Abstract
Bacteria growth depends crucially on protein synthesis, which is limited by ribosome synthesis. Ribosomal RNA (rRNA) transcription is the rate-limiting step of ribosome synthesis. It is generally proposed that the transcriptional initiation rate of rRNA operon is the primary factor that controls the rRNA synthesis. In this study, we established a convenient GFP-based reporter approach for measuring the bacterial rRNA chain elongation rate. We showed that the rRNA chain elongation rate of Escherichia coli remains constant under nutrient limitation and chloramphenicol inhibition. In contrast, rRNA chain elongation rate decreases dramatically under low temperatures. Strikingly, we found that Vibrio natriegens, the fastest growing bacteria known, has a 50% higher rRNA chain elongation rate than E. coli, which contributes to its rapid ribosome synthesis. Our study demonstrates that rRNA chain elongation rate is another important factor that affects the bacterial ribosome synthesis capacity.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Basan, M., Zhu, M., Dai, X., Warren, M., Sévin, D., Wang, Y.P., and Hwa, T. (2015). Inflating bacterial cells by increased protein synthesis. Mol Syst Biol 11, 836.
Borkowski, O., Goelzer, A., Schaffer, M., Calabre, M., Mäder, U., Aymerich, S., Jules, M., and Fromion, V. (2016). Translation elicits a growth rate-dependent, genome-wide, differential protein production in Bacillus subtilis. Mol Syst Biol 12, 870.
Bremer, H., and Dennis, P.P. (1996). Modulation of chemical composition and other parameters of the cell at different exponential growth rates. In Escherichia coli and Salmonella, Neidhardt FC, ed. (Washington, DC: Am Soc Microbiol), 2nd Ed, pp. 1553–1569.
Bremer, H., Hymes, J., and Dennis, P.P. (1974). Ribosomal RNA chain growth rate and RNA labeling patterns in Escherichia coli. J Theor Biol 45, 379–403.
Buckstein, M.H., He, J., and Rubin, H. (2008). Characterization of nucleotide pools as a function of physiological state in Escherichia coli. JB 190, 718–726.
Chen, Z., and Duan, X. (2011). Ribosomal RNA depletion for massively parallel bacterial RNA-sequencing applications. Methods Mol Biol 733, 93–103.
Dai, X., Zhu, M., Warren, M., Balakrishnan, R., Patsalo, V., Okano, H., Williamson, J.R., Fredrick, K., Wang, Y.P., and Hwa, T. (2016). Reduction of translating ribosomes enables Escherichia coli to maintain elongation rates during slow growth. Nat Microbiol 2, 16231.
Dalia, T.N., Hayes, C.A., Stolyar, S., Marx, C.J., McKinlay, J.B., and Dalia, A.B. (2017). Multiplex genome editing by natural transformation (MuGENT) for synthetic biology in Vibrio natriegens. ACS Synth Biol 6, 1650–1655.
Dennis, P.P. (1976). Effects of chloramphenicol on the transcriptional activities of ribosomal RNA and ribosomal protein genes in Escherichia coli. J Mol Biol 108, 535–546.
Dennis, P.P., Ehrenberg, M., and Bremer, H. (2004). Control of rRNA synthesis in Escherichia coli: a systems biology approach. Microbiol Mol Biol Rev 68, 639–668.
Dennis, P.P., Ehrenberg, M., Fange, D., and Bremer, H. (2009). Varying rate of RNA chain elongation during rrn transcription in Escherichia coli. J Bacteriol 191, 3740–3746.
Farewell, A., and Neidhardt, F.C. (1998). Effect of temperature on in vivo protein synthetic capacity in Escherichia coli. J Bacteriol 180, 4704–4710.
Frey, J., Chandler, M., and Caro, L. (1981). The initiation of chromosome replication in a dnaAts46 and a dnaA+ strain at various temperatures. Mol Gen Genet 182, 364–366.
Gourse, R.L., Gaal, T., Bartlett, M.S., Appleman, J.A., and Ross, W. (1996). rRNA transcription and growth rate-dependent regulation of ribosome synthesis in Escherichia coli. Annu Rev Microbiol 50, 645–677.
Harvey, R.J., and Koch, A.L. (1980). How partially inhibitory concentrations of chloramphenicol affect the growth of Escherichia coli. Antimicrob Agents Chemother 18, 323–337.
Hauryliuk, V., Atkinson, G.C., Murakami, K.S., Tenson, T., and Gerdes, K. (2015). Recent functional insights into the role of (p)ppGpp in bacterial physiology. Nat Rev Microbiol 13, 298–309.
Hoffart, E., Grenz, S., Lange, J., Nitschel, R., Müller, F., Schwentner, A., Feith, A., Lenfers-Lücker, M., Takors, R., and Blombach, B. (2017). High substrate uptake rates empower Vibrio natriegens as production host for industrial biotechnology. Appl Environ Microbiol 83.
Hui, S., Silverman, J.M., Chen, S.S., Erickson, D.W., Basan, M., Wang, J., Hwa, T., and Williamson, J.R. (2015). Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria. Mol Syst Biol 11, 784.
Iyer, S., Le, D., Park, B.R., and Kim, M. (2018). Distinct mechanisms coordinate transcription and translation under carbon and nitrogen starvation in Escherichia coli. Nat Microbiol 3, 741–748.
Iyer, S., Park, B.R., and Kim, M. (2016). Absolute quantitative measurement of transcriptional kinetic parameters in vivo. Nucleic Acids Res 44, e142.
Klumpp, S., and Hwa, T. (2008a). Growth-rate-dependent partitioning of RNA polymerases in bacteria. Proc Natl Acad Sci USA 105, 20245–20250.
Klumpp, S., and Hwa, T. (2008b). Stochasticity and traffic jams in the transcription of ribosomal RNA: Intriguing role of termination and antitermination. Proc Natl Acad Sci USA 105, 18159–18164.
Klumpp, S., Scott, M., Pedersen, S., and Hwa, T. (2013). Molecular crowding limits translation and cell growth. Proc Natl Acad Sci USA 110, 16754–16759.
Lee, H.H., Ostrov, N., Wong, B.G., Gold, M.A., Khalil, A., and Church, G. M. (2016). Vibrio natriegens, a new genomic powerhouse. bioRxiv, 058487.
Lee, H.H., Ostrov, N., Wong, B.G., Gold, M.A., Khalil, A.S., and Church, G.M. (2019). Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi. Nat Microbiol 4, 1105–1113.
Mandelstam, J. (1960). The intracellular turnover of protein and nucleic acids and its role in biochemical differentiation. Bacteriol Rev 24, 289–308.
Munafó, D.B., Langhorst, B.W., Chater, C.L., Sumner, C.J., Rodríguez, D. N., Russello, S., Gardner, A.F., Slatko, B.E., Stewart, F.J., and Sinicropi, D. (2016). Selective Depletion of Abundant RNAs to Enable Transcriptome Analysis of Low-Input and Highly Degraded Human RNA (John Wiley & Sons, Inc.).
O℉Neil, D., Glowatz, H., and Schlumpberger, M. (2013). Ribosomal RNA depletion for efficient use of RNA-seq capacity. Curr Protoc Mol Biol, Chapter 4, Unit4.19.
Paul, B.J., Ross, W., Gaal, T., and Gourse, R.L. (2004). rRNA transcription in Escherichia coli. Annu Rev Genet 38, 749–770.
Pedersen, S. (1984). Escherichia coli ribosomes translate in vivo with variable rate. EMBO J 3, 2895–2898.
Piir, K., Paier, A., Liiv, A., Tenson, T., and Maiväli, U. (2011). Ribosome degradation in growing bacteria. EMBO Rep 12, 458–462.
Santangelo, T.J., and Artsimovitch, I. (2011). Termination and antitermination: RNA polymerase runs a stop sign. Nat Rev Microbiol 9, 319–329.
Scott, M., Gunderson, C.W., Mateescu, E.M., Zhang, Z., and Hwa, T. (2010). Interdependence of cell growth and gene expression: origins and consequences. Science 330, 1099–1102.
Scott, M., Klumpp, S., Mateescu, E.M., and Hwa, T. (2014). Emergence of robust growth laws from optimal regulation of ribosome synthesis. Mol Syst Biol 10, 747.
Shen, V., and Bremer, H. (1977). Chloramphenicol-induced changes in the synthesis of ribosomal, transfer, and messenger ribonucleic acids in Escherichia coli B/r. J Bacteriol 130, 1098–1108.
Vogel, U., and Jensen, K.F. (1997). NusA is required for ribosomal antitermination and for modulation of the transcription elongation rate of both antiterminated RNA and mRNA. J Biol Chem 272, 12265–12271.
Vogel, U., and Jensen, K.F. (1994). Effects of guanosine 3′,5′-bisdiphosphate (ppGpp) on rate of transcription elongation in isoleucine-starved Escherichia coli. J Biol Chem 269, 16236–16241.
Vogel, U., and Jensen, K.F. (1995). Effects of the antiterminator BoxA on transcription elongation kinetics and ppGpp inhibition of transcription elongation in Escherichia coli. J Biol Chem 270, 18335–18340.
Waldron, C., and Lacroute, F. (1975). Effect of growth rate on the amounts of ribosomal and transfer ribonucleic acids in yeast. J Bacteriol 122, 855–865.
Weinstock, M.T., Hesek, E.D., Wilson, C.M., and Gibson, D.G. (2016). Vibrio natriegens as a fast-growing host for molecular biology. Nat Methods 13, 849–851.
Weisberg, R.A., and Gottesman, M.E. (1999). Processive antitermination. J Bacteriol 181, 359–367.
Zhu, M., and Dai, X. (2018). On the intrinsic constraint of bacterial growth rate: M. tuberculosis℉s view of the protein translation capacity. Crit Rev Microbiol 44, 455–464.
Zhu, M., and Dai, X. (2019). Growth suppression by altered (p)ppGpp levels results from non-optimal resource allocation in Escherichia coli. Nucleic Acids Res 47, 4684–4693.
Zhu, M., Dai, X., and Wang, Y.P. (2016). Real time determination of bacterial in vivo ribosome translation elongation speed based on LacZa complementation system. Nucleic Acids Res 44, e155.
Zhu, M., Mori, M., Hwa, T., and Dai, X. (2019). Disruption of transcription-translation coordination in Escherichia coli leads to premature transcriptional termination. Nat Microbiol 4, 2347–2356.
Acknowledgements
We thank members of Terry Hwa lab for useful discussion during conceptualization stages of this work. This work was supported by the National Natural Science Foundation of China (31700089, 31700039, 31870028 and 31970027) and by self-determined research funds of CCNU from the colleges’ basic research and operation of MOE (CCNU18KFY01, CCNU19TS028 and CCNU20TS023).
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Compliance and ethics The author(s) declare that they have no conflict of interest.
Electronic Supplementary Material
Rights and permissions
About this article
Cite this article
Zhu, M., Mu, H., Jia, M. et al. Control of ribosome synthesis in bacteria: the important role of rRNA chain elongation rate. Sci. China Life Sci. 64, 795–802 (2021). https://doi.org/10.1007/s11427-020-1742-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11427-020-1742-4