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>.
Creators: name: Gunbin, Konstantin
name: Kopeina, Gelina
name: Zhivotovsky, Boris
name: Zamaraev, Alexey
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 show the evolution of CD1 proteins in the Rodentia family and the diversity among its members. Based on the analysis of CD1 protein-coding regions in rodent genomes and the reconstruction of protein structures, we found that <i>Heterocephalus glaber</i> represents a unique member of the suborder Hystricomorpha with significant changes in protein sequences and structures of the CD1 family<i>. </i>Multiple lines of evidence point to the absence of CD1d and CD1e and probably a dysfunctional CD1b protein in <i>Heterocephalus glaber</i>. In addition, the impact of CD1d loss on the CD1d/Natural killer T (NKT) cell axis in the naked mole-rat and its potential implications for immune system function are discussing in detail.<br><br><b>Data description</b><br>Supplementary archive 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)Supplementary archive 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 fileSupplementary archive 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)Supplementary archive 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.plSupplementary archive 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>Supplementary archive 6 contains: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.<br>Supplementary archive 7 contains:The genomic sequence alignment of mouse chromosome 3:86902541-86907348 region containing cd1d1 gene to primary assembly of naked_mole-rat 28:5227926-5229655. The genomic sequence alignment of mouse chromosome 3: 86893258:86897687 region containing cd1d2 gene to primary assembly of naked_mole-rat 28:5227926-5229655.<br>Supplementary archive 8 contains:<br>(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) Best matched reads (*.BESTREADS.m8 file)<br><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><br><br>Supplementary table 1.Percent Identity Matrix of α-helices and β-sheets of the reconstructed CD1d, CD1d1, CD1d2, CD1e in <i>Heterocephalus glaber</i>, to neighboring species or other species with known protein sequences.<br>Supplementary table 2.Table of critical CD1d (pdb:1Z5L) residues located around the antigen binding cleft that, when mutated, show a 25-50% reduction (orange); a &gt;=50% reduction (red) in NKT cell activation (Almeida, C.F., Sundararaj, S., Le Nours, J. et al. Distinct CD1d docking strategies exhibited by diverse Type II NKT cell receptors. Nat Commun 10, 5242 (2019)). The table below shows the conservative residues at these critical positions in the reconstructed CD1d, CD1d1, CD1d2 proteins in <i>Heterocephalus glaber</i>.