powder (CaClO), and iodine (I2). The water and larval samples were collected from nauplius 6 (N6), zoea 1 (Z1), mysis 1 (M1), and postlarvae 1 (P1) shrimp growth periods. 16S rDNA high-throughput sequencing revealed that the bacterial composition of the rearing water was more complex than that of the larvae, and the bacterial community of the rearing water and the larvae fluctuated significantly at the P1 and Z1 periods, respectively. Disinfectants altered the bacterial diversity and composition of the rearing water and larvae. Specifically, in the rearing water of the P1 period, Proteobacteria abundance was increased in the HCHO group; while Bacteroidetes abundance was decreased in the ClO2, HCHO, and I2 groups but increased in the CaClO group. In the larvae of the Z1 period, Firmicutes (especially Bacillus class) abundance was increased in the CaClO group, but decreased in the ClO2, HCHO, and I2 groups. Network analyses revealed that the genera Donghicola, Roseibacterium, Candidatus-Cquiluna, and Nautella were enriched in the rearing water, while Halomonas, Vibrio, and Flavirhabdus had high abundance in the larvae. The survival of shrimp was influenced by disinfectants that were inconsistent with the bacterial community changes. These results will be helpful for using microbial characteristics to facilitate healthy shrimp nursery.

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Metagenomic insights into the rapid recovery mechanisms of prokaryotic community and spread of antibiotic resistance genes after seawater disinfection
Jiaojiao Yan, Xinxu Zhang, Xinyong Shi, Jialin Wu, Ziang Zhou, Yawen Tang, Zhen Bao, Nan Luo, Demin Zhang, Jiong Chen, Huajun Zhang
Water Research.2025; 271: 122887. CrossRef
Comparative Microbiome Analysis of Artemia spp. and Potential Role of Microbiota in Cyst Hatching
Euihyeon Lee, Kyun-Woo Lee, Yeun Park, Ayeon Choi, Kae Kyoung Kwon, Hye-Min Kang
Marine Biotechnology.2024; 26(1): 50. CrossRef
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Peng Wu, Yi Li, Aijun Yang, Xiangyu Tan, Jifeng Chu, Yifan Zhang, Yongxu Yan, Ju Tang, Hongye Yuan, Xiaoxing Zhang, Song Xiao
ACS Sensors.2024; 9(6): 2728. CrossRef
Effects of potassium monopersulfate on nitrification activity and bacterial community structure of sponge biocarrier biofilm in Litopenaeus vannamei aquaculture system
Yazhi Luan, Yang Wang, Chao Liu, Libin Lv, Ailing Xu, Zhiwen Song
Environmental Technology.2024; 45(17): 3354. CrossRef
Investigating the impact of chlorine dioxide in shrimp-rearing water on the stomach microbiome, gill transcriptome, and infection-related mortality in shrimp
Kentaro Imaizumi, Reiko Nozaki, Kayo Konishi, Hideaki Tagishi, Takanori Miura, Hidehiro Kondo, Ikuo Hirono
Journal of Applied Microbiology.2024;[Epub] CrossRef
Assessing the efficacy of bleaching powder in disinfecting marine water: Insights from the rapid recovery of microbiomes
Yawen Tang, Huajun Zhang, Jiaojiao Yan, Nan Luo, Xuezhi Fu, Xiaoyu Wu, Jialin Wu, Changjun Liu, Demin Zhang
Water Research.2023; 241: 120136. CrossRef
Stocking Density Effects on Pacific White Shrimp Litopenaeus vannamei Hatchery Performance in Algal‐Bacterial Biofloc Systems
Hu‐wei Chen, Da‐chuan Sun, Wen‐chang Liu, Shuang Li, Hong‐xin Tan
North American Journal of Aquaculture.2023; 85(1): 3. CrossRef

Review

[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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Research Support, Non-U.S. Gov't

Deoxycytidine Production by Metabolically Engineered Corynebacterium ammoniagenes: Yun-Bom Lee , Hong Baek , Sang-Kyum Kim , Hyung-Hwan Hyun; J. Microbiol. 2011;49(1):53-57. Published online March 3, 2011; DOI: https://doi.org/10.1007/s12275-011-0195-1

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Abstract: Corynebacterium ammoniagenes N424 was metabolically modified to isolate overproducers of deoxycytidine. Inosine auxotrophy (ino-) was initially introduced to prevent the flow of PRPP (phosphoribosyl pyrophosphate) into the purine biosynthetic pathway by random mutagenesis using N-methyl-N'-nitro-N-nitrosoguanidine. Following that, mutants possessing hydroxyurea resistance (HUr) were isolated to increase the activity of ribonucleoside diphosphate reductase, which catalyzes the reduction of ribonucleoside diphosphate to deoxyribonucleoside diphosphate. Then, in order to block the flow of dCTP into the TMP biosynthetic pathway via dUTP, thymine auxotrophy (thy-) was introduced into the mutant IH30 with ino- and HUr. The resulting mutant IM7, possessing the characteristics of ino-, HUr, and thy-, was deficient in dCTP deaminase and produced significantly higher amounts of deoxycytidine (81.3 mg/L) compared to its mother strain IH30 (6.2 mg/L). Deoxycytidine productivity was further enhanced by isolating the mutant IU19, which was resistant to 5-fluorouracil, an inhibitor of carbamoyl phosphate synthase. This enzyme catalyzed the synthesis of carbamoyl phosphate from glutamine, HCO3 -, and ATP. 5-Fluorouracil also inhibited aspartate transcarbamoylase, catalyzeing the condensation of carbamoyl phosphate and aspartate. Finally, 5-fluorocytosine resistance (FCr) was introduced into the mutant strain IU19 to relieve the repression caused by accumulation of pyrimidine nucleosides. The mutant strain IC14-C6 possessing all the five characteristics described above produced 226.3 mg/L of deoxycytidine, which was at least 2,000 fold higher compared to the wild type, and accumulated only a negligible amount of other pyrimidines under shake flask fermentation.

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