1887

Abstract

We analysed the response of the model bacterium to abrupt depletion of glucose after several generations of exponential growth. Glucose depletion resulted in a drastic drop in the energy charge accompanied by an extremely low GTP level and an almost total arrest of protein synthesis. Strikingly, the cell prioritized the continued synthesis of a few proteins, of which the ribosomal dimerization factor YfiA was the most highly expressed. Transcriptome analysis showed no immediate decrease in total mRNA levels despite the lowered nucleotide pools and only marginally increased levels of the transcript. Severe up-regulation of genes in the FruR, CcpA, ArgR and AhrC regulons were consistent with a downshift in carbon and energy source. Based upon the results, we suggest that transcription proceeded long enough to record the transcriptome changes from activation of the FruR, CcpA, ArgR and AhrC regulons, while protein synthesis stopped due to an extremely low GTP concentration emerging a few minutes after glucose depletion. The deletion mutant exhibited a longer lag phase upon replenishment of glucose and a faster death rate after prolonged starvation supporting that YfiA-mediated ribosomal dimerization is important for keeping long-term starved cells viable and competent for growth initiation.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.000362
2016-10-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/micro/162/10/1829.html?itemId=/content/journal/micro/10.1099/mic.0.000362&mimeType=html&fmt=ahah

References

  1. Anderson K. L., Roberts C., Disz T., Vonstein V., Hwang K., Overbeek R., Olson P. D., Projan S. J., Dunman P. M. 2006; Characterization of the Staphylococcus aureus heat shock, cold shock, stringent, and SOS responses and their effects on log-phase mRNA turnover. J Bacteriol 188:6739–6756 [View Article][PubMed]
    [Google Scholar]
  2. Atkinson D. E. 1968; The energy charge of the adenylate pool as a regulatory parameter. Interaction with feedback modifiers. Biochemistry 7:4030–4034 [View Article][PubMed]
    [Google Scholar]
  3. Barrière C., Veiga-da-Cunha M., Pons N., Guédon E., van Hijum S. A., Kok J., Kuipers O. P., Ehrlich D. S., Renault P. 2005; Fructose utilization in Lactococcus lactis as a model for low-GC gram-positive bacteria: its regulator, signal, and DNA-binding site. J Bacteriol 187:3752–3761 [View Article][PubMed]
    [Google Scholar]
  4. Brøndsted L., Hammer K. 1999; Use of the integration elements encoded by the temperate lactococcal bacteriophage TP901-1 to obtain chromosomal single-copy transcriptional fusions in Lactococcus lactis . Appl Environ Microbiol 65:752–758[PubMed]
    [Google Scholar]
  5. Carvalho B. S., Irizarry R. A. 2010; A framework for oligonucleotide microarray preprocessing. Bioinformatics 26:2363–2367 [View Article][PubMed]
    [Google Scholar]
  6. Dressaire C., Redon E., Gitton C., Loubière P., Monnet V., Cocaign-Bousquet M. 2011; Investigation of the adaptation of Lactococcus lactis to isoleucine starvation integrating dynamic transcriptome and proteome information. Microb Cell Fact 10:S18 [View Article][PubMed]
    [Google Scholar]
  7. Gasson M. J. 1983; Plasmid complements of Streptococcus lactis NCDO 712 and other lactic streptococci after protoplast-induced curing. J Bacteriol 154:1–9[PubMed]
    [Google Scholar]
  8. Gentleman R. C., Carey V. J., Bates D. M., Bolstad B., Dettling M., Dudoit S., Ellis B., Gautier L., Ge Y. et al. 2004; Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5:R80 [View Article][PubMed]
    [Google Scholar]
  9. Gualerzi C. O., Giuliodori A. M., Pon C. L. 2003; Transcriptional and post-transcriptional control of cold-shock genes. J Mol Biol 331:527–539 [View Article][PubMed]
    [Google Scholar]
  10. Holo H., Nes I. F. 1989; High-frequency transformation, by electroporation, of Lactococcus lactis subsp. cremoris grown with glycine in osmotically stabilized media. Appl Environ Microbiol 55:3119–3123[PubMed]
    [Google Scholar]
  11. Jendresen C. B., Martinussen J., Kilstrup M. 2012; The PurR regulon in Lactococcus lactis - transcriptional regulation of the purine nucleotide metabolism and translational machinery. Microbiology 158:2026–2038 [View Article][PubMed]
    [Google Scholar]
  12. Jendresen C. B., Dimitrov P., Gautier L., Liu M., Martinussen J., Kilstrup M. 2014; Towards in vivo regulon kinetics: PurR activation by 5-phosphoribosyl-α-1-pyrophosphate during purine depletion in Lactococcus lactis . Microbiology 160:1321–1331 [View Article][PubMed]
    [Google Scholar]
  13. Jensen P. R., Hammer K. 1993; Minimal requirements for exponential growth of Lactococcus lactis . Appl Environ Microbiol 59:4363–4366[PubMed]
    [Google Scholar]
  14. Jensen K. F., Fast R., Karlström O., Larsen J. N. 1986; Association of RNA polymerase having increased Km for ATP and UTP with hyperexpression of the pyrB and pyrE genes of Salmonella typhimurium . J Bacteriol 166:857–865[PubMed]
    [Google Scholar]
  15. Kilstrup M., Jacobsen S., Hammer K., Vogensen F. K. 1997; Induction of heat shock proteins DnaK, GroEL, and GroES by salt stress in Lactococcus lactis . Appl Environ Microbiol 63:1826–1837[PubMed]
    [Google Scholar]
  16. Kline B. C., McKay S. L., Tang W. W., Portnoy D. A. 2015; The Listeria monocytogenes hibernation-promoting factor is required for the formation of 100S ribosomes, optimal fitness, and pathogenesis. J Bacteriol 197:581–591 [View Article][PubMed]
    [Google Scholar]
  17. Kornberg H., Lambourne L. T. 1994; The role of phosphoenolpyruvate in the simultaneous uptake of fructose and 2-deoxyglucose by Escherichia coli . Proc Natl Acad Sci U S A 91:11080–11083 [View Article][PubMed]
    [Google Scholar]
  18. Larsen R., van Hijum S. A., Martinussen J., Kuipers O. P., Kok J. 2008; Transcriptome analysis of the Lactococcus lactis ArgR and AhrC regulons. Appl Environ Microbiol 74:4768–4771 [View Article][PubMed]
    [Google Scholar]
  19. Law J., Buist G., Haandrikman A., Kok J., Venema G., Leenhouts K. 1995; A system to generate chromosomal mutations in Lactococcus lactis which allows fast analysis of targeted genes. J Bacteriol 177:7011–7018[PubMed]
    [Google Scholar]
  20. Leenhouts K., Buist G., Bolhuis A., ten Berge A., Kiel J., Mierau I., Dabrowska M., Venema G., Kok J. 1996; A general system for generating unlabelled gene replacements in bacterial chromosomes. Mol Gen Genet 253:217–224 [View Article][PubMed]
    [Google Scholar]
  21. Magdenoska O., Martinussen J., Thykaer J., Nielsen K. F. 2013; Dispersive solid phase extraction combined with ion-pair ultra high-performance liquid chromatography tandem mass spectrometry for quantification of nucleotides in Lactococcus lactis . Anal Biochem 440:166–177 [View Article][PubMed]
    [Google Scholar]
  22. Maguin E., Prévost H., Ehrlich S. D., Gruss A. 1996; Efficient insertional mutagenesis in lactococci and other gram-positive bacteria. J Bacteriol 178:931–935[PubMed]
    [Google Scholar]
  23. Martinussen J., Wadskov-Hansen S., Hammer K. 2003; Two nucleoside uptake systems in Lactococcus lactis: competition between purine nucleosides and cytidine allows for modulation of intracellular nucleotide pools. J Bacteriol 185:1503–1508 [View Article][PubMed]
    [Google Scholar]
  24. Mesters J. R., Potapov A. P., de Graaf J. M., Kraal B. 1994; Synergism between the GTPase activities of EF-Tu.GTP and EF-G.GTP on empty ribosomes. Elongation factors as stimulators of the ribosomal oscillation between two conformations. J Mol Biol 242:644–654 [View Article][PubMed]
    [Google Scholar]
  25. Poolman B., Smid E. J., Veldkamp H., Konings W. N. 1987; Bioenergetic consequences of lactose starvation for continuously cultured Streptococcus cremoris . J Bacteriol 169:1460–1468[PubMed]
    [Google Scholar]
  26. Puri P., Eckhardt T. H., Franken L. E., Fusetti F., Stuart M. C., Boekema E. J., Kuipers O. P., Kok J., Poolman B. 2014; Lactococcus lactis YfiA is necessary and sufficient for ribosome dimerization. Mol Microbiol 91:394–407 [View Article][PubMed]
    [Google Scholar]
  27. Rallu F., Gruss A., Ehrlich S. D., Maguin E. 2000; Acid- and multistress-resistant mutants of Lactococcus lactis: identification of intracellular stress signals. Mol Microbiol 35:517–528 [View Article][PubMed]
    [Google Scholar]
  28. Redon E., Loubiere P., Cocaign-Bousquet M. 2005a; Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280:36380–36385 [View Article]
    [Google Scholar]
  29. Redon E., Loubiere P., Cocaign-Bousquet M. 2005b; Transcriptome analysis of the progressive adaptation of Lactococcus lactis to carbon starvation. J Bacteriol 187:3589–3592 [View Article]
    [Google Scholar]
  30. Reiss S., Pané-Farré J., Fuchs S., François P., Liebeke M., Schrenzel J., Lindequist U., Lalk M., Wolz C. et al. 2012; Global analysis of the Staphylococcus aureus response to mupirocin. Antimicrob Agents Chemother 56:787–804 [View Article][PubMed]
    [Google Scholar]
  31. Samartzidou H., Widger W. R. 1998; Transcriptional and posttranscriptional control of mRNA from lrtA, a light-repressed transcript in Synechococcus sp. PCC 7002. Plant Physiol 117:225–234 [View Article][PubMed]
    [Google Scholar]
  32. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning: A Laboratory Manual, 2nd edn. pp. 7–37 Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  33. Smyth G. K. 2005; Limma: Linear Models for Microarray Data. In Bioinformatics and Computational Biology Solutions Using R and Bioconductor , pp. 397–420 Edited by Gentleman R., Carey V., Huber W., Irizarry R., Dudoit S. New York, NY:: Springer; [CrossRef]
    [Google Scholar]
  34. Terzaghi B. E., Sandine W. E. 1975; Improved medium for lactic streptococci and their bacteriophages. Appl Microbiol 29:807–813[PubMed]
    [Google Scholar]
  35. Ueta M., Ohniwa R. L., Yoshida H., Maki Y., Wada C., Wada A. 2008; Role of HPF (hibernation promoting factor) in translational activity in Escherichia coli . J Biochem 143:425–433 [View Article][PubMed]
    [Google Scholar]
  36. Ueta M., Wada C., Wada A. 2010; Formation of 100S ribosomes in Staphylococcus aureus by the hibernation promoting factor homolog SaHPF. Genes Cells 15:43–58 [View Article][PubMed]
    [Google Scholar]
  37. Ueta M., Wada C., Daifuku T., Sako Y., Bessho Y., Kitamura A., Ohniwa R. L., Morikawa K., Yoshida H. et al. 2013; Conservation of two distinct types of 100S ribosome in bacteria. Genes Cells 18:554–574 [View Article][PubMed]
    [Google Scholar]
  38. Varmanen P., Ingmer H., Vogensen F. K. 2000; ctsR of Lactococcus lactis encodes a negative regulator of clp gene expression. Microbiology 146:1447–1455 [View Article][PubMed]
    [Google Scholar]
  39. Wada A. 1998; Growth phase coupled modulation of Escherichia coli ribosomes. Genes Cells 3:203–208 [View Article][PubMed]
    [Google Scholar]
  40. Wada A., Yamazaki Y., Fujita N., Ishihama A. 1990; Structure and probable genetic location of a “ribosome modulation factor” associated with 100S ribosomes in stationary-phase Escherichia coli cells. Proc Natl Acad Sci U S A 87:2657–2661 [View Article][PubMed]
    [Google Scholar]
  41. Wada A., Igarashi K., Yoshimura S., Aimoto S., Ishihama A. 1995; Ribosome modulation factor: stationary growth phase-specific inhibitor of ribosome functions from Escherichia coli . Biochem Biophys Res Commun 214:410–417 [View Article][PubMed]
    [Google Scholar]
  42. Willemoës M., Mølgaard A., Johansson E., Martinussen J. 2005; Lid L11 of the glutamine amidotransferase domain of CTP synthase mediates allosteric GTP activation of glutaminase activity. FEBS J 272:856–864 [View Article][PubMed]
    [Google Scholar]
  43. Wolf C., Hochgräfe F., Kusch H., Albrecht D., Hecker M., Engelmann S. 2008; Proteomic analysis of antioxidant strategies of Staphylococcus aureus: diverse responses to different oxidants. Proteomics 8:3139–3153 [View Article][PubMed]
    [Google Scholar]
  44. Yamagishi M., Matsushima H., Wada A., Sakagami M., Fujita N., Ishihama A. 1993; Regulation of the Escherichia coli rmf gene encoding the ribosome modulation factor: growth phase- and growth rate-dependent control. EMBO J 12:625–630[PubMed]
    [Google Scholar]
  45. Yoshida H., Wada A. 2014; The 100S ribosome: ribosomal hibernation induced by stress. Wiley Interdiscip Rev RNA 5:723–732 [View Article][PubMed]
    [Google Scholar]
  46. Zomer A. L., Buist G., Larsen R., Kok J., Kuipers O. P. 2007; Time-resolved determination of the CcpA regulon of Lactococcus lactis subsp. cremoris MG1363. J Bacteriol 189:1366–1381 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.000362
Loading
/content/journal/micro/10.1099/mic.0.000362
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error