Advertisement

Journal of Molecular Evolution

, Volume 79, Issue 3–4, pp 143–152 | Cite as

Essential is Not Irreplaceable: Fitness Dynamics of Experimental E. coli RNase P RNA Heterologous Replacement

  • Jasmine L. Loveland
  • Jocelyn Rice
  • Paula C. G. Turrini
  • Michelle Lizotte-Waniewski
  • Robert L. DoritEmail author
Original Article

Abstract

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.

Keywords

RNase P Ribozyme tRNA processing rnpB M1 RNA 

Notes

Acknowledgments

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.

Supplementary material

239_2014_9646_MOESM1_ESM.doc (5.8 mb)
Supplementary material 1 (DOC 5946 kb)

References

  1. Alifano P, Rivellini F, Piscitelli C, Arraiano CM, Bruni CB, Carlomagno MS (1994) Ribonuclease E provides substrates for ribonuclease P-dependent processing of a polycistronic mRNA. Genes Dev 8:3021–3031CrossRefPubMedGoogle Scholar
  2. Altman S (2011) Ribonuclease P. Philos Trans R Soc B-Biol Sci 366:2936–2941CrossRefGoogle Scholar
  3. Altman S, Smith JD (1971) Tyrosine tRNA precursor molecule polynucleotide sequence. Nat New Biol 233:35–39CrossRefPubMedGoogle Scholar
  4. Barrick JE, Kauth MR, Strelioff CC, Lenski RE (2010) Escherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects. Mol Biol Evol 27:1338–1347PubMedCentralCrossRefPubMedGoogle Scholar
  5. Bourgaize DB, Fournier MJ (1987) Initiation of translation is impaired in E. coli cells deficient in 4.5S RNA. Nature 325:281–284CrossRefPubMedGoogle Scholar
  6. Buck AH, Dalby AB, Poole AW, Kazantsev AV, Pace NR (2005a) Protein activation of a ribozyme: the role of bacterial RNase P protein. EMBO J 24:3360–3368PubMedCentralCrossRefPubMedGoogle Scholar
  7. Buck AH, Kazantsev AV, Dalby AB, Pace NR (2005b) Structural perspective on the activation of RNAse P RNA by protein. Nat Struct Mol Biol 12:958–964CrossRefPubMedGoogle Scholar
  8. Bull JJ, Badgett MR, Wichman HA, Huelsenbeck JP, Hillis DM, Gulati A, Ho C, Molineux IJ (1997) Exceptional convergent evolution in a virus. Genetics 147:1497–1507PubMedCentralPubMedGoogle Scholar
  9. Cases I, de Lorenzo V (2005) Promoters in the environment: transcriptional regulation in its natural context. Nat Rev Microbiol 3:105–118CrossRefPubMedGoogle Scholar
  10. Chen J-L, Nolan JM, Harris ME, Pace NR (1998) Comparative photocross-linking analysis of the tertiary structures of Escherichia coli and Bacillus subtilis RNase P RNAs. EMBO J 17:1515–1525PubMedCentralCrossRefPubMedGoogle Scholar
  11. Cherayil B, Krupp G, Schuchert P, Char S, Soll D (1987) The RNA components of Schizosaccharomyces pombe RNase P are essential for cell viability. Gene 60:157–161CrossRefPubMedGoogle Scholar
  12. Clune J, Misevic D, Ofria C, Lenski RE, Elena SF, Sanjuan R (2008) Natural selection fails to optimize mutation rates for long-term adaptation on rugged fitness landscapes. PLoS Comput Biol 4:e1000187PubMedCentralCrossRefPubMedGoogle Scholar
  13. Dong H, Kirsebom LA, Nilsson L (1996) Growth rate regulation of 4.5 S RNA and M1 RNA the catalytic subunit of Escherichia coli RNase P. J Mol Biol 261:303–308CrossRefPubMedGoogle Scholar
  14. Esakova O, Krasilnikov A (2010) Of proteins and RNA: the RNase P/MRP family. RNA 16:1725–1747PubMedCentralCrossRefPubMedGoogle Scholar
  15. Gossringer M, Kretschmer-Kazemi Far R, Hartmann RK (2006) Analysis of RNase P protein (rnpA) expression in Bacillus subtilis utilizing strains with suppressible rnpA expression. J Bacteriol 188:6816–6823PubMedCentralCrossRefPubMedGoogle Scholar
  16. Guerrier-Takada C, Gardiner K, Marsh T, Pace NR, Altman S (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35:849–857CrossRefPubMedGoogle Scholar
  17. Guo B, Abdelraouf K, Ledesma KR, Nikolaou M, Tam VH (2012) Predicting bacterial fitness cost associated with drug resistance. J Antimicrob Chemother 67:928–932CrossRefPubMedGoogle Scholar
  18. Haga S, Tanaka T, Kikuchi Y (2004) Mutational analysis of the length of the J3/4 domain of Escherichia coli ribonuclease P ribozyme. Biosci Biotechnol Biochem 68:2630–2632CrossRefPubMedGoogle Scholar
  19. Hall TA, Brown JW (2001) The ribonuclease P family. Methods Enzymol 341:56–77CrossRefPubMedGoogle Scholar
  20. Harris JK, Haas ES, Williams D et al (2001) New insight into RNase P RNA structure from comparative analysis of the archaeal RNA. RNA 7:220–232PubMedCentralCrossRefPubMedGoogle Scholar
  21. Hartmann RK, Heinrich J, Schlegl J, Schuster H (1995) Precursor of C4 antisense RNA of bacteriophages P1 and P7 is a substrate for RNase P of Escherichia coli. Proc Natl Acad Sci USA 92:5822–5826PubMedCentralCrossRefPubMedGoogle Scholar
  22. Hoang TT, Karkhoff-Schweizer RR, Kutchma AJ, Schweizer HP (1998) A broad-host-range Flp-FRT recombination system for site-specific excision of chromosomally-located DNA sequences: application for isolation of unmarked Pseudomonas aeruginosa mutants. Gene 212:77–86CrossRefPubMedGoogle Scholar
  23. Jarrous N, Gopalan V (2010) Archaeal/eukaryal RNase P: subunits, functions and RNA diversification. Nucleic Acids Res 38:7885–7894PubMedCentralCrossRefPubMedGoogle Scholar
  24. Jovanovic M, Sanchez R, Altman S, Gopalan V (2002) Elucidation of structure–function relationships in the protein subunit of bacterial RNase P using a genetic complementation approach. Nucleic Acids Res 30:5065–5073PubMedCentralCrossRefPubMedGoogle Scholar
  25. Kazantsev AV, Pace NR (2006) Bacterial RNase P: a new view of an ancient enzyme. Nat Rev Microbiol 4:729–740CrossRefPubMedGoogle Scholar
  26. Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, Muniz-Rascado L et al (2011) EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res 39:D583–D590PubMedCentralCrossRefPubMedGoogle Scholar
  27. Kim MS, Park BH, Kim S, Lee YJ, Chung JH, Lee Y (1998) Complementation of the growth defect of an rnpA49 mutant of Escherichia coli by overexpression of arginine tRNA(CCG). Biochem Mol Biol Int 46:1153–1160PubMedGoogle Scholar
  28. Komine Y, Kitabatake M, Yokogawa T, Nishikawa K, Inokuchi H (1994) A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli. Proc Natl Acad Sci USA 91:9223–9227PubMedCentralCrossRefPubMedGoogle Scholar
  29. Krasilnikov AS, Yang X, Pan T, Mondragon A (2003) Crystal structure of the specificity domain of ribonuclease P. Nature 421:760–764CrossRefPubMedGoogle Scholar
  30. Krivenko AA, Kazantsev AV, Adamidi C, Harrington DJ, Pace NR (2002) Expression, purification, crystallization and preliminary diffraction analysis of RNase P protein from Thermotoga maritima. Acta Crystallogr D Biol Crystallogr 58:1234–1236CrossRefPubMedGoogle Scholar
  31. Lawrence NP, Richman A, Amini R, Altman S (1987) Heterologous enzyme function in Escherichia coli and the selection of genes encoding the catalytic RNA subunit of RNase P. Proc Natl Acad Sci USA 84:6825–6829PubMedCentralCrossRefPubMedGoogle Scholar
  32. Lee Y, Ramamoorthy R, Park CU, Schmidt FJ (1989) Sites of initiation and pausing in the Escherichia coli rnpB (M1 RNA) transcript. J Biol Chem 264:5098–5103PubMedGoogle Scholar
  33. Lee J, Kim Y, Kang SK, Lee Y (2008) RNase P-dependent cleavage of polycistronic mRNAs within their downstream coding regions in Escherichia coli. Bull Korean Chem Soc 29:1137CrossRefGoogle Scholar
  34. Li Y, Altman S (2003) A specific endoribonuclease, RNase P, affects gene expression of polycistronic operon mRNAs. Proc Natl Acad Sci USA 100:13213–13218PubMedCentralCrossRefPubMedGoogle Scholar
  35. Li Y, Cole K, Altman S (2003) The effect of a single, temperature-sensitive mutation on global gene expression in Escherichia coli. RNA 9:518–532PubMedCentralCrossRefPubMedGoogle Scholar
  36. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25:402–408CrossRefPubMedGoogle Scholar
  37. Martinez-Antonio A, Collado-Vides J (2003) Identifying global regulators in transcriptional regulatory networks in bacteria. Curr Opin Microbiol 6:482–489CrossRefPubMedGoogle Scholar
  38. Masquida B, Westhof E (2011) RNase P: at last, the key finds its lock. RNA 17:1615–1618PubMedCentralCrossRefPubMedGoogle Scholar
  39. Meyer-Leon L, Senecoff JF, Bruckner RC, Cox MM (1984) Site-specific genetic recombination promoted by the FLP protein of the yeast 2-micron plasmid in vitro. Cold Spring Harb Symp Quant Biol 49:797–804CrossRefPubMedGoogle Scholar
  40. Mohanty BK, Kushner SR (2007) Ribonuclease P processes polycistronic tRNA transcripts in Escherichia coli independent of ribonuclease E. Nucleic Acids Res 35:7614–7625PubMedCentralCrossRefPubMedGoogle Scholar
  41. Ostrowski EA, Woods RJ, Lenski RE (2008) The genetic basis of parallel and divergent phenotypic responses in evolving populations of Escherichia coli. Proc Biol Sci 275:277–284PubMedCentralCrossRefPubMedGoogle Scholar
  42. Panagiotidis CA, Drainas D, Huang SC (1992) Modulation of ribonuclease P expression in Escherichia coli by polyamines. Int J Biochem 24:1625–1631CrossRefPubMedGoogle Scholar
  43. Peck-Miller KA, Altman S (1991) Kinetics of the processing of the precursor to 4.5 S RNA, a naturally occurring substrate for RNase P from Escherichia coli. J Mol Biol 221:1–5CrossRefPubMedGoogle Scholar
  44. Pomeranz Krummel DA, Altman S (1999) Verification of phylogenetic predictions in vivo and the importance of the tetraloop motif in a catalytic RNA. Proc Natl Acad Sci USA 96:11200–11205CrossRefPubMedGoogle Scholar
  45. 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
  46. Smits WK, Kuipers OP, Veening JW (2006) Phenotypic variation in bacteria: the role of feedback regulation. Nat Rev Microbiol 4:259–271CrossRefPubMedGoogle Scholar
  47. Sniegowski PD, Gerrish PJ (2010) Beneficial mutations and the dynamics of adaptation in asexual populations. Philos Trans R Soc Lond B Biol Sci 365:1255–1263PubMedCentralCrossRefPubMedGoogle Scholar
  48. Sniegowski PD, Gerrish PJ, Lenski RE (1997) Evolution of high mutation rates in experimental populations of E. coli. Nature 387:703–705CrossRefPubMedGoogle Scholar
  49. Syvanen M (2012) Evolutionary implications of horizontal gene transfer. Annu Rev Genet 46:341–358CrossRefPubMedGoogle Scholar
  50. Torres-Larios A, Swinger KK, Pan T, Mondragon A (2006) Structure of ribonuclease P: a universal ribozyme. Curr Opin Struct Biol 16:327–335CrossRefPubMedGoogle Scholar
  51. Travisano M, Lenski RE (1996) Long-term experimental evolution in Escherichia coli. IV. Targets of selection and the specificity of adaptation. Genetics 143:15–26PubMedCentralPubMedGoogle Scholar
  52. 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
  53. van Opijnen T, Camilli A (2013) Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms. Nat Rev Micro 11:435–442CrossRefGoogle Scholar
  54. Waugh DS, Pace NR (1990) Complementation of an RNase P RNA (rnpB) gene deletion in Escherichia coli by homologous genes from distantly related eubacteria. J Bacteriol 172:6316–6322PubMedCentralPubMedGoogle Scholar
  55. Weber C, Hartig A, Hartmann RK, Rossmanith W (2014) Playing RNase P evolution: swapping the RNA catalyst for a protein reveals functional uniformity of highly divergent enzyme forms. PLoS Genet 10:e1004506PubMedCentralCrossRefPubMedGoogle Scholar
  56. Wegscheid B, Hartmann RK (2007) In vivo and in vitro investigation of bacterial type B RNase P interaction with tRNA 3′-CCA. Nucleic Acids Res 35:2060–2073PubMedCentralCrossRefPubMedGoogle Scholar
  57. Wegscheid B, Condon C, Hartmann RK (2006) Type A and B RNase P RNAs are interchangeable in vivo despite substantial biophysical differences. EMBO Rep 7:411–417PubMedCentralPubMedGoogle Scholar
  58. Yan W, Francklyn C (1994) Cytosine 73 is a discriminator nucleotide in vivo for histidyl-tRNA in Escherichia coli. J Biol Chem 269:10022–10027PubMedGoogle Scholar
  59. 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

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Jasmine L. Loveland
    • 1
    • 2
  • Jocelyn Rice
    • 2
  • Paula C. G. Turrini
    • 2
  • Michelle Lizotte-Waniewski
    • 2
    • 3
  • Robert L. Dorit
    • 2
    Email author
  1. 1.Department of Biological SciencesStanford UniversityStanfordUSA
  2. 2.Department of Biological SciencesSmith CollegeNorthamptonUSA
  3. 3.Department of Basic Science, Schmidt College of MedicineFlorida Atlantic UniversityBoca RatonUSA

Personalised recommendations