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. 2012:12:150.
doi: 10.1673/031.012.15001.

In silico identification of novel chitinase-like proteins in the silkworm, Bombyx mori, genome

Ye Pan  1 , Peng Lü, Yong Wang, Lijing Yin, Hexiang Ma, Guohong Ma, Keping Chen, Yuanqing He
Affiliations

In silico identification of novel chitinase-like proteins in the silkworm, Bombyx mori, genome

Ye Pan et al. J Insect Sci. 2012.

Abstract

In insects, chitinases participate in the periodic shedding of old exoskeletons and the turnover of peritrophic membranes. Chitinase family members have been identified in dozens of species, including Tribolium castaneum, Drosophila melanogaster, and Anopheles gambiae. In this study, nine chitinases and three hypothetical chitinases have been identified in Bombyx mori L. (Lepidoptera: Bombycidae) through genome-wide searching. Phylogenetic analyses revealed that seven of them belong to the seven chitinase groups, respectively. BmCht25 and BmCht26 could not be grouped into the known chitinase groups, and might belong to two new groups of the chitinase family. BmCht10, BmCht25, and BmIDGF have glutamate amino acid substitutions in the active catalytic domain. Only BmCht5 and BmCht10 contain CBD domain and PEST sequences (rich in proline, glutamic acid, serine, and threonine). BmCht5 and BmCht26 are located on chromosome 7, and others (BmCht6, BmCht7, BmCht10, BmCht11, BmCht20, BmIDGF) are located on separate chromosomes of Bombyx mori, respectively. The present study provides important background information for future studies using Bombyx mori as a model organism for insect development and virus and host interaction.

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Figures

Figure 1.
Figure 1.
Phylogenetic analysis of Bombyx mori and other insect chitinase proteins. A phylogenetic tree was constructed by the neighbor-joining method based on catalytic domain sequences. Sequences used for the analysis are: NP_477298.2 (DmCht2), NP_524962.2(DmCht4), NP_572598.1 (DmCht6), NP_647768.2 (DmCht7), NP_611542.1 (DmCht8), NP_611543.3 (DmCht9), EAA46011.1 (DmCht10), NP_572361.1 (DmCht11), NP_726022.1 (DmCht12), NP_477258.1 (DmIDGF1), NP_477257.2(DmIDGF2), NP_723967.1 (DmlDGF3), NP_727374.1 (DmlDGF4), NP_61121.3 (DmlDGF5), NP_477081.1 (DmlDGF6), NP_00103451 6.3 (TcCht2), NP_001073567.1 (TcCht4), NP_0041034524.1 (TcCht5), XP_967813.1 (TcChto), NP_001036035.1 (TcCht7), NP_001038094.1 (TcCht8), NP_001038096.1 (TcCht9), NP_001036067.1 (TcCht10), XP_974461.1 (TcCht11), XP_972802.2 (TcCht12), NP_001036034.1 (TcCht13), XP_973005.1 (TcCht14), XP_973077.1 (TcCht15), NP_001034515.1 (TcCht16), XP_972719.1 (TcCht17), XP_973161.2 (TcCht18), XP_973119.2 (TcCht19), XP_970191.2(TcCht20), NP_001034517.1 (TcCht21), NP_001038095.1 (TcCht22), NP_001038092.1 (TclDGF2), NP_001038091.1 (TclDGF4), XP_315650.4 (AgCht2), XP_315351.4 (AgCht4), HQ456129 (AgCht5-1), HQ456130 (AgCht5-2), HQ456131 (AgCht5-3), HQ456132 (AgCht5-4), HQ456133 (AgCht5-5), XP_001 687765.2 (AgCht6), XP_308858.4 (AgCht7), XP_316448.2 (AgCht8), XP_307732.4 (AgCht9), XP_001238192.2 (AgCht10), XP_310662.4 (AgCht11), XP_316142.4 9 (AgCht12), XP_3 14312.4 (AgCht 13), XP_3 19801.4 (AgCht16), XP_001 688641.1 (AgCht23), XP_31 6256.4 (AgCht24), XP_001237925.1 (Ag IDGF2), XP_317398.3 (AglDGF4). High quality figures are available online.
Figure 2.
Figure 2.
In-group phylogenetic analyses of BmIDGF (A), BmCht10 (B), BmCht20 (C), BmCht25 (D), BmCht26 (E). Neighborjoining trees were constructed with selected group members of the catalytic domains. Sequences used for the analysis are: (A– C) Protein accession numbers are shown in Figure 1. (D) Culex quinquefasciatus chitinase XP_00186961 7.1, Danaus plexippus chitinase EHJ68452.1, Daphnia pulex chitinase EFX69014.1, Pediculus humanus corporis chitinase XP_002428336.1. (E) BmNPV chitinase NP_047523.1, Manduca sexta chitinase-h ABB88891.1, Danaus plexippus viral-like chitinase EHJ71822.1, Spodoptera littoralis viral-like chitinase ABA06505.1, Spodoptera exigua virus-like chitinase ADI24347.1. High quality figures are available online.
Figure 3.
Figure 3.
Schematic diagram of exon and intron organization of the chitinase genes from Bombyx mori. High quality figures are available online.
Figure 4.
Figure 4.
Chromosomal locations of Bombyx mori chitinase genes. High quality figures are available online.
Figure 5.
Figure 5.
Domain architecture of identified Bombyx mori chitinase proteins. All the sequences contain at least one catalytic domain. The programs Pfam and SMART were used to analyze the identified sequences. High quality figures are available online.
Figure 6.
Figure 6.
Multiple sequence alignment of the catalytic domains of Bombyx mori chitinase proteins. Catalytic domain sequences were retrieved from the identified B. mori chitinase proteins and the ClustalW program was used. The four conserved regions are boxed. The arrowhead indicates the important glutamate amino acid. High quality figures are available online.
Figure 7.
Figure 7.
Multiple sequence alignment of CBD domains of Bombyx mori chitinase proteins. CBD domain sequences were retrieved from the identified B. mori chitinases and analyzed using the ClustalW program. The six cysteine residues are conserved among the chitin-binding domains of B. mori chitinases. High quality figures are available online.
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