1887

Microbiology Society logo

Volume 156, Issue 8

Role of Hfq in iron-dependent and -independent gene regulation in Free

Abstract

In , iron-responsive gene regulation is mediated primarily by the ferric uptake regulator (Fur) protein. When complexed with iron, Fur represses gene expression by preventing transcription initiation. Fur can also indirectly activate gene expression via the repression of regulatory small RNAs (sRNA). One such Fur- and iron-regulated sRNA, NrrF, was previously identified in and shown to repress expression of the and genes encoding subunits of the succinate dehydrogenase complex. In the majority of Gram-negative bacteria, sRNA-mediated regulation requires a cofactor RNA-binding protein (Hfq) for proper gene regulation and stabilization. In this study, we examined the role of Hfq in NrrF-mediated regulation of the succinate dehydrogenase genes in and the effect of an mutation on iron-responsive gene regulation more broadly. We first demonstrated that the stability of NrrF, as well as the regulation of and , was unaltered in the mutant. Secondly, we established that iron-responsive gene regulation of the Fur-regulated gene was dependent on Hfq. Finally, we demonstrated that in , Hfq functions in a global manner to control expression of many ORFs and intergenic regions via iron-independent mechanisms. Collectively these studies demonstrate that in , iron- and NrrF-mediated regulation of and can occur independently of Hfq, although Hfq functions more globally to control regulation of other genes primarily by iron-independent mechanisms.

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): CDM, chemically defined media , IG, intergenic , qRT-PCR, quantitative RT-PCR and sRNA, small RNA
SGM
Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.039040-0
2010-08-01
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/micro/156/8/2316.html?itemId=/content/journal/micro/10.1099/mic.0.039040-0&mimeType=html&fmt=ahah

References

  1. Bohn C., Rigoulay C., Bouloc P. 2007; No detectable effect of RNA-binding protein Hfq absence in Staphylococcus aureus. BMC Microbiol 7:10
     [Google Scholar]
  2. Bolstad B. M., Irizarry R. A., Astrand M., Speed T. P. 2003; A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19:185–193
     [Google Scholar]
  3. Christiansen J. K., Nielsen J. S., Ebersbach T., Valentin-Hansen P., Sogaard-Andersen L., Kallipolitis B. H. 2006; Identification of small Hfq-binding RNAs in Listeria monocytogenes. RNA 12:1383–1396
     [Google Scholar]
  4. Davis B. M., Quinones M., Pratt J., Ding Y., Waldor M. K. 2005; Characterization of the small untranslated RNA RyhB and its regulon in Vibrio cholerae. J Bacteriol 187:4005–4014
     [Google Scholar]
  5. Delany I., Ieva R., Alaimo C., Rappuoli R., Scarlato V. 2003; The iron-responsive regulator Fur is transcriptionally autoregulated and not essential in Neisseria meningitidis. J Bacteriol 185:6032–6041
     [Google Scholar]
  6. Delany I., Grifantini R., Bartolini E., Rappuoli R., Scarlato V. 2006; Effect of Neisseria meningitidis fur mutations on global control of gene transcription. J Bacteriol 188:2483–2492
     [Google Scholar]
  7. Desai P. J., Angerer A., Genco C. A. 1996; Analysis of Fur binding to operator sequences within the Neisseria gonorrhoeae fbpA promoter. J Bacteriol 178:5020–5023
     [Google Scholar]
  8. Escolar L., Perez-Martin J., de Lorenzo V. 1998a; Binding of the Fur (ferric uptake regulator) repressor of Escherichia coli to arrays of the GATAAT sequence. J Mol Biol 283:537–547
     [Google Scholar]
  9. Escolar L., Perez-Martin J., de Lorenzo V. 1998b; Coordinated repression in vitro of the divergent fepA–fes promoters of Escherichia coli by the iron uptake regulation (Fur) protein. J Bacteriol 180:2579–2582
     [Google Scholar]
  10. Fantappie L., Metruccio M. M., Seib K. L., Oriente F., Cartocci F., Ferlicca M., Giuliani M., Scarlato V., Delany I. 2009; The RNA chaperone Hfq is involved in stress response and virulence in Neisseria meningitidis and is a pleiotropic regulator of protein expression. Infect Immun 77:1842–1853
     [Google Scholar]
  11. Franze de Fernandez M. T., Eoyang L., August J. T. 1968; Factor fraction required for the synthesis of bacteriophage Q β-RNA. Nature 219:588–590
     [Google Scholar]
  12. Gaballa A., Antelmann H., Aguilar C., Khakh S. K., Song K. B., Smaldone G. T., Helmann J. D. 2008; The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins. Proc Natl Acad Sci U S A 105:11927–11932
     [Google Scholar]
  13. Gottesman S. 2004; The small RNA regulators of Escherichia coli: roles and mechanisms. Annu Rev Microbiol 58:303–328
     [Google Scholar]
  14. Grifantini R., Sebastian S., Frigimelica E., Draghi M., Bartolini E., Muzzi A., Rappuoli R., Grandi G., Genco C. A. 2003; Identification of iron-activated and -repressed Fur-dependent genes by transcriptome analysis of Neisseria meningitidis group B. Proc Natl Acad Sci U S A 100:9542–9547
     [Google Scholar]
  15. Heidrich N., Chinali A., Gerth U., Brantl S. 2006; The small untranslated RNA SR1 from the Bacillus subtilis genome is involved in the regulation of arginine catabolism. Mol Microbiol 62:520–536
     [Google Scholar]
  16. Heidrich N., Moll I., Brantl S. 2007; In vitro analysis of the interaction between the small RNA SR1 and its primary target ahrC mRNA. Nucleic Acids Res 35:4331–4346
     [Google Scholar]
  17. Irizarry R. A., Hobbs B., Collin F., Beazer-Barclay Y. D., Antonellis K. J., Scherf U., Speed T. P. 2003; Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4:249–264
     [Google Scholar]
  18. Majdalani N., Vanderpool C. K., Gottesman S. 2005; Bacterial small RNA regulators. Crit Rev Biochem Mol Biol 40:93–113
     [Google Scholar]
  19. Masse E., Gottesman S. 2002; A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc Natl Acad Sci U S A 99:4620–4625
     [Google Scholar]
  20. Masse E., Escorcia F. E., Gottesman S. 2003; Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli. Genes Dev 17:2374–2383
     [Google Scholar]
  21. Masse E., Vanderpool C. K., Gottesman S. 2005; Effect of RyhB small RNA on global iron use in Escherichia coli. J Bacteriol 187:6962–6971
     [Google Scholar]
  22. Mellin J. R., Goswami S., Grogan S., Tjaden B., Genco C. A. 2007; A novel Fur- and iron-regulated small RNA, NrrF, is required for indirect Fur-mediated regulation of the sdhA and sdhC genes in Neisseria meningitidis. J Bacteriol 189:3686–3694
     [Google Scholar]
  23. Metruccio M. M., Fantappie L., Serruto D., Muzzi A., Roncarati D., Donati C., Scarlato V., Delany I. 2009; The Hfq-dependent small noncoding RNA NrrF directly mediates Fur-dependent positive regulation of succinate dehydrogenase in Neisseria meningitidis. J Bacteriol 191:1330–1342
     [Google Scholar]
  24. Miller J. H. 1972 Experiments in Molecular Genetics Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
  25. Moller T., Franch T., Hojrup P., Keene D. R., Bachinger H. P., Brennan R. G., Valentin-Hansen P. 2002; Hfq: a bacterial Sm-like protein that mediates RNA–RNA interaction. Mol Cell 9:23–30
     [Google Scholar]
  26. Morse S. A., Bartenstein L. 1980; Purine metabolism in Neisseria gonorrhoeae: the requirement for hypoxanthine. Can J Microbiol 26:13–20
     [Google Scholar]
  27. Murphy E. R., Payne S. M. 2007; RhyB, an iron-responsive small RNA molecule, regulates Shigella dysenteriae virulence. Infect Immun 75:3470–3477
     [Google Scholar]
  28. Pannekoek Y., Huis in 't Veld R., Hopman C. T., Langerak A. A., Speijer D., van der Ende A. 2009; Molecular characterization and identification of proteins regulated by Hfq in Neisseria meningitidis. FEMS Microbiol Lett 294:216–224
     [Google Scholar]
  29. Repoila F., Majdalani N., Gottesman S. 2003; Small non-coding RNAs, co-ordinators of adaptation processes in Escherichia coli: the RpoS paradigm. Mol Microbiol 48:855–861
     [Google Scholar]
  30. Silver L. E., Clark V. L. 1995; Construction of a translational lacZ fusion system to study gene regulation in Neisseria gonorrhoeae. Gene 166:101–104
     [Google Scholar]
  31. Stojiljkovic I., Hantke K. 1995; Functional domains of the Escherichia coli ferric uptake regulator protein (Fur. Mol Gen Genet 247:199–205
     [Google Scholar]
  32. Takada A., Wachi M., Kaidow A., Takamura M., Nagai K. 1997; DNA binding properties of the hfq gene of Escherichia coli. Biochem Biophys Res Commun 236:576–579
     [Google Scholar]
  33. Tettelin H., Saunder J., Heidelberg J., Jeffries A. C., Nelson K. E., Eisen J. A., Ketchum K. A., Hood D. W., Peden J. F. other authors 2000; Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science 287:1809–1815
     [Google Scholar]
  34. Urban J. H., Vogel J. 2007; Translational control and target recognition by Escherichia coli small RNAs in vivo. Nucleic Acids Res 35:1018–1037
     [Google Scholar]
  35. Večerek B., Moll I., Afonyushkin T., Kaberdin V., Bläsi U. 2003; Interaction of the RNA chaperone Hfq with mRNAs: direct and indirect roles of Hfq in iron metabolism of Escherichia coli. Mol Microbiol 50:897–909
     [Google Scholar]
  36. Windbichler N., von Pelchrzim F., Mayer O., Csaszar E., Schroeder R. 2008; Isolation of small RNA-binding proteins from E. coli. RNA Biol 5:30–40
     [Google Scholar]
  37. Zhang A., Altuvia S., Tiwari A., Argaman L., Hengge-Aronis R., Storz G. 1998; The OxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-I) protein. EMBO J 17:6061–6068
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.039040-0
Loading
Role of Hfq in iron-dependent and -independent gene regulation in Neisseria meningitidis
Microbiology 156, 2316 (2010); https://doi.org/10.1099/mic.0.039040-0
/content/journal/micro/10.1099/mic.0.039040-0
/content/journal/micro/10.1099/mic.0.039040-0
Loading

Data & Media loading...

Most cited Most Cited RSS feed

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