1887

Abstract

A large non-coding RNA, termed α-Fur, of ~1000 nt has been detected in the extreme acidophile encoded on the antisense strand to the iron-responsive master regulator (ferric uptake regulator) gene. A promoter for α was predicted bioinformatically and validated using gene fusion experiments. The promoter is situated within the coding region and in the same sense as , potentially encoding a glutamate 5-kinase. The 3′ termination site of the α transcript was determined by 3′ rapid amplification of cDNA ends to lie 7 nt downstream of the start of transcription of . Thus, α is antisense to the complete coding region of , including its predicted ribosome-binding site. The genetic context of α is conserved in several members of the genus but not in all acidophiles, indicating that it is monophyletic but not niche specific. It is hypothesized that α-Fur regulates the cellular level of Fur. This is the fourth example of an antisense RNA to , although it is the first in an extreme acidophile, and underscores the growing importance of -encoded non-coding RNAs as potential regulators involved in the microbial iron-responsive stimulon.

Funding
This study was supported by the:
  • Fondecyt (Award 1130683 and 1090451)
  • Mecesup (Award UAB 602)
  • Conicyt
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2014-03-01
2021-10-25
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References

  1. Andrews S. C., Robinson A. K., Rodríguez-Quiñones F. ( 2003). Bacterial iron homeostasis. FEMS Microbiol Rev 27:215–237 [View Article][PubMed]
    [Google Scholar]
  2. Argaman L., Hershberg R., Vogel J., Bejerano G., Wagner E. G., Margalit H., Altuvia S. ( 2001). Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr Biol 11:941–950 [View Article][PubMed]
    [Google Scholar]
  3. Baichoo N., Wang T., Ye R., Helmann J. D. ( 2002). Global analysis of the Bacillus subtilis Fur regulon and the iron starvation stimulon. Mol Microbiol 45:1613–1629 [View Article][PubMed]
    [Google Scholar]
  4. Bertin P. N., Heinrich-Salmeron A., Pelletier E., Goulhen-Chollet F., Arsène-Ploetze F., Gallien S., Lauga B., Casiot C., Calteau A. & other authors ( 2011). Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta- and proteo-genomics. ISME J 5:1735–1747 [View Article][PubMed]
    [Google Scholar]
  5. Bes M. T., Hernández J. A., Peleato M. L., Fillat M. F. ( 2001). Cloning, overexpression and interaction of recombinant Fur from the cyanobacterium Anabaena PCC 7119 with isiB and its own promoter. FEMS Microbiol Lett 194:187–192 [View Article][PubMed]
    [Google Scholar]
  6. Bonnefoy V., Holmes D. S. ( 2012). Genomic insights into microbial iron oxidation and iron uptake strategies in extremely acidic environments. Environ Microbiol 14:1597–1611 [View Article][PubMed]
    [Google Scholar]
  7. Butcher J., Sarvan S., Brunzelle J. S., Couture J.-F., Stintzi A. ( 2012). Structure and regulon of Campylobacter jejuni ferric uptake regulator Fur define apo-Fur regulation. Proc Natl Acad Sci U S A 109:10047–10052 [View Article][PubMed]
    [Google Scholar]
  8. Cornelis P., Wei Q., Andrews S. C., Vinckx T. ( 2011). Iron homeostasis and management of oxidative stress response in bacteria. Metallomics 3:540–549 [View Article][PubMed]
    [Google Scholar]
  9. Danielli A., Roncarati D., Delany I., Chiarini V., Rappuoli R., Scarlato V. ( 2006). In vivo dissection of the Helicobacter pylori Fur regulatory circuit by genome-wide location analysis. J Bacteriol 188:4654–4662 [View Article][PubMed]
    [Google Scholar]
  10. 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 [View Article][PubMed]
    [Google Scholar]
  11. De Lorenzo V., Herrero M., Giovannini F., Neilands J. B. ( 1988). Fur (ferric uptake regulation) protein and CAP (catabolite-activator protein) modulate transcription of fur gene in Escherichia coli. Eur J Biochem 173:537–546 [View Article][PubMed]
    [Google Scholar]
  12. De Lorenzo V., Herrero M., Jakubzik U., Timmis K. N. ( 1990). Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in gram-negative eubacteria. J Bacteriol 172:6568–6572[PubMed]
    [Google Scholar]
  13. 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 [View Article][PubMed]
    [Google Scholar]
  14. Denef V. J., Mueller R. S., Banfield J. F. ( 2010). AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature. ISME J 4:599–610 [View Article][PubMed]
    [Google Scholar]
  15. Ducey T. F., Jackson L., Orvis J., Dyer D. W. ( 2009). Transcript analysis of nrrF, a Fur repressed sRNA of Neisseria gonorrhoeae. Microb Pathog 46:166–170 [View Article][PubMed]
    [Google Scholar]
  16. Egal M., Casiot C., Morin G., Parmentier M., Bruneel O., Lebrun S., Elbaz-Poulichet F. ( 2009). Kinetic control on the formation of tooeleite, schwertmannite and jarosite by Acidithiobacillus ferrooxidans strains in an As(III)-rich acid mine water. Chem Geol 265:432–441 [View Article]
    [Google Scholar]
  17. Friedman Y. E., O’Brian M. R. ( 2003). A novel DNA-binding site for the ferric uptake regulator (Fur) protein from Bradyrhizobium japonicum. J Biol Chem 278:38395–38401 [View Article][PubMed]
    [Google Scholar]
  18. 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 [View Article][PubMed]
    [Google Scholar]
  19. Gao H., Zhou D., Li Y., Guo Z., Han Y., Song Y., Zhai J., Du Z., Wang X. & other authors ( 2008). The iron-responsive Fur regulon in Yersinia pestis. J Bacteriol 190:3063–3075 [View Article][PubMed]
    [Google Scholar]
  20. Gioia J., Highlander S. K. ( 2007). Identification and characterization of transcriptional regulation of the Mannheimia haemolytica ferric uptake regulator. Vet Microbiol 124:298–309 [View Article][PubMed]
    [Google Scholar]
  21. Guacucano M., Levicán G., Holmes D., Jedlicki E. ( 2000). An RT-PCR artifact in the characterization of bacterial operons. Electron J Biotechnol 3:213–216
    [Google Scholar]
  22. He Z., Xiao S., Xie X., Zhong H., Hu Y., Li Q., Gao F., Li G., Liu J., Qiu G. ( 2007). Molecular diversity of microbial community in acid mine drainages of Yunfu sulfide mine. Extremophiles 11:305–314 [View Article][PubMed]
    [Google Scholar]
  23. Hedrich S., Johnson D. B. ( 2013). Acidithiobacillus ferridurans sp. nov., an acidophilic iron-, sulfur- and hydrogen-metabolizing chemolithotrophic gammaproteobacterium. Int J Syst Evol Microbiol 63:4018–4025 [View Article][PubMed]
    [Google Scholar]
  24. Hernández J. A., Muro-Pastor A. M., Flores E., Bes M. T., Peleato M. L., Fillat M. F. ( 2006). Identification of a furA cis antisense RNA in the cyanobacterium Anabaena sp. PCC 7120. J Mol Biol 355:325–334 [View Article][PubMed]
    [Google Scholar]
  25. Hernández J. A., Alonso I., Pellicer S., Luisa Peleato M., Cases R., Strasser R. J., Barja F., Fillat M. F. ( 2010). Mutants of Anabaena sp. PCC 7120 lacking alr1690 and alpha-furA antisense RNA show a pleiotropic phenotype and altered photosynthetic machinery. J Plant Physiol 167:430–437 [View Article][PubMed]
    [Google Scholar]
  26. Hippe H. ( 2000). Leptospirillum gen. nov. (ex Markosyan 1972), nom. rev., including Leptospirillum ferrooxidans sp. nov. (ex Markosyan 1972), nom. rev. and Leptospirillum thermoferrooxidans sp. nov. (Golovacheva et al. 1992). Int J Syst Evol Microbiol 50:501–503 [View Article][PubMed]
    [Google Scholar]
  27. Hohle T. H., O’Brian M. R. ( 2009). The mntH gene encodes the major Mn2+ transporter in Bradyrhizobium japonicum and is regulated by manganese via the Fur protein. Mol Microbiol 72:399–409 [View Article][PubMed]
    [Google Scholar]
  28. Imlay J. A. ( 2008). Cellular defenses against superoxide and hydrogen peroxide. Annu Rev Biochem 77:755–776 [View Article][PubMed]
    [Google Scholar]
  29. Isabella V., Wright L. F., Barth K., Spence J. M., Grogan S., Genco C. A., Clark V. L. ( 2008). cis- and trans-acting elements involved in regulation of norB (norZ), the gene encoding nitric oxide reductase in Neisseria gonorrhoeae. Microbiology 154:226–239 [View Article][PubMed]
    [Google Scholar]
  30. Jones D. S., Albrecht H. L., Dawson K. S., Schaperdoth I., Freeman K. H., Pi Y., Pearson A., Macalady J. L. ( 2012). Community genomic analysis of an extremely acidophilic sulfur-oxidizing biofilm. ISME J 6:158–170 [View Article][PubMed]
    [Google Scholar]
  31. Kammler M., Schön C., Hantke K. ( 1993). Characterization of the ferrous iron uptake system of Escherichia coli. J Bacteriol 175:6212–6219[PubMed]
    [Google Scholar]
  32. Leathen W., Braley S. ( 1954). A new iron-oxidizing bacterium: Ferrobacillus ferrooxidans. Bacteriol Proc 1954:44
    [Google Scholar]
  33. Ledala N., Pearson S. L., Wilkinson B. J., Jayaswal R. K. ( 2007). Molecular characterization of the Fur protein of Listeria monocytogenes. Microbiology 153:1103–1111 [View Article][PubMed]
    [Google Scholar]
  34. Lee H. J., Park K. J., Lee A. Y., Park S. G., Park B. C., Lee K. H., Park S. J. ( 2003). Regulation of fur expression by RpoS and Fur in Vibrio vulnificus. J Bacteriol 185:5891–5896 [View Article][PubMed]
    [Google Scholar]
  35. Lefimil C., Jedlicki E., Holmes D. S. ( 2012). An artifact in studies of gene regulation using β-galactosidase reporter gene assays. Anal Biochem 421:333–335 [View Article][PubMed]
    [Google Scholar]
  36. Liljeqvist M., Valdés J., Holmes D. S., Dopson M. ( 2011). Draft genome of the psychrotolerant acidophile Acidithiobacillus ferrivorans SS3. J Bacteriol 193:4304–4305 [View Article][PubMed]
    [Google Scholar]
  37. Liu Z., Guiliani N., Appia-Ayme C., Borne F., Ratouchniak J., Bonnefoy V. ( 2000). Construction and characterization of a recA mutant of Thiobacillus ferrooxidans by marker exchange mutagenesis. J Bacteriol 182:2269–2276 [View Article][PubMed]
    [Google Scholar]
  38. López-Gomollón S., Hernández J. A., Wolk C. P., Peleato M. L., Fillat M. F. ( 2007). Expression of furA is modulated by NtcA and strongly enhanced in heterocysts of Anabaena sp. PCC 7120. Microbiology 153:42–50 [View Article][PubMed]
    [Google Scholar]
  39. Lowe C. A., Asghar A. H., Shalom G., Shaw J. G., Thomas M. S. ( 2001). The Burkholderia cepacia fur gene: co-localization with omlA and absence of regulation by iron. Microbiology 147:1303–1314[PubMed]
    [Google Scholar]
  40. Lybecker M. C., Samuels D. S. ( 2007). Temperature-induced regulation of RpoS by a small RNA in Borrelia burgdorferi. Mol Microbiol 64:1075–1089 [View Article][PubMed]
    [Google Scholar]
  41. Majdalani N., Cunning C., Sledjeski D., Elliott T., Gottesman S. ( 1998). DsrA RNA regulates translation of RpoS message by an anti-antisense mechanism, independent of its action as an antisilencer of transcription. Proc Natl Acad Sci U S A 95:12462–12467 [View Article][PubMed]
    [Google Scholar]
  42. Martin-Luna B., Sevilla E., Gonzalez A., Bes M. T., Fillat M. F., Peleato M. L. ( 2011). Expression of fur and its antisense α-fur from Microcystis aeruginosa PCC7806 as response to light and oxidative stress. J Plant Physiol 168:2244–2250 [View Article][PubMed]
    [Google Scholar]
  43. Massé 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 [View Article][PubMed]
    [Google Scholar]
  44. Miller J. H. ( 1972). Experiments in Molecular Genetics Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  45. Mills S. A., Marletta M. A. ( 2005). Metal binding characteristics and role of iron oxidation in the ferric uptake regulator from Escherichia coli. Biochemistry 44:13553–13559 [View Article][PubMed]
    [Google Scholar]
  46. Morfeldt E., Taylor D., von Gabain A., Arvidson S. ( 1995). Activation of alpha-toxin translation in Staphylococcus aureus by the trans-encoded antisense RNA, RNAIII. EMBO J 14:4569–4577[PubMed]
    [Google Scholar]
  47. Münch R., Hiller K., Grote A., Scheer M., Klein J., Schobert M., Jahn D. ( 2005). Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. Bioinformatics 21:4187–4189 [View Article][PubMed]
    [Google Scholar]
  48. Nandal A., Huggins C. C., Woodhall M. R., McHugh J., Rodríguez-Quiñones F., Quail M. A., Guest J. R., Andrews S. C. ( 2010). Induction of the ferritin gene (ftnA) of Escherichia coli by Fe2+-Fur is mediated by reversal of H-NS silencing and is RyhB independent. Mol Microbiol 75:637–657 [View Article][PubMed]
    [Google Scholar]
  49. Nieto P. A., Covarrubias P. C., Jedlicki E., Holmes D. S., Quatrini R. ( 2009). Selection and evaluation of reference genes for improved interrogation of microbial transcriptomes: case study with the extremophile Acidithiobacillus ferrooxidans. BMC Mol Biol 10:63–74 [View Article][PubMed]
    [Google Scholar]
  50. Ochsner U. A., Wilderman P. J., Vasil A. I., Vasil M. L. ( 2002). GeneChip expression analysis of the iron starvation response in Pseudomonas aeruginosa: identification of novel pyoverdine biosynthesis genes. Mol Microbiol 45:1277–1287 [View Article][PubMed]
    [Google Scholar]
  51. Oglesby A. G., Murphy E. R., Iyer V. R., Payne S. M. ( 2005). Fur regulates acid resistance in Shigella flexneri via RyhB and ydeP. Mol Microbiol 58:1354–1367 [View Article][PubMed]
    [Google Scholar]
  52. Osorio H., Martínez V., Veloso F., Pedroso I., Valdés J., Jedlicki E., Holmes D. S., Quatrini R. ( 2008a). Iron homeostasis strategies in acidophilic iron oxidizers: studies in Acidithiobacillus and Leptospirillum. Hydrometallurgy 94:175–179 [View Article]
    [Google Scholar]
  53. Osorio H., Martínez V., Nieto P. A., Holmes D. S., Quatrini R. ( 2008b). Microbial iron management mechanisms in extremely acidic environments: comparative genomics evidence for diversity and versatility. BMC Microbiol 8:203 [View Article][PubMed]
    [Google Scholar]
  54. Outten F. W., Wood M. J., Munoz F. M., Storz G. ( 2003). The SufE protein and the SufBCD complex enhance SufS cysteine desulfurase activity as part of a sulfur transfer pathway for Fe-S cluster assembly in Escherichia coli. J Biol Chem 278:45713–45719 [View Article][PubMed]
    [Google Scholar]
  55. Pokorna B., Mandl M., Borilova S., Ceskova P., Markova R., Janiczek O. ( 2007). Kinetic constant variability in bacterial oxidation of elemental sulfur. Appl Environ Microbiol 73:3752–3754 [View Article][PubMed]
    [Google Scholar]
  56. Prévost K., Salvail H., Desnoyers G., Jacques J. F., Phaneuf E., Massé E. ( 2007). The small RNA RyhB activates the translation of shiA mRNA encoding a permease of shikimate, a compound involved in siderophore synthesis. Mol Microbiol 64:1260–1273 [View Article][PubMed]
    [Google Scholar]
  57. Quatrini R., Jedlicki E., Holmes D. S. ( 2005a). Genomic insights into the iron uptake mechanisms of the biomining microorganism Acidithiobacillus ferrooxidans. J Ind Microbiol Biotechnol 32:606–614 [View Article][PubMed]
    [Google Scholar]
  58. Quatrini R., Lefimil C., Holmes D. S., Jedlicki E. ( 2005b). The ferric iron uptake regulator (Fur) from the extreme acidophile Acidithiobacillus ferrooxidans. Microbiology 151:2005–2015 [View Article][PubMed]
    [Google Scholar]
  59. Quatrini R., Lefimil C., Veloso F. A., Pedroso I., Holmes D. S., Jedlicki E. ( 2007). Bioinformatic prediction and experimental verification of Fur-regulated genes in the extreme acidophile Acidithiobacillus ferrooxidans. Nucleic Acids Res 35:2153–2166 [View Article][PubMed]
    [Google Scholar]
  60. Quatrini R., Appia-Ayme C., Denis Y., Jedlicki E., Holmes D. S., Bonnefoy V. ( 2009). Extending the models for iron and sulfur oxidation in the extreme acidophile Acidithiobacillus ferrooxidans. BMC Genomics 10:394 [View Article][PubMed]
    [Google Scholar]
  61. Rawlings D. E. ( 2005). Characteristics and adaptability of iron- and sulfur-oxidizing microorganisms used for the recovery of metals from minerals and their concentrates. Microb Cell Fact 4:13–28 [View Article][PubMed]
    [Google Scholar]
  62. Razzell W. E., Trusell P. C. ( 1963). Isolation and properties of an iron-oxidizing Thiobacillus. J Bacteriol 85:595–603[PubMed]
    [Google Scholar]
  63. Salvail H., Massé E. ( 2012). Regulating iron storage and metabolism with RNA: an overview of posttranscriptional controls of intracellular iron homeostasis. Wiley Interdiscip Rev RNA 3:26–36 [View Article][PubMed]
    [Google Scholar]
  64. Savic D., Lazic M., Veljkovic V., Vrvic M. ( 2005). A kinetic model of ferrous iron oxidation by Acidithiobacillus ferrooxidans in a batch culture. CI & CEQ 11:59–62 [View Article]
    [Google Scholar]
  65. Sevilla E., Martín-Luna B., González A., Gonzalo-Asensio J. A., Peleato M. L., Fillat M. F. ( 2011). Identification of three novel antisense RNAs in the fur locus from unicellular cyanobacteria. Microbiology 157:3398–3404 [View Article][PubMed]
    [Google Scholar]
  66. Smaldone G. T., Antelmann H., Gaballa A., Helmann J. D. ( 2012). The FsrA sRNA and FbpB protein mediate the iron-dependent induction of the Bacillus subtilis LutABC iron-sulfur-containing oxidases. J Bacteriol 194:2586–2593 [View Article][PubMed]
    [Google Scholar]
  67. Tomizuka N., Yagisawa M., Someya J., Takahara Y. ( 1976). Continuous leaching of uranium by Thiobacillus ferrooxidans. Agric Biol Chem 40:1019–1025 [View Article]
    [Google Scholar]
  68. Valdés J., Pedroso I., Quatrini R., Dodson R. J., Tettelin H., Blake R. II, Eisen J. A., Holmes D. S. ( 2008). Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. BMC Genomics 9:597 [View Article][PubMed]
    [Google Scholar]
  69. Valdés J., Ossandón F., Quatrini R., Dopson M., Holmes D. S. ( 2011). Draft genome sequence of the extremely acidophilic biomining bacterium Acidithiobacillus thiooxidans ATCC 19377 provides insights into the evolution of the Acidithiobacillus genus. J Bacteriol 193:7003–7004 [View Article][PubMed]
    [Google Scholar]
  70. Vasil M. L., Ochsner U. A. ( 1999). The response of Pseudomonas aeruginosa to iron: genetics, biochemistry and virulence. Mol Microbiol 34:399–413 [View Article][PubMed]
    [Google Scholar]
  71. Watnick P. I., Eto T., Takahashi H., Calderwood S. B. ( 1997). Purification of Vibrio cholerae Fur and estimation of its intracellular abundance by antibody sandwich enzyme-linked immunosorbent assay. J Bacteriol 179:243–247[PubMed]
    [Google Scholar]
  72. Williams R. J. ( 2012). Iron in evolution. FEBS Lett 586:479–484 [View Article][PubMed]
    [Google Scholar]
  73. Yu C., Genco C. A. ( 2012). Fur-mediated activation of gene transcription in the human pathogen Neisseria gonorrhoeae. J Bacteriol 194:1730–1742 [View Article][PubMed]
    [Google Scholar]
  74. Zhang Z., Gosset G., Barabote R., Gonzalez C. S., Cuevas W. A., Saier M. H. Jr ( 2005). Functional interactions between the carbon and iron utilization regulators, Crp and Fur, in Escherichia coli. J Bacteriol 187:980–990 [View Article][PubMed]
    [Google Scholar]
  75. Zheng M., Doan B., Schneider T. D., Storz G. ( 1999). OxyR and SoxRS regulation of fur. J Bacteriol 181:4639–4643[PubMed]
    [Google Scholar]
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