Sequence conservation, phylogenetic relationships, and expression profiles of nondigestive serine proteases and serine protease homologs in Manduca sexta

Abstract

Serine protease (SP) and serine protease homolog (SPH) genes in insects encode a large family of proteins involved in digestion, development, immunity, and other processes. While 68 digestive SPs and their close homologs are reported in a companion paper (Kuwar et al., 2015), we have identified 125 other SPs/SPHs in Manduca sexta and studied their structure, evolution, and expression. Fifty-two of them contain cystine-stabilized structures for molecular recognition, including clip, LDLa, Sushi, Wonton, TSP, CUB, Frizzle, and SR domains. There are nineteen groups of genes evolved from relatively recent gene duplication and sequence divergence. Thirty-five SPs and seven SPHs contain 1, 2 or 5 clip domains. Multiple sequence alignment and molecular modeling of the 54 clip domains have revealed structural diversity of these regulatory modules. Sequence comparison with their homologs in Drosophila melanogaster, Anopheles gambiae and Tribolium castaneum allows us to classify them into five subfamilies: A are SPHs with 1 or 5 group-3 clip domains, B are SPs with 1 or 2 group-2 clip domains, C, D1 and D2 are SPs with a single clip domain in group-1a, 1b and 1c, respectively. We have classified into six categories the 125 expression profiles of SP-related proteins in fat body, brain, midgut, Malpighian tubule, testis, and ovary at different stages, suggesting that they participate in various physiological processes. Through RNA-Seq-based gene annotation and expression profiling, as well as intragenomic sequence comparisons, we have established a framework of information for future biochemical research of nondigestive SPs and SPHs in this model species.

Are feeding preferences and insecticide resistance associated with the size of detoxifying enzyme families in insect herbivores?

“…Other gene families may be more relevant in some cases, for example the UDPglucuronosyltransferases (UGTs) and ABC transporters in relation to plant secondary metabolites [45,46] and various digestive hydrolases in relation to their primary metabolites [16,47]. We also acknowledge that simple counts of genes in the various families will mean that members of the families that have nothing to do with detoxification are given equal weighting to specific genes and clades of genes that are likely to be important, such as the CYP6 and CYP4 P450s, the Clade 1 CCEs, and the Delta and Epsilon GSTs [5,13,48].…”

Integrated modeling of protein-coding genes in the Manduca sexta genome using RNA-Seq data from the biochemical model insect

“…2A); 2) over 17,000 undetermined nucleotide (NNN) regions (average: 1,118 bp; range: 1-124,308 bp) (Fig. 2B) may contain genes or gene elements, even though they only account for 4.71% of the entire assembly; 3) conserved and novel repetitive elements, accounting for 25% of Msex 1.0 (X et al, 2014), and other highly similar sequences may cause errors in this assembly (Cao et al, 2014). Consequently, gene modeling can be a challenge in some cases.…”

Phylogenetic analysis and expression profiling of the pattern recognition receptors: Insights into molecular recognition of invading pathogens in Manduca sexta

“…Our previous expression analyses of non-digestive serine protease-related protein, C-type lectin-domain protein, and immune effector genes revealed an interesting trend that transcription of most immunity-related genes are up-regulated in fat body and midgut from pre-wandering to early pupal stage (Cao et al, 2015b; Rao et al, 2015; He et al, 2015). Since immune function for most of the genes reported herein, especially LRRPs, lacks experimental support, we tried to use their expression patterns to predict this feature.…”