- The discovery of potent immunostimulatory CpG-ODNs widely distributed in bacterial genomes
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Juan Liu , Yan Wei , Yongling Lu , Yangyuling Li , Qian Chen , Yan Li
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J. Microbiol. 2020;58(2):153-162. Published online December 23, 2019
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DOI: https://doi.org/10.1007/s12275-020-9289-y
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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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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
- Comparing the sugar profiles and primary structures of alkali-extracted water-soluble polysaccharides in cell wall between the yeast and mycelial phases from Tremella fuciformis
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Hanyu Zhu , Yuan Yuan , Juan Liu , Liesheng Zheng , Liguo Chen , Aimin Ma
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J. Microbiol. 2016;54(5):381-386. Published online April 20, 2016
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DOI: https://doi.org/10.1007/s12275-016-5533-x
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989
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Abstract
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To gain insights into dimorphism, cell wall polysaccharides
from Tremella fuciformis strains were obtained from alkaliextracted
water-soluble fractions PTF-M38 (from the mycelial
form), PTF-Y3 and PTF-Y8 (from the yeast form) of
T. fuciformis strains were used to gain some insights into
dimorphism study. Their chemical properties and structural
features were investigated using gel permeation chromatography,
gas chromatography, UV and IR spectrophotometry
and Congo red binding reactions. The results indicated that
the backbones of PTF-M38, PTF-Y3 and PTF-Y8 were configured
with α-linkages with average molecular weights of
1.24, 1.08, and 1.19 kDa, respectively. PTF-M38 was mainly
composed of xylose, mannose, glucose, and galactose in a
ratio of 1:1.47:0.48:0.34, while PTF-Y3 and PTF-Y8 were
mainly composed of xylose, mannose and glucose in a ratio
of 1:1.65:4.06 and 1:1.21:0.44, respectively. The sugar profiles
of PTF-M38, PTF-Y3 and PTF-Y8 were also established
for further comparison. These profiles showed that all three
polysaccharides contained the same sugars but in different
ratios, and the carbon sources (xylose, mannose, glucose, and
galactose) affected the sugar ratios within the polysaccharides.
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Citations
Citations to this article as recorded by - Comparative anti-photoaging effects of polysaccharides from Tremella fuciformis fruiting bodies and spores in Caenorhabditis elegans
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Polymers.2022; 14(8): 1514. CrossRef - Study of Dimorphism Transition Mechanism of Tremella fuciformis Based on Comparative Proteomics
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Bobo Lin, Gangliang Huang
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Hanyu Zhu, Dongmei Liu, Liesheng Zheng, Liguo Chen, Aimin Ma
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International Journal of Immunopathology and Pharmacology.2021;[Epub] CrossRef - Tremella fuciformis TFCUV5 Mycelial Culture-derived Exopolysaccharide Production and Its Anti-aging Effects on Skin Cells
Min-Ho Jo, Byeol Kim, Jung-Hyun Ju, Sun-Yeon Heo, Keug-Hyun Ahn, Hye Ja Lee, Hyun-Sook Yeom, Hansu Jang, Min-Soo Kim, Chul-Ho Kim, Baek-Rock Oh
Biotechnology and Bioprocess Engineering.2021; 26(5): 738. CrossRef - Cloning and functional characterization of gpd and α-tubulin promoters from Annulohypoxylon stygium, a companion fungus of Tremella fuciformis
Dongmei Liu, Hanyu Zhu, Dwi Pujiana, Liesheng Zheng, Liguo Chen, Aimin Ma
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- An Improved Method for Extracting Bacteria from Soil for High Molecular Weight DNA Recovery and BAC Library Construction
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Juan Liu , Jingquan Li , Li Feng , Hui Cao , Zhongli Cui
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J. Microbiol. 2010;48(6):728-733. Published online January 9, 2011
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DOI: https://doi.org/10.1007/s12275-010-0139-1
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888
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Separation of bacterial cells from soil is a key step in the construction of metagenomic BAC libraries with large DNA inserts. Our results showed that when combined with sodium pyro-phosphate and homogenization for soil dispersion, sucrose density gradient centrifugation (SDGC) was more effective at separating bacteria from soil than was low speed centrifugation (LSC). More than 70% of the cells, along with some soil colloids, were recovered with one round of centrifugation. A solution of 0.8% NaCl was used to resuspend these cell and soil pellets for purification with nycodenz density gradient centrifugation (NDGC). After purification, more than 30% of the bacterial cells in the primary soil were extracted. This procedure effectively removed soil contamination and yielded sufficient cells for high molecular weight (HMW) DNA isolation. Ribosomal intergenic spacer analysis (RISA) showed that the microbial community structure of the extracted cells was
similar to that of the primary soil, suggesting that this extraction procedure did not significantly change the the soil bacteria community structure. HMW DNA was isolated from bacterial cells extracted from red soil for metagenomic BAC library construction. This library contained DNA inserts of more than 200 Mb with an
average size of 75 kb.
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