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

Abstract

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.

Analysis of chitin-binding proteins from Manduca sexta provides new insights into evolution of peritrophin A-type chitin-binding domains in insects

“…A search of the insect genome databases using these five M. sexta CPAP1 proteins identified presumptive orthologs in several insect genomes, including T. castaneum, and D. melanogaster. Similar results were independently obtained recently (Ioannidou et al, 2014). Therefore, five new groups including these proteins (named CPAP1-K to CPAP1-O) were created.…”

“…CPAP1s and CPAP3s) are highly conserved across several orders of insects (Ioannidou et al, 2014;Jasrapuria et al, 2010;Willis et al, 2012). Functional studies of multiple CPAPs in T. castaneum by RNAi have shown that CPAPs play essential nonredundant roles in T. castaneum (Jasrapuria et al, 2012).…”

Annotation and expression analysis of cuticular proteins from the tobacco hornworm, Manduca sexta

“…Many CPs can be classified by the conserved sequence motifs they contain (Ioannidou et al ., 2014; Willis et al ., 2012). The largest group is known as CPs with the Rebers and Riddiford motif (CPR) that contain a core 28 amino acid sequence that is now recognized as part of a larger 63 amino acid consensus sequence (pfam00379) (Rebers and Riddiford, 1988; Willis et al ., 2012).…”

Two major cuticular proteins are required for assembly of horizontal laminae and vertical pore canals in rigid cuticle of Tribolium castaneum

“…Many of the insect structural CPs have been classified into 12 different families as defined by unique amino acid sequence motifs characteristic of each of the families (Willis, 2010;Ioannidou et al, 2014). The largest family is the CPR family whose members contain the Rebers & Riddiford (R&R) Consensus (Rebers and Riddiford, 1988).…”