Affiliation:
1. Department of Biology, University of Ottawa, Ontario, Canada
2. Ottawa Institute of Systems Biology, University of Ottawa, Ontario, Canada
Abstract
AbstractMicroorganisms require efficient translation to grow and replicate rapidly, and translation is often rate-limited by initiation. A prominent feature that facilitates translation initiation in bacteria is the Shine–Dalgarno (SD) sequence. However, there is much debate over its conservation in Cyanobacteria and in chloroplasts which presumably originated from endosymbiosis of ancient Cyanobacteria. Elucidating the utilization of SD sequences in Cyanobacteria and in chloroplasts is therefore important to understand whether 1) SD role in Cyanobacterial translation has been reduced prior to chloroplast endosymbiosis or 2) translation in Cyanobacteria and in plastid has been subjected to different evolutionary pressures. To test these alternatives, we employed genomic, proteomic, and transcriptomic data to trace differences in SD usage among Synechocystis species, Microcystis aeruginosa, cyanophages, Nicotiana tabacum chloroplast, and Arabidopsis thaliana chloroplast. We corrected their mis-annotated 16S rRNA 3′ terminus using an RNA-Seq-based approach to determine their SD/anti-SD locational constraints using an improved measurement DtoStart. We found that cyanophages well-mimic Cyanobacteria in SD usage because both have been under the same selection pressure for SD-mediated initiation. Whereas chloroplasts lost this similarity because the need for SD-facilitated initiation has been reduced in plastids having much reduced genome size and different ribosomal proteins as a result of host-symbiont coevolution. Consequently, SD sequence significantly increases protein expression in Cyanobacteria but not in chloroplasts, and only Cyanobacterial genes compensate for a lack of SD sequence by having weaker secondary structures at the 5′ UTR. Our results suggest different evolutionary pressures operate on translation initiation in Cyanobacteria and in chloroplast.
Funder
Natural Sciences and Engineering Research Council of Canada
NSERC Doctoral Scholarship
Publisher
Oxford University Press (OUP)
Subject
Genetics,Ecology, Evolution, Behavior and Systematics
Reference61 articles.
1. How changes in anti-SD sequences would affect SD sequences in Escherichia coli and Bacillus subtilis;Abolbaghaei,2017
2. Basic local alignment search tool;Altschul;J Mol Biol,1990
3. RAM ribosomes are defective proofreaders;Andersson;Mol Gen Genet,1983
4. Highly resolved systems biology to dissect the etioplast-to-chloroplast transition in tobacco leaves;Armarego-Marriott;Plant Physiol,2019
5. Trimmomatic: a flexible trimmer for Illumina sequence data;Bolger;Bioinformatics,2014
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