A phylogenetic analysis of the ubiquitin superfamily based on sequence and structural information

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• 作者：Zhen Yang (1) (2)
  Haikui Chen (3)
  Xiaobo Yang (1)
  Xueshuai Wan (1)
  Lian He (1)
  Ruoyu Miao (1)
  Huayu Yang (1)
  Yang Zhong (4)
  Li Wang (5)
  Haitao Zhao (1)
  
• 关键词：Ubiquitin ; Phylogeny ; Motif ; Gene family
• 刊名：Molecular Biology Reports
• 出版年：2014
• 出版时间：September 2014
• 年：2014
• 卷：41
• 期：9
• 页码：6083-6088
• 全文大小：1,327 KB
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• 作者单位：Zhen Yang (1) (2)
  Haikui Chen (3)
  Xiaobo Yang (1)
  Xueshuai Wan (1)
  Lian He (1)
  Ruoyu Miao (1)
  Huayu Yang (1)
  Yang Zhong (4)
  Li Wang (5)
  Haitao Zhao (1)
  
  1. Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science, CAMS & PUMC, Beijing, 100730, China
  2. Institute of Biomedical Sciences, Fudan University, Shanghai, 200433, China
  3. Department of Life Science, Beifang University of Nationalities, Yinchuan, 730000, China
  4. Institute of Biodiversity Science and Geobiology, Tibet University, Lhasa, 850000, China
  5. Shanghai Center for Bioinformation Technology, Shanghai, 200235, China
  
• ISSN：1573-4978

文摘

Ubiquitin belongs to an important class of protein modifier and gene expression regulator proteins that participates in various cellular processes. A large number of ubiquitin-related proteins have been identified during the last two decades. However, the evolutionary history of this ancient gene family remains largely unknown. We analyzed the members of the superfamily using both sequence- and structure-based methodology to better understand the evolution of ubiquitin-related proteins. As a part of these analyses we used the MEME algorithm to extract common sequence motifs across the superfamily, and we inferred the phylogeny and distribution of the superfamily members across multiple species. A total of 23 families were identified in the gene family. Several common sequence motifs were revealed and evaluated. We also found that the number of genes for ubiquitin-related proteins encoded within a specific genome correlates with the biological complexity of that particular species. This analysis should provide valuable insight into the sequence/function relationships and evolutionary history of ubiquitin and ubiquitin-related proteins.