Supplementary data for the <i>Konstantin V Gunbin, Gelina S Kopeina, Boris Zhivotovsky, Alexey V Zamaraev. </i><b>Features of the CD1 gene family in rodents and the uniqueness of the immune </b><b>system of naked mole-rat</b>. Immunology &amp; Cell Biology
Creators: name: Gunbin, Konstantin
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 310206
subject: Sequence analysis
classificationCode: 310205
subject: Proteomics and metabolomics

description: <b>Abstract</b><br>Cluster of Differentiation 1 (CD1) proteins are widely expressed throughout jawed vertebrates and present lipid antigens to specific CD1-restricted T lymphocytes. CD1 molecules play an important role in immune defense with the presence or absence of particular CD1 proteins frequently associated with the functional characteristics of the immune system. Here, we demonstrate the evolution of CD1 proteins in the Rodentia family and the diversity among their members. Based on the analysis of CD1 protein-coding regions in rodent genomes and reconstruct protein structures by AlphaFold we have demonstrated the absence of functional structure of CD1d and CD1e proteins in <i>Heterocephalus glaber</i> and probably dysfunctional CD1b due to presence of an unstructured region. Additionally, we discuss in detail the impact of CD1d loss on the CD1d/Natural killer T (NKT) cells axis in the naked mole rat and its potential effect on the function of immune system.<br><br><b>Data description</b><br>Suppl. 1 contains:(1) The query sequences and query database (ancprots.fa and ancprots.dmnd files)<br>(2) Search results obtained by diamond on dynamically downloaded fastq files (*.m8 files)<br>(3) The NCBI SRA acession lists (*.txt files)<br>(4) The Perl scripts for sequence retrieval and data parsing (intermediate data removed to save disk resources)Suppl. 2 contains:<br>(1) The query sequences (ancprots.fa file)(2) The Perl script that summarizes data from *.m8 files (see Suppl. 1)<br>(3) The output generated by the script (see (2)): *.txt fileSuppl. 3 contains:<br>(1) The pipeline consists of 4 Perl scripts for dumping and selecting NCBI SRA reads that have similarity with query sequences. This pipeline starts from *.m8 files (see Suppl. 1)<br>(2) The result that was created by a pipeline stages 0-2 (*.checked.fa file)Suppl. 4 contains:<br>(1) The query sequences (ancprots.fa file)(2) The results of the 3rd pipeline stage (see Suppl. 3) are stored in *sum.fa files (for 3 translation frames)<br>(3) The main Perl script (recProtein.pl) which summarizes proteins from translated reads(4) The *sum.recpr.fa and *sum.tab.txt files produced by the main Perl script<br>(5) The formatted and selected results (see (4)) are available in the form of *.fas and *.leg* files, along with simple Perl scripts for sequence formatting and selection, such as *legenda.pl and recProteinExtract.plSuppl. 5 contains:<br>(1) The *.docx file summarizes AlphaFold2 raw results<br>(2) The raw AlphaFold2 results can be found in zip archives for every protein<br>(3) The Perl script for converting old json PAE data format to new format that used in PAE Viewer (http://www.subtiwiki.uni-goettingen.de/v4/paeViewerDemo)<br>(4) The *.txt file summarized results from Foldseek search (queries: <i>Heterocephalus glaber</i> CD1 potential proteins), PAE_Viewer, and PDB Pairwise Structure Alignment (jFATCAT-flexible)<br><br>Supplementary figure S1. Domain structure of human CD1a,b,c,d,e proteins. The heavy chain is composed of α1, α2 and α3 domains which is non-covalently associated with β-microglobulin. The antigen-binding hydrophobic cleft is formed by α1+α2 domains. The α3 domain attaches CD1 molecules to membranes through a transmembrane segment.Supplementary figure S2. The distribution of normalized translated peptide (from retrieved reads) lengths without stop-codons for all <i>Heterocephalus glaber</i> potential proteins.<br>Supplementary figure S3. The Predicted Aligned Error (PAE) plots and 3D predicted structures of CD1b,d,e of <i>Heterocephalus glaber</i>, showing selected regions of low confidence (purple on the PAE plots and 3D structure) and the orientation of adjacent parts of the structures (orange and cyan on the 3D structure) to the disordered region.