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Evolutionary Classification of Homeodomains

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Abstract

Purpose and Methods: We performed multiple comparisons between available amino acid (aa) sequences of homeodomain(HOM)-containing proteins from a wide spectrum of animals to create an evolutionary classification of the proteins.

Results: Based on results of statistical and special computational analyses of over 500 homeodomain aa sequences (HOMs) a novel system of concepts describing complex structural correlations between homologous proteins is proposed. This system includes such notions as differentiated isofunctionality of aa, chemotype, stereotype, local functional motifs, gradual conservativeness of aa positions, and group-specific domain patterns, as well as major categories of the evolutionary classification of HOMs (Division, Type, Branch, Class, Family, Series, Variety, Sort). Using this approach, a complete structural systematics of HOMs belonging to proteomes of eukaryotic animals is proposed.

Conclusions: The proposed structural classification of HOMs is in full agreement with the bulk of experimental data revealing complex functional similarities and differences among HOMs in terms of their expression patterns in developing embryos. It turn, this classification can provide answers regarding homology among homeodomains when experimental data are conflicting.

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REFERENCES

  1. Gindilis VM, Ageev SV: HuNeG project: The progress report of 1993–94 on the Scottish Rite SRP Huneg grant award, Oct 1994, pp 1-31. (Office of the SRP, P.O. Box 519, 33 Marret Road, Lexington, MA 02173)

  2. Scott MP, Tamkun JW, Hartzell GW: The structure and function of the homeodomain. Biochim Biophys Acta 1989;989:25-48

    Google Scholar 

  3. Burglin TR: A comprehensive classification of homeobox genes: In Guidebook to the Homeobox Genes, D Duboule (ed). New York, Oxford University Press, 1994, pp 25-71

    Google Scholar 

  4. Stein S, Fritsch R, Lemaire L, Kessel M: Checklist: Vertebrate homebox genes. Mech Dev 1996;55:91-108

    Google Scholar 

  5. Abouhief E, Akam M, Dickinson WJ, Holland PWH, Meyer A, Patel NH, Raff RA, Roth Wray GA: Homology and developmental gene. Trends Genet 1997;13:432-433

    Google Scholar 

  6. Gindilis V, Banikazemi M, Vyasankin A, Verlinsky O, Matveyev I, Verlinsky Y: Borders, patterns, and distinctive families of homeodomains. J Assist Reprod Genet 1994;11:244-269

    Google Scholar 

  7. Gindilis VM, Verlinsky Y: Reconstruction of mutational history in the evolution of the caudal-like homeodomain family. J Mol Evol (in press)

  8. Islam SA, Luo J, Sternberg MJE: Identification and analysis of domains in proteins. Prot Eng 1995;8:513-525

    Google Scholar 

  9. Schmidt W: Phylogeny reconstruction for protein sequences based on amino acid properties. J Mol Evol 1995;41:522-530

    Google Scholar 

  10. Jiwani NG, Liebman MN: Structure-function analysis of amino acid substitutions in proteins: In Molecular Modeling, TF Kumosinski, MN Liebman (eds). Washington, DC, Am Chem Soc, 1994, pp 184-206

    Google Scholar 

  11. Bowie JU, Luthy R, Eisenberg D: A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991;253:164-170

    Google Scholar 

  12. Taylor WR: The classification of amino acid conservation. J Theor Biol 1986;119:205-218

    Google Scholar 

  13. Kidera A, Konishi Y, Oka M, Ooi T, Scheraga HA: Statistical analysis of the physical properties of the 20 naturally occuring amino acids. J Prot Chem 1985;4:23-55

    Google Scholar 

  14. Ratner V, Jarkich A, Kolchanov N: In Problems of the Molecular Evolution Theory. Novosibirsk, Nauka, 1985, pp 63-74 (in Russian)

    Google Scholar 

  15. Swanson R: A unifying concept for the amino acid code. Bull Math Biol 1984;46:187-203

    Google Scholar 

  16. Burglin TR: Analysis of TALE superclass homeobox genes. Nucleic Acids Res 1997;25:4173-4180

    Google Scholar 

  17. Duprey P, Chowdhury K, Dressler GR, Balling R, Simon D, Guenet J-L, Gruss P: A mouse gene homologous to the Drosophila gene caudal is expressed in epithelial cells from the embryonic intestine. Genes Dev 1988;2:1647-1654

    Google Scholar 

  18. Hu Y, Kazenwadel J, James R: Isolation and characterization of the murine homeobox gene Cdx-1. J Biol Chem 1993; 268:27214-27225

    Google Scholar 

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Authors and Affiliations

  1. Reproductive Genetics Institute, 836 West Wellington, Chicago, Illinois, 60657

    Viktor Gindilis, Eugene Goltsman & Yury Verlinsky

Authors
  1. Viktor Gindilis
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  2. Eugene Goltsman
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  3. Yury Verlinsky
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Gindilis, V., Goltsman, E. & Verlinsky, Y. Evolutionary Classification of Homeodomains. J Assist Reprod Genet 15, 349–357 (1998). https://doi.org/10.1023/A:1022517232580

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  • DOI: https://doi.org/10.1023/A:1022517232580

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