Nematode Epicuticlin and Collagen Sequences with YGD/GYR Amino Acid Motifs

Title

Nematode Epicuticlin and Collagen Sequences with YGD/GYR Amino Acid Motifs

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Description

Nematoda and Arthropoda have a complex exoskeleton, the cuticle, which is replaced via molts during their development. Major constituents of nematode cuticles are specific collagens and insoluble proteins called cuticlins. The epicuticle is composed of an insoluble protein called epicuticlin. Our objective was to identify and characterize genes and their encoded proteins forming the epicuticle. We were able to complete the identification of the first epicuticlin gene, Asu-epicut1 of Ascaris suum which is composed of 7 tandem repeats. The deduced protein, Asu-EPICUT1, consists of a signal peptide of 20 amino acids followed by 353 amino acids composed of seven tandem repeats (TR) of 49 or 51 amino acids each. Each repeat has three highly conserved tyrosine motives. Interestingly one of them (GYR) is the Pfam motif PF02756 present in several cuticular proteins of arthropods. Blast search in different databases using parts of epicuticular proteins as queries showed the presence of homologous proteins in 50 other nematode species. They are all characterized by TR, each composed of around 60 amino acids and two to four motifs with a conserved tyrosine. Some of the putative epicuticular proteins detected in nematodes of Clade V (Rhabditina) contain beside the tyrosine residues one cysteine residue per repeat. This new category of cuticular proteins might crosslink with specific cuticular collagens, which also have tyrosine motifs. The localization in the outermost layer of the nematode body and their unique structure renders them important candidates for biochemical and molecular interaction studies.

Publication Date

5-9-2022

Keywords

Biological sciences

Disciplines

Biochemistry | Genetics

Comments

Methods

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.

Funding

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung

Université de Neuchâtel

Copyright

This work is licensed under a CC0 1.0 Universal (CC0 1.0) Public Domain Dedication license.

Nematode Epicuticlin and Collagen Sequences with YGD/GYR Amino Acid Motifs

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