Evolution of primate orphan proteins.

Genomes contain a large number of genes that do not have recognizable homologues in other species. These genes, found in only one or a few closely related species, are known as orphan genes. Their limited distribution implies that many of them are probably involved in lineage-specific adaptive processes. One important question that has remained elusive to date is how orphan genes originate. It has been proposed that they might have arisen by gene duplication followed by a period of very rapid sequence divergence, which would have erased any traces of similarity to other evolutionarily related genes. However, this explanation does not seem plausible for genes lacking homologues in very closely related species. In the present article, we review recent efforts to identify the mechanisms of formation of primate orphan genes. These studies reveal an unexpected important role of transposable elements in the formation of novel protein-coding genes in the genomes of primates.

[1]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[2]  M. Albà,et al.  Inverse relationship between evolutionary rate and age of mammalian genes. , 2005, Molecular biology and evolution.

[3]  L. Armengol,et al.  Origin of primate orphan genes: a comparative genomics approach. , 2008, Molecular biology and evolution.

[4]  K. White,et al.  Identification of a novel retina-specific gene located in a subtelomeric region with polymorphic distribution among multiple human chromosomes. , 2001, Biochimica et biophysica acta.

[5]  Evan E. Eichler,et al.  Positive selection of a gene family during the emergence of humans and African apes , 2001, Nature.

[6]  Yun Ding,et al.  On the origin of new genes in Drosophila. , 2008, Genome research.

[7]  Nikolaus Blin,et al.  Dermcidin: a novel human antibiotic peptide secreted by sweat glands , 2001, Nature Immunology.

[8]  Colin N. Dewey,et al.  Initial sequencing and comparative analysis of the mouse genome. , 2002 .

[9]  Huifeng Jiang,et al.  De Novo Origination of a New Protein-Coding Gene in Saccharomyces cerevisiae , 2008, Genetics.

[10]  K. Sperling,et al.  Irreversible repression of DNA synthesis in Fanconi anemia cells is alleviated by the product of a novel cyclin-related gene , 1995, Molecular and cellular biology.

[11]  Roderic Guigó,et al.  DNA Composition, Codon Usage and Exon Prediction , 1997 .

[12]  James A. Cuff,et al.  Distinguishing protein-coding and noncoding genes in the human genome , 2007, Proceedings of the National Academy of Sciences.

[13]  A. Nekrutenko,et al.  Transposable elements are found in a large number of human protein-coding genes. , 2001, Trends in genetics : TIG.

[14]  D. Tautz,et al.  An evolutionary analysis of orphan genes in Drosophila. , 2003, Genome research.

[15]  Ziheng Yang.  PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[16]  Sung-Hou Kim,et al.  Evolution of protein structural classes and protein sequence families , 2006, Proceedings of the National Academy of Sciences.

[17]  S. Jablonka,et al.  A new gene family (FAM9) of low-copy repeats in Xp22.3 expressed exclusively in testis: implications for recombinations in this region. , 2002, Genomics.

[18]  M. Albà,et al.  On homology searches by protein Blast and the characterization of the age of genes , 2007, BMC Evolutionary Biology.

[19]  M. Albà,et al.  Accelerated Evolution of Genes of Recent Origin , 2008 .

[20]  David K. Smith,et al.  Accelerated Evolutionary Rate May Be Responsible for the Emergence of Lineage-Specific Genes in Ascomycota , 2006, Journal of Molecular Evolution.

[21]  C. Figdor,et al.  A Human Minor Histocompatibility Antigen Specific for B Cell Acute Lymphoblastic Leukemia , 1999, The Journal of experimental medicine.

[22]  Jun Wang,et al.  Identification and characterization of insect-specific proteins by genome data analysis , 2007, BMC Genomics.

[23]  J. Brosius,et al.  From "junk" to gene: curriculum vitae of a primate receptor isoform gene. , 2004, Journal of molecular biology.

[24]  Andrew D Kern,et al.  Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[25]  Kevin R. Thornton,et al.  The origin of new genes: glimpses from the young and old , 2003, Nature Reviews Genetics.