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Identification and characterization of human PPFIA4 gene in silico
1M&M Medical BioInformatics, Narashino 275-0022, Japan.
Insights
This study identifies the complete coding sequence of the human PPFIA4 gene, revealing its structure and potential roles in protein interactions and cellular transport. It characterizes PPFIA4 as a kinesin-cargo linker.
Area of Science:
- Molecular Biology
- Genetics
- Bioinformatics
Background:
- The human PPFIA1 gene encodes a KIF1A-binding protein involved in protein trafficking.
- Previous studies had only identified partial cDNA sequences for human and rat PPFIA4.
- The complete coding sequence and comprehensive characterization of PPFIA4 were previously unknown.
Purpose of the Study:
- To determine the complete coding sequence of the human PPFIA4 gene using bioinformatics.
- To characterize the PPFIA4 gene, its protein domains, and its relationship to other PPFIA family members.
- To identify potential binding interactions and cellular functions of PPFIA4.
Main Methods:
- Bioinformatic analysis of human genome sequences (AC096632.3, AL451082.6) to identify PPFIA4 exons.
- Comparative sequence analysis to determine amino acid identity with other PPFIA family members.
- Identification and characterization of conserved protein domains (PFIH1-4, SAM1-3) and functional motifs.
Main Results:
- The complete coding sequence of human PPFIA4 (1186 amino acids) was determined.
- PPFIA4 shares significant amino acid identity with PPFIA2, PPFIA1, and PPFIA3.
- PPFIA4 possesses distinct structural features, including the absence of a C-terminal GRIP binding domain but includes a bipartite nuclear localization signal within the PFIH4 domain. The PFIH2-PFIH3 domains bind KIF1A, and SAM1-3 domains bind LAR PTPases and PPFIBP proteins.
Conclusions:
- This study provides the first comprehensive characterization of the human PPFIA4 gene and its encoded protein.
- PPFIA4 is a novel member of the PPFIA family of kinesin-cargo linkers with distinct functional domains.
- The identified structural features suggest specific roles for PPFIA4 in intracellular trafficking and protein complex formation.
Abstract:
Human PPFIA1 (also known as LIP.1 or Liprin alpha1) gene, located within CCND1-FGF4-EMS1 amplicon at human chromosome 11q13.3, encodes KIF1A-binding protein, which is implicated in trafficking of LAR subfamily PTPases and AMPA-type glutamate receptors. Human PPFIA4 (AF034801) and rat Ppfia4 (AY057064) are 5'-truncated partial cDNAs, and the complete coding sequence of PPFIA4 ortholog of any species remained to be identified. Here, we determined the complete coding sequence of human PPFIA4 gene by using bioinformatics. Exons 1-12 of PPFIA4 gene were located within human genome sequence AC096632.3, while exons 11-29 within AL451082.6. PPFIA4-MYOG locus (human chromosome 1q32.1) was paralogous to PPFIA2-LIN7A-MYF5-MYF6 locus (12q21.31), which was also paralogous to PPFIA3-LIN7B locus (19q13.41). PPFIA4 (1186 aa) showed 70.9%, 67.1%, and 61.8% total-amino-acid identity with PPFIA2, PPFIA1, and PPFIA3, respectively. PPFIA family members consist of PFIH1, PFIH2, PFIH3, PFIH4 domains and three SAM (Sterile alpha motif) domains. C-terminal binding domain for GRIP proteins (VRTYSC motif) was present in PPFIA1, PPFIA2 and PPFIA3, but not in PPFIA4. Bipartite nuclear localization signal was included within PFIH4 domain. PFIH2 domain was identical to ERM or Smc domain. The region spanning PFIH2-PFIH3 domains is the binding domain for KIF1A. The region spanning SAM1-SAM3 domains is the binding domain for LAR subfamily PTPases and PPFIBP (Liprin beta) family proteins. This is the first report on comprehensive characterization of PPFIA4 belonging to the PPFIA family of kinesin-cargo linkers.