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Open Access Highly Accessed Research article

Identification and characterization of insect-specific proteins by genome data analysis

Guojie Zhang123, Hongsheng Wang1, Junjie Shi2, Xiaoling Wang2, Hongkun Zheng2, Gane Ka-Shu Wong2, Terry Clark4, Wen Wang3, Jun Wang25 and Le Kang1*

Author Affiliations

1 State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology Chinese Academy of Sciences, Haidian Beijing 100080, China

2 Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing 101300, China

3 CAS-Max Plank Junior Research Group, Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Science (CAS), Kunming, Yunnan 650223, China

4 Department of Electrical Engineering and Computer Science, The University of Kansas, 2001 Eaton Hall, Lawrence, KS 66044, USA

5 Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230, Odense M, Denmark

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BMC Genomics 2007, 8:93  doi:10.1186/1471-2164-8-93

Published: 4 April 2007

Abstract

Background

Insects constitute the vast majority of known species with their importance including biodiversity, agricultural, and human health concerns. It is likely that the successful adaptation of the Insecta clade depends on specific components in its proteome that give rise to specialized features. However, proteome determination is an intensive undertaking. Here we present results from a computational method that uses genome analysis to characterize insect and eukaryote proteomes as an approximation complementary to experimental approaches.

Results

Homologs in common to Drosophila melanogaster, Anopheles gambiae, Bombyx mori, Tribolium castaneum, and Apis mellifera were compared to the complete genomes of three non-insect eukaryotes (opisthokonts) Homo sapiens, Caenorhabditis elegans and Saccharomyces cerevisiae. This operation yielded 154 groups of orthologous proteins in Drosophila to be insect-specific homologs; 466 groups were determined to be common to eukaryotes (represented by three opisthokonts). ESTs from the hemimetabolous insect Locust migratoria were also considered in order to approximate their corresponding genes in the insect-specific homologs. Stress and stimulus response proteins were found to constitute a higher fraction in the insect-specific homologs than in the homologs common to eukaryotes.

Conclusion

The significant representation of stress response and stimulus response proteins in proteins determined to be insect-specific, along with specific cuticle and pheromone/odorant binding proteins, suggest that communication and adaptation to environments may distinguish insect evolution relative to other eukaryotes. The tendency for low Ka/Ks ratios in the insect-specific protein set suggests purifying selection pressure. The generally larger number of paralogs in the insect-specific proteins may indicate adaptation to environment changes. Instances in our insect-specific protein set have been arrived at through experiments reported in the literature, supporting the accuracy of our approach.