Abstract
The periodic variations obtained by correlating the relative positions of purines and pyrimidines (and of the four bases thymine, cytosine, adenine, and guanine) in a wide variety of genomes of wholly or partly known sequence suggest that there may be enough of an earlier comma-free coding system (i.e., only readable in one frame) still present to permit determination of the reading frame and approximate extent of the present protein coding stretches. The characteristics of these variations support the hypothesis that these primitive messages were formed of coding triplets having the form RNY (R = purine; Y = pyrimidine; and N = purine or pyrimidine). The base sequences and reading frames that have a minimal deviation from such a message are still good predictors of actual coding regions and reading frames in spite of the many mutations that have occurred since such a genetic code was last in use. In fact, the right frame for almost all the proteins in a number of viruses and various prokaryotes and eukaryotes is deduced purely from purine/pyrimidine information and not by using the normal start and stop signals.
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- Baralle F. Complete nucleotide sequence of the 5' noncoding region of human alpha-and beta-globin mRNA. Cell. 1977 Dec;12(4):1085–1095. doi: 10.1016/0092-8674(77)90171-4. [DOI] [PubMed] [Google Scholar]
- Barrell B. G., Air G. M., Hutchison C. A., 3rd Overlapping genes in bacteriophage phiX174. Nature. 1976 Nov 4;264(5581):34–41. doi: 10.1038/264034a0. [DOI] [PubMed] [Google Scholar]
- Barrell B. G., Bankier A. T., Drouin J. A different genetic code in human mitochondria. Nature. 1979 Nov 8;282(5735):189–194. doi: 10.1038/282189a0. [DOI] [PubMed] [Google Scholar]
- Beck E., Sommer R., Auerswald E. A., Kurz C., Zink B., Osterburg G., Schaller H., Sugimoto K., Sugisaki H., Okamoto T. Nucleotide sequence of bacteriophage fd DNA. Nucleic Acids Res. 1978 Dec;5(12):4495–4503. doi: 10.1093/nar/5.12.4495. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Crick F. H., Brenner S., Klug A., Pieczenik G. A speculation on the origin of protein synthesis. Orig Life. 1976 Dec;7(4):389–397. doi: 10.1007/BF00927934. [DOI] [PubMed] [Google Scholar]
- Crick F. H., Griffith J. S., Orgel L. E. CODES WITHOUT COMMAS. Proc Natl Acad Sci U S A. 1957 May 15;43(5):416–421. doi: 10.1073/pnas.43.5.416. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Efstratiadis A., Kafatos F. C., Maniatis T. The primary structure of rabbit beta-globin mRNA as determined from cloned DNA. Cell. 1977 Apr;10(4):571–585. doi: 10.1016/0092-8674(77)90090-3. [DOI] [PubMed] [Google Scholar]
- Fiers W., Contreras R., Duerinck F., Haegeman G., Iserentant D., Merregaert J., Min Jou W., Molemans F., Raeymaekers A., Van den Berghe A. Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene. Nature. 1976 Apr 8;260(5551):500–507. doi: 10.1038/260500a0. [DOI] [PubMed] [Google Scholar]
- Fuller W., Hodgson A. Conformation of the anticodon loop intRNA. Nature. 1967 Aug 19;215(5103):817–821. doi: 10.1038/215817a0. [DOI] [PubMed] [Google Scholar]
- Godson G. N., Barrell B. G., Staden R., Fiddes J. C. Nucleotide sequence of bacteriophage G4 DNA. Nature. 1978 Nov 16;276(5685):236–247. doi: 10.1038/276236a0. [DOI] [PubMed] [Google Scholar]
- Goodman M., Moore G. W., Matsuda G. Darwinian evolution in the genealogy of haemoglobin. Nature. 1975 Feb 20;253(5493):603–608. doi: 10.1038/253603a0. [DOI] [PubMed] [Google Scholar]
- Horii T., Ogawa T., Ogawa H. Organization of the recA gene of Escherichia coli. Proc Natl Acad Sci U S A. 1980 Jan;77(1):313–317. doi: 10.1073/pnas.77.1.313. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jou W. M., Verhoeyen M., Devos R., Saman E., Fang R., Huylebroeck D., Fiers W., Threlfall G., Barber C., Carey N. Complete structure of the hemagglutinin gene from the human influenza A/Victoria/3/75 (H3N2) strain as determined from cloned DNA. Cell. 1980 Mar;19(3):683–696. doi: 10.1016/s0092-8674(80)80045-6. [DOI] [PubMed] [Google Scholar]
- Jukes T. H., King J. L. Evolutionary nucleotide replacements in DNA. Nature. 1979 Oct 18;281(5732):605–606. doi: 10.1038/281605a0. [DOI] [PubMed] [Google Scholar]
- Kimura M. Evolutionary rate at the molecular level. Nature. 1968 Feb 17;217(5129):624–626. doi: 10.1038/217624a0. [DOI] [PubMed] [Google Scholar]
- King J. L., Jukes T. H. Non-Darwinian evolution. Science. 1969 May 16;164(3881):788–798. doi: 10.1126/science.164.3881.788. [DOI] [PubMed] [Google Scholar]
- Konkel D. A., Tilghman S. M., Leder P. The sequence of the chromosomal mouse beta-globin major gene: homologies in capping, splicing and poly(A) sites. Cell. 1978 Dec;15(4):1125–1132. doi: 10.1016/0092-8674(78)90040-5. [DOI] [PubMed] [Google Scholar]
- Kronenberg H. M., McDevitt B. E., Majzoub J. A., Nathans J., Sharp P. A., Potts J. T., Jr, Rich A. Cloning and nucleotide sequence of DNA coding for bovine preproparathyroid hormone. Proc Natl Acad Sci U S A. 1979 Oct;76(10):4981–4985. doi: 10.1073/pnas.76.10.4981. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Marcoli R., Iida S., Bickle T. A. The DNA sequence of an IS/-flanked transposon coding for resistance to chloramphenicol and fusidic acid. FEBS Lett. 1980 Jan 28;110(1):11–14. doi: 10.1016/0014-5793(80)80011-1. [DOI] [PubMed] [Google Scholar]
- McReynolds L., O'Malley B. W., Nisbet A. D., Fothergill J. E., Givol D., Fields S., Robertson M., Brownlee G. G. Sequence of chicken ovalbumin mRNA. Nature. 1978 Jun 29;273(5665):723–728. doi: 10.1038/273723a0. [DOI] [PubMed] [Google Scholar]
- Nakamura K., Pirtle R. M., Pirtle I. L., Takeishi K., Inouye M. Messenger ribonucleic acid of the lipoprotein of the Escherichia coli outer membrane. II. The complete nucleotide sequence. J Biol Chem. 1980 Jan 10;255(1):210–216. [PubMed] [Google Scholar]
- Nakanishi S., Inoue A., Kita T., Nakamura M., Chang A. C., Cohen S. N., Numa S. Nucleotide sequence of cloned cDNA for bovine corticotropin-beta-lipotropin precursor. Nature. 1979 Mar 29;278(5703):423–427. doi: 10.1038/278423a0. [DOI] [PubMed] [Google Scholar]
- Nichols B. P., Yanofsky C. Nucleotide sequences of trpA of Salmonella typhimurium and Escherichia coli: an evolutionary comparison. Proc Natl Acad Sci U S A. 1979 Oct;76(10):5244–5248. doi: 10.1073/pnas.76.10.5244. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Nishioka Y., Leder P. The complete sequence of a chromosomal mouse alpha--globin gene reveals elements conserved throughout vertebrate evolution. Cell. 1979 Nov;18(3):875–882. doi: 10.1016/0092-8674(79)90139-9. [DOI] [PubMed] [Google Scholar]
- Porter A. G., Barber C., Carey N. H., Hallewell R. A., Threlfall G., Emtage J. S. Complete nucleotide sequence of an influenza virus haemagglutinin gene from cloned DNA. Nature. 1979 Nov 29;282(5738):471–477. doi: 10.1038/282471a0. [DOI] [PubMed] [Google Scholar]
- Post L. E., Strycharz G. D., Nomura M., Lewis H., Dennis P. P. Nucleotide sequence of the ribosomal protein gene cluster adjacent to the gene for RNA polymerase subunit beta in Escherichia coli. Proc Natl Acad Sci U S A. 1979 Apr;76(4):1697–1701. doi: 10.1073/pnas.76.4.1697. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Reddy V. B., Thimmappaya B., Dhar R., Subramanian K. N., Zain B. S., Pan J., Ghosh P. K., Celma M. L., Weissman S. M. The genome of simian virus 40. Science. 1978 May 5;200(4341):494–502. doi: 10.1126/science.205947. [DOI] [PubMed] [Google Scholar]
- Robertson M. A., Staden R., Tanaka Y., Catterall J. F., O'Malley B. W., Brownlee G. G. Sequence of three introns in the chick ovalbumin gene. Nature. 1979 Mar 22;278(5702):370–372. doi: 10.1038/278370a0. [DOI] [PubMed] [Google Scholar]
- Sanger F., Coulson A. R., Friedmann T., Air G. M., Barrell B. G., Brown N. L., Fiddes J. C., Hutchison C. A., 3rd, Slocombe P. M., Smith M. The nucleotide sequence of bacteriophage phiX174. J Mol Biol. 1978 Oct 25;125(2):225–246. doi: 10.1016/0022-2836(78)90346-7. [DOI] [PubMed] [Google Scholar]
- Schaffner W., Kunz G., Daetwyler H., Telford J., Smith H. O., Birnstiel M. L. Genes and spacers of cloned sea urchin histone DNA analyzed by sequencing. Cell. 1978 Jul;14(3):655–671. doi: 10.1016/0092-8674(78)90249-0. [DOI] [PubMed] [Google Scholar]
- Woese C. Molecular mechanics of translation: a reciprocating ratchet mechanism. Nature. 1970 May 30;226(5248):817–820. doi: 10.1038/226817a0. [DOI] [PubMed] [Google Scholar]