CutProtFam-Pred: detection and classification of putative structural cuticular proteins from sequence alone, based on profile hidden Markov models.

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.

Ioannidou ZS ，Theodoropoulou MC ，Papandreou NC ，Willis JH ，Hamodrakas SJ ... -  《-》

Preliminary characterization of putative structural cuticular proteins in the malaria vector Anopheles sinensis.

The insect cuticle protects against environmental stresses such as insecticides, physical injury, dehydration and pathogenic microorganisms. Structural cuticular proteins (CPs) are the primary components of the cuticle, and are of interest for physiology-based pest management methods. Anopheles sinensis CPs are poorly characterised at present, and therefore we performed whole-genome sequence analysis and re-analysed available transcriptome data to identify potential insecticide resistance-associated CPs. Genome analysis revealed 238 putative CPs belonging to 11 different families; 136 proteins possessing a Rebers and Riddiford motif (CPR), 12 CPs analogous to peritrophins with a single chitin-binding domain (CPAP1), eight CPs analogous to peritrophins with three chitin-binding domains (CPAP3), four proteins with a 44 amino acid motif (CPF), five CPF-like (CPFL) proteins, nine Tweedle proteins, three proteins of low complexity with alanine residues (CPLCA), 26 proteins of low complexity with conserved glycine residues (CPLCG), seven proteins of low complexity with invariant W residues (CPLCW), 27 proteins of low complexity with proline residues (CPLCP), and one protein with two or three copies of a C-X -C motif (CPCFC). Two CPs belonging to the CPR and CPAP3 families were over-expressed in a deltamethrin-resistant strain. These results establish an information framework for An. sinensis CPs that provides a basis for further molecular research. © 2017 Society of Chemical Industry.

Zhou D ，Duan B ，Sun Y ，Ma L ，Zhu C ，Shen B ... -  《-》

Structural cuticular proteins from arthropods: annotation, nomenclature, and sequence characteristics in the genomics era.

The availability of whole genome sequences of several arthropods has provided new insights into structural cuticular proteins (CPs), in particular the distribution of different families, the recognition that these proteins may comprise almost 2% of the protein coding genes of some species, and the identification of features that should aid in the annotation of new genomes and EST libraries as they become available. Twelve CP families are described: CPR (named after the Rebers and Riddiford Consensus); CPF (named because it has a highly conserved region consisting of about forty-four amino acids); CPFL (like the CPFs in a conserved C-terminal region); the TWDL family, named after a picturesque phenotype of one mutant member; four families in addition to TWDL with a preponderance of low complexity sequence that are not member of the families listed above. These were named after particular diagnostic features as CPLCA, CPLCG, CPLCW, CPLCP. There are also CPG, a lepidopteran family with an abundance of glycines, the apidermin family, named after three proteins in Apis mellifera, and CPAP1 and CPAP3, named because they have features analogous to peritrophins, namely one or three chitin-binding domains. Also described are common motifs and features. Four unusual CPs are discussed in detail. Data that facilitated the analysis of sequence variation of single CP genes in natural populations are analyzed.

Willis JH 《-》

Drosophila cuticular proteins with the R&R Consensus: annotation and classification with a new tool for discriminating RR-1 and RR-2 sequences.

Karouzou MV ，Spyropoulos Y ，Iconomidou VA ，Cornman RS ，Hamodrakas SJ ，Willis JH ... -  《INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY》

Identification of Cuticular Protein Genes in the Colorado Potato Beetle Leptinotarsa decemlineata (Coleoptera: Chrysomelidae).

Structural cuticular proteins (CPs) are the primary components of insect cuticle, linings of salivary gland, foregut, hindgut and tracheae, and midgut peritrophic membrane. Variation of CPs in insect cuticle can cause penetration resistance to insecticides. Moreover, depletion of specific CP by RNA interference may be a suitable way for the development of potential pest control traits. Leptinotarsa decemlineata (Say) CPs are poorly characterized at present, and therefore, we mined the genome and transcriptome data to better annotate and classify L. decemlineata CPs in this study, by comparison with the annotated CPs of Tribolium castaneum Browse (Coleoptera: Tenebrionidae). We identified 175 CP genes. Except one miscellaneous CP with an 18-amino acid motif, these CPs were classified into 7 families based on motifs and phylogenetic analyses (CPs with a Rebers and Riddiford motif, CPR; CPs analogous to peritrophins, CPAP3 and CPAP1; CPs with a tweedle motif, TWDL; CPs with a 44-amino acid motif, CPF; CPs that are CPF-like, CPFL; and CPs with two to three copies of C-X5-C motif, CPCFC). Leptinotarsa decemlineata CPRs could be categorized into three subfamilies: RR-1 (50), RR-2 (85), and RR-3 (2). The RR-1 proteins had an additional motif with a conserved YTADENGF sequence. The RR-2 members possessed a conserved RDGDVVKG region and three copes of G-x(3)-VV. Few genes were found in TWDL (9), CPAP1 (9), CPAP3 (8), CPF (5), CPFL (4), and CPCFC (2) families. The findings provide valuable information to explore molecular modes of penetration resistance to insecticides and to develop dsRNA-based control method in L. decemlineata.

Wang YW ，Li YZ ，Li GQ ，Wan PJ ，Li C ... -  《-》