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Codes of Biosequences

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The Codes of Life

Part of the book series: Biosemiotics ((BSEM,volume 1))

Contrary to common belief that the nucleotide sequences only encode proteins, there are numerous additional codes, each of a different nature. The codes, at DNA, RNA, and protein sequence levels, are superposed, i.e. the same nucleotide in a given sequence may be simultaneously involved in several different encoded functions, at different levels. Such coexistence is possible due to degeneracy of the messages present in the sequence. Protein sequences are degenerate as well: involved not only in the functions related to the protein, but also adjusting to sequence requirements at the DNA level.

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References

  • Aharonovsky E, Trifonov EN (2005) Protein sequence modules. J Biomol Str Dyn 23:237–242

    CAS  Google Scholar 

  • Aparicio S, et al. (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297:1301–1310

    Article  CAS  PubMed  Google Scholar 

  • Bacolla A, Collins JR, Gold B et al. (2006) Long homopurine* homopyrimidine sequences are characteristic of genes expressed in brain and the pseudoautosomal region. Nucl Acids Res 34:2663–2675

    Article  CAS  PubMed  Google Scholar 

  • Berezovsky IN, Trifonov EN (2001) Evolutionary aspects of protein structure and folding. Mol Biol 35:233–239

    Article  CAS  Google Scholar 

  • Berezovsky IN, Trifonov EN (2002) Loop fold structure of proteins: resolution of Levinthal’s paradox. J Biomolec Str Dyn 20:5–6

    CAS  Google Scholar 

  • Berezovsky IN, Grosberg AY, Trifonov EN (2000) Closed loops of nearly standard size: common basic element of protein structure. FEBS Lett 466:283–286

    Article  CAS  PubMed  Google Scholar 

  • Berezovsky IN, Kirzhner VM, Kirzhner A et al. (2003a) Protein sequences yield a proteomic code. J Biomol Struct Dyn 21:317–325

    CAS  PubMed  Google Scholar 

  • Berezovsky IN, Kirzhner A, Kirzhner VM, Trifonov EN (2003b) Spelling protein structure. J Biomol Struct Dyn 21:327–339

    CAS  PubMed  Google Scholar 

  • Berman AL, Kolker E, Trifonov EN (1994) Underlying order in protein sequence organization. Proc Natl Acad Sci USA 91:4044–4047

    Article  CAS  PubMed  Google Scholar 

  • Bolshoy A, McNamara P, Harrington RE, Trifonov EN (1991) Curved DNA without AA: experimental estimation of all 16 wedge angles. Proc Natl Acad Sci USA 88:2312–2316

    Article  CAS  PubMed  Google Scholar 

  • Breathnach R, Chambon P (1981) Organization and expression of eukaryotic split genes coding for proteins. Ann Rev Bioch 50:349–383

    Article  CAS  Google Scholar 

  • Cohanim AB, Kashi Y, Trifonov EN (2005) Yeast nucleosome DNA pattern: deconvolution from genome sequences of S. cerevisiae. J Biomol Str Dyn 22:687–694

    CAS  Google Scholar 

  • Cohanim AB, Kashi Y, Trifonov EN (2006a) Three sequence rules for chromatin. J Biomol Struct Dyn 23:559–566

    CAS  PubMed  Google Scholar 

  • Cohanim AB, Trifonov EN, Kashi Y (2006b) Specific selection pressure on the third codon positions: contribution to 10 - 11 base periodicity in prokaryotic genomes. J Molec Evol (in press)

    Google Scholar 

  • Denisov DA, Shpigelman ES, Trifonov EN (1997) Protective nucleosome centering at splice sites as suggested by sequence-directed mapping of the nucleosomes. Gene 205:145–149

    Article  CAS  PubMed  Google Scholar 

  • D’Onofrio G, Bernardi G (1992) A universal compositional correlation among codon positions. Gene 110:81–88

    Article  PubMed  Google Scholar 

  • Doolittle RF (1988) More molecular opportunism. Nature 336:18

    Article  CAS  PubMed  Google Scholar 

  • Fire A, Xu S, Montgomery MK et al. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806–811

    Article  CAS  PubMed  Google Scholar 

  • Fondon JW, Garner HR (2004) Molecular origin of rapid and continuous morphological evolution. Proc Natl Acad Sci USA 101:18058–18063

    Article  CAS  PubMed  Google Scholar 

  • Gabdank I, Barash D, Trifonov EN (2006) Tracing ancient mRNA hairpins. J Biomol Str Dyn 24:163–170

    CAS  Google Scholar 

  • Gott JM, Emeson RB (2000) Functions and mechanisms of RNA editing. Ann Rev Genet 34:499–531

    Article  CAS  PubMed  Google Scholar 

  • Hinegardner R (1976) Evolution of genome size. In: Ayala FJ (ed) Molecular Evolution. Sinauer Association, Sunderland

    Google Scholar 

  • Holliday R (1968) Genetic recombination in fungi. In: Peacock WJ, Brock RD (eds) Replication and Recombination of Genetic Material. Australian Academy of Science, Canberra, Australia

    Google Scholar 

  • Holliday R (1991) Quantitative genetic variation and developmental clocks. J Theor Biol 151:351–358

    Article  CAS  PubMed  Google Scholar 

  • Khorana HG, Büchi H, Ghosh H et al. (1966) Polynucleotide synthesis and the genetic code. Cold Spring Harb Symp Quant Biol 31:39–49

    CAS  PubMed  Google Scholar 

  • King DG (1994) Triple repeat DNA as a highly mutable regulatory mechanism. Science 263:595–596

    CAS  PubMed  Google Scholar 

  • King DG, Soller M, Kashi Y (1997) Evolutionary tuning knobs. Endeavor 21:36–40

    Article  Google Scholar 

  • Kiyama R, Trifonov EN (2002) What positiones nucleosomes? A model. FEBS Lett 523:7–11

    Article  CAS  PubMed  Google Scholar 

  • Kogan S, Trifonov EN (2005) Gene splice sites correlate with nucleosome positions. Gene 352:57–62

    Article  CAS  PubMed  Google Scholar 

  • Kogan SB, Kato M, Kiyama R, Trifonov EN (2006) Sequence structure of human nucleosome DNA. J Biomol Struct Dyn 24:43–48

    CAS  PubMed  Google Scholar 

  • Kolker E, Trifonov EN (1995) Periodic recurrence of methionines: Fossil of gene fusion? Proc Natl Acad Sci USA 92:557–560

    Article  CAS  PubMed  Google Scholar 

  • Kolker E, Tjaden BC, Hubley R et al. (2002) Spectral analysis of distributions: finding periodic components in eukaryotic enzyme length data. OMICS: J Integr Biol 6:123–130

    Article  CAS  Google Scholar 

  • Koop BF, Hood L (1994) Striking sequence similarity over almost 100 kilobases of human and mouse T-cell receptor DNA. Nature Genet 7:48–53

    Article  CAS  PubMed  Google Scholar 

  • Künzler P, Matsuo K, Schaffner W (1995) Pathological, physiological, and evolutionary aspects of short unstable DNA repeats in the human genome. Biol Chem Hoppe-Seyler 376:201–211

    PubMed  Google Scholar 

  • Lagunez-Otero J, Trifonov EN (1992) mRNA periodical infrastructure complementary to the proof-reading site in the ribosome. J Biomol Struct Dyn 10:455–464

    CAS  PubMed  Google Scholar 

  • Makhoul CH, Trifonov EN (2002) Distribution of rare triplets along mRNA and their relation to protein folding. J Biomol Struct Dyn 20:413–420

    CAS  PubMed  Google Scholar 

  • Mengeritsky G, Trifonov EN (1983) Nucleotide sequence-directed mapping of the nucleosomes. Nucl Acids Res 11:3833–3851

    Article  CAS  PubMed  Google Scholar 

  • Mount SM (1982) A catalogue of splice junction sequences. Nucl Acids Res 10:459–472

    Article  CAS  PubMed  Google Scholar 

  • Nalimov VV (1981) In the labyrinths of language: A Mathematician’s Journey. ISI Press, Philadelphia, USA

    Google Scholar 

  • Nirenberg M, Caskey T, Marshall R et al. (1966) The RNA code and protein synthesis. Cold Spring Harb Symp Quant Biol 31:11–24

    CAS  PubMed  Google Scholar 

  • Noll M, Zimmer S, Engel A, Dubochet J (1980) Self-assembly of single and closely spaced nucleosome core particles. Nucl Acids Res 8:21–42

    Article  CAS  PubMed  Google Scholar 

  • Normark S, Bergstrom S, Edlund T et al (1983) Overlapping genes. Ann Rev Genet 17:499–525

    Article  CAS  PubMed  Google Scholar 

  • Ochoa S (1963) Synthetic polynucleotides and the amino acid code. Cold Spring Harb Symp Quant Biol 28:559–567

    Google Scholar 

  • Peleg G, Katzir G, Peleg O et al. (2006) Hereditary family signature of facial expression. Proc Natl Acad Sci USA 103:15921–15926

    Article  CAS  PubMed  Google Scholar 

  • Reanney DC (1976) Extrachromosomal elements as possible agents of adaption and development. Bact Rev 40:552–590

    CAS  PubMed  Google Scholar 

  • Schaap T (1971) Dual information in DNA and the evolution of the genetic code. J Theor Biol 32:293–298

    Article  CAS  PubMed  Google Scholar 

  • Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom A, Field Y, Moore IK, Wang JP, Widom J (2006) A genome code for nucleosome positioning. Nature 442:772–778

    Article  CAS  PubMed  Google Scholar 

  • Shore D, Langowski J, Baldwin RL (1981) DNA flexibility studied by covalent closure of short fragments into circles. Proc Natl Acad Sci USA 78:4833–4838

    Article  CAS  PubMed  Google Scholar 

  • Shpigelman ES, Trifonov EN, Bolshoy A (1993) CURVATURE: software for the analysis of curved DNA. CABIOS 9:435–440

    CAS  PubMed  Google Scholar 

  • Sobolevsky Y, Trifonov EN (2005) Conserved sequences of prokaryotic proteomes and their compositional age. J Mol Evol 61:591–596

    Article  CAS  PubMed  Google Scholar 

  • Sobolevsky Y, Trifonov EN (2006) Protein modules conserved since LUCA. J Mol Evol 63:622–634

    Article  CAS  PubMed  Google Scholar 

  • Tompa P, Scasz C, Buday L (2005) Structural disorder throws new light on moonlighting. Trends Bioch Sci 30:484–489

    Article  CAS  Google Scholar 

  • Trifonov EN (1980) Sequence-dependent deformational anisotropy of chromatin DNA. Nucl Acids Res 8:4041–4053

    Article  CAS  PubMed  Google Scholar 

  • Trifonov EN (1981) Structure of DNA in chromatin. In: Schweiger H (ed) International Cell Biology 1980–1981. Springer-Verlag, Berlin

    Google Scholar 

  • Trifonov EN (1987) Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16S rRNA nucleotide sequences. J Mol Biol 194:643–652

    Article  CAS  PubMed  Google Scholar 

  • Trifonov EN (1989) The multiple codes of nucleotide sequences. Bull Math Biol 51:417–432

    CAS  PubMed  Google Scholar 

  • Trifonov EN (1991) DNA in profile. Trends Biochem Sci 16:467–470

    Article  CAS  PubMed  Google Scholar 

  • Trifonov EN (1990) Making sense of the human genome. In: Sarma RH, Sarma MH (eds) Structure and Methods, vol. 1, Human Genome Initiative and DNA Recombination. Adenine Press, New York

    Google Scholar 

  • Trifonov EN (1995) Segmented structure of protein sequences and early evolution of genome by combinatorial fusion of DNA elements. J Mol Evol 40:337–342

    Article  CAS  PubMed  Google Scholar 

  • Trifonov EN (1996) Interfering contexts of regulatory sequence elements. CABIOS 12:423–429

    CAS  PubMed  Google Scholar 

  • Trifonov EN (1997) Genetic sequences as product of compression by inclusive superposition of many codes. Mol Biol 31:759–767

    CAS  Google Scholar 

  • Trifonov EN (1999) Elucidating sequence codes: three codes for evolution. Annals NY Acad Sci 870:330–338

    Article  CAS  Google Scholar 

  • Trifonov EN (2000a) Earliest pages of bioinformatics. Bioinformatics 16:5–9

    Article  CAS  PubMed  Google Scholar 

  • Trifonov EN (2000b) Consensus temporal order of amino acids and evolution of the triplet code. Gene 261:139–151

    Article  CAS  PubMed  Google Scholar 

  • Trifonov EN (2002) Segmented genome: elementary units of genome structure. Russian J Genet. 38:659–663

    Article  CAS  Google Scholar 

  • Trifonov EN (2004) The triplet code from first principles. J Biomol Struct Dyn 22:1–11

    CAS  PubMed  Google Scholar 

  • Trifonov EN (2006) Theory of early molecular evolution: predictions and confirmations. In: Eisenhaber F (ed) Discovering Biomolecular Mechanisms with Computational Biology. Landes Bioscience, Georgetown

    Google Scholar 

  • Trifonov EN, Berezovsky IN (2003) Evolutionary aspects of protein structure and folding, Curr Opinion Struct Biol 13:110–114

    Article  CAS  Google Scholar 

  • Trifonov EN, Bettecken T (1997) Sequence fossils, triplet expansion, and reconstruction of earliest codons. Gene 205:1–6

    Article  CAS  PubMed  Google Scholar 

  • Trifonov EN, Sussman JL (1980) The pitch of chromatin DNA is reflected in its nucleotide sequence. Proc Natl Acad Sci USA 77:3816–3820

    Article  CAS  PubMed  Google Scholar 

  • Trifonov EN, Kirzhner A, Kirzhner VM, Berezovsky IN (2001) Distinct stages of protein evolution as suggested by protein sequence analysis. J Mol Evol 53:394–401

    Article  CAS  PubMed  Google Scholar 

  • Trifonov EN, Kogan S, Cohanim AB (2006a) Latest on the nucleosome positioning sequence patterns. In: Kiyama R, Shimizu M (eds) DNA Structure, Chromatin and Gene Expression. Transworld Research Network. Trivandrum, India

    Google Scholar 

  • Trifonov EN, Gabdank I, Barash D, Sobolevsky Y (2006b) Primordia vita. Deconvolution from modern sequences. Origin Life Evol Biosph 36(5–6):559–565

    CAS  Google Scholar 

  • Ulanovsky LE, Trifonov EN (1986) A different view point on the chromatin higher order structure: steric exclusion effects. In: Sarma RH, Sarma MH (eds) Biomolecular stereodynamics III. Adenine Press, New York

    Google Scholar 

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Trifonov, E.N. (2008). Codes of Biosequences. In: Barbieri, M., Hoffmeyer, J. (eds) The Codes of Life. Biosemiotics, vol 1. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-6340-4_1

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