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Genes encoding proteins with peritrophin A-type chitin-binding domains in Tribolium castaneum are grouped into three distinct families based on phylogeny, expression and function

Department of Biochemistry, Kansas State University, 141 Chalmers Hall, Manhattan, KS 66506-3702, USA.
Insect biochemistry and molecular biology (Impact Factor: 3.42). 02/2010; 40(3):214-27. DOI: 10.1016/j.ibmb.2010.01.011
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ABSTRACT This study is focused on the characterization and expression of genes in the red flour beetle, Tribolium castaneum, encoding proteins that possess one or more six-cysteine-containing chitin-binding domains related to the peritrophin A domain (ChtBD2). An exhaustive bioinformatics search of the genome of T. castaneum queried with ChtBD2 sequences yielded 13 previously characterized chitin metabolic enzymes and 29 additional proteins with signal peptides as well as one to 14 ChtBD2s. Using phylogenetic analyses, these additional 29 proteins were classified into three large families. The first family includes 11 proteins closely related to the peritrophins, each containing one to 14 ChtBD2s. These are midgut-specific and are expressed only during feeding stages. We propose the name "Peritrophic Matrix Proteins" (PMP) for this family. The second family contains eight proteins encoded by seven genes (one gene codes for 2 splice variants), which are closely related to gasp/obstructor-like proteins that contain 3 ChtBD2s each. The third family has ten proteins that are of diverse sizes and sequences with only one ChtBD2 each. The genes of the second and third families are expressed in non-midgut tissues throughout all stages of development. We propose the names "Cuticular Proteins Analogous to Peritophins 3" (CPAP3) for the second family that has three ChtBD2s and "Cuticular Proteins Analogous to Peritophins 1 (CPAP1) for the third family that has 1 ChtBD2. Even though proteins of both CPAP1 and CPAP3 families have the "peritrophin A" domain, they are expressed only in cuticle-forming tissues. We determined the exon-intron organization of the genes, encoding these 29 proteins as well as the domain organization of the encoded proteins with ChtBD2s. All 29 proteins have predicted cleavable signal peptides and ChtBD2s, suggesting that they interact with chitin in extracellular locations. Comparison of ChtBD2s-containing proteins in different insect species belonging to different orders suggests that ChtBD2s are ancient protein domains whose affinity for chitin in extracellular matrices has been exploited many times for a range of biological functions. The differences in the expression profiles of PMPs and CPAPs indicate that even though they share the peritrophin A motif for chitin binding, these three families of proteins have quite distinct biological functions.

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Available from: Subbaratnam Muthukrishnan, Mar 20, 2015
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    • "The chitin-binding proteins identified are classified into four different classes based on their sequence similarity, domain organization and tissue/stage specificity of gene expression. They include chitin metabolism enzymes (chitinases and chitin deacetylases ), cuticular proteins analogous to peritrophins (CPAPs), which are proteins expressed in cuticle-forming tissues with either one (CPAP1s) or three CBDs (CPAP3s), and peritrophic matrix proteins (PMPs), which are expressed in the midgut and can contain from one to several CBDs (Jasrapuria et al., 2010; Tellam et al., 1999). 2.2. "
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    ABSTRACT: In insects, chitin is a major structural component of the cuticle and the peritrophic membrane (PM). In nature, chitin is always associated with proteins among which chitin-binding proteins (CBPs) are the most important for forming, maintaining and regulating the functions of these extracellular structures. In this study, a genome-wide search for genes encoding proteins with ChtBD2-type (peritrophin A-type) chitin-binding domains (CBDs) was conducted. A total of 53 genes encoding 56 CBPs were identified, including 15 CPAP1s (cuticular proteins analogous to peritrophins with 1 CBD), 11 CPAP3s (CPAPs with 3 CBDs) and 17 PMPs (PM proteins) with a variable number of CBDs, which are structural components of cuticle or of the PM. CBDs were also identified in enzymes of chitin metabolism including 6 chitinases and 7 chitin deacetylases encoded by 6 and 5 genes, respectively. RNA-seq analysis confirmed that PMP and CPAP genes have differential spatial expression patterns. The expression of PMP genes is midgut-specific, while CPAP genes are widely expressed in different cuticle forming tissues. Phylogenetic analysis of CBDs of proteins in insects belonging to different orders revealed that CPAP1s from different species constitute a separate family with 16 different groups, including 6 new groups identified in this study. The CPAP3s are clustered into a separate family of 7 groups present in all insect orders. Altogether, they reveal that duplication events of CBDs in CPAP1s and CPAP3s occurred prior to the evolutionary radiation of insect species. In contrast to the CPAPs, all CBDs from individual PMPs are generally clustered and distinct from other PMPs in the same species in phylogenetic analyses, indicating that the duplication of CBDs in each of these PMPs occurred after divergence of insect species. Phylogenetic analysis of these three CBP families showed that the CBDs in CPAP1s form a clearly separate family, while those found in PMPs and CPAP3s were clustered together in the phylogenetic tree. For chitinases and chitin deacetylases, most of phylogenetic analysis performed with the CBD sequences resulted in similar clustering to the one obtained by using catalytic domain sequences alone, suggesting that CBDs were incorporated into these enzymes and evolved in tandem with the catalytic domains before the diversification of different insect orders. Based on these results, the evolution of CBDs in insect CBPs is discussed to provide a new insight into the CBD sequence structure and diversity, and their evolution and expression in insects.
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    • "Pascoa et al. (2002) found an amount of free heme bound to the Aedes aegypti PM equivalent to hydrolysis of 2ul of a typical 3ul bloodmeal. To determine whether our peptides were in fact peritrophins associated with a midgut PM, as opposed to non-specific cuticular proteins analogous to peritrophins (CPAPs, see Jasrapuria et al. (2010)) which also exhibit Peritrophin-A domain homologs, we aligned our nine candidate peptide domains to a selection of those from the classification of Jasrapuria et al. (2010) and produced a maximum-likelihood tree which grouped all 21 of our sequences in a Peritrophic Matrix Protein (PMP) clade at a bootstrap support of 99% (Fig. S1). This indicates our candidates are in fact likely associated with the midgut PM and involved in digestion. "
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    PeerJ 02/2015; 3:e807(5). DOI:10.7717/peerj.807 · 2.10 Impact Factor
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    • " leads to an abnormal shape of eggs that fail to hatch indicates an essential additional role for TcPMP5 - B in egg development . Every insect species whose genome has been extensively sequenced has an assortment of PMP genes that encode proteins with a wide range in the number of CBM14 domains ( Dinglasan et al . , 2009 ; Hegedus et al . , 2009 ; Jasrapuria et al . , 2010 ; Venancio et al . , 2009 ) . Some of these PMP genes have mucin repeats ( Bolognesi et al . , 2008 ; Hegedus et al . , 2009 ; Morris et al . , 2009 ; Wang and Granados , 2000 ) . It is tempting to speculate , that the strategy of a gradient of decreasing permeability of the PM from the anterior to the posterior regions of the midgut po"
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