Journal of Microbiology

Journal Articles

Evaluation of Cyc1 protein stability in Acidithiobacillus ferrooxidans bacterium after E121D mutation by molecular dynamics simulation to improve electron transfer: Mahnaz Shojapour , Somayeh Farahmand , Faezeh Fatemi , Marzieh Dehghan Shasaltaneh; J. Microbiol. 2022;60(5):526-532. Published online March 14, 2022; DOI: https://doi.org/10.1007/s12275-022-1645-7

48 View
0 Download
1 Web of Science
1 Crossref

Cyc1 (Cytochrome c552) is a protein in the electron transport chain of the Acidithiobacillus ferrooxidans (Af) bacteria which obtain their energy from oxidation Fe2+ to Fe3+. The electrons are directed through Cyc2, RCY (rusticyanin), Cyc1, and Cox aa3 proteins to O2. Cyc1 protein consists of two chains, A and B. In the present study, a novel mutation (E121D) in the A chain of Cyc1 protein was selected due to electron receiving from Histidine 143 of RCY. Then, the changes performed in the E121D mutant were evaluated by MD simulations analyzes. Cyc1 and RCY proteins were docked by a Patchdock server. By E121D mutation, the connection between Zn 1388 of chain B and aspartate 121 of chain A weaken. Asp 121 gets farther from Zn 1388. Therefore, the aspartate gets closer to Cu 1156 of the RCY leading to the higher stability of the RCY/ Cyc1 complex. Further, an acidic residue (Glu121) becomes a more acidic residue (Asp121) and improves the electron transfer to Cyc1 protein. The results of RMSF analysis showed further ligand flexibility in mutation. This leads to fluctuation of the active site and increases redox potential at the mutation point and the speed of electron transfer. This study also predicts that in all respiratory chain proteins, electrons probably enter the first active site via glutamate and exit histidine in the second active site of each respiratory chain protein.

Citations

Citations to this article as recorded by

Point mutation consideration in CcO protein of the electron transfer chain by MD simulation
Mahnaz Shojapour, Somayeh Farahmand
Journal of Molecular Graphics and Modelling.2022; 117: 108309. CrossRef

Vibrio vulnificus PlpA facilitates necrotic host cell death induced by the pore forming MARTX toxin: Changyi Cho , Sanghyeon Choi , Myung Hee Kim , Byoung Sik Kim; J. Microbiol. 2022;60(2):224-233. Published online February 1, 2022; DOI: https://doi.org/10.1007/s12275-022-1448-x

49 View
0 Download
7 Web of Science
6 Crossref

Abstract

Opportunistic pathogen Vibrio vulnificus causes severe systemic infection in humans with high mortality. Although multiple exotoxins have been characterized in V. vulnificus, their interactions and potential synergistic roles in pathogen-induced host cell death have not been investigated previously. By employing a series of multiple exotoxin deletion mutants, we investigated whether specific exotoxins of the pathogen functioned together to achieve severe and rapid necrotic cell death. Human epithelial cells treated with V. vulnificus with a plpA deletion background exhibited an unusually prolonged cell blebbing, suggesting the importance of PlpA, a phospholipase A2, in rapid necrotic cell death by this pathogen. Additional deletion of the rtxA gene encoding the multifunctional autoprocessing repeats-in-toxin (MARTX) toxin did not result in necrotic cell blebs. However, if the rtxA gene was engineered to produce an effector-free MARTX toxin, the cell blebbing was observed, indicating that the pore forming activity of the MARTX toxin is sufficient, but the MARTX toxin effector domains are not necessary, for the blebbing. When a recombinant PlpA was treated on the blebbed cells, the blebs were completely disrupted. Consistent with this, MARTX toxin-pendent rapid release of cytosolic lactate dehydrogenase was significantly delayed in the plpA deletion background. Mutations in other exotoxins such as elastase, cytolysin/hemolysin, and/or extracellular metalloprotease did not affect the bleb formation or disruption. Together, these findings indicate that the pore forming MARTX toxin and the phospholipase A2, PlpA, cooperate sequentially to achieve rapid necrotic cell death by inducing cell blebbing and disrupting the blebs, respectively.

Citations

Citations to this article as recorded by

Genome-wide phenotypic profiling of transcription factors and identification of novel targets to control the virulence of Vibrio vulnificus
Dayoung Sung, Garam Choi, Minji Ahn, Hokyung Byun, Tae Young Kim, Hojun Lee, Zee-Won Lee, Ji Yong Park, Young Hyun Jung, Ho Jae Han, Sang Ho Choi
Nucleic Acids Research.2024;[Epub] CrossRef
Vibrio-infecting bacteriophages and their potential to control biofilm
Ana Cevallos-Urena, Jeong Yeon Kim, Byoung Sik Kim
Food Science and Biotechnology.2023; 32(12): 1719. CrossRef
Pathogenic Mechanism of Vibrio Vulnificus Infection
Kun Lu, Yang Li, Rui Chen, Hua Yang, Yong Wang, Wei Xiong, Fang Xu, Qijun Yuan, Haihui Liang, Xian Xiao, Renqiang Huang, Zhipeng Chen, Chunou Tian, Songqing Wang
Future Microbiology.2023; 18(6): 373. CrossRef
Functional conservation of specialized ribosomes bearing genome-encoded variant rRNAs in Vibrio species
Younkyung Choi, Eunkyoung Shin, Minho Lee, Ji-Hyun Yeom, Kangseok Lee, Bashir Sajo Mienda
PLOS ONE.2023; 18(12): e0289072. CrossRef
Complex regulatory networks of virulence factors in Vibrio vulnificus
Garam Choi, Sang Ho Choi
Trends in Microbiology.2022; 30(12): 1205. CrossRef
MARTX toxin of Vibrio vulnificus induces RBC phosphatidylserine exposure that can contribute to thrombosis
Han Young Chung, Yiying Bian, Kyung-Min Lim, Byoung Sik Kim, Sang Ho Choi
Nature Communications.2022;[Epub] CrossRef

The discovery of potent immunostimulatory CpG-ODNs widely distributed in bacterial genomes: Juan Liu , Yan Wei , Yongling Lu , Yangyuling Li , Qian Chen , Yan Li; J. Microbiol. 2020;58(2):153-162. Published online December 23, 2019; DOI: https://doi.org/10.1007/s12275-020-9289-y

39 View
0 Download
4 Web of Science
2 Crossref

Abstract

Oligodeoxynucleotides containing unmethylated CpG dinucleotides (CpG-ODN) can be specifically recognized by Toll-like receptor 9 (TLR9), provoking innate immune responses. Designed according to this structural feature, many synthetic phosphorothioate CpG-ODNs successfully activate macrophages. However, it is difficult to find potent stimulatory CpG-DNA fragments in microbial genomes. Therefore, whether microbial CpG-DNA substantially contributes to infectious and immune diseases remains controversial. In this study, high-throughput scanning was carried out for thousands of bacterial genomes with bioinformatics tools to comprehensively evaluate the distribution of CpG-DNA fragments. A random sampling test was then performed to verify their immunostimulatory properties by experiments in vitro and in vivo. Natural TLR9-dependent and potent stimulatory CpG-DNA fragments were found in microbial genomes. Interestingly, highly conserved stimulatory CpG-DNA fragments were found in 16S and 23S rDNA sequences with multiple copies, while others were species-specific. Additionally, we found that the reported active motifs were mostly nonstimulatory in natural CpG fragments. This evidence indicates that the previous structural descriptions of functional CpG-ODNs are incomplete. Our study has assessed the distribution of microbial CpG-DNA fragments, and identified natural stimulatory CpG-DNA fragments. These findings provide a deeper understanding of CpG-ODN structures and new evidence for microbial DNA inflammatory function and pathogenicity.

Citations

Citations to this article as recorded by

Advances in protein subunit vaccines against H1N1/09 influenza
Yu Zhang, Jingyao Gao, Wenqi Xu, Xingyu Huo, Jingyan Wang, Yirui Xu, Wenting Ding, Zeliang Guo, Rongzeng Liu
Frontiers in Immunology.2024;[Epub] CrossRef
Cell-free DNA beyond a biomarker for rejection: Biological trigger of tissue injury and potential therapeutics
Naoko Tsuji, Sean Agbor-Enoh
The Journal of Heart and Lung Transplantation.2021; 40(6): 405. CrossRef

Research Support, Non-U.S. Gov'ts

Innate signaling mechanisms controlling Mycobacterium chelonae-mediated CCL2 and CCL5 expression in macrophages: Yi Sak Kim , Ji Hye Kim , Minjeong Woo , Tae-sung Kim Kim , Kyung Mok Sohn , Young-Ha Lee , Eun-Kyeong Jo , Jae-Min Yuk; J. Microbiol. 2015;53(12):864-874. Published online December 2, 2015; DOI: https://doi.org/10.1007/s12275-015-5348-1

39 View
0 Download
3 Crossref

Abstract

Mycobacterium chelonae (Mch) is an atypical rapidly growing mycobacterium (RGM) that belongs to the M. chelonae complex, which can cause a variety of human infections. During this type of mycobacterial infection, macrophagederived chemokines play an important role in the mediation of intracellular communication and immune surveillance by which they orchestrate cellular immunity. However, the intracellular signaling pathways involved in the macrophage- induced chemokine production during Mch infections remain unknown. Thus, the present study aimed to determine the molecular mechanisms by which Mch activates the gene expressions of chemokine (C-C motif) ligand 2 (CCL2) and CCL5 in murine bone marrow-derived macrophages (BMDMs) and in vivo mouse model. Toll-like receptor 2 (TLR2)-deficient mice showed increased bacterial burden in spleen and lung and decreased protein expression of CCL2 and CCL5 in serum. Additionally, Mch infection triggered the mRNA and protein expression of CCL2 and CCL5 in BMDMs via TLR2 and myeloid differentiation primary response gene 88 (MyD88) signaling and that it rapidly activated nuclear factor (NF)-κB signaling, which is required for the Mch-induced expressions of CCL2 and CCL5 in BMDMs. Moreover, while the innate receptor Dectin-1 was only partly involved in the Mch-induced expression of the CCL2 and CCL5 chemokines in BMDMs, the generation of intracellular reactive oxygen species (ROS) was an important contributor to these processes. Taken together, the present data indicate that the TLR2, MyD88, and NF-κB pathways, Dectin-1 signaling, and intracellular ROS generation contribute to the Mch-mediated expression of chemokine genes in BMDMs.

Citations

Citations to this article as recorded by

The Rise of Non-Tuberculosis Mycobacterial Lung Disease
Champa N. Ratnatunga, Viviana P. Lutzky, Andreas Kupz, Denise L. Doolan, David W. Reid, Matthew Field, Scott C. Bell, Rachel M. Thomson, John J. Miles
Frontiers in Immunology.2020;[Epub] CrossRef
A Comparative Analysis of Edwardsiella tarda-Induced Transcriptome Profiles in RAW264.7 Cells Reveals New Insights into the Strategy of Bacterial Immune Evasion
Huili Li, Boguang Sun, Xianhui Ning, Shuai Jiang, Li Sun
International Journal of Molecular Sciences.2019; 20(22): 5724. CrossRef
Abnormal Microglia and Enhanced Inflammation-Related Gene Transcription in Mice with Conditional Deletion ofCtcfinCamk2a-Cre-Expressing Neurons
Bryan E. McGill, Ruteja A. Barve, Susan E. Maloney, Amy Strickland, Nicholas Rensing, Peter L. Wang, Michael Wong, Richard Head, David F. Wozniak, Jeffrey Milbrandt
The Journal of Neuroscience.2018; 38(1): 200. CrossRef

Newly Identified CpG ODNs, M5-30 and M6-395, Stimulate MouseNewly Identified CpG ODNs, M5-30 and M6-395, Stimulate Mouse Immune Cells to Secrete TNF-α and Enhance Th1-Mediated Immunity: Sun-Shim Choi , Eunkyung Chung , Yu-Jin Jung; J. Microbiol. 2010;48(4):512-517. Published online August 20, 2010; DOI: https://doi.org/10.1007/s12275-010-0053-6

37 View
0 Download
13 Scopus

Abstract: Bacterial CpG motifs are known to induce both innate and adaptive immunity in infected hosts via toll-like receptor 9 (TLR9). Because small oligonucleotides (ODNs) mimicking bacterial CpG motifs are easily synthesized, they have found use as immunomodulatory agents in a number of disease models. We have developed a novel bioinformatics approach to identify effective CpG ODN sequences and evaluate their function as TLR9 ligands in a murine system. Among the CpG ODNs we identified, M5-30 and M6-395 showed significant ability to stimulate TNF-α and IFN-γ production in a mouse macrophage cell line and mouse splenocytes, respectively. We also found that these CpG ODNs activated cells through the canonical NF-κB signaling pathway. Moreover, both CpG ODNs were able to induce Th1-mediated immunity in Mycobacterium tuberculosis (Mtb)-infected mice. Our results demonstrate that M5-30 and M6-395 function as TLR9-specific ligands, making them useful in the study of TLR9 functionality and signaling in mice.

First
Prev
Page of 1
Next
Last

Search