• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of geneticsGeneticsCurrent IssueInformation for AuthorsEditorial BoardSubscribeSubmit a Manuscript
Genetics. Aug 2004; 167(4): 1813–1820.
PMCID: PMC1470981

A genomic basis for the evolution of vertebrate transcription factors containing amino Acid runs.

Abstract

We have previously shown that polyAla (A) tract-containing proteins frequently present runs of glycine (G), proline (P), and histidine (H) and that, in their ORFs, GC content at all codon positions is higher than that in the rest of the genome. In this study, we present new analyses of these human proteins/ORFs. We detected striking differences in codon usage for A, G, and P in and out of runs. After dividing the ORFs, we found that 5' halves were richer in runs than 3' halves. Afterward, when removing the runs, we observed that the run-rich halves (grouped irrespectively of their 5' or 3' position) had a marked statistical tendency to have more homo- and hetero-dicodons for A, G, P, and H than the run-poor halves. This suggests that, in addition to the necessary GC-rich genomic background, a specific codon organization is probably required to generate these coding repeats. Homo-dicodons may indeed provide primers for run formation through polymerase slippage. The compositional analysis of human HOX genes, the most polyAla-rich family, and their comparison with their zebrafish homologs, support these hypotheses and suggest possible effects of genomic environment on ORF evolution and organismal diversification.

Full Text

The Full Text of this article is available as a PDF (140K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Han K, Manley JL. Functional domains of the Drosophila Engrailed protein. EMBO J. 1993 Jul;12(7):2723–2733. [PMC free article] [PubMed]
  • Han K, Manley JL. Transcriptional repression by the Drosophila even-skipped protein: definition of a minimal repression domain. Genes Dev. 1993 Mar;7(3):491–503. [PubMed]
  • Harris SE, Chand AL, Winship IM, Gersak K, Aittomäki K, Shelling AN. Identification of novel mutations in FOXL2 associated with premature ovarian failure. Mol Hum Reprod. 2002 Aug;8(8):729–733. [PubMed]
  • Hishinuma A, Ohyama Y, Kuribayashi T, Nagakubo N, Namatame T, Shibayama K, Arisaka O, Matsuura N, Ieiri T. Polymorphism of the polyalanine tract of thyroid transcription factor-2 gene in patients with thyroid dysgenesis. Eur J Endocrinol. 2001 Oct;145(4):385–389. [PubMed]
  • Karlin Samuel, Brocchieri Luciano, Bergman Aviv, Mrazek Jan, Gentles Andrew J. Amino acid runs in eukaryotic proteomes and disease associations. Proc Natl Acad Sci U S A. 2002 Jan 8;99(1):333–338. [PMC free article] [PubMed]
  • Lavoie Hugo, Debeane Francois, Trinh Quoc-Dien, Turcotte Jean-Francois, Corbeil-Girard Louis-Philippe, Dicaire Marie-Josée, Saint-Denis Anik, Pagé Martin, Rouleau Guy A, Brais Bernard. Polymorphism, shared functions and convergent evolution of genes with sequences coding for polyalanine domains. Hum Mol Genet. 2003 Nov 15;12(22):2967–2979. [PubMed]
  • Montoya-Burgos Juan Ignacio, Boursot Pierre, Galtier Nicolas. Recombination explains isochores in mammalian genomes. Trends Genet. 2003 Mar;19(3):128–130. [PubMed]
  • Aïssani B, Bernardi G. CpG islands: features and distribution in the genomes of vertebrates. Gene. 1991 Oct 15;106(2):173–183. [PubMed]
  • Nakachi Y, Hayakawa T, Oota H, Sumiyama K, Wang L, Ueda S. Nucleotide compositional constraints on genomes generate alanine-, glycine-, and proline-rich structures in transcription factors. Mol Biol Evol. 1997 Oct;14(10):1042–1049. [PubMed]
  • Amores A, Force A, Yan YL, Joly L, Amemiya C, Fritz A, Ho RK, Langeland J, Prince V, Wang YL, et al. Zebrafish hox clusters and vertebrate genome evolution. Science. 1998 Nov 27;282(5394):1711–1714. [PubMed]
  • Pesole G, Liuni S, Grillo G, Saccone C. Structural and compositional features of untranslated regions of eukaryotic mRNAs. Gene. 1997 Dec 31;205(1-2):95–102. [PubMed]
  • Queitsch Christine, Sangster Todd A, Lindquist Susan. Hsp90 as a capacitor of phenotypic variation. Nature. 2002 Jun 6;417(6889):618–624. [PubMed]
  • Bernardi G. Isochores and the evolutionary genomics of vertebrates. Gene. 2000 Jan 4;241(1):3–17. [PubMed]
  • Ronshaugen Matthew, McGinnis Nadine, McGinnis William. Hox protein mutation and macroevolution of the insect body plan. Nature. 2002 Feb 21;415(6874):914–917. [PubMed]
  • Brown Lucia Y, Brown Stephen A. Alanine tracts: the expanding story of human illness and trinucleotide repeats. Trends Genet. 2004 Jan;20(1):51–58. [PubMed]
  • Ross CA. When more is less: pathogenesis of glutamine repeat neurodegenerative diseases. Neuron. 1995 Sep;15(3):493–496. [PubMed]
  • Cocquet Julie, De Baere Elfride, Caburet Sandrine, Veitia Reiner A. Compositional biases and polyalanine runs in humans. Genetics. 2003 Nov;165(3):1613–1617. [PMC free article] [PubMed]
  • Rozen Steve, Skaletsky Helen, Marszalek Janet D, Minx Patrick J, Cordum Holland S, Waterston Robert H, Wilson Richard K, Page David C. Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. Nature. 2003 Jun 19;423(6942):873–876. [PubMed]
  • Ruddle FH, Bartels JL, Bentley KL, Kappen C, Murtha MT, Pendleton JW. Evolution of Hox genes. Annu Rev Genet. 1994;28:423–442. [PubMed]
  • De Baere Elfride, Beysen Diane, Oley Christine, Lorenz Birgit, Cocquet Julie, De Sutter Paul, Devriendt Koen, Dixon Michael, Fellous Marc, Fryns Jean-Pierre, et al. FOXL2 and BPES: mutational hotspots, phenotypic variability, and revision of the genotype-phenotype correlation. Am J Hum Genet. 2003 Feb;72(2):478–487. [PMC free article] [PubMed]
  • Sumiyama K, Washio-Watanabe K, Saitou N, Hayakawa T, Ueda S. Class III POU genes: generation of homopolymeric amino acid repeats under GC pressure in mammals. J Mol Evol. 1996 Sep;43(3):170–178. [PubMed]
  • Eyre-Walker A, Hurst LD. The evolution of isochores. Nat Rev Genet. 2001 Jul;2(7):549–555. [PubMed]
  • Toyota Tomoko, Yoshitsugu Kiyoshi, Ebihara Mitsuru, Yamada Kazuo, Ohba Hisako, Fukasawa Masayuki, Minabe Yoshio, Nakamura Kazuhiko, Sekine Yoshimoto, Takei Noriyoshi, et al. Association between schizophrenia with ocular misalignment and polyalanine length variation in PMX2B. Hum Mol Genet. 2004 Mar 1;13(5):551–561. [PubMed]
  • Finnerty JR, Martindale MQ. The evolution of the Hox cluster: insights from outgroups. Curr Opin Genet Dev. 1998 Dec;8(6):681–687. [PubMed]
  • Galant Ron, Carroll Sean B. Evolution of a transcriptional repression domain in an insect Hox protein. Nature. 2002 Feb 21;415(6874):910–913. [PubMed]
  • Gehring WJ, Affolter M, Bürglin T. Homeodomain proteins. Annu Rev Biochem. 1994;63:487–526. [PubMed]

Articles from Genetics are provided here courtesy of Genetics Society of America

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...