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Nucleic Acids Res. 2015 Feb 18;43(3):1783-94. doi: 10.1093/nar/gkv040. Epub 2015 Jan 23.

Engineered ribosomal RNA operon copy-number variants of E. coli reveal the evolutionary trade-offs shaping rRNA operon number.

Author information

1
Institute of Biochemistry, Synthetic and Systems Biology Unit, Biological Research Centre of the Hungarian Academy of Sciences, Szeged 6726, Hungary.
2
Scarab Genomics LLC, Madison, WI 53713, USA.
3
Dept. of Bacteriology, Univ. of Wisconsin-Madison, Madison, WI 53706, USA.
4
Institute of Biochemistry, Synthetic and Systems Biology Unit, Biological Research Centre of the Hungarian Academy of Sciences, Szeged 6726, Hungary posfaigy@nucleus.szbk.u-szeged.hu.

Abstract

Ribosomal RNA (rrn) operons, characteristically present in several copies in bacterial genomes (7 in E. coli), play a central role in cellular physiology. We investigated the factors determining the optimal number of rrn operons in E. coli by constructing isogenic variants with 5-10 operons. We found that the total RNA and protein content, as well as the size of the cells reflected the number of rrn operons. While growth parameters showed only minor differences, competition experiments revealed a clear pattern: 7-8 copies were optimal under conditions of fluctuating, occasionally rich nutrient influx and lower numbers were favored in stable, nutrient-limited environments. We found that the advantages of quick adjustment to nutrient availability, rapid growth and economic regulation of ribosome number all contribute to the selection of the optimal rrn operon number. Our results suggest that the wt rrn operon number of E. coli reflects the natural, 'feast and famine' life-style of the bacterium, however, different copy numbers might be beneficial under different environmental conditions. Understanding the impact of the copy number of rrn operons on the fitness of the cell is an important step towards the creation of functional and robust genomes, the ultimate goal of synthetic biology.

PMID:
25618851
PMCID:
PMC4330394
DOI:
10.1093/nar/gkv040
[Indexed for MEDLINE]
Free PMC Article

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