Domain organization and phylogenetic analysis of the chitinase-like family of proteins in three species of insects

Department of Biochemistry, Kansas State University, Manhattan, KS 66506, USA.
Insect Biochemistry and Molecular Biology (Impact Factor: 3.45). 05/2008; 38(4):452-66. DOI: 10.1016/j.ibmb.2007.06.010
Source: PubMed


A bioinformatics-based investigation of three insect species with completed genome sequences has revealed that insect chitinase-like proteins (glycosylhydrolase family 18) are encoded by a rather large and diverse group of genes. We identified 16, 16 and 13 putative chitinase-like genes in the genomic databases of the red flour beetle, Tribolium castaneum, the fruit fly, Drosophila melanogaster, and the malaria mosquito, Anopheles gambiae, respectively. Chitinase-like proteins encoded by this gene family were classified into five groups based on phylogenetic analyses. Group I chitinases are secreted proteins that are the most abundant such enzymes in molting fluid and/or integument, and represent the prototype enzyme of the family, with a single copy each of the catalytic domain and chitin-binding domain (ChBD) connected by an S/T-rich linker polypeptide. Group II chitinases are unusually larger-sized secreted proteins that contain multiple catalytic domains and ChBDs. Group III chitinases contain two catalytic domains and are predicted to be membrane-anchored proteins. Group IV chitinases are the most divergent. They usually lack a ChBD and/or an S/T-rich linker domain, and are known or predicted to be secreted proteins found in gut or fat body. Group V proteins include the putative chitinase-like imaginal disc growth factors (IDGFs). In each of the three insect genomes, multiple genes encode group IV and group V chitinase-like proteins. In contrast, groups I-III are each represented by only a singe gene in each species.

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Available from: Qingsong Zhu, Jul 30, 2014
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    • "Catalytic GH18 domains (white boxes), chitin-binding CB14 domains (dark and red boxes), transmembrane spans (hatched boxes), polycystic kidney disease 1 PKD1 domain (white circle), and linker regions (lines) are indicated. The tree on the left is a representation of the grouping obtained by phylogenetic analysis as shown in Fig. 4. DmCHT1 and DmCHT3 (de la Vega et al., 1998; Zhu et al., 2004), do not belong to these groups as they were later identified to be the catalytic domains of the larger DmCHT10 gene of Drosophila, which belongs to group II (Zhu et al., 2008a). The first group (group IX) includes several proteins previously identified as GH18 " Stabilin-1 interacting chitinase-like proteins " (GH18_SI-CLP; [cd08276]). "
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    ABSTRACT: Chitin is one of the most abundant biomaterials in nature. The biosynthesis and degradation of chitin in insects are complex and dynamically regulated to cope with insect growth and development. Chitin metabolism in insects is known to involve numerous enzymes, including chitin synthases (synthesis of chitin), chitin deacetylases (modification of chitin by deacetylation) and chitinases (degradation of chitin by hydrolysis). In this study, we conducted a genome-wide search and analysis of genes encoding these chitin metabolism enzymes in Manduca sexta. Our analysis confirmed that only two chitin synthases are present in M. sexta as in most other arthropods. Eleven chitin deacetylases (encoded by nine genes) were identified, with at least one representative in each of the five phylogenetic groups that have been described for chitin deacetylases to date. Eleven genes encoding for family 18 chitinases (GH18) were found in the M. sexta genome. Based on the presence of conserved sequence motifs in the catalytic sequences and phylogenetic relationships, two of the M. sexta chitinases did not cluster with any of the current eight phylogenetic groups of chitinases: two new groups were created (groups IX and X) and their characteristics are described. The result of the analysis of the Lepidoptera-specific chitinase-h (group h) is consistent with its proposed bacterial origin. By analyzing chitinases from fourteen species that belong to seven different phylogenetic groups, we reveal that the chitinase genes appear to have evolved sequentially in the arthropod lineage to achieve the current high level of diversity observed in M. sexta. Based on the sequence conservation of the catalytic domains and on their developmental stage- and tissue-specific expression, we propose putative functions for each group in each category of enzymes.
    Insect Biochemistry and Molecular Biology 06/2015; 62:114-126. DOI:10.1016/j.ibmb.2015.01.006 · 3.45 Impact Factor
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    • "Similar observations of non-redundancy of CBPs functions in exoskeleton organization and tracheal tubulogenesis have also been described in D. melanogaster (Luschnig et al., 2006; Petkau et al., 2012). In addition to these three families of CBPs, several chitin metabolism enzymes associated with the PM and/or cuticle also contain ChtBD2 domains, such as some chitinases (CHTs) and chitin deacetylases (CDAs) (Dixit et al., 2008; Merzendorfer and Zimoch, 2003; Zhu et al., 2008). Although chitin-binding proteins (CBPs) have received increasing attention in the last two decades, molecular details of their interaction with chitin in the structural formation and functions of cuticle and PM remain to be better understood (Iconomidou et al., 2005; Jasrapuria et al., 2010). "
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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.
    Insect Biochemistry and Molecular Biology 06/2015; 62:127-141. DOI:10.1016/j.ibmb.2014.12.002 · 3.45 Impact Factor
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    • "The conserved sequence in CR_II, DWEYP, is an essential characteristic of a putative chitinase. The residue E is a putative protein donor essential for catalytic activity (Zhu et al., 2008a). In NlCht3, all four regions were poorly conserved ; the residue E was replaced by R, suggesting that NlCht3 does not have chitinase catalytic activity (Fig. 5). "
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    ABSTRACT: Chitinases are important enzymes required for chitin degradation and reconstruction in insects. Based on a bioinformatics investigation, we identified 12 genes encoding putative chitinase-like proteins, including 10 chitinases (Cht), one imaginal disc growth factor (IDGF) and one endo-β-N-acetylglucosaminidase (ENGase) in the genome of the brown planthopper, Nilaparvata lugens (Hemiptera: Delphacidae). These 12 genes were clustered into nine different groups, with 11 in glycoside hydrolase family 18 groups (groups I-VIII) and one in the ENGase group. Developmental and tissue-specific expression pattern analysis revealed that the transcript levels of eight genes peaked periodically during moulting and were mainly expressed in the integument, except NlCht2, NlCht4, NlIDGF and NlENGase. NlCht2, NlIDGF and NlENGase were expressed at all stages with slight periodical changes and mainly expressed in the female reproductive organs in adults, whereas NlCht4 was highly expressed only at the adult stage in the male reproductive organs. Lethal phenotypes were observed in insects challenged by double-stranded RNAs for NlCht1, NlCht5, NlCht7, NlCht9 and NlCht10 during moulting, suggesting their significant roles in old cuticle degradation. NlCht1 was the most sensitive gene, inducing 50% mortality even at 0.01 ng per insect. Our results illustrate the structural and functional differences of chitinase-like family genes and provide potential targets for RNA interference-based rice planthopper management.
    Insect Molecular Biology 10/2014; 24(1). DOI:10.1111/imb.12133 · 2.59 Impact Factor
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