10.5061/DRYAD.FTTDZ08VS
Betschart, Bruno
0000-0001-6057-9374
University of Neuchâtel
Bisoffi, Marco
Chapman University
Alaeddine, Ferial
University of Neuchâtel
Identification and characterization of epicuticular proteins of nematodes
sharing motifs with cuticular proteins of arthropods
Dryad
dataset
2022
FOS: Biological sciences
Swiss National Science Foundation
https://ror.org/00yjd3n13
University of Neuchâtel
https://ror.org/00vasag41
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
008439
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
26764
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
33961
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
047194
2022-05-09T00:00:00Z
2022-05-09T00:00:00Z
en
https://doi.org/10.1016/0166-6851(96)02668-0
http://doc.rero.ch/record/4865
https://doi.org/10.1371/journal.pone.0274751
374343 bytes
9
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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 A.suum 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 A. suum; 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 C. elegans 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.