Essential is Not Irreplaceable: Fitness Dynamics of Experimental E. coli RNase P RNA Heterologous Replacement
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While critical cellular components—such as the RNA moiety of bacterial ribonuclease P—can sometimes be replaced with a highly divergent homolog, the cellular response to such perturbations is often unexpectedly complex. RNase P is a ubiquitous and essential ribonucleoprotein involved in the processing of multiple RNA substrates, including tRNAs, small non-coding RNAs and intergenic operons. In Bacteria, RNase P RNAs have been subdivided—based on their secondary and tertiary structures—into two major groups (A and B), each with a distinct phylogenetic distribution. Despite the vast phylogenetic and structural gap that separates the two RNase P RNA classes, previous work suggested their interchangeability. Here, we explore in detail the functional and fitness consequences of replacing the endogenous Type-A Escherichia coli RNase P RNA with a Type-B homolog derived from Bacillus subtilis, and show that E. coli cells forced to survive with a chimeric RNase P as their sole source of RNase P activity exhibit extremely variable responses. The chimeric RNase P alters growth rates—used here as an indirect measure of fitness—in unpredictable ways, ranging from 3- to 20-fold reductions in maximal growth rate. The transcriptional behavior of cells harboring the chimeric RNAse P is also perturbed, affecting the levels of at least 79 different transcripts. Such transcriptional plasticity represents an important mechanism of transient adaptation which, when coupled with the emergence and eventual fixation of compensatory mutations, enables the cells to overcome the disruption of this tightly coevolving ribonucleoprotein.
KeywordsRNase P Ribozyme tRNA processing rnpB M1 RNA
This study was supported by NASA Grant NNX08AE90G and NSF Grant 9981394, as well as by funds from the Blakeslee Fund at Smith College. We thank Chris White-Ziegler, Laura Katz, and Adam Hall for comments on earlier versions of this manuscript. We thank Chris White-Ziegler, Scott Edmands, Adam Hall, and Wen Li for technical assistance. We are especially grateful to Dr. Norman Pace for permission to reproduce the structures shown in Figure 1, and for his thoughtful reading of this work. We also thank our two anonymous reviewers for their helpful comments which greatly improved the manuscript.
Conflict of interest
The authors declare they have no conflict of interest.
- Pope CF, McHugh TD, Gillespie SH (2009) Methods to determine fitness in bacteria. In: Gillespie SH, McHugh TD (eds) Antibiotic resistance protocols. Humana Press, Totowa, pp 113–121Google Scholar
- Turrini PCG, Loveland JL, Dorit RL (2012) By any other name: heterologous replacement of the Escherichia coli RNase P protein subunit has in vivo fitness consequences. PLoS ONE 7:e32456Google Scholar
- Yang IV, Chen E, Hasseman JP, Liang W, Frank BC, Wang S, Sharov V, Saeed AI, White J, Li J (2002) Within the fold: assessing differential expression measures and reproducibility in microarray assays. Genome Biol 3(1–0062):12Google Scholar