host factor 1 protein


Summary: An integration host factor that was originally identified as a bacterial protein required for the integration of bacteriophage Q beta (ALLOLEVIVIRUS). Its cellular function may be to regulate mRNA stability and processing in that it binds tightly to poly(A) RNA and interferes with ribosome binding.

Top Publications

  1. Chao Y, Vogel J. The role of Hfq in bacterial pathogens. Curr Opin Microbiol. 2010;13:24-33 pubmed publisher
    ..Hfq also facilitates post-transcriptional cross-talk between the core and variable genome regions of bacterial pathogens, and might help integrate horizontally acquired virulence genes into existing regulatory networks. ..
  2. Brennan R, Link T. Hfq structure, function and ligand binding. Curr Opin Microbiol. 2007;10:125-33 pubmed
    ..Fluorescence resonance energy transfer (FRET) studies directly demonstrated the role of Hfq as a chaperone that facilitates the interaction between sRNAs and target mRNAs. There are still, however, some unresolved questions. ..
  3. Schuppli D, Georgijevic J, Weber H. Synergism of mutations in bacteriophage Qbeta RNA affecting host factor dependence of Qbeta replicase. J Mol Biol. 2000;295:149-54 pubmed
    ..It appears to contribute little to the Hfq independence but may enhance RNA stability by re-establishing the possibility of forming a long-range base-pairing interaction involving the immediate 3'-terminal sequence...
  4. Vytvytska O, Moll I, Kaberdin V, von Gabain A, Blasi U. Hfq (HF1) stimulates ompA mRNA decay by interfering with ribosome binding. Genes Dev. 2000;14:1109-18 pubmed
    ..The data are discussed in terms of a model wherein Hfq regulates the stability of ompA mRNA by competing with 30S ribosomes for binding to the ompA 5'-UTR. ..
  5. Sun X, Wartell R. Escherichia coli Hfq binds A18 and DsrA domain II with similar 2:1 Hfq6/RNA stoichiometry using different surface sites. Biochemistry. 2006;45:4875-87 pubmed
    ..Titration experiments indicate a 2:1 Hfq(6)/RNA stoichiometry for the strong binding complexes of Hfq with either A(18) or DsrA(DII) and suggests that RNA-induced dimer formation of Hfq(6) is a common feature of Hfq-RNA interactions. ..
  6. Chen S, Zhang A, Blyn L, Storz G. MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli. J Bacteriol. 2004;186:6689-97 pubmed
    ..We suggest that the MicF and MicC RNAs act in conjunction with the EnvZ-OmpR two-component system to control the OmpF/OmpC protein ratio in response to a variety of environmental stimuli. ..
  7. Hajnsdorf E, Boni I. Multiple activities of RNA-binding proteins S1 and Hfq. Biochimie. 2012;94:1544-53 pubmed publisher
    ..This review is focused on the diversity of functions that can be performed by these abundant RNA-binding bacterial proteins. ..
  8. Valentin Hansen P, Eriksen M, Udesen C. The bacterial Sm-like protein Hfq: a key player in RNA transactions. Mol Microbiol. 2004;51:1525-33 pubmed
    ..Here, we summarize the history of Hfq and highlight results that have led to an important gain in insight into the physiology, biochemistry and evolution of Hfq and its homologues. ..
  9. Geissmann T, Touati D. Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator. EMBO J. 2004;23:396-405 pubmed
    ..Thus, Hfq is a critical chaperone in vivo and in vitro, changing the folding of the target mRNA to make it subject to the small RNA regulator. ..

More Information


  1. Heidrich N, Moll I, Brantl S. In vitro analysis of the interaction between the small RNA SR1 and its primary target ahrC mRNA. Nucleic Acids Res. 2007;35:4331-46 pubmed
    ..The intracellular concentrations of SR1 were calculated under different growth conditions. ..
  2. Bardill J, Zhao X, Hammer B. The Vibrio cholerae quorum sensing response is mediated by Hfq-dependent sRNA/mRNA base pairing interactions. Mol Microbiol. 2011;80:1381-94 pubmed publisher
    ..These results demonstrate that the V. cholerae QS response is mediated by base pairing interactions between Qrr sRNAs and hapR mRNA. ..
  3. Ding Y, Davis B, Waldor M. Hfq is essential for Vibrio cholerae virulence and downregulates sigma expression. Mol Microbiol. 2004;53:345-54 pubmed
    ..However, increased sigma(E) does not appear to account for this strain's reduced virulence. It is likely that sRNAs, in conjunction with Hfq, are critical regulators of V. cholerae pathogenicity. ..
  4. Sittka A, Sharma C, Rolle K, Vogel J. Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes. RNA Biol. 2009;6:266-75 pubmed
    ..It also suggests that the expression of heterologous RNA-binding proteins combined with deep sequencing analysis of RNA ligands can be used as a molecular tool to dissect individual steps of RNA metabolism in vivo...
  5. Takada A, Wachi M, Nagai K. Negative regulatory role of the Escherichia coli hfq gene in cell division. Biochem Biophys Res Commun. 1999;266:579-83 pubmed
    ..Increased ftsZ mRNA levels were also observed in the hfq::cat mutant in the stationary phase. These results suggest a negative regulatory role of the DNA-, RNA-binding protein Hfq in cell division in the stationary phase. ..
  6. Vassilieva I, Nikulin A, Blasi U, Moll I, Garber M. Crystallization of Hfq protein: a bacterial gene-expression regulator. Acta Crystallogr D Biol Crystallogr. 2003;59:1061-3 pubmed
    ..41, c = 170.36 A. The crystals belong to space group I4 and diffract to 2.1 A resolution. Two hexamers are predicted per asymmetric unit...
  7. Pfeiffer V, Sittka A, Tomer R, Tedin K, Brinkmann V, Vogel J. A small non-coding RNA of the invasion gene island (SPI-1) represses outer membrane protein synthesis from the Salmonella core genome. Mol Microbiol. 2007;66:1174-91 pubmed
    ..This study identifies the first regulatory RNA of an enterobacterial pathogenicity island, and new roles for Hfq and HilD in SPI-1 gene expression. ..
  8. Sharma A, Payne S. Induction of expression of hfq by DksA is essential for Shigella flexneri virulence. Mol Microbiol. 2006;62:469-79 pubmed
  9. Azam T, Hiraga S, Ishihama A. Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid. Genes Cells. 2000;5:613-26 pubmed
    ..coli could be classified into two groups. One group proteins was distributed uniformly within the nucleoid, but the other group of proteins showed an irregular distribution, forming immuno-stained spots or clumps. ..
  10. Zhang A, Wassarman K, Ortega J, Steven A, Storz G. The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs. Mol Cell. 2002;9:11-22 pubmed
    ..We also show that Hfq increases the OxyS RNA interaction with its target messages and propose that the enhancement of RNA-RNA pairing may be a general function of Hfq, Sm, and Sm-like proteins...
  11. Afonyushkin T, Vecerek B, Moll I, Blasi U, Kaberdin V. Both RNase E and RNase III control the stability of sodB mRNA upon translational inhibition by the small regulatory RNA RyhB. Nucleic Acids Res. 2005;33:1678-89 pubmed
    ..These data are discussed in terms of a model, which accounts for the observed roles of RNase E and RNase III in sodB mRNA turnover. ..
  12. Arluison V, Folichon M, Marco S, Derreumaux P, Pellegrini O, Seguin J, et al. The C-terminal domain of Escherichia coli Hfq increases the stability of the hexamer. Eur J Biochem. 2004;271:1258-65 pubmed
    ..On the basis of these results, we propose that the C-terminal domain could protect the interface between the subunits and stabilize the hexameric Hfq structure. The origin of this C-terminal domain is also discussed. ..
  13. Sauter C, Basquin J, Suck D. Sm-like proteins in Eubacteria: the crystal structure of the Hfq protein from Escherichia coli. Nucleic Acids Res. 2003;31:4091-8 pubmed
    ..Finally, a detailed structural comparison shows that the Sm-fold is remarkably well conserved in bacteria, Archaea and Eukarya, and represents a universal and modular building unit for oligomeric RNA binding proteins...
  14. Caswell C, Gaines J, Ciborowski P, Smith D, Borchers C, Roux C, et al. Identification of two small regulatory RNAs linked to virulence in Brucella abortus 2308. Mol Microbiol. 2012;85:345-60 pubmed publisher
    ..In an Escherichia coli two-plasmid reporter system, overexpression of either AbcR1 or AbcR2 was sufficient for regulation of target mRNAs, indicating that the AbcR sRNAs from B. abortus 2308 perform redundant regulatory functions...
  15. Vincent H, Henderson C, Ragan T, Garza Garcia A, Cary P, Gowers D, et al. Characterization of Vibrio cholerae Hfq provides novel insights into the role of the Hfq C-terminal region. J Mol Biol. 2012;420:56-69 pubmed publisher
    ..Overall, the similarities and differences in the fundamental properties of V. cholerae and E. coli Hfq provide insight into their assembly and molecular mechanisms...
  16. Sittka A, Pfeiffer V, Tedin K, Vogel J. The RNA chaperone Hfq is essential for the virulence of Salmonella typhimurium. Mol Microbiol. 2007;63:193-217 pubmed
    ..In addition, the hfq mutation appears to cause a chronic activation of the RpoE-mediated envelope stress response which is likely due to a misregulation of membrane protein expression. ..
  17. Morita T, Maki K, Aiba H. RNase E-based ribonucleoprotein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Genes Dev. 2005;19:2176-86 pubmed
    ..The formation of ribonucleoprotein complexes containing RNases could be a general way by which small RNAs destabilize target mRNAs in both prokaryotes and eukaryotes. ..
  18. Sobrero P, Valverde C. Evidences of autoregulation of hfq expression in Sinorhizobium meliloti strain 2011. Arch Microbiol. 2011;193:629-39 pubmed publisher
    ..meliloti Hfq protein autocontrols its expression at the translational level, a phenomenon that was evident in the natural host S. meliloti as well as in the heterologous host E. coli. ..
  19. Hämmerle H, Beich Frandsen M, Vecerek B, Rajkowitsch L, Carugo O, Djinovic Carugo K, et al. Structural and biochemical studies on ATP binding and hydrolysis by the Escherichia coli RNA chaperone Hfq. PLoS ONE. 2012;7:e50892 pubmed publisher
    ..Taken together, these studies strongly suggest that ATP is dispensable for and does not interfere with Hfq-mediated RNA transactions. ..
  20. Schiano C, Bellows L, Lathem W. The small RNA chaperone Hfq is required for the virulence of Yersinia pseudotuberculosis. Infect Immun. 2010;78:2034-44 pubmed publisher
    ..pseudotuberculosis by participating in the regulation of multiple steps in the pathogenic process and further highlight the unique role of Hfq in the virulence of individual pathogens. ..
  21. Zhang Y, Hong G. Post-transcriptional regulation of NifA expression by Hfq and RNase E complex in Rhizobium leguminosarum bv. viciae. Acta Biochim Biophys Sin (Shanghai). 2009;41:719-30 pubmed
    ..A possible explanation based on predicted RNA secondary structure of the NifA 5'-untranslated region was that the cleavage made ribosome-binding sites accessible for translation. ..
  22. Rabhi M, Espeli O, Schwartz A, Cayrol B, Rahmouni A, Arluison V, et al. The Sm-like RNA chaperone Hfq mediates transcription antitermination at Rho-dependent terminators. EMBO J. 2011;30:2805-16 pubmed publisher
    ..These data unveil a new Hfq function and a novel transcription regulatory mechanism with potentially important implications for bacterial RNA metabolism, gene silencing, and pathogenicity. ..
  23. Balbontin R, Fiorini F, Figueroa Bossi N, Casadesus J, Bossi L. Recognition of heptameric seed sequence underlies multi-target regulation by RybB small RNA in Salmonella enterica. Mol Microbiol. 2010;78:380-94 pubmed
    ..Altogether, our results indicate that an heptameric 'seed' sequence is sufficient to confer susceptibility to RybB regulation. ..
  24. Vecerek B, Moll I, Afonyushkin T, Kaberdin V, Blasi U. Interaction of the RNA chaperone Hfq with mRNAs: direct and indirect roles of Hfq in iron metabolism of Escherichia coli. Mol Microbiol. 2003;50:897-909 pubmed
    ..These data assign a role to Hfq in regulation of iron uptake and in switching off of iron scavenger genes. ..
  25. Moll I, Afonyushkin T, Vytvytska O, Kaberdin V, Bl si U. Coincident Hfq binding and RNase E cleavage sites on mRNA and small regulatory RNAs. RNA. 2003;9:1308-14 pubmed
    ..It is commonly believed that the RNA chaperone Hfq facilitates or promotes the interaction between sRNAs and their mRNA targets. This study reveals another role for Hfq, that is, protection of sRNAs from endonucleolytic attack...
  26. Kawamoto H, Koide Y, Morita T, Aiba H. Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq. Mol Microbiol. 2006;61:1013-22 pubmed
    ..We also showed in vitro that SgrS forms a stable duplex with the ptsG mRNA, and that Hfq markedly facilitates the rate of duplex formation. ..
  27. Roop R, Gee J, Robertson G, Richardson J, Ng W, Winkler M. Brucella stationary-phase gene expression and virulence. Annu Rev Microbiol. 2003;57:57-76 pubmed publisher
  28. Durand S, Storz G. Reprogramming of anaerobic metabolism by the FnrS small RNA. Mol Microbiol. 2010;75:1215-31 pubmed publisher
    ..We thus suggest that FnrS extends the FNR regulon and increases the efficiency of anaerobic metabolism by repressing the synthesis of enzymes that are not needed under these conditions. ..
  29. Le Derout J, Boni I, Regnier P, Hajnsdorf E. Hfq affects mRNA levels independently of degradation. BMC Mol Biol. 2010;11:17 pubmed publisher
  30. Lee T, Feig A. The RNA binding protein Hfq interacts specifically with tRNAs. RNA. 2008;14:514-23 pubmed publisher
    ..We infer that tRNA binding and reduced fidelity are linked by a role for Hfq in tRNA modification. ..
  31. Udekwu K, Darfeuille F, Vogel J, Reimegård J, Holmqvist E, Wagner E. Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA. Genes Dev. 2005;19:2355-66 pubmed
    ..MicA requires the presence of the Hfq protein, although the mechanistic basis for this remains unclear. ..
  32. Mass E, Escorcia F, Gottesman S. Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli. Genes Dev. 2003;17:2374-83 pubmed publisher
    ..Thus, this large class of regulatory RNAs share an unexpected intrinsic mechanism for shutting off their action...
  33. Moll I, Leitsch D, Steinhauser T, Bl si U. RNA chaperone activity of the Sm-like Hfq protein. EMBO Rep. 2003;4:284-9 pubmed publisher
    ..We also show that the Hfq-induced structural changes in ompA mRNA are maintained after proteolytic digestion of the protein, which classifies Hfq as an RNA chaperone...
  34. Arluison V, Derreumaux P, Allemand F, Folichon M, Hajnsdorf E, R gnier P. Structural Modelling of the Sm-like Protein Hfq from Escherichia coli. J Mol Biol. 2002;320:705-12 pubmed
    ..This structure accounts for the physico-chemical properties of Hfq and highlights amino acid residues that could interact with RNA...
  35. Zhang A, Altuvia S, Tiwari A, Argaman L, Hengge Aronis R, Storz G. The OxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-I) protein. EMBO J. 1998;17:6061-8 pubmed
    ..Co-immunoprecipitation and gel mobility shift experiments revealed that the OxyS RNA binds Hfq, suggesting that OxyS represses rpoS translation by altering Hfq activity. ..
  36. Zhang A, Schu D, Tjaden B, Storz G, Gottesman S. Mutations in interaction surfaces differentially impact E. coli Hfq association with small RNAs and their mRNA targets. J Mol Biol. 2013;425:3678-97 pubmed publisher
    ..We discuss the implications of these observations for Hfq binding to RNA and mechanisms of action. ..
  37. Morita T, Aiba H. RNase E action at a distance: degradation of target mRNAs mediated by an Hfq-binding small RNA in bacteria. Genes Dev. 2011;25:294-8 pubmed publisher
    ..The study has provided an important insight into the initial events of sRNA-induced degradation of target mRNAs. ..
  38. Silva I, Saramago M, Dressaire C, Domingues S, Viegas S, Arraiano C. Importance and key events of prokaryotic RNA decay: the ultimate fate of an RNA molecule. Wiley Interdiscip Rev RNA. 2011;2:818-36 pubmed publisher
    ..All of the above-mentioned aspects are discussed in the present review, which also highlights the principal differences between the RNA degradation pathways for the two main Gram-negative and Gram-positive bacterial models. ..
  39. Brown L, Elliott T. Mutations that increase expression of the rpoS gene and decrease its dependence on hfq function in Salmonella typhimurium. J Bacteriol. 1997;179:656-62 pubmed
  40. Kim Y, Wood T. Toxins Hha and CspD and small RNA regulator Hfq are involved in persister cell formation through MqsR in Escherichia coli. Biochem Biophys Res Commun. 2010;391:209-13 pubmed publisher
  41. Sonnleitner E, Sorger Domenigg T, Madej M, Findeiss S, Hackermüller J, Huttenhofer A, et al. Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools. Microbiology. 2008;154:3175-87 pubmed publisher
    ..In addition, based on surveys with structure-based bioinformatic tools, we provide an electronic compilation of putative sRNA and non-coding RNA genes of PAO1 based on their evolutionarily conserved structure. ..
  42. Nikulin A, Stolboushkina E, Perederina A, Vassilieva I, Blaesi U, Moll I, et al. Structure of Pseudomonas aeruginosa Hfq protein. Acta Crystallogr D Biol Crystallogr. 2005;61:141-6 pubmed publisher
  43. Mass E, Majdalani N, Gottesman S. Regulatory roles for small RNAs in bacteria. Curr Opin Microbiol. 2003;6:120-4 pubmed
    ..Small RNAs can both positively and negatively regulate translation, can simultaneously regulate multiple mRNA targets, and can change the pattern of polarity within an operon...
  44. Vasil eva I, Garber M. [The regulatory role of the Hfq protein in bacterial cells]. Mol Biol (Mosk). 2002;36:970-7 pubmed
    ..A similarity of Hfq and eukaryotic mRNA splicing proteins is discussed. Data are reviewed on the roles of Hfq in poly(A) metabolism and formation of the bacterial nucleoid and on the Hfq interaction with untranslated regulatory RNAs. ..
  45. Barra Bily L, Fontenelle C, Jan G, Flechard M, Trautwetter A, Pandey S, et al. Proteomic alterations explain phenotypic changes in Sinorhizobium meliloti lacking the RNA chaperone Hfq. J Bacteriol. 2010;192:1719-29 pubmed publisher
    ..Some proteins required for efficient symbiosis are reduced in the hfq mutant, contributing to the drastic defect in nodulation observed in this mutant...
  46. Ansong C, Yoon H, Porwollik S, Mottaz Brewer H, Petritis B, Jaitly N, et al. Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella: implications for virulence and global protein translation. PLoS ONE. 2009;4:e4809 pubmed publisher
  47. Zhang Y, Sun S, Wu T, Wang J, Liu C, Chen L, et al. Identifying Hfq-binding small RNA targets in Escherichia coli. Biochem Biophys Res Commun. 2006;343:950-5 pubmed
    ..Using a new alignment algorithm, most known negatively regulated targets of Hfq-binding sRNAs were identified. The results also show several interesting aspects of the regulatory function of Hfq-binding sRNAs. ..
  48. Valderas M, Alcantara R, Baumgartner J, Bellaire B, Robertson G, Ng W, et al. Role of HdeA in acid resistance and virulence in Brucella abortus 2308. Vet Microbiol. 2005;107:307-12 pubmed
    ..These experimental findings indicate that the brucellae rely upon additional gene products to resist the acidic conditions they encounter in the phagosomal compartment of host macrophages. ..
  49. Kawamoto H, Morita T, Shimizu A, Inada T, Aiba H. Implication of membrane localization of target mRNA in the action of a small RNA: mechanism of post-transcriptional regulation of glucose transporter in Escherichia coli. Genes Dev. 2005;19:328-38 pubmed
  50. Panja S, Woodson S. Hexamer to monomer equilibrium of E. coli Hfq in solution and its impact on RNA annealing. J Mol Biol. 2012;417:406-12 pubmed publisher
    ..These results suggest that RNA binding is coupled to hexamer assembly and that the biochemical activity of Hfq reflects the equilibrium between different quaternary structures. ..
  51. Lenz D, Mok K, Lilley B, Kulkarni R, Wingreen N, Bassler B. The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell. 2004;118:69-82 pubmed publisher
    ..We propose that Hfq, together with these sRNAs, creates an ultrasensitive regulatory switch that controls the critical transition into the high cell density, quorum-sensing mode...
  52. Mass E, Gottesman S. A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc Natl Acad Sci U S A. 2002;99:4620-5 pubmed publisher
  53. Tsui H, Leung H, Winkler M. Characterization of broadly pleiotropic phenotypes caused by an hfq insertion mutation in Escherichia coli K-12. Mol Microbiol. 1994;13:35-49 pubmed
    ..Together, these results show that hfq function plays a fundamental role in Escherichia coli physiology and that hfq and the hflA-region are in the amiB-mutL-miaA-hfq-hflX superoperon...