CutProtFam-Pred: Detection and classification of putative structural cuticular proteins from sequence alone, based on profile Hidden Markov Models

• Published in: Insect biochemistry and molecular biology 2014-09, Vol.52, p.51-59
• Main Authors: Ioannidou, Zoi S., Theodoropoulou, Margarita C., Papandreou, Nikos C., Willis, Judith H., Hamodrakas, Stavros J.
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Animals; Arthropod cuticle; Arthropod Proteins - chemistry; Arthropod Proteins - genetics; Arthropod Proteins - metabolism; Arthropods - chemistry; Arthropods - genetics; Arthropods - metabolism; Chitin - chemistry; Chitin - genetics; Chitin - metabolism; Computational Biology - methods; Cuticular proteins; Markov Chains; Molecular Sequence Data; Multigene Family; Phylogeny; Profile Hidden Markov Models (pHMMs); Proteome; Sequence Alignment; Sequence Analysis, Protein; Structural cuticular protein families
• ISSN: 0965-1748; 1879-0240
• DOI: 10.1016/j.ibmb.2014.06.004

The arthropod cuticle is a composite, bipartite system, made of chitin filaments embedded in a proteinaceous matrix. The physical properties of cuticle are determined by the structure and the interactions of its two major components, cuticular proteins (CPs) and chitin. The proteinaceous matrix consists mainly of structural cuticular proteins. The majority of the structural proteins that have been described to date belong to the CPR family, and they are identified by the conserved R&R region (Rebers and Riddiford Consensus). Two major subfamilies of the CPR family RR-1 and RR-2, have also been identified from conservation at sequence level and some correlation with the cuticle type. Recently, several novel families, also containing characteristic conserved regions, have been described. The package HMMER v3.0 (http://hmmer.janelia.org/) was used to build characteristic profile Hidden Markov Models based on the characteristic regions for 8 of these families, (CPF, CPAP3, CPAP1, CPCFC, CPLCA, CPLCG, CPLCW, Tweedle). In brief, these families can be described as having: CPF (a conserved region with 44 amino acids); CPAP1 and CPAP-3 (analogous to peritrophins, with 1 and 3 chitin-binding domains, respectively); CPCFC (2 or 3 C-x(5)-C repeats); and four of five low complexity (LC) families, each with characteristic domains. Using these models, as well as the models previously created for the two major subfamilies of the CPR family, RR-1 and RR-2 (Karouzou et al., 2007), we developed CutProtFam-Pred, an on-line tool (http://bioinformatics.biol.uoa.gr/CutProtFam-Pred) that allows one to query sequences from proteomes or translated transcriptomes, for the accurate detection and classification of putative structural cuticular proteins. The tool has been applied successfully to diverse arthropod proteomes including a crustacean (Daphnia pulex) and a chelicerate (Tetranychus urticae), but at this taxonomic distance only CPRs and CPAPs were recovered. [Display omitted] •pHMMs created for 8 of the 12 newly characterized cuticular protein families.•Detection of CPR, CPAP1, CPAP3, CPCFC, CPF, CPLCA, CPLCG, CPLCW, Tweedle proteins.•4 other families did not have enough conservation for sequence-based models.•Development of CutProtFam-Pred, a publicly available on-line web tool.•CutProtFam-Pred will be useful in the functional annotation of arthropod proteomes.