Article
Biochemistry & Molecular Biology
Cheng-Hai Yan, Fang-Hui Chen, Yu-Lu Yang, Yu-Fan Zhan, Richard A. Herman, Lu-Chan Gong, Sheng Sheng, Jun Wang
Summary: This study successfully constructed a csgD deletion mutant Delta csgD using the CRISPR/Cas9 gene-editing system, and found that Delta csgD exhibited decreased biofilm formation, inhibited mobility and adhesion, and significantly decreased resistance to acid, alkali, and osmotic stress conditions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Olga Lamprecht, Maryia Ratnikava, Paulina Jacek, Eugen Kaganovitch, Nina Buettner, Kirstin Fritz, Ina Biazruchka, Robin P. Koehler, Julian P. Pietsch, Victor P. Sourjik
Summary: The formation of bacterial biofilms leads to the differentiation of matrix-embedded communities into subpopulations with different gene expression and physiology. In this study, the role of cyclic di-GMP (c-di-GMP) regulation in the activation of curli genes in Escherichia coli was investigated. The expression of curli genes was found to be bimodal in both planktonic and biofilm cultures, even in the absence of external spatial cues. While regulation by c-di-GMP was not necessary for gene activation, it influenced the frequency and dynamics of gene induction and reduced variability between cells and growth conditions.
Review
Biotechnology & Applied Microbiology
Xiaohan Huang, Qiaoqiao Song, Shuqi Guo, Qiang Fei
Summary: This review summarizes several transcription regulation strategies applied in methylotrophs and discusses their applications and prospects.
BIORESOURCES AND BIOPROCESSING
(2022)
Article
Biochemistry & Molecular Biology
Ikki Kobayashi, Kenji Mochizuki, Jun Teramoto, Sousuke Imamura, Kazuhiro Takaya, Akira Ishihama, Tomohiro Shimada
Summary: Understanding the functional information of all genes and the biological mechanism based on the comprehensive genome regulation mechanism is an important task in life science. YgfI, an uncharacterized LysR family transcription factor in Escherichia coli, was found to be involved in biofilm formation, hydrogen peroxide resistance, and antibiotic resistance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Genetics & Heredity
Guido van Mierlo, Olga Pushkarev, Judith F. Kribelbauer, Bart Deplancke
Summary: Regulation of gene expression is a complex process, and recent studies have shown that chromatin modules, which result from interactions between cis-regulatory elements (CREs) and 3D structures, play an important role. This article reviews methods for identifying chromatin modules, summarizes possible mechanisms for CRE interactions within these modules, and discusses challenges in understanding the functional 3D genome.
TRENDS IN GENETICS
(2023)
Article
Microbiology
Tania Gaviria-Cantin, Andres Felipe Vargas, Youssef El Mouali, Carlos Jonay Jimenez, Annika Cimdins-Ahne, Cristina Madrid, Ute Romling, Carlos Balsalobre
Summary: Biofilm formation of Salmonella typhimurium and Escherichia coli is a common ancient multicellular behavior with important roles in cell-cell and inter-organism interactions. The orphan transcriptional regulator CsgD plays a central role in the regulation of rdar morphotype expression, and GreA/GreB are required for the expression of csgD operon and the rdar morphotype.
Review
Immunology
Virginia E. Glazier
Summary: Candida sp. is a common fungal commensal in the human microbiome and can cause both superficial and systemic infections. The transcription factor Efg1, extensively studied in Candida, plays a central role in pathogenicity, but several important unanswered questions remain.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Oceanography
Shao Yina, Wang Jiahao, Zhang Yi, Li Chenghua
Summary: F-type lectins, also known as Fucolectins, are carbohydrate-binding proteins that play important roles in innate immune responses. Two homologous Fucolectin genes, AjFTL-1 and AjFTL-2, were found to exhibit different expression patterns in response to immune stimulation, with NF-kappa B playing a key role in their transcriptional regulation. The study suggests that different Fucolectin members in marine invertebrates have distinct transcriptional regulations and expression patterns, potentially influencing immune defenses during pathogen infections.
JOURNAL OF OCEAN UNIVERSITY OF CHINA
(2021)
Article
Microbiology
Haley Stokas, Heather L. Rhodes, Marit B. Simmons, Richard Zhang, Catherine C. Wright, Georgiana E. Purdya
Summary: In this study, we characterized a mutant of Mycobacterium tuberculosis lacking Rv3249c and found that it directly represses the alkB-rubA-rubB operon. The mutant showed better survival inside macrophages, but had defects in growing on host-associated carbon sources and biofilm formation. These results highlight the importance of the AlkBRubAB system in the intracellular survival of M. tuberculosis.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biotechnology & Applied Microbiology
Zhenyang Liao, Fei Dong, Juan Liu, Lele Xu, Amy Marshall-Colon, Ray Ming
Summary: This research analyzed the developmental stages of papaya pistil and identified differentially expressed genes related to pistil development and sex differentiation. Transcription factor and hormone-related genes were revealed based on functional and regulatory network analysis. These findings provide new insights into the molecular mechanism of pistil development and sex differentiation in papaya.
Article
Microbiology
Tao Gong, Xiaoya He, Jiamin Chen, Boyu Tang, Ting Zheng, Meiling Jing, Yongwang Lin, Yangyang Pan, Qizhao Ma, Yuqing Li, Xuedong Zhou
Summary: The RcrR gene plays a crucial role in the growth, biofilm formation, and multiple sugar transportation of Streptococcus mutans. Its deletion leads to impaired biofilm formation and altered expression of sugar transportation-related genes. RcrR acts as a transcription activator to regulate the two PTS systems and influences sugar transportation and biofilm formation.
Article
Biochemistry & Molecular Biology
Kamal Ajit, Bruce D. Murphy, Arnab Banerjee
Summary: Embryonic diapause is a mysterious phenomenon found in various species with established regulatory mechanisms, yet much remains to be discovered. This study used a computational approach to identify unique transcription factors and signaling pathways regulating diapause, consolidating them into a model of known regulatory mechanisms. Certain transcription factors were highlighted as potential 'master transcription factors,' and evidence of independent evolution for regulatory elements involved in diapause was suggested through promoter analysis.
Article
Plant Sciences
Yueying Liu, Xinyu Wang, Zongjian Li, Jing Tu, Ya-nan Lu, Xiaohang Hu, Qingzhu Zhang, Zhimin Zheng
Summary: This study identified the RcMYB106 transcription factor as a key regulator of capsule spine development in castor through genetic analysis. It was found that a deletion or a single nucleotide polymorphism in the RcMYB106 gene led to the spineless capsule phenotype. The study also proposed a potential regulatory mechanism involving the downstream gene RcWIN1, but further experimentation is needed.
Review
Physiology
Federica Zinghirino, Xena Giada Pappalardo, Angela Messina, Giuseppe Nicosia, Vito De Pinto, Francesca Guarino
Summary: Despite similarity in sequence and structure, VDAC1 and VDAC2 have different biological roles in normal and pathological conditions. VDAC1 and VDAC2 are expressed at higher levels in human and mouse tissues, except for VDAC3 which is more highly expressed in the reproductive system. The expression of VDAC genes is mainly regulated by transcription factors involved in controlling cell growth, proliferation and differentiation, apoptosis, and bioenergetic metabolism.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Oncology
Guangliang Bai, Ning Wei, Fang Li, Peng Zhao, Zhen Meng, Bo Zou, Yujiao Liu, Kai Xu, Keyi Li, Chao Yao, Peng Yang
Summary: This study investigated the role of TCTN1 in oral squamous cell carcinoma (OSCC). The results showed that TCTN1 was associated with the clinical stage and grade of the tumor. Knockdown of TCTN1 suppressed the proliferative, migratory, and invasive capacity of OSCC cells. TFAP2A was suggested as a potential regulator of TCTN1 mRNA expression. These findings highlight the direct association between TCTN1 and OSCC and suggest the TFAP2A/TCTN1 axis as a possible therapeutic target for OSCC.
Article
Microbiology
Tomohiro Shimada, Kaneyoshi Yamamoto, Masahiro Nakano, Hiroki Watanabe, David Schleheck, Akira Ishihama
Article
Microbiology
Genki Akanuma, Tomoaki Tagana, Maho Sawada, Shota Suzuki, Tomohiro Shimada, Kan Tanaka, Fujio Kawamura, Yasuyuki Kato-Yamada
Article
Multidisciplinary Sciences
Takayuki Shimizu, Sylwia M. Kacprzak, Nobuyoshi Mochizuki, Akira Nagatani, Satoru Watanabe, Tomohiro Shimada, Kan Tanaka, Yuuki Hayashi, Munehito Arai, Dario Leister, Haruko Okamoto, Matthew J. Terry, Tatsuru Masuda
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Correction
Multidisciplinary Sciences
Tomohiro Shimada, Yui Yokoyama, Takumi Anzai, Kaneyoshi Yamamoto, Akira Ishihama
SCIENTIFIC REPORTS
(2020)
Article
Microbiology
Hiroshi Ogasawara, Toshiyuki Ishizuka, Shuhei Hotta, Michiko Aoki, Tomohiro Shimada, Akira Ishihama
Article
Genetics & Heredity
Takumi Anzai, Sousuke Imamura, Akira Ishihama, Tomohiro Shimada
MICROBIAL GENOMICS
(2020)
Article
Biochemistry & Molecular Biology
Tomohiro Shimada, Kohta Nakazawa, Tomoyuki Tachikawa, Natsumi Saito, Tatsuya Niwa, Hideki Taguchi, Kan Tanaka
Summary: Acetate overflow refers to the metabolic process where a large portion of carbon from glucose is catabolized and excreted as acetate by E. coli cells. Mutants lacking enzymes in this pathway show growth lag after glucose depletion, with underlying mechanisms involving changes in enzyme levels and coenzyme A availability. Understanding the role of acetate overflow in metabolic regulation can have applications in biotechnology.
Article
Genetics & Heredity
Tomohiro Shimada, Shun Furuhata, Akira Ishihama
Summary: The study identified a set of 'constitutive' promoters recognized by specific sigma subunits of RNA polymerase in E. coli, as well as uncovered the dual roles of the RpoN holoenzyme as a repressor and transcriptase for the same set of genes. The research also demonstrated the promoter activity of NtrC-dependent and -independent RpoN promoters under nitrogen starvation conditions.
MICROBIAL GENOMICS
(2021)
Article
Biochemistry & Molecular Biology
Ikki Kobayashi, Kenji Mochizuki, Jun Teramoto, Sousuke Imamura, Kazuhiro Takaya, Akira Ishihama, Tomohiro Shimada
Summary: Understanding the functional information of all genes and the biological mechanism based on the comprehensive genome regulation mechanism is an important task in life science. YgfI, an uncharacterized LysR family transcription factor in Escherichia coli, was found to be involved in biofilm formation, hydrogen peroxide resistance, and antibiotic resistance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Tomohiro Shimada, Rie Murayama, Tomoki Mashima, Natsuko Kawano, Akira Ishihama
Summary: Genomic SELEX screening identified the binding sites of YiaU, a LysR family transcription factor, on the Escherichia coli K-12 genome. It was found that YiaU regulates genes that are involved in biofilm formation, antibiotic resistance, and complement sensitivity.
Article
Biochemistry & Molecular Biology
Hideji Yoshida, Tomohiro Shimada, Akira Ishihama
Summary: Bacteria respond to stress by regulating gene expression at the transcriptional and translational levels. In this study, the binding of metal-responsive transcription factors (TFs) to the promoter regions of rsd and rmf was examined, and the effects of these TFs on the expression of rsd and rmf were studied in E. coli strains deficient in each TF gene. The results show that several metal-responsive TFs and metal ions influence rsd and rmf gene expression while regulating transcriptional and translational activities.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Editorial Material
Biochemistry & Molecular Biology
Tomohiro Shimada, Hideji Yoshida
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Hiraku Takada, Kaede Kijima, Akira Ishiguro, Akira Ishihama, Tomohiro Shimada
Summary: This study reveals that the master regulator FlhDC mediates all flagellum-forming genes in E. coli through a transcriptional regulatory cascade. The researchers also identified new target genes involved in the sugar utilization phosphotransferase system, sugar catabolic pathway of glycolysis, and other carbon source metabolic pathways. The results suggest that FlhDC activates these new targets, providing coordinated regulation between flagella formation, operation, and energy production.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Takumi Anzai, Kaede Kijima, Miki Fujimori, Soma Nakamoto, Akira Ishihama, Tomohiro Shimada
Summary: LldR is a lactate-responsive transcription factor that regulates the lldPRD operon and plays a significant role in adapting to lactate-induced acid stress. In addition to lactate utilization, LldR is involved in regulating genes related to glutamate-dependent acid resistance and membrane lipid composition.
MICROBIAL GENOMICS
(2023)
Review
Microbiology
Akira Ishihama, Tomohiro Shimada
Summary: This review summarizes the regulatory targets of more than 150 transcription factors from E. coli K-12, which can be classified into four families: nucleoid-associated bifunctional TFs, global regulators, local regulators, and single-target regulators. The nucleoid-associated TFs H-NS and StpA together play a silencing role for a set of non-essential genes, with LeuO and other global regulators indicated for anti-silencing.Overall, the hierarchy of TF network is proposed as a key framework of the bacterial genome regulation.
FEMS MICROBIOLOGY REVIEWS
(2021)
