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

Abstract

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.

Fig.1

Comparisons of RR-2 Consensus regions from 4 different groups of arthropods. WebLogos were constructed at <http://weblogo.berkeley.edu/logo.cgi> (Schneider and Stephens, 1990; Crooks et al., 2004). Details on sequences used are in Supplementary Information File 8. A. Chelicerata based on 33 sequences. B. Crustacea based on 16 sequences. C. Lepidoptera based on 87 B. mori sequences. D. Diptera based on 101 An. gambiae sequences.

Fig. 2

WebLogos (see Fig. 1) of RR-1 Consensus regions compared to RR-2. Details on sequences used are in Supplementary Information File 8. A. Crustacea based on 48 sequences. B. Representative lepidopteran, Bombyx mori, 52 sequences. C. Representative dipteran, Anopheles gambiae, 51 sequences. D. RR-2 sequences from combination of data used for panels C and D of Fig. 1.

Fig. 3

WebLogos (see Fig. 1) for three cuticular protein families. Details on sequences used are in Supplementary File 8. A. TWDL Family. Twenty-four sequences from 8 species in 6 orders of insects were used to create this figure. The continuous sequence was split to facilitate recognition of the four conserved regions. B. CPLCG Family. Note the highly conserved GHPG at residues 5, 8,11,14. Eighty-six sequences from dipterans were used. This is a shortened version of the WebLogo that appears in Cornman and Willis (2009). See Supplementary Information File 2 for WebLogo of CPLCGs from non-dipterans. C. CPLCW Family. The 27 CPLCW sequences of this mosquito-restricted family were used. Unlike other WebLogos, the alignment for this one required gaps of 5, 6, or 8 amino acids between position 18 and 27 to accommodate the longer Ae. aegypti sequences. This is a shortened version of the WebLogo that appears in Cornman and Willis (2009).

Fig. 4

WebLogos (see Fig. 1). See Supplementary Information File 8 for details on sequences used. A. CPLCA Family. The WebLogo is based on three sequences from each of four species, An. gambiae, Ae. agegypi, C. pipiens and D. melanogaster that had the closest match to AgamCPLCA1. This region corresponds to the retinin domain. This is a shortened version of the WebLogo that appears in Cornman and Willis (2009). B. The 18 amino acid repeat from 40 sequences from 26 proteins from 5 insect orders and two crustaceans. C. BcNCP1, 29 repeat regions from orthologs in 11 species in 8 insect orders and Crustacea. Only one species of Drosophila was used.

Fig. 5

Comparison of sequences discussed in relation to resilin. References are in the text. A. Alignment of peptides derived from various proteins as indicated on the figure. B. Comparison of glycine content in various resilin and resilin-like proteins. The first four have the R&R Consensus, the last two lack that region. Additional identifiers for these proteins are: Dmelresilin (CG15920) and AgamCPR152 (AGAP012487-PA). Manual annotation modified the sequences for both AmelCPR15 and NvitCPR25. The modified sequences are given in Supplementary Material 8.