Analysis of Sequence Periodicity in E. Coli Proteins: Empirical Investigation of the "duplication and Divergence" Theory of Protein Evolution

Overview

Journal J Mol Evol

Specialty Biochemistry

Date 2003 Oct 18

PMID 14562959

Citations 3

Authors

Derek Gatherer

Neil R McEwan

Affiliations

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Abstract

Periodicity was quantified in 4289 Escherichia coli K12 confirmed and putative protein sequences, using a simple chi-square technique previously shown to reveal triplet period periodicity in coding DNA. Periodicities were calculated from period n = 2 to period n = 50 in nine different alphabetic representations of the proteins. By comparison with a randomly generated proteome of the same compositional content, the E. coli proteome does not contain a significant excess of periodic proteins. However, 60 proteins do appear to be significantly periodic in at least one alphabetic representation, after Bonferroni correction, at p < 0.01, and 30 at p < 0.001. These are compared with significantly periodic proteins of solved three-dimensional structure, detected by an identical analysis of the sequences from a protein structure database. It is concluded that there is no evidence for the presence of a proteome-wide quasi-periodicity as predicted by the "duplication and divergence" model of protein evolution and that the major periodicity detected is a consequence of the repetitive tendencies within alpha-helices. However, it is not possible to explain all sequence periodicities in terms of observable secondary structure, as in cases where sequence periodicity can be compared to solved structure, there is often no structural regularity that would provide an obvious explanation in terms of natural selection on protein function.

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References

Ohno S . Repeats of base oligomers as the primordial coding sequences of the primeval earth and their vestiges in modern genes. J Mol Evol. 1984; 20(3-4):313-21. DOI: 10.1007/BF02104737. View

Eisenberg D, Weiss R, Terwilliger T . The hydrophobic moment detects periodicity in protein hydrophobicity. Proc Natl Acad Sci U S A. 1984; 81(1):140-4. PMC: 344626. DOI: 10.1073/pnas.81.1.140. View

Stanfel L . A new approach to clustering the amino acids. J Theor Biol. 1996; 183(2):195-205. DOI: 10.1006/jtbi.1996.0213. View

Berman H, Westbrook J, Feng Z, Gilliland G, Bhat T, Weissig H . The Protein Data Bank. Nucleic Acids Res. 1999; 28(1):235-42. PMC: 102472. DOI: 10.1093/nar/28.1.235. View

Zhurkin V . Periodicity in DNA primary structure is defined by secondary structure of the coded protein. Nucleic Acids Res. 1981; 9(8):1963-71. PMC: 326816. DOI: 10.1093/nar/9.8.1963. View

Ycas M . Origin of periodic proteins. Fed Proc. 1976; 35(10):2139-40. View

Ohno S . Codon preference is but an illusion created by the construction principle of coding sequences. Proc Natl Acad Sci U S A. 1988; 85(12):4378-82. PMC: 280432. DOI: 10.1073/pnas.85.12.4378. View

Shulman M, STEINBERG C, WESTMORELAND N . The coding function of nucleotide sequences can be discerned by statistical analysis. J Theor Biol. 1981; 88(3):409-20. DOI: 10.1016/0022-5193(81)90274-5. View

Barker W, Dayhoff M . Evolution of lipoproteins deduced from protein sequence data. Comp Biochem Physiol B. 1977; 57(4):309-15. DOI: 10.1016/0305-0491(77)90060-8. View

10.

Katti M, Ranjekar P, Gupta V . Amino acid repeat patterns in protein sequences: their diversity and structural-functional implications. Protein Sci. 2000; 9(6):1203-9. PMC: 2144659. DOI: 10.1110/ps.9.6.1203. View

11.

Pattabiraman N, Namboodiri K, LOWREY A, Gaber B . NRL-3D: a sequence-structure database derived from the protein data bank (PDB) and searchable within the PIR environment. Protein Seq Data Anal. 1990; 3(5):387-405. View

12.

Ivanov O, Ivanov C . Some evidence for the universality of structural periodicity in proteins. J Mol Evol. 1980; 16(1):47-68. DOI: 10.1007/BF01732069. View

13.

Wuilmart C, Urbain J . Alpha secondary structures generate weak but recurrent periodicity in proteins. Eur J Biochem. 1984; 139(1):35-40. DOI: 10.1111/j.1432-1033.1984.tb07972.x. View

14.

Elleman T, CREWTHER W, Van Der Touw J . Amino acid sequences of alpha-helical segments from S-carboxymethylkerateine-A. Statistical analysis. Biochem J. 1978; 173(2):387-91. PMC: 1185790. DOI: 10.1042/bj1730387. View

15.

Ivanov O, Kenderov P, Revalski J . The structural periodicity of E. coli ribosomal proteins. Orig Life. 1984; 14(1-4):557-64. DOI: 10.1007/BF00933704. View

16.

Vaara M . Eight bacterial proteins, including UDP-N-acetylglucosamine acyltransferase (LpxA) and three other transferases of Escherichia coli, consist of a six-residue periodicity theme. FEMS Microbiol Lett. 1992; 76(3):249-54. DOI: 10.1016/0378-1097(92)90344-n. View