Molecular Biology Reports

, Volume 41, Issue 9, pp 6083–6088 | Cite as

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

  • Zhen Yang
  • Haikui Chen
  • Xiaobo Yang
  • Xueshuai Wan
  • Lian He
  • Ruoyu Miao
  • Huayu Yang
  • Yang Zhong
  • Li Wang
  • Haitao Zhao


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.


Ubiquitin Phylogeny Motif Gene family 



This work was supported by International Science and Technology Cooperation Projects (2010DFB33720), the scientific research project of Ningxia Higher Education (2010JY001), National Natural Science Foundation of China (31000583 and 31071137), and Program for New Century Excellent Talents in University (NCET-11-0288).

Conflict of interest

The authors declare that they have no competing interests.

Supplementary material

11033_2014_3486_MOESM1_ESM.docx (22 kb)
Supplementary material 1 (DOCX 21 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • 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. 1.Department of Liver SurgeryPeking Union Medical College Hospital, Chinese Academy of Medical Science, CAMS & PUMCBeijingChina
  2. 2.Institute of Biomedical SciencesFudan UniversityShanghaiChina
  3. 3.Department of Life ScienceBeifang University of NationalitiesYinchuanChina
  4. 4.Institute of Biodiversity Science and GeobiologyTibet UniversityLhasaChina
  5. 5.Shanghai Center for Bioinformation TechnologyShanghaiChina

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