Alterations in rRNA-mRNA interaction during plastid evolution.
Translation initiation depends on the recognition of mRNA by a ribosome. For this to occur, prokaryotes primarily use the Shine-Dalgarno (SD) interaction, where the 3'-tail of small subunit rRNA (core motif: 3'CCUCC) forms base pairs with a complementary signal sequence in the 5'-untranslated region of mRNA. Here, we examined what happened to SD interactions during the evolution of a cyanobacterial endosymbiont into modern plastids (including chloroplasts). Our analysis of available complete plastid genome sequences revealed that the majority of plastids retained SD interactions but with varying levels of usage. Parallel losses of SD interactions took place in plastids of Chlorophyta, Euglenophyta, and Chromerida/Apicomplexa lineages, presumably related to their extensive reductive evolution. Interestingly, we discovered that the classical SD interaction (3'CCUCC/5'GGAGG [rRNA/mRNA]) was replaced by an altered SD interaction (3'CCCU/5'GGGA or 3'CUUCC/5'GAAGG) through coordinated changes in the sequences of the core rRNA motif and its paired mRNA signal. These changes in plastids of Chlorophyta and Euglenophyta proceeded through intermediate stages that allowed both the classical and altered SD interactions. This coevolution between the rRNA motif and the mRNA signal demonstrates unexpected plasticity in the translation initiation machinery.
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Minato-ku, Tokyo, JapanThe Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan.
Kyungtaek
K
Lim
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Minato-ku, Tokyo, JapanThe Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan.
Ichizo
I
Kobayashi
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Minato-ku, Tokyo, JapanThe Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan knakai@ims.u-tokyo.ac.jp.
Kenta
K
Nakai
D000460:Chlorophyta / Q000235:genetics; D000458:Cyanobacteria / Q000235:genetics; D016822:Euglenida / Q000235:genetics; D019143:Evolution, Molecular; D054627:Genome, Plastid; D010802:Phylogeny; D018087:Plastids / Q000145:classification* / Q000235:genetics*; D012333:RNA, Messenger / Q000378:metabolism*; D012335:RNA, Ribosomal / Q000378:metabolism*
D012333:RNA, Messenger; D012335:RNA, Ribosomal
Shine–Dalgarno sequence; chloroplast; endosymbiosis; ribosome; translation