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BMC evolutionary biology
10 07, 2020;20 (1): 130.

Molecular evolutionary and structural analysis of human UCHL1 gene demonstrates the relevant role of intragenic epistasis in Parkinson's disease and other neurological disorders.

Muhammad Saqib Nawaz, Razia Asghar, Nashaiman Pervaiz, Shahid Ali, Irfan Hussain, Peiqi Xing, Yiming Bao, Amir Ali Abbasi
Author Information
  1. Muhammad Saqib Nawaz: National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
  2. Razia Asghar: National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
  3. Nashaiman Pervaiz: National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
  4. Shahid Ali: National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
  5. Irfan Hussain: National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
  6. Peiqi Xing: National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
  7. Yiming Bao: National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China. baoym@big.ac.cn.
  8. Amir Ali Abbasi: National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan. abbasiam@qau.edu.pk. ORCID
PMID: 33028204 DOI: 10.1186/s12862-020-01684-7

Abstract

BACKGROUND: Parkinson's disease (PD) is the second most common neurodegenerative disorder. PD associated human UCHL1 (Ubiquitin C-terminal hydrolase L1) gene belongs to the family of deubiquitinases and is known to be highly expressed in neurons (1-2% in soluble form). Several functions of UCHL1 have been proposed including ubiquitin hydrolyze activity, ubiquitin ligase activity and stabilization of the mono-ubiquitin. Mutations in human UCHL1 gene have been associated with PD and other neurodegenerative disorders. The present study aims to decipher the sequence evolutionary pattern and structural dynamics of UCHL1. Furthermore, structural and interactional analysis of UCHL1 was performed to help elucidate the pathogenesis of PD.
RESULTS: The phylogenetic tree topology suggests that the UCHL1 gene had originated in early gnathostome evolutionary history. Evolutionary rate analysis of orthologous sequences reveals strong purifying selection on UCHL1. Comparative structural analysis of UCHL1 pinpoints an important protein segment spanning amino acid residues 32 to 39 within secretion site with crucial implications in evolution and PD pathogenesis through a well known phenomenon called intragenic epistasis. Identified critical protein segment appears to play an indispensable role in protein stability, proper protein conformation as well as harboring critical interaction sites.
CONCLUSIONS: Conclusively, the critical protein segment of UCHL1 identified in the present study not only demonstrates the relevant role of intraprotein conformational epistasis in the pathophysiology of PD but also offers a novel therapeutic target for the disease.

Keywords

Epistasis Neurodegenerative diseases Parkinson’s disease SNCA UCHL1

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Grants

  1. 2016YFE0206600/National Key Research and Development Program of China
  2. XXH13505-05/The 13th Five-year Informatization Plan of Chinese Academy of Sciences

MeSH Term

Epistasis, Genetic
Evolution, Molecular
Humans
Parkinson Disease
Phylogeny
Ubiquitin
Ubiquitin Thiolesterase

Chemicals

UCHL1 protein, human
Ubiquitin
Ubiquitin Thiolesterase
Journal Article Research Support, Non-U.S. Gov't

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