Journal of Microbiology

Journal Articles

Development of a Novel D‑Lactic Acid Production Platform Based on Lactobacillus saerimneri TBRC 5746: Kitisak Sansatchanon , Pipat Sudying , Peerada Promdonkoy , Yutthana Kingcha , Wonnop Visessanguan , Sutipa Tanapongpipat , Weerawat Runguphan , Kanokarn Kocharin; J. Microbiol. 2023;61(9):853-863. Published online September 14, 2023; DOI: https://doi.org/10.1007/s12275-023-00077-x

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D-Lactic acid is a chiral, three-carbon organic acid, that bolsters the thermostability of polylactic acid. In this study, we developed a microbial production platform for the high-titer production of D-lactic acid. We screened 600 isolates of lactic acid bacteria (LAB) and identified twelve strains that exclusively produced D-lactic acid in high titers. Of these strains, Lactobacillus saerimneri TBRC 5746 was selected for further development because of its homofermentative metabolism. We investigated the effects of high temperature and the use of cheap, renewable carbon sources on lactic acid production and observed a titer of 99.4 g/L and a yield of 0.90 g/g glucose (90% of the theoretical yield). However, we also observed L-lactic acid production, which reduced the product’s optical purity. We then used CRISPR/dCas9-assisted transcriptional repression to repress the two Lldh genes in the genome of L. saerimneri TBRC 5746, resulting in a 38% increase in D-lactic acid production and an improvement in optical purity. This is the first demonstration of CRISPR/dCas9-assisted transcriptional repression in this microbial host and represents progress toward efficient microbial production of D-lactic acid.

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Converting a D-/L lactic acid bacteria to its d-type counterpart via a combined chemical mutagenesis and biosensor screening method, and its application in lignocellulosic biorefinery
Xingwang Ma, Kang Yan, Yuwei Zhang, Xiaoyu Xie, Shujie Zou, Yuanyuan Sha, Rui Zhai, Zhaoxian Xu, Mingjie Jin
Bioresource Technology.2025; 428: 132471. CrossRef
Industrial–scale production of various bio–commodities by engineered microbial cell factories: Strategies of engineering in microbial robustness
Ju-Hyeong Jung, Vinoth Kumar Ponnusamy, Gopalakrishnan Kumar, Bartłomiej Igliński, Vinod Kumar, Grzegorz Piechota
Chemical Engineering Journal.2024; 502: 157679. CrossRef
Microbial Cell Factories: Biodiversity, Pathway Construction, Robustness, and Industrial Applicability
Rida Chaudhary, Ali Nawaz, Mireille Fouillaud, Laurent Dufossé, Ikram ul Haq, Hamid Mukhtar
Microbiology Research.2024; 15(1): 247. CrossRef
Adaptive Evolution for the Efficient Production of High-Quality d-Lactic Acid Using Engineered Klebsiella pneumoniae
Bo Jiang, Jiezheng Liu, Jingnan Wang, Guang Zhao, Zhe Zhao
Microorganisms.2024; 12(6): 1167. CrossRef
Enhancing D-lactic acid production from non-detoxified corn stover hydrolysate via innovative F127-IEA hydrogel-mediated immobilization of Lactobacillus bulgaricus T15
Yuhan Zheng, Feiyang Sun, Siyi Liu, Gang Wang, Huan Chen, Yongxin Guo, Xiufeng Wang, Maia Lia Escobar Bonora, Sitong Zhang, Yanli Li, Guang Chen
Frontiers in Microbiology.2024;[Epub] CrossRef

Metformin Regulates Gut Microbiota Abundance to Suppress M2 Skewing of Macrophages and Colorectal Tumorigenesis in Mice: Linfeng Fan , Xiangfu Zeng , Guofeng Xu; J. Microbiol. 2023;61(1):109-120. Published online January 26, 2023; DOI: https://doi.org/10.1007/s12275-022-00010-8

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The correlation of imbalanced gut microbiota with the onset and progression of colorectal cancer (CRC) has become clear. This work investigates the effect of metformin on gut microbiota and genesis of CRC in mice. Human fecal samples were collected from healthy control (HC) donors and CRC patients. Compared to HC donors, CRC patients had reduced abundance of gut microbiota; however, they had increased abundance of detrimental Bacteroidetes. Mice were injected with azomethane (AOM) to induce colorectal tumorigenesis models. Treatment of CRC patients-sourced fecal microbiota promoted tumorigenesis, and it increased the expression of Ki67, β-catenin, COX-2, and Cyclin D1 in mouse colon tissues. Further treatment of metformin blocked the colorectal tumorigenesis in mice. Fecal microbiota from the metformin-treated mice was collected, which showed decreased Bacteroidetes abundance and suppressed AOM-induced colorectal tumorigenesis in mice as well. Moreover, the metformin- modified microbiota promoted the M1 macrophage-related markers IL-6 and iNOS but suppressed the M2 macrophage-related markers IL-4R and Arg1 in mouse colon tissues. In conclusion, this study suggests that metformin-mediated gut microbiota alteration suppresses macrophage M2 polarization to block colorectal tumorigenesis.

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Metformin alleviates colitis-associated colorectal cancer via inhibition of the TLR4/MyD88/NFκB/MAPK pathway and macrophage M2 polarization
Xueying Lai, Bin Liu, Yu Wan, Ping Zhou, Wanjun Li, Wei Hu, Wei Gong
International Immunopharmacology.2025; 144: 113683. CrossRef
Metformin as an immunomodulatory agent in enhancing head and neck squamous cell carcinoma therapies
Wenting Li, Nanshu Liu, Mingwei Chen, Dongjuan Liu, Sai Liu
Biochimica et Biophysica Acta (BBA) - Reviews on Cancer.2025; 1880(2): 189262. CrossRef
Intestinal dysbiosis and colorectal cancer
Ziran Kang, Shanshan Jiang, Jing-Yuan Fang, Huimin Chen
Chinese Medical Journal.2025; 138(11): 1266. CrossRef
Metformin induces diarrhea in mice under over-eating conditions
Kotomi Chikama, Hiroshi Takemroi, Momoka Mizoguchi, Saho Furukawa, Koutarou Terada, Masafumi Ito, Hirotsugu Hirano, Takanori Miura, Koichi Doi, Megumi Horiya, Takehiro Kato, Daisuke Yabe, Takashi Shibata
Diabetology International.2025; 16(3): 568. CrossRef
Clinical efficacy of metformin in familial adenomatous polyposis and the effect of intestinal flora
Linxin Zhou, Linfu Zheng, Binbin Xu, Zhou Ye, Dazhou Li, Wen Wang
Orphanet Journal of Rare Diseases.2024;[Epub] CrossRef
An AMPK agonist suppresses the progress of colorectal cancer by regulating the polarization of TAM to M1 through inhibition of HIF-1α and mTOR signal pathway
Yuanyuan Cao, Mingyi Wo, Chan Xu, Xianming Fei, Juan Jin, Zhiming Shan
Journal of Cancer Research and Therapeutics.2023; 19(6): 1560. CrossRef

[PROTOCOL]Analyzing viral epitranscriptomes using nanopore direct RNA sequencing: Ari Hong , Dongwan Kim , V. Narry Kim , Hyeshik Chang; J. Microbiol. 2022;60(9):867-876. Published online August 24, 2022; DOI: https://doi.org/10.1007/s12275-022-2324-4

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RNA modifications are a common occurrence across all domains of life. Several chemical modifications, including N6- methyladenosine, have also been found in viral transcripts and viral RNA genomes. Some of the modifications increase the viral replication efficiency while also helping the virus to evade the host immune system. Nonetheless, there are numerous examples in which the host's RNA modification enzymes function as antiviral factors. Although established methods like MeRIP-seq and miCLIP can provide a transcriptome- wide overview of how viral RNA is modified, it is difficult to distinguish between the complex overlapping viral transcript isoforms using the short read-based techniques. Nanopore direct RNA sequencing (DRS) provides both long reads and direct signal readings, which may carry information about the modifications. Here, we describe a refined protocol for analyzing the RNA modifications in viral transcriptomes using nanopore technology.

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From DNA Methylation and Histone Modifications to Non-Coding RNAs: Evaluating Tools for Epigenetic Research
Ines Benčik, Lara Saftić Martinović, Tea Mladenić, Saša Ostojić, Sanja Dević Pavlić
Applied Sciences.2025; 15(18): 9940. CrossRef
Computational methods for the analysis of long-read RNA-seq data
Kristina Santucci, Yuning Cheng, Si-Mei Xu, Michael Janitz
Genomics.2025; 117(6): 111144. CrossRef
Enhanced detection of RNA modifications in Escherichia coli utilizing direct RNA sequencing
Zhihao Guo, Yanwen Shao, Lu Tan, Beifang Lu, Xin Deng, Sheng Chen, Runsheng Li
Cell Reports Methods.2025; 5(9): 101168. CrossRef
Utilization of nanopore direct RNA sequencing to analyze viral RNA modifications
Lu Tan, Zhihao Guo, Xiaoming Wang, Dal Young Kim, Runsheng Li, Pedro H. Oliveira
mSystems.2024;[Epub] CrossRef
Current progress in strategies to profile transcriptomic m6A modifications
Yuening Yang, Yanming Lu, Yan Wang, Xianghui Wen, Changhai Qi, Weilan Piao, Hua Jin
Frontiers in Cell and Developmental Biology.2024;[Epub] CrossRef
Improved sub-genomic RNA prediction with the ARTIC protocol
Thomas Baudeau, Kristoffer Sahlin
Nucleic Acids Research.2024; 52(17): e82. CrossRef
Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases
Stephen Spatz, Claudio L. Afonso
Veterinary Sciences.2024; 11(6): 239. CrossRef
Quantitative profiling N1-methyladenosine (m1A) RNA methylation from Oxford nanopore direct RNA sequencing data
Shenglun Chen, Jia Meng, Yuxin Zhang
Methods.2024; 228: 30. CrossRef
Multicellular, IVT-derived, unmodified human transcriptome for nanopore-direct RNA analysis
Caroline A. McCormick, Stuart Akeson, Sepideh Tavakoli, Dylan Bloch, Isabel N. Klink, Miten Jain, Sara H. Rouhanifard
Gigabyte.2024; 2024: 1. CrossRef
Dissecting the effects of METTL3 on alternative splicing in prostate cancer
Lin Wang, Ling Shi, Yonghao Liang, Judy Kin-Wing Ng, Chan Hoi Yin, Lingyi Wang, Jinpao Hou, Yiwei Wang, Cathy Sin-Hang Fung, Peter Ka-Fung Chiu, Chi-Fai Ng, Stephen Kwok-Wing Tsui
Frontiers in Oncology.2023;[Epub] CrossRef

Analysis of a bac operon-silenced strain suggests pleiotropic effects of bacilysin in Bacillus subtilis: Ozan Ertekin , Meltem Kutnu , Aslı Aras Ta&# , Mustafa Demir , Ayten Yazgan Karata&# , Gülay Özcengiz; J. Microbiol. 2020;58(4):297-313. Published online January 28, 2020; DOI: https://doi.org/10.1007/s12275-020-9064-0

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Bacilysin, as the simplest peptide antibiotic made up of only L-alanine and L-anticapsin, is produced and excreted by Bacillus subtilis under the control of quorum sensing. We analyzed bacilysin-nonproducing strain OGU1 which was obtained by bacA-targeted pMutin T3 insertion into the parental strain genome resulting in a genomic organization (bacA􍿁::lacZ::erm::bacABCDEF) to form an IPTG-inducible bac operon. Although IPTG induction provided 3- to 5-fold increment in the transcription of bac operon genes, no bacilysin activity was detectable in bioassays and inability of the OGU1 to form bacilysin was confirmed by UPLC-mass spectrometry analysis. Phenotypic analyses revealed the deficiencies in OGU1 with respect to colony pigmentation, spore coat proteins, spore resistance and germination, which could be rescued by external addition of bacilysin concentrate into its cultures. 2DE MALDI-TOF/MS and nanoLC-MS/MS were used as complementary approaches to compare cytosolic proteomes of OGU1. 2-DE identified 159 differentially expressed proteins corresponding to 121 distinct ORFs. In nanoLCMS/ MS, 76 proteins were differentially expressed in OGU1. Quantitative transcript analyses of selected genes validated the proteomic findings. Overall, the results pointed to the impact of bacilysin on expression of certain proteins of sporulation and morphogenesis; the members of mother cell compartment- specific σE and σK regulons in particular, quorum sensing and two component-global regulatory systems, peptide transport, stress response as well as CodY- and ScoCregulated proteins.

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Exploring Bacillus velezensis in a biomedical context: a systematic review
Eduarda Guimarães Sousa, Gabriela Munis Campos, Ludmila Silva Quaresma, Thaís Fernandes Mendonça Mota, Nédia de Castilhos Ghisi, Gabriel Camargos Gomes, Rhayane Cristina Viegas Santos, Beatriz Gamarano Rocha de Souza, Éric Guédon, Siomar de Castro Soares,
Academia Molecular Biology and Genomics.2025;[Epub] CrossRef
Biocontrol Ability of Strain Bacillus amyloliquefaciens SQ-2 against Table Grape Rot Caused by Aspergillus tubingensis
Suran Li, Shuangshuang Dai, Lei Huang, Yumeng Cui, Ming Ying
Journal of Agricultural and Food Chemistry.2024; 72(44): 24374. CrossRef
Isolation and identification of a novel Bacillus velezensis strain JIN4 and its potential for biocontrol of kiwifruit bacterial canker caused by Pseudomonas syringae pv. actinidiae
Xin Zhao, Yang Zhai, Lin Wei, Fei Xia, Yuanru Yang, Yongjian Yi, Hongying Wang, Caisheng Qiu, Feng Wang, Liangbin Zeng
Frontiers in Plant Science.2024;[Epub] CrossRef
Signatures of kin selection in a natural population of the bacteria Bacillus subtilis
Laurence J Belcher, Anna E Dewar, Chunhui Hao, Melanie Ghoul, Stuart A West
Evolution Letters.2023; 7(5): 315. CrossRef
Comparative biological network analysis for differentially expressed proteins as a function of bacilysin biosynthesis in Bacillus subtilis
Meltem Kutnu, Elif Tekin İşlerel, Nurcan Tunçbağ, Gülay Özcengiz
Integrative Biology.2022; 14(5): 99. CrossRef
Probiotic effects of the Bacillus velezensis GY65 strain in the mandarin fish, Siniperca chuatsi
Jiachuan Wang, Defeng Zhang, Yajun Wang, Zhijun Liu, Lijuan Liu, Cunbin Shi
Aquaculture Reports.2021; 21: 100902. CrossRef
Bacilysin within the Bacillus subtilis group: gene prevalence versus antagonistic activity against Gram-negative foodborne pathogens
Catherine Nannan, Huong Quynh Vu, Annika Gillis, Simon Caulier, Thuy Thanh Thi Nguyen, Jacques Mahillon
Journal of Biotechnology.2021; 327: 28. CrossRef
Impact of spatial proximity on territoriality among human skin bacteria
Jhonatan A. Hernandez-Valdes, Lu Zhou, Marcel P. de Vries, Oscar P. Kuipers
npj Biofilms and Microbiomes.2020;[Epub] CrossRef

Transcriptomic and proteomic profiling revealed global changes in Streptococcus thermophilus during pH-controlled batch fermentations: Yali Qiao , Cong Leng , Gefei Liu , Yanjiao Zhang , Xuepeng Lv , Hongyu Chen , Jiahui Sun , Zhen Feng; J. Microbiol. 2019;57(9):769-780. Published online June 14, 2019; DOI: https://doi.org/10.1007/s12275-019-8604-y

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Understanding global changes of physiological processes at the molecular level during the growth of Streptococcus thermophilus is essential for the rational design of cultivation media and the optimization of bioprocesses. Transcriptomics and proteomics were combined to investigate the global changes at the transcript and protein level during the growth of S. thermophilus. The expression of 1396 genes (FDR ≤ 0.001) and 876 proteins (P < 0.05) changed significantly over time. The most remarkable growth phase dependent changes occurred in the late-lag phase and were related to heterofermentation, glycolysis, peptidoglycan biosynthesis, conversion between amino acids and stress response. The present
results
could provide theoretical guidance for high-cell-density culture, help design cultivation media, and help attain a high biomass of S. thermophilus.

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The dual nature of plant growth-promoting bacteria: Benefits, risks, and pathways to sustainable deployment
Hassan Etesami
Current Research in Microbial Sciences.2025; 9: 100421. CrossRef
Metabolic and Transcriptomic-Based Characterization of Streptococcus salivarius ssp. thermophilus Snew Fermentation in Milk
Ye Wang, Haijie Zhao, Huilin Zhang, Baochao Hou, Weilian Hung, Jian He, Chao Liang, Baolei Li, Chaoxin Man, Yujun Jiang, Yu Zhang, Ling Guo
Foods.2025; 14(3): 530. CrossRef
The contribution of microorganisms to sustainable development: towards a green future through synthetic biology and systems biology
Alaa T. Qumsani
Journal of Umm Al-Qura University for Applied Sciences.2024;[Epub] CrossRef
Multi-omics analysis for mechanistic understanding of microbial-mediated synthesis of silver nanoparticles
Wenjing Liu, Aofan Wang, Xitong Li, Jishi Wang, Xiaowei Liu, Yujie Zhao, Zeying He, Jingjing Du
Chemical Engineering Journal.2024; 497: 154410. CrossRef
Arginine deiminase pathway of Tetragenococcus halophilus contributes to improve the acid tolerance of lactic acid bacteria
Huan Yang, Dingkang Wang, Yao Jin, Rongqing Zhou, Jun Huang, Chongde Wu
Food Microbiology.2023; 113: 104281. CrossRef
Current advances for omics-guided process optimization of microbial manufacturing
Shengtong Wan, Xin Liu, Wentao Sun, Bo Lv, Chun Li
Bioresources and Bioprocessing.2023;[Epub] CrossRef
Proteomic perspectives on thermotolerant microbes: an updated review
Chandraprakash Yamini, Govindasamy Sharmila, Chandrasekaran Muthukumaran, Kumar Pavithran, Narasimhan Manojkumar
Molecular Biology Reports.2022; 49(1): 629. CrossRef
Comparative transcriptome analysis for the biosynthesis of antioxidant exopolysaccharide in Streptococcus thermophilusCS6
Yang Zhou, Yanhua Cui, Xiaojun Qu
Journal of the Science of Food and Agriculture.2022; 102(12): 5321. CrossRef
Genome-Scale Metabolic Modeling Combined with Transcriptome Profiling Provides Mechanistic Understanding of Streptococcus thermophilus CH8 Metabolism
Martin H. Rau, Paula Gaspar, Maiken Lund Jensen, Asger Geppel, Ana Rute Neves, Ahmad A. Zeidan, Danilo Ercolini
Applied and Environmental Microbiology.2022;[Epub] CrossRef
Foodomic-Based Approach for the Control and Quality Improvement of Dairy Products
Rubén Agregán, Noemí Echegaray, Asad Nawaz, Christophe Hano, Gholamreza Gohari, Mirian Pateiro, José M. Lorenzo
Metabolites.2021; 11(12): 818. CrossRef
Milk Fermentation by Lacticaseibacillus rhamnosus GG and Streptococcus thermophilus SY-102: Proteolytic Profile and ACE-Inhibitory Activity
Jessica Lizbeth Sebastián-Nicolas, Elizabeth Contreras-López, Juan Ramírez-Godínez, Alma Elizabeth Cruz-Guerrero, Gabriela Mariana Rodríguez-Serrano, Javier Añorve-Morga, Judith Jaimez-Ordaz, Araceli Castañeda-Ovando, Emmanuel Pérez-Escalante, Alexis Ayal
Fermentation.2021; 7(4): 215. CrossRef
Regulatory Mechanisms of L-Lactic Acid and Taste Substances in Chinese Acid Rice Soup (Rice-Acid) Fermented With a Lacticaseibacillus paracasei and Kluyveromyces marxianus
Na Liu, Likang Qin, Song Miao
Frontiers in Microbiology.2021;[Epub] CrossRef
Metabolic Pathway Profiling in Intracellular and Extracellular Environments of Streptococcus thermophilus During pH-Controlled Batch Fermentations
Yali Qiao, Gefei Liu, Xuepeng Lv, Xuejing Fan, Yanjiao Zhang, Li Meng, Mingzhi Ai, Zhen Feng
Frontiers in Microbiology.2020;[Epub] CrossRef

Review

MINIREVIEW] Cure of tuberculosis using nanotechnology: An overview: Rout George Kerry , Sushanto Gouda , Bikram Sil , Gitishree Das , Han-Seung Shin , Gajanan Ghodake , Jayanta Kumar Patra; J. Microbiol. 2018;56(5):287-299. Published online May 2, 2018; DOI: https://doi.org/10.1007/s12275-018-7414-y

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Mycobacterium tuberculosis is the causative agent of tuberculosis (TB), a major health issue of the present era. The bacterium inhabits the host macrophage and other immune cells where it modulates the lysosome trafficking protein, hinders the formation of phagolysosome, and blocks the TNF receptor- dependent apoptosis of host macrophage/monocytes. Other limitations such as resistance to and low bioavailability and bio-distribution of conventional drugs aid to their high virulence and human mortality. This review highlights the use of nanotechnology-based approaches for drug formulation and delivery which could open new avenues to limit the pathogenicity of tuberculosis. Moreover phytochemicals, such as alkaloids, phenols, saponins, steroids, tannins, and terpenoids, extracted from terrestrial plants and mangroves seem promising against M. tuberculosis through different molecular mechanisms. Further understanding of the genomics and proteomics of this pathogenic microbe could also help overcome various research gaps in the path of developing a suitable therapy against tuberculosis.

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Mechanisms of Antibiotic Resistance and Novel Therapeutic Approaches for Mycobacterium tuberculosis: A Narrative Review With a Focus on Tuberculosis Mutations in Iran
Ali Bayat Bodaghi, Aref Shariati, Jebreil Shamseddin, Amir Bayat Bodaghi, Mina Rezaei, Abbas Farahani
Health Science Reports.2025;[Epub] CrossRef
Multi-purpose prototypes for extrapulmonary Mycobacterium tuberculosis targeting: A regenerative medicine perspective
Mashudu T. Mphaphuli, Mduduzi N. Sithole, Pradeep Kumar, Pierre P.D. Kondiah, Mostafa Mabrouk, Yahya E. Choonara
Journal of Drug Delivery Science and Technology.2023; 89: 105039. CrossRef
Clay minerals-based drug delivery systems for anti-tuberculosis drugs
Saeida Saadat, Deepak Rawtani, Garvita Parikh
Journal of Drug Delivery Science and Technology.2022; 76: 103755. CrossRef
A Systematic Review on Antituberculosis Drug Discovery and Antimycobacterial Potential of Biologically Synthesized Silver Nanoparticles: Overview and Future Perspectives
Christian K. Ezeh, Chibuzor N. Eze, Uju M. E. Dibua, Stephen C. Emencheta
Infectious Microbes and Diseases.2022; 4(4): 139. CrossRef
Treatment of Tuberculosis in Nano Era: Recent Avenues
Ritu Rathi, Manju Nagpal, Malkiet Kaur, Priyansh Ballouria, Redhima Dutta, Geeta Aggarwal, Sandeep Arora
Current Bioactive Compounds.2022;[Epub] CrossRef
Detection of Mycobacterium Tuberculosis by Magnetic Nanoparticle Capture-Polymerase Chain Reaction
Zhanying Li, Lei Zhao, Lili Diao, Pei Wang, Conglu Che, Yanqing Tian, Xiuzheng Wang
Science of Advanced Materials.2021; 13(11): 2116. CrossRef
Inhalable linezolid loaded PLGA nanoparticles for treatment of tuberculosis: Design, development and in vitro evaluation
Sunny Shah, Dhanya Cristopher, Shweta Sharma, Moinuddin Soniwala, Jayant Chavda
Journal of Drug Delivery Science and Technology.2020; 60: 102013. CrossRef
Enhancement of cell proliferation and motility of mammalian cells grown in co-culture with Pichia pastoris expressing recombinant human FGF-2
Henry Hieu M. Le, David Vang, Nadia Amer, Tou Vue, Colwin Yee, Hyam Kaou, Joseph S. Harrison, Nan Xiao, Joan Lin-Cereghino, Geoff P. Lin-Cereghino, Der Thor
Protein Expression and Purification.2020; 176: 105724. CrossRef
Silver Nanoparticles for the Therapy of Tuberculosis

Alexandru-Flaviu Tăbăran, Cristian Tudor Matea, Teodora Mocan, Alexandra Tăbăran, Marian Mihaiu, Cornel Iancu, Lucian Mocan
International Journal of Nanomedicine.2020; Volume 15: 2231. CrossRef

Journal Articles

Proteome analysis reveals global response to deletion of mrflbA in Monascus ruber: Qingqing Yan , Zhouwei Zhang , Yishan Yang , Fusheng Chen , Yanchun Shao; J. Microbiol. 2018;56(4):255-263. Published online February 28, 2018; DOI: https://doi.org/10.1007/s12275-018-7425-8

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Abstract PDF

Monascus spp. are commonly used for a wide variety of applications in the food and pharmaceutical industries. In previous studies, the knock-out of mrflbA (a putative regulator of the G protein α subunit) in M. ruber led to autolysis of the mycelia, decreased pigmentation and lowered mycotoxin production. Therefore, we aimed to obtain a comprehensive overview of the underlying mechanism of mrflbA deletion at the proteome level. A two-dimensional gel electrophoresis analysis of mycelial proteins indicated that the abundance of 178 proteins was altered in the ΔmrflbA strain, 33 of which were identified with high confidence. The identified proteins are involved in a range of activities, including carbohydrate and amino acid metabolism, hyphal development and the oxidative stress response, protein modification, and the regulation of cell signaling. Consistent with these findings, the activity of antioxidative enzymes and chitinase was elevated in the supernatant of the ΔmrflbA strain. Furthermore, deletion of mrflbA resulted in the transcriptional reduction of secondary metabolites (pigment and mycotoxin). In short, the mutant phenotypes induced by the deletion of mrflbA were consistent with changes in the expression levels of associated proteins, providing direct evidence of the regulatory functions mediated by mrflbA in M. ruber.

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Histone deacetylase MrHos3 negatively regulates the production of citrinin and pigments in Monascus ruber
Qianrui Liu, Yunfan Zheng, Baixue Liu, Fufang Tang, Yanchun Shao
Journal of Basic Microbiology.2023; 63(10): 1128. CrossRef
Histone deacetylase MrRpd3 plays a major regulational role in the mycotoxin production of Monascus ruber
Yunfan Zheng, Yueyan Huang, Zejing Mao, Yanchun Shao
Food Control.2022; 132: 108457. CrossRef
Characterization of key upstream asexual developmental regulators in Monascus ruber M7
Lili Jia, Yuyun Huang, Jae-Hyuk Yu, Marc Stadler, Yanchun Shao, Wanping Chen, Fusheng Chen
Food Bioscience.2022; 50: 102153. CrossRef
Quantitative Proteomics Analysis by Sequential Window Acquisition of All Theoretical Mass Spectra–Mass Spectrometry Reveals Inhibition Mechanism of Pigments and Citrinin Production of Monascus Response to High Ammonium Chloride Concentration
Bo Zhou, Yifan Ma, Yuan Tian, Jingbo Li, Haiyan Zhong
Journal of Agricultural and Food Chemistry.2020; 68(3): 808. CrossRef

The protein and neutral lipid composition of lipid droplets isolated from the fission yeast, Schizosaccharomyces pombe: Alex Meyers , Karuna Chourey , Taylor M. Weiskittel , Susan Pfiffner , John R. Dunlap , Robert L. Hettich , Paul Dalhaimer; J. Microbiol. 2017;55(2):112-122. Published online January 26, 2017; DOI: https://doi.org/10.1007/s12275-017-6205-1

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Lipid droplets consist of a core of neutral lipids surrounded by a phospholipid monolayer with bound proteins. Much of the information on lipid droplet function comes from proteomic and lipodomic studies that identify the components of droplets isolated from organisms throughout the phylogenetic tree. Here, we add to that important inventory by reporting lipid droplet factors from the fission yeast, Schizosaccharomyces pombe. Unique to this study was the fact that cells were cultured in three different environments: 1) late log growth phase in glucose-based media, 2) stationary phase in glucosebased media, and 3) late log growth phase in media containing oleic acid. We confirmed colocalization of major factors with lipid droplets using live-cell fluorescent microscopy. We also analyzed droplets from each of the three conditions for sterol ester (SE) and triacylglycerol (TAG) content, along with their respective fatty acid compositions. We identified a previously undiscovered lipid droplet protein, Vip1p, which affects droplet size distribution. The results provide further insight into the workings of these ubiquitous organelles.

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Cbf11 and Mga2 function together to activate transcription of lipid metabolism genes and promote mitotic fidelity in fission yeast
Anna Marešová, Michaela Grulyová, Miluše Hradilová, Viacheslav Zemlianski, Jarmila Princová, Martin Převorovský, Cathy Savage-Dunn
PLOS Genetics.2024; 20(12): e1011509. CrossRef
Mild Heat Stress Alters the Physical State and Structure of Membranes in Triacylglycerol-Deficient Fission Yeast, Schizosaccharomyces pombe
Péter Gudmann, Imre Gombos, Mária Péter, Gábor Balogh, Zsolt Török, László Vígh, Attila Glatz
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Kohei Yoneda, Yohei Ishibashi, Masaki Yoshida, Makoto M. Watanabe, Makoto Ito, Iwane Suzuki
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Mehmet Oguz Gok, Natalie Ortiz Speer, W. Mike Henne, Jonathan R. Friedman, James Olzmann
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Abdou Rachid Thiam, Elina Ikonen
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Brandon C. Farmer, Adeline E. Walsh, Jude C. Kluemper, Lance A. Johnson
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Proteomic characterization of the outer membrane vesicle of the halophilic marine bacterium Novosphingobium pentaromativorans US6-1: Sung Ho Yun , Sang-Yeop Lee , Chi-Won Choi , Hayoung Lee , Hyun-Joo Ro , Sangmi Jun , Yong Min Kwon , Kae Kyoung Kwon , Sang-Jin Kim , Gun-Hwa Kim , Seung Il Kim; J. Microbiol. 2017;55(1):56-62. Published online December 30, 2016; DOI: https://doi.org/10.1007/s12275-017-6581-6

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Novosphingobium pentaromativorans US6-1 is a Gram-negative halophilic marine bacterium able to utilize several polycyclic aromatic hydrocarbons such as phenanthrene, pyrene, and benzo[a]pyrene. In this study, using transmission electron microscopy, we confirmed that N. pentaromativorans US6-1 produces outer membrane vesicles (OMVs). N. pentaromativorans OMVs (hereafter OMVNovo) are spherical in shape, and the average diameter of OMVNovo is 25–70 nm. Proteomic analysis revealed that outer membrane proteins and periplasmic proteins of N. pentaromativorans are the major protein components of OMVNovo. Comparative proteomic analysis with the membrane-associated protein fraction and correlation analysis demonstrated that the outer membrane proteins of OMVNovo originated from the membrane- associated protein fraction. To the best of our knowledge, this study is the first to characterize OMV purified from halophilic marine bacteria.

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Proteomic and Functional Analyses of a Novel Porin-like Protein in Xanthomonas oryzae pv. oryzae: Hye-Jee Park , Sang-Won Lee , Sang-Wook Han; J. Microbiol. 2014;52(12):1030-1035. Published online November 29, 2014; DOI: https://doi.org/10.1007/s12275-014-4442-0

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Abstract PDF

Proteomic analysis is a useful technique for postulating and elucidating protein functions. In the present work, a shotgun proteomic analysis was used to identify functions of the PXO_03968 gene (previously known as the ax21) from Xanthomonas oryzae pv. oryzae (Xoo), a causal agent for bacterial blight disease in rice. Structural prediction performed on the protein sequence encoded by PXO_03968 reveals that it encodes a putative porin-like protein, possessing a β-barrel domain with 10 β-strands and a signal peptide at the Nterminus. We renamed the gene as an omp1X (outer membrane protein 1 in Xoo), generated its knock out mutant (XooΔomp1X), and compared the protein expression level in the mutant to that in the wild type. A total of 106 proteins displayed more than 1.5-fold difference in expression between the mutant and the wild type strains. COG analysis revealed that these proteins are involved in cell motility as well as signal transduction. In addition, phenotypic analysis demonstrated that motility and biofilm formation in XooΔomp1X are lower than the wild type. These results provide new insights into the functions of outer membrane proteins in Gram-negative bacteria.

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Vladimir Mikhailovich, Rustam Heydarov, Danila Zimenkov, Igor Chebotar
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Vladimir M. Mikhailovich, Rustam N. Geydarov, Julia A. Bocharova, Igor V. Chebotar
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p‐Aminobenzoic acid inhibits the growth of soybean pathogen Xanthomonas axonopodis pv. glycines by altering outer membrane integrity
Yong‐Hui Jiang, Ting Liu, Xin‐Chi Shi, Daniela D Herrera‐Balandrano, Mei‐Ting Xu, Su‐Yan Wang, Pedro Laborda
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Deciphering the functions of the outer membrane porin OprBXo involved in virulence, motility, exopolysaccharide production, biofilm formation and stress tolerance in Xanthomonas oryzae pv. oryzae
Nahee Bae, Hye‐Jee Park, Hanbi Park, Minyoung Kim, Sang‐Wook Han
Molecular Plant Pathology.2018; 19(12): 2527. CrossRef
The Ax21 protein influences virulence and biofilm formation in Stenotrophomonas maltophilia
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Lsp family proteins regulate antibiotic biosynthesis in Lysobacter enzymogenes OH11
Ruping Wang, Huiyong Xu, Yangyang Zhao, Juan Zhang, Gary Y Yuen, Guoliang Qian, Fengquan Liu
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Characterization of Thermostable Deblocking Aminopeptidases of Archaeon Thermococcus onnurineus NA1 by Proteomic and Biochemical Approaches: Yeol Gyun Lee , Sun-Hee Leem , Young-Ho Chung , Seung Il Kim; J. Microbiol. 2012;50(5):792-797. Published online November 4, 2012; DOI: https://doi.org/10.1007/s12275-012-2461-2

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Abstract

Thermococcus onnurineus NA1 is a hyperthermophilic archaeon that grows optimally at >80°C. The deblocking aminopeptidase (DAP) (TNA1-DAP1) encoded in Ton_1032 of T. onnurineus NA1 is considered a major DAP. However, four genes encoding putative DAP have been identified from a genomic analysis of T. onnurineus NA1. A proteomic analysis revealed that all four DAPs were differentially induced in YPS culture medium and, particularly, two DAPs (TNA1-DAP1 and TNA1-DAP2) were dominantly expressed in T. onnurineus NA1. The biochemical properties and enzyme activity of DAPs induced in an E. coli expression system suggested that the two major DAPs play complementary roles in T. onnurineus NA1.

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Proteomic Insights into Sulfur Metabolism in the Hydrogen-Producing Hyperthermophilic Archaeon Thermococcus onnurineus NA1
Yoon-Jung Moon, Joseph Kwon, Sung-Ho Yun, Hye Lim, Jonghyun Kim, Soo Kim, Sung Kang, Jung-Hyun Lee, Seung Kim, Young-Ho Chung
International Journal of Molecular Sciences.2015; 16(5): 9167. CrossRef
Characterization of Streptococcus pneumoniae N-acetylglucosamine-6-phosphate deacetylase as a novel diagnostic marker
Chi-Won Choi, Hee-Young An, Yong Ju Lee, Yeol Gyun Lee, Sung Ho Yun, Edmond Changkyun Park, Yeonhee Hong, Gun-Hwa Kim, Jae-Eun Park, Sun Jong Baek, Hyun Sik Kim, Seung Il Kim
Journal of Microbiology.2013; 51(5): 659. CrossRef

Physiological and Metabolic Responses for Hexadecane Degradation in Acinetobacter oleivorans DR1: Jaejoon Jung , Jaemin Noh , Woojun Park; J. Microbiol. 2011;49(2):208-215. Published online May 3, 2011; DOI: https://doi.org/10.1007/s12275-011-0395-8

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Abstract PDF: The hexadecane degradation of Acinetobacter oleivorans DR1 was evaluated with changes in temperature and ionic salt contents. Hexadecane degradation of strain DR1 was reduced markedly by the presence of sodium chloride (but not potassium chloride). High temperature (37°C) was also shown to inhibit the motility, biofilm formation, and hexadecane biodegradation. The biofilm formation of strain DR1 on the oil-water interface might prove to be a critical physiological feature for the degradation of hexadecane. The positive relationship between biofilm formation and hexadecane degradation could be observed at 30°C, but not at low temperatures (25°C). Alterations in cell hydrophobicity and EPS production by temperature and salts were not correlated with biofilm formation and hexadecane degradation. Our proteomic analyses have demonstrated that metabolic changes through the glyoxylate pathway are important for efficient degradation of hexadecane. Proteins involved in fatty acid metabolism, gluconeogenesis, and oxidative stress defense proteins appear to be highly expressed during biodegradation of hexadecane. These results suggested that biofilm formation and oxidative stress defense are important physiological responses for hexadecane degradation along with metabolic switch to glyoxylate pathway in strain DR1.

Proteomic Analysis of Acinetobacter baumannii in Biofilm and Planktonic Growth Mode: Ji-Hyun Shin , Hee-Woo Lee , Sung-Min Kim , Jungmin Kim; J. Microbiol. 2009;47(6):728-735. Published online February 4, 2010; DOI: https://doi.org/10.1007/s12275-009-0158-y

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Recently, multidrug-resistant clinical isolates of Acinetobacter baumannii have been found to have a high capacity to form biofilm. It is well known that bacterial cells within biofilms are highly resistant to antibiotics, UV light, acid exposure, dehydration, and phagocytosis in comparison to their planktonic counterparts, which suggests that the cells in a biofilm have altered metabolic activity. To determine which proteins are up-regulated in A. baumannii biofilm cells, we performed a proteomic analysis. A clinical isolate of A. baumannii 1656-2, which was characterized to have a high biofilm forming ability, was cultivated under biofilm and planktonic conditions. Outer membrane enriched A. baumannii 1656-2 proteins were separated by two-dimensional (2-D) gel electrophoresis and the differentially expressed proteins were identified by MALDI-TOF mass spectrometry. The proteins up-regulated or expressed only in biofilm cells of A. baumannii are categorized as follows: (i) proteins processing environmental information such as the outer membrane receptor protein involved in mostly Fe transport, a sensor histidine kinase/response regulator, and diguanylate cyclase (PAS-GGEDF-EAL domain); (ii) proteins involved in metabolism such as NAD- linked malate dehydrogenase, nucleoside-diphosphate sugar epimerase, putative GalE, ProFAR isomerase, and N-acetylmuramoyl-L-alanine amidase; (iii) bacterial antibiotic resistance related proteins; and (iv) proteins related to gene repair such as exodeoxyribonuclease III and GidA. This proteomic analysis provides a fundamental platform for further studies to reveal the role of biofilm in the persistence and tolerance of A. baumannii.

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Helicobacter pylori Proteins Response to Nitric Oxide Stress: Wei Qu , Yabin Zhou , Chunhong Shao , Yundong Sun , Qunye Zhang , Chunyan Chen , Jihui Jia; J. Microbiol. 2009;47(4):486-493. Published online September 9, 2009; DOI: https://doi.org/10.1007/s12275-008-0266-0

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Abstract PDF: Helicobacter pylori is a highly pathogenic microorganism with various strategies to evade human immune responses. Nitric oxide (NO) and reactive nitrogen species (RNS) generated via nitric oxide synthase pathway are important effectors during the innate immune response. However, the mechanisms of H. pylori to survive the nitrosative stress are not clear. Here the proteomic approach has been used to define the adaptive response of H. pylori to nitrosative stress. Proteomic analysis showed that 38 protein spots were regulated by NO donor, sodium nitroprusside (SNP). These proteins were involved in protein processing, antioxidation, general stress response, and virulence, as well as some unknown functions. Particularly, some of them were participated in iron metabolism, potentially under the control of ferric uptake regulator (Fur). Real time PCR revealed that fur was induced under nitrosative stress, consistent with our deduction. One stress-related protein up-regulated under nitrosative conditions was thioredoxin reductase (TrxR). Inactivation of fur or trxR can lead to increased susceptivity to nitrosative stress respectively. These studies described the adaptive response of H. pylori to nitric oxide stress, and analyzed the relevant role of Fur regulon and TrxR in nitrosative stress management.

Note] Comparative Analysis of 2,4,6-Trinitrotoluene (TNT)-Induced Cellular Responses and Proteomes in Pseudomonas sp. HK-6 in Two Types of Media: Yun-Seok Cho , Bheong-Uk Lee , Hyung-Yeel Kahng , Kye-Heon Oh; J. Microbiol. 2009;47(2):220-224. Published online May 2, 2009; DOI: https://doi.org/10.1007/s12275-008-0108-0

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Abstract PDF: TNT-induced cellular responses and proteomes in Pseudomonas sp. HK-6 were comparatively analyzed in two different media: basal salts (BS) and Luria broth (LB). HK-6 cells could not degrade more than 0.5 mM TNT with BS medium, while in LB medium, they exhibited the enhanced capability to degrade as much as 3.0 mM TNT. Analysis of total cellular fatty acids in HK-6 cells suggested that the relative abundance of several saturated or unsaturated fatty acids is altered under TNT-mediated stress conditions. Scanning electron microscopy showed the presence of perforations, irregular rod formations, and wrinkled extracellular surfaces in cells under TNT stress. Proteomic analysis of soluble protein fractions from HK-6 <br>cultures grown with TNT as a substrate revealed 11 protein spots induced by TNT. Among these, seven proteins (including Alg8, AlgB, NirB, and the AhpC/Tsa family) were detected only in LB medium containing TNT. The proteins AspS, Tsf, and assimilatory nitrate reductase were increasingly expressed only in BS medium containing TNT. The protein dGTPase was found to be induced and expressed when cells were grown in either type of TNT-containing media. These results provide a better understanding of the cytotoxicity and survival mechanism used by Pseudomonas sp. HK-6 when placed under TNT stress conditions.

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