Home LiteratureArticle Details
PMID: 6795634 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Extraordinarily high evolutionary rate of pseudogenes: evidence for the presence of selective pressure against changes between synonymous codons.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 78 ·No. 9 ·1981-09-00 ·Pages 5739-43

Miyata T, Hayashida H

Abstract

Comparisons of nucleotide sequences of several pseudogenes described to date, including alpha- and beta-globin and immunoglobulin kappa-type variable domain pseudogenes, with those of functional counterparts revealed that pseudogenes accumulate mutations at an extremely high rate uniformly over their entirety. It is remarkable that the evolutionary rate exceeds the rate of changes between synonymous codons, the highest known rate, in functional genes. Because no pseudogenes appear to function, this result strongly supports the neutral theory. In addition this result apparently indicates the presence of selective pressure against changes between synonymous codons in functional genes. Close examinations of codon utilization patterns in pseudogenes and functional genes revealed a significant correlation between the rate of changes at synonymous codon sites and the strength of bias in code word usage. This implies that even synonymous codon changes are not completely free from selective pressure but are constrained in part, although presumably weakly, depending on the degree of bias in code word usage. We also reexamined alignment between mouse beta h3 (pseudogene) and beta maj sequences and found a unique structure of the beta h3 that is homologous in sequence to the beta maj gene overall but contains a long deletion (about 150 base pairs) in the middle of the gene.

MeSH Terms
Animals Base Sequence Binding Sites, Antibody/genetics Biological Evolution Codon Genes Globins/genetics Immunoglobulin Light Chains/genetics Immunoglobulin Variable Region/genetics Immunoglobulin kappa-Chains/genetics Mice Selection, Genetic
Chemicals
Codon Immunoglobulin Light Chains Immunoglobulin Variable Region Immunoglobulin kappa-Chains Globins
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Miyata T
Hayashida H
References (36)
36 references, click to expand
  1. Evolutionary rate at the molecular level.
    Nature. 1968 Feb 17;217(5129):624-6 PMID: 5637732
  2. Rapidly evolving mouse alpha-globin-related pseudo gene and its evolutionary history.
    Proc Natl Acad Sci U S A. 1981 Jan;78(1):450-3 PMID: 6941257
  3. Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution.
    Nature. 1977 May 19;267(5608):275-6 PMID: 865622
  4. A pseudogene structure in 5S DNA of Xenopus laevis.
    Cell. 1977 Sep;12(1):109-20 PMID: 561661
  5. The primary sequence of rabbit alpha-globin mRNA.
    Cell. 1978 Sep;15(1):43-54 PMID: 699050
  6. Sequences at the somatic recombination sites of immunoglobulin light-chain genes.
    Nature. 1979 Jul 26;280(5720):288-94 PMID: 111144
  7. A kappa-immunoglobulin gene is formed by site-specific recombination without further somatic mutation.
    Nature. 1979 Aug 2;280(5721):370-5 PMID: 111146
  8. Comparison of total sequence of a cloned rabbit beta-globin gene and its flanking regions with a homologous mouse sequence.
    Science. 1979 Oct 19;206(4416):337-44 PMID: 482942
  9. Sequences of five potential recombination sites encoded close to an immunoglobulin kappa constant region gene.
    Proc Natl Acad Sci U S A. 1979 Jul;76(7):3450-4 PMID: 115000
  10. Are snRNPs involved in splicing?
    Nature. 1980 Jan 10;283(5743):220-4 PMID: 7350545
  11. Molecular cloning and sequence analysis of adult chicken betal globin cDNA.
    Nucleic Acids Res. 1979 Nov 10;7(5):1137-46 PMID: 514809
  12. The evolution and sequence comparison of two recently diverged mouse chromosomal beta--globin genes.
    Cell. 1979 Nov;18(3):865-73 PMID: 519759
  13. The complete sequence of a chromosomal mouse alpha--globin gene reveals elements conserved throughout vertebrate evolution.
    Cell. 1979 Nov;18(3):875-82 PMID: 519760
  14. The preferential codon usages in variable and constant regions of immunoglobulin genes are quite distinct from each other.
    Nucleic Acids Res. 1979 Dec 20;7(8):2431-8 PMID: 523321
  15. Secondary structure of MS2 phage RNA and bias in code word usage.
    Nucleic Acids Res. 1979 Dec 11;7(7):2073-9 PMID: 537920
  16. Organization and complete sequence of identical embryonic and plasmacytoma kappa V-region genes.
    J Biol Chem. 1980 Apr 25;255(8):3691-4 PMID: 6767723
  17. Nucleotide sequence divergence of mouse immunoglobulin gamma 1 and gamma 2b chain genes and the hypothesis of intervening sequence-mediated domain transfer.
    Proc Natl Acad Sci U S A. 1980 Apr;77(4):2143-7 PMID: 6769121
  18. Molecular cloning and characterization of the human beta-like globin gene cluster.
    Cell. 1980 Apr;19(4):959-72 PMID: 6155216
  19. The isolation of the beta A-, beta C-, and gamma-globin genes and a presumptive embryonic globin gene from a goat DNA recombinant library.
    J Biol Chem. 1980 Jul 10;255(13):6355-67 PMID: 6248519
  20. Unusual alpha-globin-like gene that has cleanly lost both globin intervening sequences.
    Proc Natl Acad Sci U S A. 1980 May;77(5):2806-9 PMID: 6930668
  21. A mouse alpha-globin-related pseudogene lacking intervening sequences.
    Nature. 1980 Jul 17;286(5770):222-6 PMID: 6250049
  22. A mutant immunoglobulin light chain is formed by aberrant DNA- and RNA-splicing events.
    Nature. 1980 Aug 21;286(5775):779-83 PMID: 6772973
  23. DNA sequence organization of the beta-globin complex in the BALB/c mouse.
    Cell. 1980 Aug;21(1):159-68 PMID: 6250710
  24. The structure of a human alpha-globin pseudogene and its relationship to alpha-globin gene duplication.
    Cell. 1980 Sep;21(2):537-44 PMID: 7407925
  25. The nucleotide sequence of a rabbit beta-globin pseudogene.
    Cell. 1980 Sep;21(2):545-53 PMID: 7407926
  26. Two types of somatic recombination are necessary for the generation of complete immunoglobulin heavy-chain genes.
    Nature. 1980 Aug 14;286(5774):676-83 PMID: 6774258
  27. Mouse globin system: a functional and evolutionary analysis.
    Science. 1980 Sep 19;209(4463):1336-42 PMID: 7414319
  28. Euglena gracilis chloroplast ribosomal RNA transcription units. II. Nucleotide sequence homology between the 16 S--23 S ribosomal RNA spacer and the 16 S ribosomal RNA leader regions.
    J Biol Chem. 1980 Nov 25;255(22):10997-1003 PMID: 6253497
  29. Complete nucleotide sequence of a cloned chicken alpha-globin cDNA.
    Nucleic Acids Res. 1980 Mar 25;8(6):1187-99 PMID: 6253930
  30. Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type.
    Nucleic Acids Res. 1980 May 10;8(9):1893-912 PMID: 6159596
  31. The nucleotide sequence of the human beta-globin gene.
    Cell. 1980 Oct;21(3):647-51 PMID: 6254664
  32. Molecular evolution of mRNA: a method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application.
    J Mol Evol. 1980 Sep;16(1):23-36 PMID: 6449605
  33. Human immunoglobulin variable region genes--DNA sequences of two V kappa genes and a pseudogene.
    Nature. 1980 Dec 25;288(5792):730-3 PMID: 6779204
  34. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.
    J Mol Evol. 1980 Dec;16(2):111-20 PMID: 7463489
  35. Nucleotide sequence divergence and functional constraint in mRNA evolution.
    Proc Natl Acad Sci U S A. 1980 Dec;77(12):7328-32 PMID: 6938980
  36. On some principles governing molecular evolution.
    Proc Natl Acad Sci U S A. 1974 Jul;71(7):2848-52 PMID: 4527913
Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.78.9.5739
Published
1981-09-00
Pages
5739-43
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC348847
Subset
IM
External Links
PubMed source DOI: 10.1073/pnas.78.9.5739 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2