Analysis of Translation Initiation Sites in the Complete
Genome of Mycoplasma genitalium Suggests That
This Bacterium Uses Alternative Signal for Translation
Initiation
Rintaro Saito

Masaru Tomita

12rsaito@mag.keio.ac.jp

13

mt@sfc.keio.ac.jp

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

1 Introduction
Although the Shine-Dalgarno (SD) sequence [5] is widely accepted as the signal sequence for ribosomemRNA binding in procaryotic translation initiation, this sequence is not well conserved among genes
within or among species. This is especially striking in Mycoplasma genitalium [2], where no obvious
conserved sequence can be observed upstream of start codons[1]. To investigate the possibility ofan alternative sequence pattern to account for the lack of SD sequences, we have conducted computer analyses of translation initiation sites (ORF start sites) in the complete genome sequence of M.
genitalium [3].

2 Materials and Methods
Frequencies of all 64 triplets in within 500 bases upstream from start codons are computed. Then standardized frequencies (Sf ) of each triplet at each position with respect to start codons were calculated
according to the following formula:
Sf= pno 0np

0np(1 p)N(0; 1);

where n is the number of sequences to analyze, p is frequency of speci c triplets that appear in thesequences, and no is the number of the speci c triplets that were observed at speci c position.

3 Results and Discussion
Triplets with signi cant frequencies are listed in Fig. 1(a). Frequency of triplet \TAA" was the mostsigni cant one. We have plotted frequency of \TAA" around start codons. An outstanding peakin the frequency of the triplet \TAA" was observed between positions 027 to 04 (Fig. 1(b)). Thesimilar peak was still observed even when stop codons (TAA) of the preceding genes were eliminatedfrom our analysis by only counting translation initiation sites with their preceding genes oppositelyoriented (head-on genes) (Fig. 1(c)). The fact that the complementary triplet \TTA" does not exist
in the 3'-terminus of 16S rRNA of M. genitalium1 leads us to suspect the existence of an alternative
mechanism for translation initiation in M. genitalium [4].
1

The 3'-terminal sequence of M. genitalium 16S rRNA is \gggggtggatcacctc". Thus the predicted ribosome binding
sequence would be \gaggtgatccaccccc".

262

(a)
Position

06
07
012
06
03

Sf

Triplet

9:89

taa

6:38

tta

5:90

taa

5:87

ata

5:59

gta

Position

019
011
015
04

Sf
5:47

Triplet

5:29

aaa

5:19

taa

5:17

agt

(b)

tta

(c)

Frequency x 10-3

Frequency x 10-3
TAATAA

140.00140.00130.00130.00120.00120.00110.00110.00100.00100.00

90.00

90.00

80.00

80.00

70.00

70.00

60.00

60.00

50.00

50.00

40.00

40.00

30.00

30.00

20.00

20.00

10.00

10.00

0.00

0.00
Position-200.00-100.00

0.00

100.00200.00

Position-200.00-100.00

0.00

100.00200.00Figure 1: (a) Signi cant triplets that appears upstream of start codons and their positions and standardized frequencies. (b) Frequency of TAA triplets around start codons in M. genitalium. (c)Frequency of TAA triplets around start codons of head-on genes (Smoothed).

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

References[1] Dalphin M.E. et al., The translational signal database, TransTerm, is now a relational database,Nuc. Acid. Res., 26:335{337, 1998.
[2] Dybvig, K. and Voelker, L., Molecular Biology of Mycoplasmas, Annu. Rev. Microbiol., 50:25{57,1996.
[3] Fraser, C.M. et al., The minimal gene complement of Mycoplasma genitalium, Science, 270:397{403, 1995.
[4] Loechel, S., Inamine, J.M., and Hu, P.-C., A novel translation initiation region from Mycoplasma
genitalium that functions in Escherichia coli, Nuc. Acid. Res., 19:6905{6911, 1991.
[5] Shine, J. and Dalgarno, L., The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA:
Complementarity to nonsense triplets and ribosome binding sites, Proc. Natl. Acad. Sci. USA,71:1342{1346, 1974.

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