Domain organization and phylogenetic analysis of proteins from the chitin deacetylase gene family of Tribolium castaneum and three other species of insects

Authors: DIXIT, RADHIKA - KANSAS STATE UNIVERSITY; ARAKANE, YASUYUKI - KANSAS STATE UNIVERSITY; SPECHT, CHARLES - UNIVERSITY OF MASSACHUSET; RICHARD, CHAD - KANSAS STATE UNIVERSITY; KRAMER, KARL - 5430-05-30 RETIRED; Beeman, Richard; MUTHUKRISHNAN, SUBBARATNAM - KANSAS STATE UNIVERSITY

Submitted to: Insect Biochemistry and Molecular Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/6/2007
Publication Date: 3/1/2008
Citation: Dixit, R., Arakane, Y., Specht, C.A., Richard, C., Kramer, K.J., Beeman, R.W., Muthukrishnan, S. 2008. Domain organization and phylogenetic analysis of proteins from the chitin deacetylase gene family of Tribolium castaneum and three other species of insects. Insect Biochemistry and Molecular Biology 38: 440-451.

Interpretive Summary: Chitin is the main component of insect exoskeleton, conferring both rigidity and flexibility, and protecting the insect from injury, predation, infection, and desiccation. Chitin is also the major component of a membrane that coats the lining of the midgut, protecting it from abrasion and self-digestion. Until recently, very little has been known about the enzymes that are needed for modifying the the properties of the freshly-synthesized, raw chitin to form the finished product with all its variations according to the requirements in the various body regions for cuticle that is either hard or soft, stiff or flexible, thick or thin. We used bioinformatics to identify nine different chitin deacetylase genes in the red flour beetle. Each of these enzymes appears to have a different function, and to modify the properties of cuticle in different regions of the insect exoskeleton. Each of these newly-discovered genes can become a target in screening assays for new biopesticides that disrupt molting and related physiological processes.

Technical Abstract: A bioinformatics investigation of four insect species with annotated genome sequences identified a family of genes encoding chitin deacetylase (CDA)-like proteins, with 5-9 members depending on the species. CDAs (EC 3.5.1.41) are chitin-modifying enzymes that deacetylate the b-1,4-linked N-acetylglucosamine homopolymer. Partial deacetylation forms a heteropolysaccharide that also contains some glucosamine residues, while complete deacetylation produces the homopolymer chitosan, consisting exclusively of glucosamine. The genomes of the red flour beetle, Tribolium castaneum, the fruit fly, Drosophila melanogaster, the malaria mosquito, Anopheles gambiae, and the honey bee, Apis mellifera contain 9, 6, 5, and 5 genes, respectively, that encode proteins with a chitin deacetylase motif. The presence of alternative exons in two of the genes, TcCDA2 and TcCDA5, increases the protein diversity further. Insect CDA-like proteins were classified into five orthologous groups based on phylogenetic analysis and the presence of additional motifs. Group I enzymes include CDA1 and isoforms of CDA2, each containing in addition to a polysaccharide deacetylase-like catalytic domain, a chitin-binding peritrophin-A domain (ChBD) and a low-density lipoprotein receptor class A domain (LDLa). Group II is composed of CDA3 orthologs from each insect species with the same domain organization as group I CDAs but differing substantially in sequence. Group III includes CDA4s, which have the ChBD domain but do not have the LDLa domain. Group IV comprises CDA5s, which are the largest CDAs because of a very long intervening region separating the ChBD and catalytic domains. Among the four insect species, Tribolium is unique in having four CDA genes in group V, whereas the other insect genomes have either one or none. Most of the CDA-like proteins have a putative signal peptide consistent with their role in modifying extracellular chitin in both cuticle and peritrophic membrane during morphogenesis and molting.