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MBE Advance Access published online on July 28, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msg203
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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Accepted June 18, 2003
© 2003 Society for Molecular Biology and Evolution

Original Articles

Comparative Analysis of Amino Acid Usage and Protein Length Distribution between Alternatively and Non-Alternatively Spliced Genes across Six Eukaryotic Genomes

Yonglong Zhuang 1, Fei Ma 1*, Jesse Li-Ling 2, Xiaofeng Xu 3, and Yanda Li 1

1 Institute of Bioinformatics, Tsinghua University, Beijing, 100084 China
2 Department of Medical Genetics, China Medical University, Shenyang, 110001 China
3 Life Science College, Nanjing Normal University, Nanjing, 210097 China

* To whom correspondence should be addressed. E-mail: bphma{at}mail.tsinghua.edu.cn.


  Abstract

Alternative splicing has been discovered in nearly all metazoan organisms as a mechanism to increase the diversity of gene products. However, the origin and evolution of alternatively spliced genes are yet poorly understood. To understand the mechanisms for the evolution of alternatively spliced genes, it may be important to study the differences between alternatively and non-alternatively spliced genes. The aim of this research was to compare amino acid usage and protein length distribution between alternatively and non-alternatively spliced genes across six nearly complete eukaryotic genomes including those of human (Homo sapiens), mouse (Mus musculus), rat (Rattus norvegicus), fruit fly (Drosophila melanogaster), C. elegans, and bovine (Bos taurus). Our results have suggested that (1) Across the six species, alternatively and non-alternatively spliced genes have very similar tendency for amino acids usage for not only the overall scale but also those highly expressed genes, with all of the highly expressed genes having preferred amino acids including A, E, G, K, L, P, S, V, R, T and D. (2) For not only the overall genes but also those highly expressed ones, the average length of the protein products of alternatively spliced genes is significantly greater than that of non-alternatively spliced ones. On the other hand, distributions of protein lengths for the two groups of genes are very similar among all six species. Based on above results, we propose that alternatively spliced genes may have originated from non-alternatively spliced ones through events such as DNA mutations or gene fusion.

Key Words: amino acid usage, alternatively spliced genes, protein length distribution, eukaryotes, evolution


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Y. Lian and H. R. Garner
Evidence for the regulation of alternative splicing via complementary DNA sequence repeats
Bioinformatics, April 15, 2005; 21(8): 1358 - 1364.
[Abstract] [Full Text] [PDF]


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