Journal of Microbiology

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Discovery of novel glycoside hydrolases from C-glycoside-degrading bacteria using sequence similarity network analysis: Bin Wei , Ya-Kun Wang , Jin-Biao Yu , Si-Jia Wang , Yan-Lei Yu , Xue-Wei Xu , Hong Wang; J. Microbiol. 2021;59(10):931-940. Published online September 23, 2021; DOI: https://doi.org/10.1007/s12275-021-1292-4

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C-Glycosides are an important type of natural product with significant bioactivities, and the C-glycosidic bonds of C-glycosides can be cleaved by several intestinal bacteria, as exemplified by the human faeces-derived puerarin-degrading bacterium Dorea strain PUE. However, glycoside hydrolases in these bacteria, which may be involved in the C-glycosidic bond cleavage of C-glycosides, remain largely unknown. In this study, the genomes of the closest phylogenetic neighbours of five puerarin-degrading intestinal bacteria (including Dorea strain PUE) were retrieved, and the protein-coding genes in the genomes were subjected to sequence similarity network (SSN) analysis. Only four clusters of genes were annotated as glycoside hydrolases and observed in the genome of D. longicatena DSM 13814T (the closest phylogenetic neighbour of Dorea strain PUE); therefore, genes from D. longicatena DSM 13814T belonging to these clusters were selected to overexpress recombinant proteins (CG1, CG2, CG3, and CG4) in Escherichia coli BL21(DE3). In vitro assays indicated that CG4 efficiently cleaved the O-glycosidic bond of daidzin and showed moderate β-D-glucosidase and β-D-xylosidase activity. CG2 showed weak activity in hydrolyzing daidzin and pNP- β-D-fucopyranoside, while CG3 was identified as a highly selective and efficient α-glycosidase. Interestingly, CG3 and CG4 could be selectively inhibited by daidzein, explaining their different performance in kinetic studies. Molecular docking studies predicted the molecular determinants of CG2, CG3, and CG4 in substrate selectivity and inhibition propensity. The present study identified three novel and distinctive glycoside hydrolases, highlighting the potential of SSN in the discovery of novel enzymes from genomic data.

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Two-step computational redesign of Bacillus subtilis cellulase and β-glucanase for enhanced thermostability and activity
Huan Zhang, Tong Zhu, Qinglin Zhai, Qiansi Chen, Xuanshuo Zhang, Yiqiang Chen, Wei He, Jingjing Li, Jianqiang Fan, Jiemeng Tao, Xingchuan Hu, Lingfeng Qi, Chaochao Wang, Kuanqi Liao, Yanchun Chen, Yinglu Cui, Shanyi Chen, Bian Wu
International Journal of Biological Macromolecules.2025; 285: 138274. CrossRef
A newly isolated human intestinal strain deglycosylating flavonoid C-glycosides
Sha Wang, Siqi Liu, Jing Wang, Jiayue Tao, Mengjiao Wu, Wenfu Ma, Rufeng Wang
Archives of Microbiology.2022;[Epub] CrossRef

Mitochondrial genome and diverse inheritance patterns in Pleurotus pulmonarius: Li-Yun Ye+ , You-Jin Deng+ , Irum Mukhtar , Guo-Liang Meng , Yan-Jiao Song , Bing Cheng , Jin-bing Hao , Xiao-Ping Wu; J. Microbiol. 2020;58(2):142-152. Published online January 29, 2020; DOI: https://doi.org/10.1007/s12275-020-9318-x

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Abstract

Pleurotus pulmonarius, a member of the Pleurotaceae family in Basidiomycota, is an edible, economically important mushroom in most Asian countries. In this study, the complete mitochondrial genomes (mtDNA) of three P. pulmonarius strains – two monokaryotic commercial (J1-13 and ZA3) and one wild (X1-15) – were sequenced and analyzed. In ZA3 and X1-15, the mtDNA molecule was found to be a single circle of 68,305 bp and 73,435 bp, respectively. Both strains contain 14 core protein-coding genes and two ribosomal RNA (rRNA) subunit genes. The ZA3 strain has 22 transfer RNA (tRNA) genes and nine introns: eight in cytochrome c oxidase subunit 1 (cox1), and one in the rRNA large subunit (rnl). Monokaryotic J1-13 and ZA3 mtDNAs were found to be similar in their structure. However, the wild strain X1-15 contains 25 tRNA genes and only seven introns in cox1. Open reading frames (ORFs) of ZA3/J1-13 and X1-15 encode LAGLIDADG, ribosomal protein S3, and DNA polymerase II. In addition, mtDNA inheritance in J1-13, ZA3, and X1-15 was also studied.
Results
showed that the mtDNA inheritance pattern was uniparental and closely related to dikaryotic hyphal location with respect to the parent. Results also show that mtDNA inheritance is influenced by both the parental nuclear genome and mitogenome in the zone of contact between two compatible parents. In summary, this analysis provides valuable information and a basis for further studies to improve our understanding of the inheritance of fungal mtDNA.

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Comparative analyses of Pleurotus pulmonarius mitochondrial genomes reveal two major lineages of mini oyster mushroom cultivars
Yang Yu, Tianhai Liu, Yong Wang, Lixu Liu, Xiaolan He, Jianwei Li, Francis M. Martin, Weihong Peng, Hao Tan
Computational and Structural Biotechnology Journal.2024; 23: 905. CrossRef
Intraspecific and interspecific variations in the synonymous codon usage in mitochondrial genomes of 8 pleurotus strains
Wei Gao, Xiaodie Chen, Jing He, Ajia Sha, Yingyong Luo, Wenqi Xiao, Zhuang Xiong, Qiang Li
BMC Genomics.2024;[Epub] CrossRef
Identification of s9ap used as an endogenous reference gene in qualitative and real-time quantitative PCR detection of Pleurotus eryngii
Yuanmiao Wei, Yao Liu, Ling Li, Shuna Xiang, Hanyue Zhang, Ying Shang
Molecular Biology Reports.2023; 50(1): 621. CrossRef
Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Auricularia villosula, an edible wild mushroom in China
Xiaoguo Wang, Shiyan Wei, Shengjin Wu, Jun Tang, Jiaojun Wei, Zengliang Liu, Liangliang Qi
Biologia.2023; 78(12): 3713. CrossRef
The Effect of Mitochondria on Ganoderma lucidum Growth and Bioactive Components Based on Transcriptomics
Liyun Ye, Xiaofang He, Congbao Su, Haiying Feng, Guoliang Meng, Bingzhi Chen, Xiaoping Wu
Journal of Fungi.2022; 8(11): 1182. CrossRef
Genome Assembly and Genetic Traits of the Pleuromutilin-Producer Clitopilus passeckerianus DSM1602
Thomas Schafhauser, Daniel Wibberg, Antonia Binder, Christian Rückert, Tobias Busche, Wolfgang Wohlleben, Jörn Kalinowski
Journal of Fungi.2022; 8(8): 862. CrossRef

Characterization of the Deletion Endpoints in Yeast Saccharomyces cerevisiae Mitochondrial oxi3 Gene Large-Deletion Mutants: Nam, Su Gil , Kim, Bok Whan , Kim, Sang Ho; J. Microbiol. 1995;33(1):16-20.

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Abstract: Previous results in our laboratory showed that there are site-specific large deletions in yeast Saccharomyces cerevisiae 777-3A mitochondrial oxi3 gene and most of them fall into A and B class only. The B-class mutants were analyzed by PCR and sequencing. About 420 bp deletion junction fragments were successfully amplified and subjected to direct sequencing. Based on the sequencing results, the deletion endpoints of class B-deletions were identified at a distance of 8,222 bp; interestingly, one end(position 26180 coincided with the 3’ splice site(intron/exon junction) of first intron aI1, the other end(position 10,839) was located in the middle of the fifth intron (aI5) of the gene, especially in an open reading frame(ORF).

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