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10. Characterization of Plasmid Co-Harboring NDM-1 and SHV-12 from a Multidrug-Resistant Citrobacter freundii Strain ZT01-0079 in China

Author

Zhang,Tingyan, Lin,Yanfeng, Li,Peihan, Li,Zhonghong, Liu,Xiong, Li,Jinhui, Li,Lizhong, Wang,Kaiying, Liu,Zhongdong, Li,Peng, Lu,Lanfen, Wang,Hongyan, Zhang,Tingyan, Lin,Yanfeng, Li,Peihan, Li,Zhonghong, Liu,Xiong, Li,Jinhui, Li,Lizhong, Wang,Kaiying, Liu,Zhongdong, Li,Peng, Lu,Lanfen, and Wang,Hongyan

Abstract

Tingyan Zhang,1,2,* Yanfeng Lin,2,3,* Peihan Li,2,3,* Zhonghong Li,2 Xiong Liu,2 Jinhui Li,2 Lizhong Li,2 Kaiying Wang,2,3 Zhongdong Liu,1 Peng Li,2 Lanfen Lu,4 Hongyan Wang1 1School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou, People’s Republic of China; 2Chinese PLA Center for Disease Control and Prevention, Beijing, People’s Republic of China; 3Academy of Military Medical Sciences, Beijing, People’s Republic of China; 4Department of Laboratory Diagnosis, Sun Yat-Sen University Affiliated Zhongshan Hospital, Zhongshan, Guangdong, People’s Republic of China*These authors contributed equally to this workCorrespondence: Peng Li; Hongyan Wang Email jiekenlee@126.com; 18623717897@163.comBackground: The emergence of multidrug-resistant Citrobacter freundii poses daunting challenges to the treatment of clinical infections. The purpose of this study was to characterize the genome of a C. freundii strain with an IncX3 plasmid encoding both the blaNDM-1 and blaSHV-12 genes.Methods: Strain ZT01-0079 was isolated from a clinical urine sample. The Vitek2 system was used for identification and antimicrobial susceptibility testing. The presence of blaNDM-1 was detected by PCR and sequencing. Conjugation experiments and Southern blotting were performed to determine the transferability of the blaNDM-1- carrying plasmid. Nanopore and Illumina sequencing were performed to better understand the genomic characteristics of the strain.Results: Strain ZT01-0079 was identified as C. freundii, and the coexistence of blaNDM-1 and multiple drug resistance genes was confirmed. Electrophoresis and Southern blotting showed that blaNDM-1 was located on a ∼ 53kb IncX3 plasmid. The NDM-1-encoding plasmid was successfully transferred at a frequency of 1.68× 10− 3. Both the blaNDM-1 and blaSHV-12 genes were located on the self-transferable IncX3 plasmid.Conclusion: The rapid spread of the IncX3 p

Published
2021

15. Metagenomic Diagnosis for a Culture-Negative Sample From a Patient With Severe Pneumonia by Nanopore and Next-Generation Sequencing

Author

Wang, Kaiying, primary, Li, Peihan, additional, Lin, Yanfeng, additional, Chen, Hongbin, additional, Yang, Lang, additional, Li, Jinhui, additional, Zhang, Tingyan, additional, Chen, Qichao, additional, Li, Zhonghong, additional, Du, Xinying, additional, Zhou, Yusen, additional, Li, Peng, additional, Wang, Hui, additional, and Song, Hongbin, additional

Published
2020
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18. Genome-Wide Analysis of the Cyclin Gene Family in Tomato

Author

Xiaofeng Cai, Zhang Tingyan, Junhong Zhang, Zhibiao Ye, Xin Wang, and Yongen Lu

Subjects
Molecular Sequence Data, Cyclin A, Arabidopsis, tomato, Genome, Chromosomes, Plant, Article, Catalysis, lcsh:Chemistry, Inorganic Chemistry, Cyclin Gene, Cyclin D1, Solanum lycopersicum, cyclin, Cyclins, Gene duplication, Amino Acid Sequence, phylogenetic analysis, gene duplication, gene expression, gibberellin, Physical and Theoretical Chemistry, lcsh:QH301-705.5, Molecular Biology, Gene, Phylogeny, Spectroscopy, Plant Proteins, Cyclin, Genetics, biology, fungi, Organic Chemistry, food and beverages, General Medicine, Computer Science Applications, lcsh:Biology (General), lcsh:QD1-999, biology.protein, Sequence Alignment, Genome, Plant, Cyclin A2
Abstract

Cyclins play important roles in cell division and cell expansion. They also interact with cyclin-dependent kinases to control cell cycle progression in plants. Our genome-wide analysis identified 52 expressed cyclin genes in tomato. Phylogenetic analysis of the deduced amino sequences of tomato and Arabidopsis cyclin genes divided them into 10 types, A-, B-, C-, D-, H-, L-, T-, U-, SDS- and J18. Pfam analysis indicated that most tomato cyclins contain a cyclin-N domain. C-, H- and J18 types only contain a cyclin-C domain, and U-type cyclins contain another potential cyclin domain. All of the cyclin genes are distributed throughout the tomato genome except for chromosome 8, and 30 of them were found to be segmentally duplicated; they are found on the duplicate segments of chromosome 1, 2, 3, 4, 5, 6, 10, 11 and 12, suggesting that tomato cyclin genes experienced a mass of segmental duplication. Quantitative real-time polymerase chain reaction analysis indicates that the expression patterns of tomato cyclin genes were significantly different in vegetative and reproductive stages. Transcription of most cyclin genes can be enhanced or repressed by exogenous application of gibberellin, which implies that gibberellin maybe a direct regulator of cyclin genes. The study presented here may be useful as a guide for further functional research on tomato cyclins.

Published
2013

19. Genome-wide Analysis of Plant-specific Dof Transcription Factor Family in Tomato

Author

Jie Ye, Taotao Wang, Yuyang Zhang, Chanjuan Zhang, Xiaofeng Cai, Junhong Zhang, Zhibiao Ye, Hanxia Li, Tixu Hu, and Zhang Tingyan

Subjects
Zinc finger, Genetics, biology, fungi, food and beverages, Plant Science, biology.organism_classification, Biochemistry, General Biochemistry, Genetics and Molecular Biology, Arabidopsis, Gene expression, Gene duplication, Gene family, Transcription factor, Gene, Segmental duplication
Abstract

The Dof (DNA binding with One Finger) family encoding single zinc finger proteins has been known as a family of plant-specific transcription factors. These transcription factors are involved in a variety of functions of importance for different biological processes in plants. In the current study, we identified 34 Dof family genes in tomato, distributed on 11 chromosomes. A complete overview of SlDof genes in tomato is presented, including the gene structures, chromosome locations, phylogeny, protein motifs and evolution pattern. Phylogenetic analysis of 34 SlDof proteins resulted in four classes constituting six clusters. In addition, a comparative analysis between these genes in tomato, Arabidopsis and rice was also performed. The tomato Dof family expansion has been dated to recent duplication events, and segmental duplication is predominant for the SlDof genes. Furthermore, the SlDof genes displayed differential expression either in their transcript abundance or in their expression patterns under normal growth conditions. This is the first step towards genome-wide analyses of the Dof genes in tomato. Our study provides a very useful reference for cloning and functional analysis of the members of this gene family in tomato and other species.

Published
2013

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