果蝇基因组中新型几丁质酶样蛋白的计算鉴定

Computational identification of novel chitinase-like proteins in the Drosophila melanogaster genome.

作者信息

Zhu Qingsong, Deng Youping, Vanka Phaneendra, Brown Susan J, Muthukrishnan Subbaratnam, Kramer Karl J

机构信息

Department of Biochemistry, Kansas State University, Manhattan, KS 66506, USA.

出版信息

Bioinformatics. 2004 Jan 22;20(2):161-9. doi: 10.1093/bioinformatics/bth020.

DOI:10.1093/bioinformatics/bth020

PMID:14734306

Abstract

MOTIVATION

Multiple chitinases as well as lectins closely related to them have been characterized previously from many insect species and the corresponding genes/cDNAs have been cloned. However, the identification of the entire assortment of genes for chitinase family proteins and their differences in biochemical properties have not been carried out in any individual insect species. The completion of the entire DNA sequence of Drosophila melanogaster (fruit fly) genome and identification of open reading frames presents an opportunity to study the structures and functions of chitinase-like proteins, and also to identify new members of this family in Drosophila. We are, therefore, interested in studying the functional genomics of chitinase-like gene families in insects.

METHODS

We searched the Drosophila protein sequences database using fully characterized insect chitinase sequences and BLASTP software, identified all the putative chitinase-like proteins encoded in Drosophila genome, and predicted their structures using domain analysis tools. A phylogenetic analysis of the chitinase-like proteins from Drosophila and several other insect species was carried out. The structures of these chitinases were modeled using homology modeling software.

RESULTS

Our analysis revealed the presence of 18 chitinase-like proteins in the Drosophila protein database. Among these are seven novel chitinase-like proteins that contain four signature amino acid sequences of chitinases belonging to family 18 glycosylhydrolases, including both acidic and hydrophobic amino acid residues critical for enzyme activity. All the proteins contain at least one catalytic domain with one having four catalytic domains. Phylogenetic analysis of chitinase-like proteins from Drosophila and other insects revealed an evolutionary relationship among all these proteins, which indicated gene duplication and domain shuffling to generate the observed diversity in the encoded proteins. Homology modeling showed that all the Drosophila chitinase-like proteins contain one or more catalytic domains with a (alpha/beta)8 barrel-like structure. Our results suggest that insects utilize multiple family 18 chitinolytic enzymes and also non-enzymatic chitinase-like proteins for degrading/remodeling/binding to chitin in different insect anatomical extracellular structures, such as the cuticle, peritrophic membrane, trachea and mouth parts during insect development, and possibly for other roles including chitin synthesis.

AVAILABILITY

Perl program and supplementary material are available at http://www.ksu.edu/bioinformatics/supplementary.htm

摘要

动机

此前已从许多昆虫物种中鉴定出多种几丁质酶以及与其密切相关的凝集素，并且相应的基因/ cDNA已被克隆。然而，尚未在任何单个昆虫物种中对几丁质酶家族蛋白的完整基因种类及其生化特性差异进行鉴定。黑腹果蝇（果蝇）基因组完整DNA序列的完成以及开放阅读框的鉴定为研究几丁质酶样蛋白的结构和功能提供了机会，同时也有助于在果蝇中鉴定该家族的新成员。因此，我们对研究昆虫中几丁质酶样基因家族的功能基因组学感兴趣。

方法

我们使用已充分表征的昆虫几丁质酶序列和BLASTP软件搜索果蝇蛋白质序列数据库，鉴定果蝇基因组中编码的所有假定的几丁质酶样蛋白，并使用结构域分析工具预测其结构。对果蝇和其他几种昆虫物种的几丁质酶样蛋白进行了系统发育分析。使用同源建模软件对这些几丁质酶的结构进行了建模。

结果

我们的分析表明，果蝇蛋白质数据库中存在18种几丁质酶样蛋白。其中有7种新的几丁质酶样蛋白，它们包含属于18家族糖基水解酶的几丁质酶的四个特征氨基酸序列，包括对酶活性至关重要的酸性和疏水性氨基酸残基。所有蛋白质至少包含一个催化结构域，其中一个具有四个催化结构域。对果蝇和其他昆虫的几丁质酶样蛋白的系统发育分析揭示了所有这些蛋白之间的进化关系，这表明基因复制和结构域改组产生了编码蛋白中观察到的多样性。同源建模表明，所有果蝇几丁质酶样蛋白都包含一个或多个具有（α/β）8桶状结构的催化结构域。我们的结果表明，昆虫利用多种18家族几丁质分解酶以及非酶促几丁质酶样蛋白在昆虫发育过程中降解/重塑/结合不同昆虫解剖学细胞外结构中的几丁质，如表皮、围食膜、气管和口器，并且可能用于包括几丁质合成在内的其他作用。