Computer Analysis of Base Pairing Free-Energy between
Shine-Dalgarno Sequence and 16S rRNA in Various

Yuko Osada

Procaryotes
12osada@sfc.keio.ac.jp
12
3Rintaro Saito

12

rsaito@sfc.keio.ac.jp

Masaru Tomita

13

mt@sfc.keio.ac.jp

Laboratory for Bioinformatics
Graduate School of Media and Governance
Department of Environmental Information
Keio University, 5322 Endo, Fujisawa 252-8520, Japan

1 Introduction
It is well accepted that the 3' end of 16S rRNA is directly involved in the procaryotic translation
initiation by pairing with the Shine-Dalgarno (SD) sequence, which is located in the ribosome-bindingsite of mRNA. According to the Shine and Dalgarno, E. coli's 5'UTR has the pattern of \AGGAG"(SD sequence), which is complement of 16S rRNA's 3' end sequence [1]. However, not all 5'UTRs ofE. coli have this pattern.
In this work, we systematically calculated free-energy values of the base pairing between the 3'
end of 16S rRNA and the 5' UTR of mRNA, in order to detect the mRNA binding sequence in 16SrRNA for various procaryotes.

2 Materials and Methods
With window gauge of 20bps, we exhaustively compute free energy values of base pairing of 5'UTR sequence of each gene with the 3' end sequence of 16S rRNA, using parameters based on thermodynamic
studies [2].
In this way, free-energy value is computed for each base position of each gene. We then takeaverage of those free-energy values for each base position, and plotted them to visualize base-pairing
patterns of the whole genome.

3 Results and discussion
The average free-energy values sharply drop about 15 bps upstream of the start codon in E. coli,
which is consistent with the model that the 3' end of 16S rRNA interacts with the SD sequence. H.
in uenzae and B. subtilis shows quite a similar pattern, indicating that the organisms have basicallythe same translation initiation mechanism (Fig. 1).
Other species, such as M. genitalium, M. pneumoniae, B. burgdorferi, H. pylori and Synechocystis
PCC6803, also show free-energy drops, although the drops are less evident (Fig. 2) and the shapes ofthe drops is signi cantly di erent from those in Fig. 1.
No free-energy drops can be seen in the genomes of Aquifex aeolicus and three archibacteria, M.
jannaschii, M. thermoautotrophicum and A. fulgidus (Fig. 3), suggesting that 16S rRNA of those
procaryotes does not base pair with a speci c region of mRNA. Those results lead us to suspect thatthese procaryotes employ an alternative mechanism for translation initiation.

Acknowledgements
This work is supported in part by a grant-in-aid for Scienti c Research on Priority Areas `Genome
Science' from The Ministry of Education, Science, Sports and Culture in Japan.
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References[1] Shine, J. and Dalgarno, L., The 3'-terminal sequence of Escherichia coli 16S ribosomal
RNA:Complementarity to nonsense triplets and ribosome binding sites, Proc. Nat. Acad. Sci.
USA, 71:1342{1346, 1974.
[2] Turner, D.H. et al., Improved parameters for prediction of RNA structure, Cold Spring Harb.
Symp. Quant. Biol., 52:123{133, 1987.
Free-energy
E.coliB.subtilis
H.influenzae

-7.00

-7.50

-8.00

-8.50

-9.00

-9.50

-10.00-10.50-11.00-11.50
Position-50.00-40.00-30.00-20.00-10.000.00

Figure 1: Sharp drops in free-energy values.
Free-energy
M.genitalium
M.pneumoniae
B.burgdorferi
H.pylori
Synechocystis

-7.00

-7.50

-8.00

-8.50

-9.00

-9.50

-10.00-10.50-11.00-11.50
Position-50.00-40.00-30.00-20.00-10.000.00

Figure 2: Less evident drops.
Free-energy
A.aeolicus
M.jannaschii
M.thermoautotrophicum
A.fulgidus

-7.00

-7.50

-8.00

-8.50

-9.00

-9.50

-10.00-10.50-11.00-11.50
Position-50.00-40.00-30.00-20.00-10.000.00

Figure 3: No signi cant drops.

259