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

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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.

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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

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

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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.

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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

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