Download - Dr. Maik Friedel

Maik Friedel, Swetlana Nikolajewa, Thomas Wilhelm
Theoretical Systems Biology, FLI-Jena, Germany
http://www.fli-leibniz.de/tsb
Abstract:
We hypothesize that in the early days of translation pre-tRNAs were able to recognize codons in both directions. In order to guarantee
termination and to avoid incorrect elongation the reverse stop codons should have had no own pre-tRNA. We studied the number
of tRNA genes of 16 archaea, 81 bacteria and 7 eucaryotes. It was surprising that still today reverse stop codons do not
have their own tRNAs (just one exception in human). Furthermore, patterns in our new classification scheme of
the genetic code support speculations that the contemporary triplet code developed from an ancient
doublet code. In order to avoid the frame shift problem one has to assume a triplet reading
frame also in doublet coding times, which would indicate an information wasting
of each third base. Our hypothesis provides a possible solution for this
information wasting problem. Moreover, it could also account
for additional so far unexplained facts about
amino acid – codon assignments.
Codon – Anticodon pairs and their corresponding
number of tRNA genes.
• STOP codons have no own tRNAs.
• Reverse STOP codons also have no own tRNAs!
Codons and the reverse codons code for either the same or a similar amino acid:
Code
Strong codons
(6 H-bonds)
Mixed codons
(5 H-bonds)
Mixed codons
(5 H-bonds)
Weak codons
(4 H-bonds)
000
Pro CC (C/U)
Ser UC (C/U)
Leu CU (C/U)
Phe UU (C/U)
• The middle base of a codon determines important physical properties of the corresponding amino
acid.
001
Pro CC (A/G)
Ser UC (A/G)
Leu CU (A/G)
Leu UU (A/G)
• 16 self reverse codons correspond to 15 different amino acids.
100
Ala GC (C/U)
Thr AC (C/U)
Val GU (C/U)
Ile AU (C/U)
101
Ala GC (A/G)
Thr AC (A/G)
Val GU (A/G)
Ile/Met AU
• The triplet genetic code had a doublet predecessor.
(A/G)
010
Arg CG (C/U)
Cys UG (C/U)
His CA (C/U)
Tyr UA (C/U)
011
Arg CG (A/G)
Stop/Trp UG
Gln CA (A/G)
Stop UA (A/G)
110
Gly GG (C/U)
Ser AG (C/U)
Asp GA (C/U)
Asn AA (C/U)
111
Gly GG (A/G)
Arg AG (A/G)
Glu GA (A/G)
Lys AA (A/G)
(A/G)
• Amino acids corresponding to codons and their reverse codons are evolutionary conserved.
Copley SD et al. PNAS, 102:4442–4447, 2005
A mechanism for the association of amino acids with their codons and the origin of the
genetic code.
• There was always a triplet reading frame.
Landweber L, Chem Biol. 9(2):237-44, 2000.
Custom codons come in threes, fours, and fives.
Our new classification scheme of the genetic code is based on a purine (1) – pyrimidine (0) coding.
Red arrows indicate codon reverse codon pairs (XYZ<->ZYX).
A new classification scheme of the genetic code
Wilhelm T., Nikolajewa S., J. Mol. Evol. 59:598 – 605, 2004
Reverse recognition conjecture:
In ancient times pre-tRNA was able to bind the pre-mRNA in both
directions.
A0
A1
U
C
C
U A
A
A0
A U G
Fig. 2
C
U A
A0
0A
C
C
U A
A
A U N
5‘
N U A
3‘
codon
U
5‘
3‘
reverse codon
Conclusion
Fig. 1
The new hypothesis can explain all above stated facts and assumptions. It can lead to a new
understanding of the early evolution of life. We assume that this sloppy translation increased
the diversity of similar proteins and thus contributed to an accelerated evolution.
The new classification scheme of the genetic code, its early evolution, and tRNA usage
Nikolajewa S., Friedel M., Beyer A., Wilhelm T., J. Comp. Biol. & Bioinf., 2006 (in press)