Transcript Document

N. A. Zaytseva1, F. A. Kondrashov2, P. K. Vlasov2
1Siberian Federal University, Krasnoyarsk, Russia
2Centre for Genomic Regulation, Barcelona, Spain
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The global tRNA evolution within the total
sequence space has not been explored.
The lack of data on the distribution and
evolution of the sequences makes a
significant gap in our understanding of
evolution of amino acids and genetic code.
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•
Goal
Demonstration of transition possibility one
group tRNA to another
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Tasks
1) To obtain a picture of groups tRNA
distribution
2) To assess the divergence of sequences
within each group of tRNA
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The analysis is based on the model of the
ongoing expansion of the protein universe.
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The rate of divergence of distant homologues
is analogous to speed in Hubble’s analysis;
the distance between sequences is
analogous to physical distance.
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5787 sequences of mitochondrial tRNAs
(Tetrapoda) were analyzed
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The sequences were retrieved from
http://www.umich.edu/~kondrash/Database/
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The general database (Tetrapoda) was divided
into four databases: Mammalia, Aves,
Amphibia and Reptilia
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Step 1. The consensus sequences for each
group of tRNA were determined.
Step 2. The values of effective radius were
computed.
Step 3. The distances from all the sequences
to each consensus were calculated.
Step 4. The sequences, which are located in
the effective radius of another groups, were
identified.
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Consensus/
Group of tRNA
His
His
Ile
LeuU Tyr
77%
LeuU
68%
18%
48%
19%
Gly
Arg
•
Arg
51%
Ile
Tyr
Gly
3%
7%
Picture 1— Reduced version of intersection
matrix (Tetrapoda).
Group of tRNA
Tyr
His
Ile
Leu
Average value (for 21
group)
Effective radius
0,3333
0,2916
0,3125
0,2916
0,3026
Table 1 — Values of effective radius for some
tRNA groups.
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Table 2— Average value of effective radius for
each database.
Tetrapoda
Reptilia
0,3026
0,2954
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Amphibia Mammalia
0,2668
0,2004
Aves
0,1240
Table 3— Number of tRNA sequences in each
database.
Tetrapoda
5760
Reptilia
650
Amphibia
Mammalia Aves
1106
3076
945
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0.35
0.3
0.25
0.2
effective
radius 0.15
R² = 0.8782
0.1
0.05
0
140
190
240
290
340
390
time, million of year
Picture 2— Correlation between effective radius
and origin time of group.
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0.4
0.35
0.3
effective 0.25
radius
0.2
0.15
0.1
0
5
10
15
20
25
normalized time
Picture 3— Correlation between value of effective
radius and chronology of amino acids origin.
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Histidine, isoleucine, lecine and tyrosine form
cluster. In the center of cluster the tyrosine
group is located.
There is a correlation between the effective
radius and origin time of group of species
taken into consideration.
The value of the effective radius is
independent on the chronology of amino
acids origin.
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When the investigation is finished, we will
have a better understanding of the nature of
tRNA distribution in sequence space.
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Fyodor Kondrashov
Peter Vlasov
Michael Sadovsky
This work was supported by grant from Russian government
department of Science and Education to Siberian Federal
University «The genetic researcher of the Siberian larch»
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