Global fitness landscapes of the Shine-Dalgarno sequence
- Syue-Ting Kuo1,6,
- Ruey-Lin Jahn2,6,
- Yuan-Ju Cheng1,6,
- Yi-Lan Chen3,
- Yun-Ju Lee1,
- Florian Hollfelder4,
- Jin-Der Wen3,5 and
- Hsin-Hung David Chou1,3
- 1Department of Life Science, National Taiwan University, Taipei 10617, Taiwan;
- 2Department of Electrical Engineering, National Taiwan University, Taipei 10617, Taiwan;
- 3Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan;
- 4Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom;
- 5Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
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↵6 These authors contributed equally to this work.
Abstract
Shine-Dalgarno sequences (SD) in prokaryotic mRNA facilitate protein translation by pairing with rRNA in ribosomes. Although conventionally defined as AG-rich motifs, recent genomic surveys reveal great sequence diversity, questioning how SD functions. Here, we determined the molecular fitness (i.e., translation efficiency) of 49 synthetic 9-nt SD genotypes in three distinct mRNA contexts in Escherichia coli. We uncovered generic principles governing the SD fitness landscapes: (1) Guanine contents, rather than canonical SD motifs, best predict the fitness of both synthetic and endogenous SD; (2) the genotype-fitness correlation of SD promotes its evolvability by steadily supplying beneficial mutations across fitness landscapes; and (3) the frequency and magnitude of deleterious mutations increase with background fitness, and adjacent nucleotides in SD show stronger epistasis. Epistasis results from disruption of the continuous base pairing between SD and rRNA. This “chain-breaking” epistasis creates sinkholes in SD fitness landscapes and may profoundly impact the evolution and function of prokaryotic translation initiation and other RNA-mediated processes. Collectively, our work yields functional insights into the SD sequence variation in prokaryotic genomes, identifies a simple design principle to guide bioengineering and bioinformatic analysis of SD, and illuminates the fundamentals of fitness landscapes and molecular evolution.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.260182.119.
- Received December 13, 2019.
- Accepted April 21, 2020.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
