So Nakagawa a, Yoshihito Niimura b, Kin-ichiro Miura c,1, and Takashi Gojobori a,d,2
-Author Affiliations
aCenter for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima 411-8540, Japan;
bDepartment of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan;
cDepartment of Medical Genome Science, Graduate School of Frontier Science, University of Tokyo, Kashiwa 277-8562, Japan; and
dBiomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
Communicated by Tomoko Ohta, National Institute of Genetics, Mishima, Japan, February 23, 2010 (received for review December 7, 2009)
Abstract
It is generally believed that prokaryotic translation is initiated by the interaction between the Shine-Dalgarno (SD) sequence in the 5′ UTR of an mRNA and the anti-SD sequence in the 3′ end of a 16S ribosomal RNA. However, there are two exceptional mechanisms, which do not require the SD sequence for translation initiation: one is mediated by a ribosomal protein S1 (RPS1) and the other used leaderless mRNA that lacks its 5′ UTR. To understand the evolutionary changes of the mechanisms of translation initiation, we examined how universal the SD sequence is as an effective initiator for translation among prokaryotes. We identified the SD sequence from 277 species (249 eubacteria and 28 archaebacteria). We also devised an SD index that is a proportion of SD-containing genes in which the differences of GC contents are taken into account. We found that the SD indices varied among prokaryotic species, but were similar within each phylum. Although the anti-SD sequence is conserved among species, loss of the SD sequence seems to have occurred multiple times, independently, in different phyla. For those phyla, RPS1-mediated or leaderless mRNA-used mechanisms of translation initiation are considered to be working to a greater extent. Moreover, we also found that some species, such as Cyanobacteria, may acquire new mechanisms of translation initiation. Our findings indicate that, although translation initiation is indispensable for all protein-coding genes in the genome of every species, its mechanisms have dynamically changed during evolution.
It is generally believed that prokaryotic translation is initiated by the interaction between the Shine-Dalgarno (SD) sequence in the 5′ UTR of an mRNA and the anti-SD sequence in the 3′ end of a 16S ribosomal RNA. However, there are two exceptional mechanisms, which do not require the SD sequence for translation initiation: one is mediated by a ribosomal protein S1 (RPS1) and the other used leaderless mRNA that lacks its 5′ UTR. To understand the evolutionary changes of the mechanisms of translation initiation, we examined how universal the SD sequence is as an effective initiator for translation among prokaryotes. We identified the SD sequence from 277 species (249 eubacteria and 28 archaebacteria). We also devised an SD index that is a proportion of SD-containing genes in which the differences of GC contents are taken into account. We found that the SD indices varied among prokaryotic species, but were similar within each phylum. Although the anti-SD sequence is conserved among species, loss of the SD sequence seems to have occurred multiple times, independently, in different phyla. For those phyla, RPS1-mediated or leaderless mRNA-used mechanisms of translation initiation are considered to be working to a greater extent. Moreover, we also found that some species, such as Cyanobacteria, may acquire new mechanisms of translation initiation. Our findings indicate that, although translation initiation is indispensable for all protein-coding genes in the genome of every species, its mechanisms have dynamically changed during evolution.
dynamic evolution Shine-Dalgarno sequence ribosomal protein S1
Footnotes
2To whom correspondence should be addressed. E-mail:tgojobor@genes.nig.ac.jp.
Author contributions: S.N., Y.N., K.-i.M., and T.G. designed research; S.N. performed research; S.N. contributed new reagents/analytic tools; S.N. analyzed data; and S.N., Y.N., and T.G. wrote the paper.
↵1Deceased September 21, 2009.
The authors declare no conflict of interest.
This article contains supporting information online at www.pnas.org/cgi/content/full/1002036107/DCSupplemental.
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