Gene Has Its Inherent Signi cantly Repetitive Tuples
Nobuyuki Uchikoga

Akira Suyama

uchiko@genji.c.u-tokyo.ac.jp

suyama@dna.c.u-tokyo.ac.jp

Department of Life Sciences, The University of Tokyo
3-8-1 Komaba, Meguro-ku, Tokyo 153, Japan

1 Introduction
Nonenzymatic synthesis of nucleic acid yields only short oligomer compared with enzymatic synthesis
using the modern machinery. It leads us to a question how nucleic acid chains, which are long enoughto encode the functional polypeptide chains, were created in primordial soup. To answer this question,
S. Ohno proposed a model of primordial sequences composed of repeats of short base oligomers [1].
This model is very attractive. However, the universality of the model still remains open to question
because he derived the model from base sequences of some genes with unusually regular oligomericrepeats.
In 1996, we examined the universality of the model by analyzing base sequences of about eighty
genes with di erent functions classi ed into the major three biospheres (Archaea, Bacteria, Eukaryotae) on the phylogenetic tree of life. This examination showed that the model of the primordial codingsequences is likely to be universal because homologous tuples appear frequently in both coding andnoncoding regions of the present living organisms [2]. However, this conclusion did not indicate thatspeci c base sequences of homologous tuples exist universally in both coding and noncoding regionsof modern genes. In our previous work, we then investigated the distribution of sets of signi cantly
repetitive tuples with the same base sequence. The conclusion of the previous work showed thatsigni cantly repetitive tuple with the same base sequence is speci c to each gene and each biosphere[3].
Although the conclusion of the previous work, signi cantly repetitive tuples with homologous
base sequence in both coding and noncoding regions can be regarded as vestiges of primordial genes
because base sequences of genes could have been changed while primordial sequences have diverged tomodern genes. These conclusions above led us to examine the distribution of signi cantly repetitive
homologous tuples by analyzing base sequences of genes classi ed into three biospheres.

2 Method
For each tuple, the signi cance, x, of the frequency of the occurrence of a tuple in a sample basesequence is given by
f0 0 N p
x = p;N p(1 0 p)
where f0 is the observed number of a tuple, N is the total number of a tuple in a base sequence
examined, and p is the probability of the occurrence of a tuple in random sequences whose basecomposition is same with a sample sequence. We de ned the signi cantly repetitive tuple (SRT) as atuple with x > 3.

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Table 1: The ratio of the number of the homologous whole gene SRTs shared with ALL genes (%) toall SRTs existing in each biosphere. (Boldface is the ratio larger than 45).
Genes chosen from data base randomly
5-tuple 6-tuple 7-tuple The number of genes
Archaea
11.8
20.3
0.3
21
Bacteria
0.1
12.0
0.7
44
6.7
10.3
1.0
21
Eukaryotae
Nine contiguous genes on E. coli genome around dnaA
(f135, gryB, recF, dnaN, dnaA, rmpH, rnpA, yidC, thdF)
5-tuple6-tuple7-tupleThe number of genes

1.0

14.4

0.7

9

Heat Shock Protein 70 Family
5-tuple6-tuple7-tupleThe number of genes

Archaea

94.3

79.9

28.1

3

Bacteria

55.8

80.6

55.6

8

Eukaryotae

17.5

47.4

18.4

21

3 Results and Discussion
We analyzed three sets of base sequences of gene. One is the set of about eighty genes chosen fromdatabase randomly. Another is the set of nine contiguous genes around dnaA on E.coli genome. The
last is Heat Shock Protein 70 family in each biosphere.
We paid special attention to SRTs observed in both coding and noncoding regions of each genebecause the primordial genes could become not only coding sequences but also noncoding sequences ofmodern genomes. We also paid attention to whole gene SRTs shared with all genes because primordial
sequences might have diverged to modern genes. It is believed that base sequences of SRTs could havebeen changed while primordial sequences diverging. In this work, we de ne homologous tuples aresets of tuples with base mismatches less than two bases. These whole gene SRTs can be regarded asvestiges of primordial genes. Table 1 shows the distribution of whole gene SRTs shared with all genes.
Table shows that more homologous whole gene SRTs are shared with Heat Shock Protein 70 family
than two other gene sets. These homologous whole gene SRTs are in not only coding region but also
noncoding region. Such SRTs appear frequently in one gene family. These facts imply that thehomologous whole gene SRTs can be regarded as vestiges of the primordial words. The gene family
may have a speci c set of primordial genes whose base sequences are similar to each other.

Acknowledgements
This work was supported in part by a Grant-in-Aid for Scienti c Research on Priority Areas from The
Ministry of Education, Science, Sports and Culture in Japan.

References[1] Ohno, S., Repeats of base oligomers as the primordial coding sequences of the primeval Earthand their vestiges in modern genes, J. Mol. Evol., 20:313{321, 1984.
[2] Uchikoga, N and Suyama, A., Vestiges of primordial word in base sequences of modern genomes,
Genome Informatics 1996, Universal Academy Press, 242{243, 1996.
[3] Uchikoga, N and Suyama, A., Distribution of Signi cantly Repetitive Tuples Implying Primordialgenes, Genome Informatics 1997, Universal Academy Press, 350{351, 1997.
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