Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: The anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity

被引：33

作者：

Liu Y.-J. ^{[1
,2
]}

Zheng D. ^{[3
]}

Balasubramanian S. ^{[2
]}

Carriero N. ^{[2
]}

Khurana E. ^{[2
]}

Robilotto R. ^{[4
]}

Gerstein M.B. ^{[2
,4
,5
]}

机构：

[1] Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA

[2] Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520

[3] Albert Einstein College of Medicine of Yeshiva University, Department of Neurology, Rose F. Kennedy Center, Bronx, NY 10461

[4] Program in Computational Biology and Bioinformatics, Yale University, New Haven

[5] Department of Computer Science, Yale University, New Haven, CT 06520, Bass 432

来源：

BMC Genomics | / 10卷 / 1期

基金：

美国国家卫生研究院;

关键词：

Glycolytic Enzyme; Segmental Duplication; Chimpanzee Genome; Assembly Version; ENSEMBL Release;

D O I：

10.1186/1471-2164-10-480

中图分类号：

学科分类号：

摘要：

Background: Pseudogenes provide a record of the molecular evolution of genes. As glycolysis is such a highly conserved and fundamental metabolic pathway, the pseudogenes of glycolytic enzymes comprise a standardized genomic measuring stick and an ideal platform for studying molecular evolution. One of the glycolytic enzymes, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), has already been noted to have one of the largest numbers of associated pseudogenes, among all proteins. Results: We assembled the first comprehensive catalog of the processed and duplicated pseudogenes of glycolytic enzymes in many vertebrate model-organism genomes, including human, chimpanzee, mouse, rat, chicken, zebrafish, pufferfish, fruitfly, and worm (available at http://pseudogene.org/glycolysis/). We found that glycolytic pseudogenes are predominantly processed, i.e. retrotransposed from the mRNA of their parent genes. Although each glycolytic enzyme plays a unique role, GAPDH has by far the most pseudogenes, perhaps reflecting its large number of non-glycolytic functions or its possession of a particularly retrotranspositionally active sub-sequence. Furthermore, the number of GAPDH pseudogenes varies significantly among the genomes we studied: none in zebrafish, pufferfish, fruitfly, and worm, 1 in chicken, 50 in chimpanzee, 62 in human, 331 in mouse, and 364 in rat. Next, we developed a simple method of identifying conserved syntenic blocks (consistently applicable to the wide range of organisms in the study) by using orthologous genes as anchors delimiting a conserved block between a pair of genomes. This approach showed that few glycolytic pseudogenes are shared between primate and rodent lineages. Finally, by estimating pseudogene ages using Kimura's two-parameter model of nucleotide substitution, we found evidence for bursts of retrotranspositional activity approximately 42, 36, and 26 million years ago in the human, mouse, and rat lineages, respectively. Conclusion: Overall, we performed a consistent analysis of one group of pseudogenes across multiple genomes, finding evidence that most of them were created within the last 50 million years, subsequent to the divergence of rodent and primate lineages. © 2009 Liu et al; licensee BioMed Central Ltd.

引用

共 60 条

[1]

Zhang Z., Harrison P., Gerstein M., Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome, Genome Res, 12, 10, pp. 1466-1482, (2002)

[2]

Zhang Z., Harrison P.M., Liu Y., Gerstein M., Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome, Genome Res, 13, 12, pp. 2541-2558, (2003)

[3]

Zhang Z., Carriero N., Gerstein M., Comparative analysis of processed pseudogenes in the mouse and human genomes, Trends Genet, 20, 2, pp. 62-67, (2004)

[4]

Zhang Z., Gerstein M., Large-scale analysis of pseudogenes in the human genome, Curr Opin Genet Dev, 14, 4, pp. 328-335, (2004)

[5]

Ohshima K., Hattori M., Yada T., Gojobori T., Sakaki Y., Okada N., Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates, Genome Biol, 4, 11, (2003)

[6]

Torrents D., Suyama M., Zdobnov E., Bork P., A genome-wide survey of human pseudogenes, Genome Res, 13, 12, pp. 2559-2567, (2003)

[7]

Bischof J.M., Chiang A.P., Scheetz T.E., Stone E.M., Casavant T.L., Sheffield V.C., Braun T.A., Genome-wide identification of pseudogenes capable of disease-causing gene conversion, Hum Mutat, 27, 6, pp. 545-552, (2006)

[8]

Lerat E., Ochman H., Psi-Phi: exploring the outer limits of bacterial pseudogenes, Genome Res, 14, 11, pp. 2273-2278, (2004)

[9]

Lerat E., Ochman H., Recognizing the pseudogenes in bacterial genomes, Nucleic Acids Res, 33, 10, pp. 3125-3132, (2005)

[10]

Ochman H., Davalos L.M., The nature and dynamics of bacterial genomes, Science, 311, 5768, pp. 1730-1733, (2006)

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