Journal of Microbiology

Reviews

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

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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.

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

Extensive Genomic Rearrangement of Catalase-Less Cyanobloom-Forming Microcystis aeruginosa in Freshwater Ecosystems: Minkyung Kim, Jaejoon Jung, Wonjae Kim, Yerim Park, Che Ok Jeon, Woojun Park; J. Microbiol. 2024;62(11):933-950. Published online October 8, 2024; DOI: https://doi.org/10.1007/s12275-024-00172-7

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Abstract: Many of the world's freshwater ecosystems suffer from cyanobacteria-mediated blooms and their toxins. However, a mechanistic understanding of why and how Microcystis aeruginosa dominates over other freshwater cyanobacteria during warmer summers is lacking. This paper utilizes comparative genomics with other cyanobacteria and literature reviews to predict the gene functions and genomic architectures of M. aeruginosa based on complete genomes. The primary aim is to understand this species' survival and competitive strategies in warmer freshwater environments. M. aeruginosa strains exhibiting a high proportion of insertion sequences (~ 11%) possess genomic structures with low synteny across different strains. This indicates the occurrence of extensive genomic rearrangements and the presence of many possible diverse genotypes that result in greater population heterogeneities than those in other cyanobacteria in order to increase survivability during rapidly changing and threatening environmental challenges. Catalase-less M. aeruginosa strains are even vulnerable to low light intensity in freshwater environments with strong ultraviolet radiation. However, they can continuously grow with the help of various defense genes (e.g., egtBD, cruA, and mysABCD) and associated bacteria. The strong defense strategies against biological threats (e.g., antagonistic bacteria, protozoa, and cyanophages) are attributed to dense exopolysaccharide (EPS)-mediated aggregate formation with efficient buoyancy and the secondary metabolites of M. aeruginosa cells. Our review with extensive genome analysis suggests that the ecological vulnerability of M. aeruginosa cells can be overcome by diverse genotypes, secondary defense metabolites, reinforced EPS, and associated bacteria.

The crosstalk between bacteria and host autophagy: host defense or bacteria offense: Lin Zheng , Fang Wei , Guolin Li; J. Microbiol. 2022;60(5):451-460. Published online April 29, 2022; DOI: https://doi.org/10.1007/s12275-022-2009-z

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Abstract

Xenophagy is a specific selective autophagy for the elimination of intracellular bacteria. Current evidence suggests that the processes for host autophagy system to recognize and eliminate invading bacteria are complex, and vary according to different pathogens. Although both ubiquitin-dependent and ubiquitin-independent autophagy exist in host to defense invading bacteria, successful pathogens have evolved diverse strategies to escape from or paralyze host autophagy system. In this review, we discuss the mechanisms of host autophagy system to recognize and eliminate intracellular pathogens and the mechanisms of different pathogens to escape from or paralyze host autophagy system, with a particular focus on the most extensively studied bacteria.

Citations

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Complement C3 deposition restricts the proliferation of internalized Staphylococcus aureus by promoting autophagy
Yining Deng, Yunke Zhang, Tong Wu, Kang Niu, Xiaoyu Jiao, Wenge Ma, Chen Peng, Wenxue Wu
Frontiers in Cellular and Infection Microbiology.2024;[Epub] CrossRef
Innate immune response of host cells infected with Salmonella
Hongfei Fan, Juane Lu, Hao Wu, Haihua Ruan, Wenjun Song, Y.-T. Yu, P.P. Piccaluga, S. Xie
BIO Web of Conferences.2024; 111: 01022. CrossRef
Exploring the Connections: Autophagy, Gut Microbiota, and Inflammatory Bowel Disease Pathogenesis
Arunkumar Subramanian, Afrarahamed J, Tamilanban T, Vinoth Kumarasamy, M Yasmin Begum, Mahendran Sekar, Vetriselvan Subramaniyan, Ling Shing Wong, Adel Al Fatease
Journal of Inflammation Research.2024; Volume 17: 10453. CrossRef
Programmed cell death and Salmonella pathogenesis: an interactive overview
Yu Zhang, Maodou Xu, Yujiao Guo, Li Chen, Wanwipa Vongsangnak, Qi Xu, Lizhi Lu
Frontiers in Microbiology.2024;[Epub] CrossRef
Bacterial lipoprotein plays an important role in the macrophage autophagy and apoptosis induced by Salmonella typhimurium and Staphylococcus aureus
Shanshan Jiang, Jinyao He, Lijie Zhang, Qiaojiajie Zhao, Shuqi Zhao
Open Life Sciences.2023;[Epub] CrossRef
Xenophagy as a Strategy for Mycobacterium leprae Elimination during Type 1 or Type 2 Leprosy Reactions: A Systematic Review
Débora Dantas Nucci Cerqueira, Ana Letícia Silva Pereira, Ana Elisa Coelho da Costa, Tarcísio Joaquim de Souza, Matheus Santos de Sousa Fernandes, Fabrício Oliveira Souto, Patrícia d’Emery Alves Santos
Pathogens.2023; 12(12): 1455. CrossRef
Brucella BtpB Manipulates Apoptosis and Autophagic Flux in RAW264.7 Cells
Junmei Li, Lin Qi, Ziyang Diao, Mengyu Zhang, Bin Li, Yunyi Zhai, Mingyue Hao, Dong Zhou, Wei Liu, Yaping Jin, Aihua Wang
International Journal of Molecular Sciences.2022; 23(22): 14439. CrossRef

Journal Articles

Screening of small molecules attenuating biofilm formation of Acinetobacter baumannii by inhibition of ompA promoter activity: Seok Hyeon Na , Hyejin Jeon , Man Hwan Oh , Yoo Jeong Kim , Je Chul Lee; J. Microbiol. 2021;59(9):871-878. Published online August 27, 2021; DOI: https://doi.org/10.1007/s12275-021-1394-z

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Abstract

Anti-virulence therapeutic strategies are promising alternatives against drug-resistant pathogens. Outer membrane protein A (OmpA) plays a versatile role in the pathogenesis and antimicrobial resistance of Acinetobacter baumannii. Therefore, OmpA is an innovative target for anti-virulence therapy against A. baumannii. This study aimed to develop a high-throughput screening (HTS) system to discover small molecules inhibiting the ompA promoter activity of A. baumannii and screen chemical compounds using the bacterial growth-based HTS system. The ompA promoter and open reading frame of nptI fusion plasmids that controlled the expression of nptI encoding resistance to kanamycin by the ompA promoter were constructed and then transformed into A. baumannii ATCC 17978. This reporter strain was applied to screen small molecules inhibiting the ompA promoter activity in a chemical library. Of the 7,520 chemical compounds, 15 exhibited ≥ 70% growth inhibition of the report strain cultured in media containing kanamycin. Three compounds inhibited the expression of ompA and OmpA in the outer membrane of A. baumannii ATCC 17978, which subsequently reduced biofilm formation. In conclusion, our reporter strain is useful for large-scale screening of small molecules inhibiting the ompA expression in A. baumannii. Hit compounds identified by the HTS system are promising scaffolds to develop novel therapeutics against A. baumannii.

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A peptide targeting outer membrane protein A of Acinetobacter baumannii exhibits antibacterial activity by reducing bacterial pathogenicity
Hui Zhao, Yue Hu, Dan Nie, Na Li, Zhou Chen, Shan Zhou, Mingkai Li, Xiaoyan Xue, James E. Leggett
Antimicrobial Agents and Chemotherapy.2024;[Epub] CrossRef
Acinetobacter baumannii OmpA-like porins: functional characterization of bacterial physiology, antibiotic-resistance, and virulence
Daniela Scribano, Elena Cheri, Arianna Pompilio, Giovanni Di Bonaventura, Manuel Belli, Mario Cristina, Luigi Sansone, Carlo Zagaglia, Meysam Sarshar, Anna Teresa Palamara, Cecilia Ambrosi
Communications Biology.2024;[Epub] CrossRef
Anti-OmpA antibodies as potential inhibitors of Acinetobacter baumannii biofilm formation, adherence to, and proliferation in A549 human alveolar epithelial cells
Hamideh Barati, Zahra Fekrirad, Mohammadreza Jalali Nadoushan, Iraj Rasooli
Microbial Pathogenesis.2024; 186: 106473. CrossRef
Current and novel therapies for management of Acinetobacter baumannii -associated pneumonia
Aye Mya Sithu Shein, Parichart Hongsing, O’Rorke Kevin Smith, Phatthranit Phattharapornjaroen, Kazuhiko Miyanaga, Longzhu Cui, Hitoshi Ishikawa, Mohan Amarasiri, Peter N. Monk, Anthony Kicic, Tanittha Chatsuwan, Daniel Pletzer, Paul G. Higgins, Shuichi Ab
Critical Reviews in Microbiology.2024; : 1. CrossRef
Understanding the mechanisms of antimicrobial resistance and potential therapeutic approaches against the Gram-negative pathogen Acinetobacter baumannii
Vishwani Jamwal, Tashi Palmo, Kuljit Singh
RSC Medicinal Chemistry.2024; 15(12): 3925. CrossRef
Acinetobacter baumannii outer membrane protein A induces autophagy in bone marrow‐derived dendritic cells involving the PI3K/mTOR pathway
Hongyi Tan, Liyan Cao
Immunity, Inflammation and Disease.2023;[Epub] CrossRef
Advances in research on virulence factors ofAcinetobacter baumanniiand their potential as novel therapeutic targets
Jian-Xia Zhou, Ding-Yun Feng, Xia Li, Jia-Xin Zhu, Wen-Bin Wu, Tian-tuo Zhang
Journal of Applied Microbiology.2023;[Epub] CrossRef
Famotidine Enhances Rifampicin Activity against Acinetobacter baumannii by Affecting OmpA
Meng-na Zhang, Xiao-ou Zhao, Qi Cui, Dao-mi Zhu, Muhammad Asif Wisal, Han-dong Yu, Ling-cong Kong, Hong-xia Ma, Laurie E. Comstock
Journal of Bacteriology.2023;[Epub] CrossRef
Factors mediating Acinetobacter baumannii biofilm formation: Opportunities for developing therapeutics
Kirti Upmanyu, Qazi Mohd. Rizwanul Haq, Ruchi Singh
Current Research in Microbial Sciences.2022; 3: 100131. CrossRef
Evaluation the reactivity of a peptide-based monoclonal antibody derived from OmpA with drug resistant pulsotypes of Acinetobacter baumannii as a potential therapeutic approach
Omid Yeganeh, Mahdi Shabani, Parviz Pakzad, Nariman Mosaffa, Ali Hashemi
Annals of Clinical Microbiology and Antimicrobials.2022;[Epub] CrossRef
Therapeutic Effects of Inhibitor of ompA Expression against Carbapenem-Resistant Acinetobacter baumannii Strains
Seok-Hyeon Na, Hyejin Jeon, Man-Hwan Oh, Yoo-Jeong Kim, Mingi Chu, Ill-Young Lee, Je-Chul Lee
International Journal of Molecular Sciences.2021; 22(22): 12257. CrossRef
DksA Modulates Antimicrobial Susceptibility of Acinetobacter baumannii
Nayeong Kim, Joo-Hee Son, Kyeongmin Kim, Hyo-Jeong Kim, Minsang Shin, Je-Chul Lee
Antibiotics.2021; 10(12): 1472. CrossRef

Similarities and differences between 6S RNAs from Bradyrhizobium japonicum and Sinorhizobium meliloti: Olga Y. Burenina , Daria A. Elkina , Anzhela Y. Migur , Tatiana S. Oretskaya , Elena Evguenieva-Hackenberg , RolK. Hartmann , Elena A. Kubareva; J. Microbiol. 2020;58(11):945-956. Published online October 30, 2020; DOI: https://doi.org/10.1007/s12275-020-0283-1

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Abstract

6S RNA, a conserved and abundant small non-coding RNA found in most bacteria, regulates gene expression by inhibiting RNA polymerase (RNAP) holoenzyme. 6S RNAs from α-proteobacteria have been studied poorly so far. Here, we present a first in-depth analysis of 6S RNAs from two α-proteobacteria species, Bradyrhizobium japonicum and Sinorhizobium meliloti. Although both belong to the order Rhizobiales and are typical nitrogen-fixing symbionts of legumes, their 6S RNA expression profiles were found to differ: B. japonicum 6S RNA accumulated in the stationary phase, thus being reminiscent of Escherichia coli 6S RNA, whereas S. meliloti 6S RNA level peaked at the transition to the stationary phase, similarly to Rhodobacter sphaeroides 6S RNA. We demonstrated in vitro that both RNAs have hallmarks of 6S RNAs: they bind to the σ70-type RNAP holoenzyme and serve as templates for de novo transcription of so-called product RNAs (pRNAs) ranging in length from ~13 to 24 nucleotides, with further evidence of the synthesis of even longer pRNAs. Likewise, stably bound pRNAs were found to rearrange the 6S RNA structure to induce its dissociation from RNAP. Compared with B. japonicum 6S RNA, considerable conformational heterogeneity was observed for S. meliloti 6S RNA and its complexes with pRNAs, even though the two 6S RNAs share ~75% sequence identity. Overall, our findings suggest that the two rhizobial 6S RNAs have diverged with respect to their regulatory impact on gene expression throughout the bacterial life cycle.

Citations

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Bacteria Adaptation Mechanisms to Stress Conditions with Small Non-Coding RNAs Participation
A. S. Karpov, D. A. Elkina, T. S. Oretskaya, E. A. Kubareva
Биоорганическая химия.2023; 49(6): 555. CrossRef
Bacterial Adaptation Mechanisms to Stress Conditions with Small Non-Coding RNAs Participation (A Review)
A. S. Karpov, D. A. Elkina, T. S. Oretskaya, E. A. Kubareva
Russian Journal of Bioorganic Chemistry.2023; 49(6): 1198. CrossRef
Structural and Functional Insight into the Mechanism of Bacillus subtilis 6S-1 RNA Release from RNA Polymerase
Sweetha Ganapathy, Philipp G. Hoch, Marcus Lechner, Malte Bussiek, Roland K. Hartmann
Non-Coding RNA.2022; 8(1): 20. CrossRef
Involvement of E. coli 6S RNA in Oxidative Stress Response
Olga Y. Burenina, Daria A. Elkina, Anna Ovcharenko, Valeria A. Bannikova, M. Amri C. Schlüter, Tatiana S. Oretskaya, Roland K. Hartmann, Elena A. Kubareva
International Journal of Molecular Sciences.2022; 23(7): 3653. CrossRef
Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search
Viola Vaňková Hausnerová, Olga Marvalová, Michaela Šiková, Mahmoud Shoman, Jarmila Havelková, Milada Kambová, Martina Janoušková, Dilip Kumar, Petr Halada, Marek Schwarz, Libor Krásný, Jarmila Hnilicová, Josef Pánek
Frontiers in Microbiology.2022;[Epub] CrossRef
Detection of Small Products of Transcription from 6S RNA (pRNA) by “Mirror-Like” Northern Blot Hybridization
O. Y. Burenina, T. S. Oretskaya, E. A. Kubareva
Russian Journal of Bioorganic Chemistry.2021; 47(2): 478. CrossRef

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