DOI: 10.5061/dryad.fttdz08vs
title: Identification and characterization of epicuticular proteins of nematodes sharing motifs with cuticular proteins of arthropods

description: Specific collagens and insoluble proteins called cuticlins are major
 constituents of the nematode cuticles. The epicuticle, which forms the
 outermost electron-dense layer of the cuticle, is composed of another
 category of insoluble proteins called epicuticlins. It is distinct from
 the insoluble cuticlins localized in the cortical layer and the fibrous
 ribbon underneath lateral alae. Our objective was to identify and
 characterize genes and their encoded proteins forming the epicuticle. The
 combination between previously obtained laboratory results and recently
 made available data through the whole-genome shotgun contigs (WGS) and the
 transcriptome Shotgun Assembly (TSA) sequencing projects of Ascaris suum
 allowed us to identify the first epicuticlin gene, Asu-epic-1, on the
 chromosome VI. This gene is formed of exon1 (55 bp) and exon2 (1067 bp),
 separated by an intron of 1593 bp. Exon 2 is formed of tandem repeats (TR)
 whose number varies in different cDNA and genomic clones of Asu-epic-1.
 These variations could be due to slippage of the polymerases during DNA
 replication and RNA transcription leading to insertions and deletions
 (Indels). The deduced protein, Asu-EPIC-1, consists of a signal peptide of
 20 amino acids followed by 353 amino acids composed of seven TR of 49 or
 51 amino acids each. Three highly conserved tyrosine motifs characterize
 each repeat. The GYR motif is the Pfam motif PF02756 present in several
 cuticular proteins of arthropods. Asu-EPIC-1 is an intrinsically
 disordered protein (IDP) containing seven predicted molecular recognition
 features (MoRFs). This type of protein undergoes a disorder-to-order
 transition upon binding protein partners. Three epicuticular sequences
 have been identified in A. suum, Ascaris lumbricoides, and Toxocara canis.
 Homologous epicuticular proteins were identified in over 50 other nematode
 species. The potential of this new category of proteins in forming the
 nematode cuticle through covalent interactions with other cuticular
 components, particularly with collagens, is discussed. Their localization
 in the outermost layer of the nematode body and their unique structure
 render them crucial candidates for biochemical and molecular interaction
 studies and targets for new biotechnological and biomedical applications.
description: The public accessible cDNA
 (X92101.2, 31B1A; AJ408885.1, C1; AJ408886.1, C2; AJ408887.1, C3) and
 genomic clones (AJ408888.1, G1; AJ408889.1, G2; AJ408890.1, G3), coding
 for <em>A.suum </em>epicuticlins, were used for a comparison
 of their common properties through alignments using
 Jalview. Based on the
 conserved common characteristics (aagaggaa), nucleotide Blasts were
 carried out on the following databases: NCBI (https://blast.ncbi.nlm.nih.gov/Blast.cgi) nucleotide collection, whole-genome shotgun contigs (wgs) of <em>A. suum</em>; WormbaseParasite  and the EMBL-EBI services. Protein Blasts were carried out again on the same platforms and also using the protein knowledge platform UniProt. Multiple or pairwise nucleotide or protein sequence alignments were carried out using the EMBL-EBI services: Clustal Omega for multiple alignments and Needle or Matcher for pairwise alignments. Radar was used for the automatic alignment of protein repeats and Phobius to identify signal peptides. For the analysis of the <em>C. elegans</em> genes, Wormbase was the authoritative data source. Following Expasy services (https://www.expasy.org/) were applied for the in-depth study of the epicuticlins: STRING, ProtParam and Compute pI/MW.