Journal of Microbiology

Journal Articles

An Optimized Method for Reconstruction of Transcriptional Regulatory Networks in Bacteria Using ChIP-exo and RNA-seq Datasets: Minchang Jang, Joon Young Park, Gayeon Lee, Donghyuk Kim; J. Microbiol. 2024;62(12):1075-1088. Published online November 11, 2024; DOI: https://doi.org/10.1007/s12275-024-00181-6

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Transcriptional regulatory networks (TRNs) in bacteria are crucial for elucidating the mechanisms that regulate gene expression and cellular responses to environmental stimuli. These networks delineate the interactions between transcription factors (TFs) and their target genes, thereby uncovering the regulatory processes that modulate gene expression under varying environmental conditions. Analyzing TRNs offers valuable insights into bacterial adaptation, stress responses, and metabolic optimization from an evolutionary standpoint. Additionally, understanding TRNs can drive the development of novel antimicrobial therapies and the engineering of microbial strains for biofuel and bioproduct production. This protocol integrates advanced data analysis pipelines, including ChEAP, DEOCSU, and DESeq2, to analyze omics datasets that encompass genome-wide TF binding sites and transcriptome profiles derived from ChIP-exo and RNA-seq experiments. This approach minimizes both the time required and the risk of bias, making it accessible to non-expert users. Key steps in the protocol include preprocessing and peak calling from ChIP-exo data, differential expression analysis of RNA-seq data, and motif and regulon analysis. This method offers a comprehensive and efficient framework for TRN reconstruction across various bacterial strains, enhancing both the accuracy and reliability of the analysis while providing valuable insights for basic and applied research.

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ChIP-mini: a low-input ChIP-exo protocol for elucidating DNA-binding protein dynamics in intracellular pathogens
Joon Young Park, Minchang Jang, Eunna Choi, Sang-Mok Lee, Ina Bang, Jihoon Woo, Seonggyu Kim, Eun-Jin Lee, Donghyuk Kim
Nucleic Acids Research.2025;[Epub] CrossRef

Genetically Engineered CLDN18.2 CAR-T Cells Expressing Synthetic PD1/CD28 Fusion Receptors Produced Using a Lentiviral Vector: Heon Ju Lee, Seo Jin Hwang, Eun Hee Jeong, Mi Hee Chang; J. Microbiol. 2024;62(7):555-568. Published online May 3, 2024; DOI: https://doi.org/10.1007/s12275-024-00133-0

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Abstract: This study aimed to develop synthetic Claudin18.2 (CLDN18.2) chimeric antigen receptor (CAR)-T (CAR-T) cells as a treatment for advanced gastric cancer using lentiviral vector genetic engineering technology that targets the CLDN18.2 antigen and simultaneously overcomes the immunosuppressive environment caused by programmed cell death protein 1 (PD-1). Synthetic CAR T cells are a promising approach in cancer immunotherapy but face many challenges in solid tumors. One of the major problems is immunosuppression caused by PD-1. CLDN18.2, a gastric-specific membrane protein, is considered a potential therapeutic target for gastric and other cancers. In our study, CLDN18.2 CAR was a second-generation CAR with inducible T-cell costimulatory (CD278), and CLDN18.2-PD1/CD28 CAR was a third-generation CAR, wherein the synthetic PD1/CD28 chimeric-switch receptor (CSR) was added to the second-generation CAR. In vitro, we detected the secretion levels of different cytokines and the killing ability of CAR-T cells. We found that the secretion of cytokines such as interferon-gamma (IFN-γ) and tumor necrosis factor-alpha (TNF-α) secreted by three types of CAR-T cells was increased, and the killing ability against CLDN18.2-positive GC cells was enhanced. In vivo, we established a xenograft GC model and observed the antitumor effects and off-target toxicity of CAR-T cells. These results support that synthetic anti-CLDN18.2 CAR-T cells have antitumor effect and anti-CLDN18.2-PD1/CD28 CAR could provide a promising design strategy to improve the efficacy of CAR-T cells in advanced gastric cancer.

The C-22 sterol desaturase Erg5 is responsible for ergosterol biosynthesis and conidiation in Aspergillus fumigatus: Nanbiao Long , Guowei Zhong; J. Microbiol. 2022;60(6):620-626. Published online April 18, 2022; DOI: https://doi.org/10.1007/s12275-022-1564-7

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Abstract

Aspergillus fumigatus is the most prevalent saprophytic fungi and can cause severe invasive aspergillosis in immunocompromised individuals. For infection of A. fumigatus, the small hydrophobic conidia have been shown to play a dominant role. In this study, we found that deletion of erg5, a C-22 sterol desaturase gene which function in the last two steps of ergosterol biosynthesis, was sufficient to block ergosterol biosynthesis and conidiation. The deletion phenotype was further verified by a conditional expression strain of erg5 using the inducible tet-on system. Strikingly, erg5 mutant displays increased susceptibility to antifungal azoles itraconazole. RNA sequencing analysis showed that erg5 deficiency resulted in changes in transcription mainly related to lipid, carbohydrate, and amino acid metabolism. Genes encoding ergosterol biosynthesis- related enzymes were found to be up-regulated in erg5 null mutants. However, genes involved in asexual development, including upstream regulators, melanin biosynthesis enzymes, heterotrimeric G proteins, and MAPK signaling, were down-regulated to various degrees. Furthermore, metabolomic study revealed that erg5 deficiency also resulted in altered lipid and amino acid metabolism, which was consistent with our transcriptomics analysis. Collectively, our study established a link between ergosterol biosynthesis and asexual development at the transcriptomics and metabolomics level in A. fumigatus.

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Quantitative proteomic analysis reveals Ga(III) polypyridyl catecholate complexes disrupt Aspergillus fumigatus mitochondrial function
Magdalena Piatek, Brunella Grassiri, Lewis More O’Ferrall, Anna Maria Piras, Giovanna Batoni, Semih Esin, Christine O’Connor, Darren Griffith, Anne Marie Healy, Kevin Kavanagh
JBIC Journal of Biological Inorganic Chemistry.2024; 29(7-8): 707. CrossRef
Ergosterol Is Critical for Sporogenesis in Cryptococcus neoformans
Amber R. Matha, Xiaofeng Xie, Xiaorong Lin
Journal of Fungi.2024; 10(2): 106. CrossRef
Erg4 Is Involved in Ergosterol Biosynthesis, Conidiation and Stress Response in Penicillium expansum
Zhanhong Han, Yuanyuan Zong, Xuemei Zhang, Di Gong, Bin Wang, Dov Prusky, Edward Sionov, Huali Xue, Yang Bi
Journal of Fungi.2023; 9(5): 568. CrossRef
A chromosome-scale genome assembly of the grape powdery mildew pathogen Erysiphe necator reveals its genomic architecture and previously unknown features of its biology
Alex Z. Zaccaron, Tara Neill, Jacob Corcoran, Walter F. Mahaffee, Ioannis Stergiopoulos, Gustavo H. Goldman
mBio.2023;[Epub] CrossRef

Cytophaga hutchinsonii chu_2177, encoding the O-antigen ligase, is essential for cellulose degradation: Yahong Tan , Wenxia Song , Lijuan Gao , Weican Zhang , Xuemei Lu; J. Microbiol. 2022;60(4):364-374. Published online January 7, 2022; DOI: https://doi.org/10.1007/s12275-022-1531-3

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Abstract

Cytophaga hutchinsonii can efficiently degrade crystalline cellulose, in which the cell surface cellulases secreted by the type IX secretion system (T9SS) play important roles, but the degradation mechanism remains unclear, and the anchor mechanism of cellulases on the outer membrane in C. hutchinsonii has not been studied. Here, chu_2177 was identified by transposon mutagenesis and was proved to be indispensable for cellulose utilization in C. hutchinsonii. Disruption of chu_2177 resulted in O-antigen deficiency and chu_ 177 could confer O-antigen ligase activity upon an Escherichia coli waal mutant, indicating that chu_2177 encoded the Ontigen ligase. Moreover, deletion of chu_2177 caused defects in cellulose utilization, cell motility, biofilm formation, and stress resistance. Further study showed that the endoglucanase activity was markedly decreased in the outer membrane but was increased in the culture fluid without chu_2177. Western blot proved that endoglucanase CHU_1336 was not located on the outer membrane but was released in the culture fluid of the Δ2177 mutant. Further proteomics analysis showed that many cargo proteins of T9SS were missing in the outer membrane of the Δ2177 mutant. Our study revealed that the deletion of chu_2177 affected the localization of many T9SS cargo proteins including cellulases on the outer membrane of C. hutchinsonii.

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Screening and genome-wide analysis of lignocellulose-degrading bacteria from humic soil
Tianjiao Zhang, Shuli Wei, Yajie Liu, Chao Cheng, Jie Ma, Linfang Yue, Yanrong Gao, Yuchen Cheng, Yongfeng Ren, Shaofeng Su, Xiaoqing Zhao, Zhanyuan Lu
Frontiers in Microbiology.2023;[Epub] CrossRef
The type IX secretion system: Insights into its function and connection to glycosylation in Cytophaga hutchinsonii
Wenxia Song, Xueke Zhuang, Yahong Tan, Qingsheng Qi, Xuemei Lu
Engineering Microbiology.2022; 2(3): 100038. CrossRef

Review

MINIREVIEW] On the study of microbial transcriptomes using second- and third-generation sequencing technologies: Sang Chul Choi; J. Microbiol. 2016;54(8):527-536. Published online August 2, 2016; DOI: https://doi.org/10.1007/s12275-016-6233-2

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Abstract

Second-generation sequencing technologies transformed the study of microbial transcriptomes. They helped reveal the transcription start sites and antisense transcripts of microbial species, improving the microbial genome annotation. Quantification of genome-wide gene expression levels allowed for functional studies of microbial research. Ever-evolving sequencing technologies are reshaping approaches to studying microbial transcriptomes. Recently, Oxford Nanopore Technologies delivered a sequencing platform called MinION, a third-generation sequencing technology, to the research community. We expect it to be the next sequencing technology that enables breakthroughs in life science fields. The studies of microbial transcriptomes will be no exception. In this paper, we review microbial transcriptomics studies using second- generation sequencing technology. We also discuss the prospect of microbial transcriptomics studies with thirdgeneration sequencing.

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TPX2 upregulates MMP13 to promote the progression of lipopolysaccharide-induced osteoarthritis
Jingtao Yu, Weiqi Wang, Zenghui Jiang, Huashun Liu
PeerJ.2024; 12: e17032. CrossRef
Gut Microbiota in Children with Hand Foot and Mouth Disease on 16S rRNA Gene Sequencing
Yan Zhuang, Yiyan Lin, Hongxia Sun, Zaiting Zhang, Tao Wang, Rongjun Fan, Lu Han
Current Microbiology.2023;[Epub] CrossRef
Advances in Nanopore and Photoelectron-Based High-Throughput Sequencing Technology for Single-Molecule Sequencing
Yunqi Huang, Yutong Lu, Cailing Song, Yican Wei, Yuxi Yang, Jie Ren, Meiling Wang, Congli Tang, Aayesha Riaz, Muhammad Ali Shah, Yan Deng, Hongna Liu, Wenjing Pan, Song Li
Journal of Nanoelectronics and Optoelectronics.2023; 18(4): 381. CrossRef
Full-length transcriptome sequencing reveals the molecular mechanism of potato seedlings responding to low-temperature
Chongchong Yan, Nan Zhang, Qianqian Wang, Yuying Fu, Hongyuan Zhao, Jiajia Wang, Gang Wu, Feng Wang, Xueyan Li, Huajun Liao
BMC Plant Biology.2022;[Epub] CrossRef
Nanopore sequencing of RNA and cDNA molecules in Escherichia coli
Felix Grünberger, Sébastien Ferreira-Cerca, Dina Grohmann
RNA.2022; 28(3): 400. CrossRef
Full-length transcriptome sequences of ridgetail white prawn Exopalaemon carinicauda provide insight into gene expression dynamics during thermal stress
Kunpeng Shi, Jitao Li, Jianjian Lv, Ping Liu, Jian Li, Sedong Li
Science of The Total Environment.2020; 747: 141238. CrossRef
A chromosome-scale genome assembly of a diploid alfalfa, the progenitor of autotetraploid alfalfa
Ao Li, Ai Liu, Xin Du, Jin-Yuan Chen, Mou Yin, Hong-Yin Hu, Nawal Shrestha, Sheng-Dan Wu, Hai-Qing Wang, Quan-Wen Dou, Zhi-Peng Liu, Jian-Quan Liu, Yong-Zhi Yang, Guang-Peng Ren
Horticulture Research.2020;[Epub] CrossRef
Next-generation technologies for studying host–pathogen interactions: a focus on dual transcriptomics, CRISPR/Cas9 screening and organs-on-chips
Buket Baddal
Pathogens and Disease.2019;[Epub] CrossRef
Prospects for the use of third generation sequencers for quantitative profiling of transcriptome
S.P. Radko, L.K. Kurbatov, K.G. Ptitsyn, Y.Y. Kiseleva, E.A. Ponomarenko, A.V. Lisitsa, A.I. Archakov
Biomedical Chemistry: Research and Methods.2018; 1(4): e00086. CrossRef
Two's company: studying interspecies relationships with dual RNA-seq
Thomas Wolf, Philipp Kämmer, Sascha Brunke, Jörg Linde
Current Opinion in Microbiology.2018; 42: 7. CrossRef
Taxonomy and systematics of plant probiotic bacteria in the genomic era
Lorena Carro, Imen Nouioui
AIMS Microbiology.2017; 3(3): 383. CrossRef

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