大肠杆菌RNA分子伴侶Hfq的结构以及与RNA相互作用的研究
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摘要
Hfq是细菌里重要的转录后调节因子。它能够帮助非编码sRNA与目标mRNA的配对。Hfq蛋白对于DsrA介导的rpoS mRNA在低温下的翻译激活是必须的。rpoS编码的稳态sigma因子σS是大肠杆菌中一般应激响应的核心控制因子。大肠杆菌内的Hfq蛋白是一个102个残基（11.2kDa）的Sm家族RNA分子伴侣蛋白。N端的1~65号残基（Hfq65）组成保守的Sm结构域而C端的部分（66~102号残基）则是一个没有固定结构但是却在功能上十分重要的部分。Sm结构域形成同六聚体圆盘状结构，Hfq65六聚体分子量约43kDa，Hfq全长六聚体分子量约67kDa。圆盘的两个面分别构成能与U-rich单链RNA序列结合的近端和能与A-rich单链RNA序列结合的远端。然而，Hfq蛋白与DsrA相互作用的结构信息还未知。尽管有报道称Hfq有水解ATP的能力，但是ATP结合位点和ATP水解的生物学意义都不清楚。没有严整结构的HfqCTD的折叠属性和发挥功能的机制也是一个未解之谜。我们对Hfq65和HfqCTD进行了核磁共振（NMR）谱的主链归属，并且获得了Hfq65和Hfq全长（HfqFL）蛋白异亮氨酸，亮氨酸和颉氨酸侧链甲基的选择性标记样品的甲基HMQC谱。我们发现，Hfq65和HfqFL的1H-15NHSQC以及~1H-~(13)C甲基HMQC都有显著的不同。HfqCTD和Hfq65的相互NMR滴定实验表明这两者之间没有显著的相互作用。我们用Gd(DPA)3作为顺磁标签，在PRE实验中获得了初步的结果显示在HfqFL中，HfqCTD可能与Hfq65之间有瞬时的相互作用。我们还获得了大肠杆菌Hfq与DsrA上面的主要Hfq识别区域AU_6A以及ADP的三元复合物晶体结构，以及Hfq与ADP的二元复合物晶体结构。AU_6A结合到一个Hfq的近端和另一个Hfq的远端。ADP结合到远端的嘌呤选择性结合位点并且有一些ADP用磷酸基团与另一个Hfq上近端的保守精氨酸或是谷氨酰胺侧链相互作用。这样的ADP结合模式与之前人们推测的不同。我们在ATP酶活实验中验证了这些与ADP磷酸基团接触的保守的极性残基对于ATP酶活性的重要性。我们发现ATP酶活性会降低Hfq与U-rich序列的结合亲和力。在RNA浓度远高于Hfq浓度的情况下，ATP的存在可以增强Hfq的分子伴侣活性。我们用Hfq和DsrA的片段在溶液核磁共振以及荧光偏振实验中获得的结果验证了多个Hfq六聚体在与DsrA结合时的合作现象。用Hfq全长和DsrA全长进行的荧光共振能量转移实验也支持Hfq全长在与DsrA全长相互作用时需要多个六聚体的相互合作。我们基于以上的结果，提出一个Hfq通过多个六聚体之间的合作来完成其功能的猜想。
Hfq is a bacterial post-transcriptional regulator. It facilitates base-pairing between sRNA andtarget mRNA. Hfq mediates DsrA dependent translational activation of rpoS mRNA at lowtemperatures. rpoS encodes the stationary phase sigma factorσSwhich is the central regulatorin general stress response. E.coli Hfq is a 102 amino acid residue (11.2kDa) bacterial SmRNA chaperon protein. The N-terminal 1~65 amino acid residues of Hfq protein (Hfq65)comprise a conserved Sm domain and the C-terminal part 66~102aa (HfqCTD) isnon-structured but functional essential. The Sm domain forms homo-hexameric ring structure.The molecular weights for Hfq65 and Hfq full length hexamers are 43kDa and 67kDarespectively. Distinct RNA binding sites with specificity for A-rich and U-rich ssRNArespectively has been identified on either side of the ring. However, structural information onHfq-DsrA interaction is not yet available. Though Hfq is reported to hydrolyze ATP, neitherthe ATP binding site nor the biological significance of ATP hydrolysis is known. Moreover,the structure and function of the flexible tail of HfqCTD remains an enigma. We haveassigned backbone resonances for Hfq65 and HfqCTD and acquired I, L, V methyl selectivelylabeled Hfq65 and Hfq full length (HfqFL) HMQC spectra. We found that Hfq65 and HfqFLbehaves very differently on both1H-15N HSQC and1H-13C methyl HMQC. Mutual NMRtitrations of HfqCTD with Hfq65 indicate non-prominent interaction between these twoconstructs. We have used Gd(DPA)3as paramagnetic probe and acquired preliminaryparamagnetic relaxation enhancement (PRE) results suggesting transient interactions betweenHfq65 and HfqCTD in HfqFL protein. We have also acquired ternary crystal complexstructure of E.coli Hfq bound to a major Hfq recognition region on DsrA, AU6A, togetherwith ADP and crystal complex structure of Hfq bound to ADP. AU6A binds to proximal anddistal sides of two Hfq hexamers. ADP bind to purine selective site on distal side and contactconserved arginine or glutamine residues on proximal side of another hexamer. This bindingmode is different from previously postulated. In ATPase activity assays, we confirmed thatthe residues that make contact with ADP is involved in the ATPase activity. We found thatATPase activity decreases the binding affinity of Hfq to U-rich sequence. In cases when Hfqconcentration is much lower than RNA concentration, the presence of ATP can increase thechaperoning ability of Hfq. The cooperation of two different Hfq hexamers upon nucleic acidbinding in solution is verified by fluorescence polarization and solution NMR experimentsusing fragments of Hfq and DsrA. Fluorescence resonance energy transfer conducted with fulllength Hfq and DsrA also support cooperation of Hfq hexamers upon DsrA binding. Weproposed a plausible model for Hfq mechanism in which cooperation between multiple Hfqhexamers is required.
Hfq is a bacterial post-transcriptional regulator. It facilitates base-pairing between sRNA andtarget mRNA. Hfq mediates DsrA dependent translational activation of rpoS mRNA at lowtemperatures. rpoS encodes the stationary phase sigma factorσSwhich is the central regulatorin general stress response. E.coli Hfq is a 102 amino acid residue (11.2kDa) bacterial SmRNA chaperon protein. The N-terminal 1~65 amino acid residues of Hfq protein (Hfq65)comprise a conserved Sm domain and the C-terminal part 66~102aa (HfqCTD) isnon-structured but functional essential. The Sm domain forms homo-hexameric ring structure.The molecular weights for Hfq65 and Hfq full length hexamers are 43kDa and 67kDarespectively. Distinct RNA binding sites with specificity for A-rich and U-rich ssRNArespectively has been identified on either side of the ring. However, structural information onHfq-DsrA interaction is not yet available. Though Hfq is reported to hydrolyze ATP, neitherthe ATP binding site nor the biological significance of ATP hydrolysis is known. Moreover,the structure and function of the flexible tail of HfqCTD remains an enigma. We haveassigned backbone resonances for Hfq65 and HfqCTD and acquired I, L, V methyl selectivelylabeled Hfq65 and Hfq full length (HfqFL) HMQC spectra. We found that Hfq65 and HfqFLbehaves very differently on both1H-15N HSQC and1H-13C methyl HMQC. Mutual NMRtitrations of HfqCTD with Hfq65 indicate non-prominent interaction between these twoconstructs. We have used Gd(DPA)3as paramagnetic probe and acquired preliminaryparamagnetic relaxation enhancement (PRE) results suggesting transient interactions betweenHfq65 and HfqCTD in HfqFL protein. We have also acquired ternary crystal complexstructure of E.coli Hfq bound to a major Hfq recognition region on DsrA, AU6A, togetherwith ADP and crystal complex structure of Hfq bound to ADP. AU6A binds to proximal anddistal sides of two Hfq hexamers. ADP bind to purine selective site on distal side and contactconserved arginine or glutamine residues on proximal side of another hexamer. This bindingmode is different from previously postulated. In ATPase activity assays, we confirmed thatthe residues that make contact with ADP is involved in the ATPase activity. We found thatATPase activity decreases the binding affinity of Hfq to U-rich sequence. In cases when Hfqconcentration is much lower than RNA concentration, the presence of ATP can increase thechaperoning ability of Hfq. The cooperation of two different Hfq hexamers upon nucleic acidbinding in solution is verified by fluorescence polarization and solution NMR experimentsusing fragments of Hfq and DsrA. Fluorescence resonance energy transfer conducted with fulllength Hfq and DsrA also support cooperation of Hfq hexamers upon DsrA binding. Weproposed a plausible model for Hfq mechanism in which cooperation between multiple Hfqhexamers is required.
引文
Altuvia S. 2007. Identification of bacterial small non-coding RNAs:experimental approaches. Current Opinion in Microbiology 10: 257-261.
Arluison V, Folichon M, Marco S, Derreumaux P, Pellegrini O, Seguin J,Hajnsdorf E, Regnier P. 2004. The C-terminal domain of Escherichia coliHfq increases the stability of the hexamer. European Journal of Biochemistry271: 1258-1265.
Arluison V, Mutyam SK, Mura C, Marco S, Sukhodolets MV. 2007.Sm-like protein Hfq: Location of the ATP-binding site and the effect of ATPon Hfq-RNA complexes. Protein Science 16: 1830-1841.
Bailey S. 1994. The Ccp4 Suite - Programs for Protein Crystallography.Acta Crystallographica Section D-Biological Crystallography 50: 760-763.
Bartel DP. 2009. MicroRNAs: Target Recognition and RegulatoryFunctions. Cell 136: 215-233.
Battiste JL, Wagner G. 2000. Utilization of site-directed spin labelingand high-resolution heteronuclear nuclear magnetic resonance for globalfold determination of large proteins with limited nuclear overhauser effectdata. Biochemistry 39: 5355-5365.
Beich-Frandsen M, Vecerek B, Konarev PV, Sjoblom B, Kloiber K,Hammerle H, Rajkowitsch L, Miles AJ, Kontaxis G, Wallace BA et al. 2011.Structural insights into the dynamics and function of the C-terminus of the E.coli RNA chaperone Hfq. Nucleic Acids Res 39: 4900-4915.
Bochtler M, Hartmann C, Song HK, Bourenkov GP, Bartunik HD, HuberR. 2000. The structures of HslU and the ATP-dependent protease HslU-HslV.Nature 403: 800-805.
Boisbouvier J, Amero C, Dura MA, Noirclerc-Savoye M, Perollier A,Gallet B, Plevin MJ, Vernet T, Franzetti B. 2011. A systematicmutagenesis-driven strategy for site-resolved NMR studies ofsupramolecular assemblies. J Biomol Nmr 50: 229-236.
Brennan RG, Link TM. 2007. Hfq structure, function and ligand binding.Current Opinion in Microbiology 10: 125-133.
Brescia CC, Mikulecky PJ, Feig AL, Sledjeski DD. 2003. Identificationof the Hfq-binding site on DsrA RNA: Hfq binds without altering DsrAsecondary structure. Rna-a Publication of the Rna Society 9: 33-43.
Brown L, Elliott T. 1996. Efficient translation of the RpoS sigma factor inSalmonella typhimurium requires host factor I, an RNA-binding proteinencoded by the hfq gene. Journal of Bacteriology 178: 3763-3770.
Clore GM, Iwahara J. 2009. Theory, Practice, and Applications ofParamagnetic Relaxation Enhancement for the Characterization ofTransient Low-Population States of Biological Macromolecules and TheirComplexes. Chemical Reviews 109: 4108-4139.
Clore GM, Tang C, Iwahara J. 2007. Elucidating transientmacromolecular interactions using paramagnetic relaxation enhancement.Current Opinion in Structural Biology 17: 603-616.
Crick FH. 1958. On protein synthesis. Symp Soc Exp Biol 12: 138-163.
Croce CM, Volinia S, Calin GA, Liu CG, Ambs S, Cimmino A, PetroccaF, Visone R, Iorio M, Roldo C et al. 2006. A microRNA expression signatureof human solid tumors defines cancer gene targets. P Natl Acad Sci USA 103:2257-2261.
Eddy SR. 2001. Non-coding RNA genes and the modern RNA world.Nat Rev Genet 2: 919-929.
Fender A, Elf J, Hampel K, Zimmermann B, Wagner EG. 2010. RNAsactively cycle on the Sm-like protein Hfq. Genes Dev 24: 2621-2626.
Folichon M, Arluison V, Pellegrini O, Huntzinger E, Regnier P,Hajnsdorf E. 2003. The poly(A) binding protein Hfq protects RNA fromRNase E and exoribonucleolytic degradation. Nucleic Acids Research 31:7302-7310.
Geissmann TA, Touati D. 2004. Hfq, a new chaperoning role: bindingto messenger RNA determines access for small RNA regulator. EmboJournal 23: 396-405.
Gottesman S, McCullen CA, Guillier M, Vanderpool CK, Majdalani N,Benhammou J, Thompson KM, FitzGerald PC, Sowa NA, FitzGerald DJ. 2006.Small RNA regulators and the bacterial response to stress. Cold SpringHarbor Symposia on Quantitative Biology 71: 1-11.
Guo C, Tugarinov V. 2009. Identification of HN-methyl NOEs in largeproteins using simultaneous amide-methyl TROSY-based detection. JBiomol Nmr 43: 21-30.
Hengge-Aronis R. 2002. Signal transduction and regulatorymechanisms involved in control of the sigma(S) (RpoS) subunit of RNApolymerase. Microbiol Mol Biol Rev 66: 373-395.
Henzler-Wildman K, Kern D. 2007. Dynamic personalities of proteins.Nature 450: 964-972.
Hopkins JF, Panja S, Woodson SA. 2011. Rapid binding and release ofHfq from ternary complexes during RNA annealing. Nucleic Acids Research39: 5193-5202.
Huang TG, Hackney DD. 1994. Drosophila Kinesin Minimal MotorDomain Expressed in Escherichia-Coli - Purification and KineticCharacterization. J Biol Chem 269: 16493-16501.
Hussein R, Lim HN. 2011. Disruption of small RNA signaling caused bycompetition for Hfq. Proc Natl Acad Sci 108: 1110-1115.
Hwang W, Arluison V, Hohng S. 2011. Dynamic competition of DsrAand rpoS fragments for the proximal binding site of Hfq as a means forefficient annealing. Nucleic Acids Research 39: 5131-5139.
John C, Brothers WjF, Arthur G. Palmer I, Rance M, Nicholas JS. 2007.Protein NMR Spectroscopy. Elsevier, New York.
Jousselin A, Metzinger L, Felden B. 2009. On the facultativerequirement of the bacterial RNA chaperone, Hfq. Trends Microbiol 17:399-405.
Kolter R, Yanofsky C. 1982. Attenuation in Amino-Acid BiosyntheticOperons. Annu Rev Genet 16: 113-134.
Korzhnev DM, Kloiber K, Kanelis V, Tugarinov V, Kay LE. 2004.Probing slow dynamics in high molecular weight proteins bymethyl-TROSY NMR spectroscopy: Application to a 723-residue enzyme.Journal of the American Chemical Society 126: 3964-3973.
Lazar P, Kim S, Lee Y, Lee KW. 2010. Computational approach toensure the stability of the favorable ATP binding site in E. coli Hfq. J MolGraph Model 29: 573-580.
Lease RA, Belfort M. 2000. A trans-acting RNA as a control switch inEscherichia coli: DsrA modulates function by forming alternative structures.Proc Natl Acad Sci 97: 9919-9924.
Lease RA, Cusick ME, Belfort M. 1998. Riboregulation in Escherichiacoli: DsrA RNA acts by RNA : RNA interactions at multiple loci. Proc NatlAcad Sci 95: 12456-12461.
Lease RA, Woodson SA. 2004. Cycling of the Sm-like protein Hfq onthe DsrA small regulatory RNA. Journal of Molecular Biology 344:1211-1223.
Leslie AGW. 1992. Recent changes to the MOSFLM package forprocessing film and image plate data. Joint CCP4+ESF-EAMCB Newsletteron Protein Crystallography 26.
Link TM, Valentin-Hansen P, Brennan RG. 2009. Structure ofEscherichia coli Hfq bound to polyriboadenylate RNA. Proc Natl Acad Sci106: 19286-19291.
Liu JM, Camilli A. 2010. A broadening world of bacterial small RNAs.Current Opinion in Microbiology 13: 18-23.
Lundstrom P, Vallurupalli P, Religa TL, Dahlquist FW, Kay LE. 2007. Asingle-quantum methyl C-13-relaxation dispersion experiment withimproved sensitivity. Journal of Biomolecular Nmr 38: 79-88.
Majdalani N, Cunning C, Sledjeski D, Elliott T, Gottesman S. 1998.DsrA RNA regulates translation of RpoS message by an anti-antisensemechanism, independent of its action as an antisilencer of transcription.Proc Natl Acad Sci 95: 12462-12467.
Majdalani N, Vanderpool CK, Gottesman S. 2005. Bacterial small RNAregulators. Critical Reviews in Biochemistry and Molecular Biology 40:93-113.
McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC,Read RJ. 2007. Phaser crystallographic software. Journal of AppliedCrystallography 40: 658-674.
Mikulecky PJ, Kaw MK, Brescia CC, Takach JC, Sledjeski DD, Feig AL.2004. Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoSand poly(A) RNAs. Nature Structural & Molecular Biology 11: 1206-1214.
Moll I, Leitsch D, Steinhauser T, Blasi U. 2003. RNA chaperone activityof the Sm-like Hfq protein. Embo Reports 4: 284-289.
Muffler A, Fischer D, HenggeAronis R. 1996. The RNA-binding proteinHF-I, known as a host factor for phage Q beta RNA replication, is essentialfor rpoS translation in Escherichia coli. Genes & Development 10:1143-1151.
Nudler E, Mironov AS. 2004. The riboswitch control of bacterialmetabolism. Trends Biochem Sci 29: 11-17.
Opella SJ, Ma C. 2000. Lanthanide ions bind specifically to an added"EF-hand" and orient a membrane protein in micelles for solution NMRspectroscopy. J Magn Reson 146: 381-384.
Otting G. 2008. Prospects for lanthanides in structural biology by NMR.J Biomol Nmr 42: 1-9.
Palmer AG. 2004. NMR characterization of the dynamics ofbiomacromolecules. Chemical Reviews 104: 3623-3640.
Pelletier J, Sonenberg N. 1988. Internal initiation of translation ofeukaryotic mRNA directed by a sequence derived from poliovirus RNA.Nature 334: 320-325.
Pervushin K, Riek R, Wider G, Wuthrich K. 1997. Attenuated T2relaxation by mutual cancellation of dipole-dipole coupling and chemicalshift anisotropy indicates an avenue to NMR structures of very largebiological macromolecules in solution. Proc Natl Acad Sci U S A 94:12366-12371.
Piston DW, Rizzo MA. 2005. High-contrast imaging of fluorescentprotein FRET by fluorescence polarization microscopy. Biophysical Journal88: L14-L16.
Religa TL, Sprangers R, Kay LE. 2010. Dynamic Regulation of ArchaealProteasome Gate Opening As Studied by TROSY NMR. Science 328:98-102.
Riek R, Wider G, Pervushin K, Wuthrich K. 1999. Polarization transferby cross-correlated relaxation in solution NMR with very large molecules.P Natl Acad Sci USA 96: 4918-4923.
Rumpel S, Becker S, Zweckstetter M. 2008. High-resolution structuredetermination of the CylR2 homodimer using paramagnetic relaxationenhancement and structure-based prediction of molecular alignment. JBiomol Nmr 40: 1-13.
Runnels LW, Scarlata SF. 1995. Theory and Application ofFluorescence Homotransfer to Melittin Oligomerization. Biophysical Journal69: 1569-1583.
Ruschak AM, Kay LE. 2010. Methyl groups as probes ofsupra-molecular structure, dynamics and function. J Biomol Nmr 46: 75-87.
Salzmann M, Pervushin K, Wider G, Senn H, Wuthrich K. 1998. TROSYin triple-resonance experiments: New perspectives for sequential NMRassignment of large proteins. Proc Natl Acad Sci 95: 13585-13590.
Salzmann M, Wider G, Pervushin K, Senn H, Wuthrich K. 1999.TROSY-type triple-resonance experiments for sequential NMRassignments of large proteins. J Am Chem Soc 121: 844-848.
Sauer E, Weichenrieder O. 2011. Structural basis for RNA 3'-endrecognition by Hfq. Proc Natl Acad Sci 108: 13065-13070.
Sauter C, Basquin J, Suck D. 2003. Sm-like proteins in Eubacteria: thecrystal structure of the Hfq protein from Escherichia coli. Nucleic AcidsResearch 31: 4091-4098.
Schumacher MA, Pearson RF, Moller T, Valentin-Hansen P, BrennanRG. 2002. Structures of the pleiotropic translational regulator Hfq and anHfq-RNA complex: a bacterial Sm-like protein. Embo Journal 21: 3546-3556.
Sonnleitner E, Napetschnig J, Afonyushkin T, Ecker K, Vecerek B, MollI, Kaberdin VR, Blasi U. 2004. Functional effects of variants of the RNAchaperone Hfq. Biochemical and Biophysical Research Communications 323:1017-1023.
Soper T, Mandin P, Majdalani N, Gottesman S, Woodson SA. 2010.Positive regulation by small RNAs and the role of Hfq. P Natl Acad Sci USA107: 9602-9607.
Soper TJ, Woodson SA. 2008. The rpoS mRNA leader recruits Hfq tofacilitate annealing with DsrA sRNA. Rna-a Publication of the Rna Society 14:1907-1917.
Sprangers R, Velyvis A, Kay LE. 2007. Solution NMR of supramolecularcomplexes: providing new insights into function. Nature Methods 4:697-703.
Steward LE, Gilmore MG, M. A., Williams D, Okawa Y, Holguin B,James NG, Ross JA, Aoki KR, Jameson DM. 2011. Depolarization afterresonance energy transfer (DARET): A sensitive fluorescence-based assayfor botulinum neurotoxin protease activity. Analytical Biochemistry 413:36-42.
Su XC, Liang HB, Loscha KV, Otting G. 2009. [Ln(DPA)(3)](3-) Is aConvenient Paramagnetic Shift Reagent for Protein NMR Studies. J AmChem Soc 131: 10352-+.
Su XC, Man B, Beeren S, Liang H, Simonsen S, Schmitz C, Huber T,Messerle BA, Otting G. 2008. A dipicolinic acid tag for rigid lanthanidetagging of proteins and paramagnetic NMR spectroscopy. J Am Chem Soc130: 10486-+.
Sukhodolets MV, Garges S. 2003. Interaction of Escherichia coli RNApolymerase with the ribosomal protein S1 and the Sm-like ATPase Hfq.Biochemistry 42: 8022-8034.
Sun XG, Wartell RM. 2006. Escherichia coli Hfq binds A(18) and DsrAdomain II with similar 2 : 1 Hfq(6)/RNA stoichiometry using differentsurface sites. Biochemistry 45: 4875-4887.
Tugarinov V, Hwang PM, Ollerenshaw JE, Kay LE. 2003.Cross-correlated relaxation enhanced 1H[bond]13C NMR spectroscopy ofmethyl groups in very high molecular weight proteins and proteincomplexes. J Am Chem Soc 125: 10420-10428.
Tugarinov V, Kay LE. 2003. Ile, Leu, and Val methyl assignments of the723-residue malate synthase G using a new labeling strategy and novelNMR methods. J Am Chem Soc 125: 13868-13878.
Tugarinov V, Kay LE. 2004. An isotope labeling strategy for methylTROSY spectroscopy. Journal of Biomolecular Nmr 28: 165-172.
Updegrove TB, Correia JJ, Chen Y, Terry C, Wartell RM. 2011. Thestoichiometry of the Escherichia coli Hfq protein bound to RNA. Rna-aPublication of the Rna Society 17: 489-500.
Updegrove TB, Correia JJ, Galletto R, Bujalowski W, Wartell RM. 2010.E. coli DNA associated with isolated Hfq interacts with Hfq's distal surfaceand C-terminal domain. Biochimica Et Biophysica Acta-Gene RegulatoryMechanisms 1799: 588-596.
Vecerek B, Rajkowitsch L, Sonnleitner E, Schroeder R, Blasi U. 2008.The C-terminal domain of Escherichia coli Hfq is required for regulation.Nucleic Acids Research 36: 133-143.
Venditti V, Fawzi NL, Clore GM. 2011. Automated sequence- andstereo-specific assignment of methyl-labeled proteins by paramagneticrelaxation and methyl-methyl nuclear overhauser enhancementspectroscopy. J Biomol Nmr.
Vogel J, Luisi BF. 2011. Hfq and its constellation of RNA. Nature ReviewsMicrobiology 9: 578-589.
Walden WE, Selezneva AI, Dupuy J, Volbeda A, Fontecilla-Camps JC,Theil EC, Volz K. 2006. Structure of dual function iron regulatory protein 1complexed with ferritin IRE-RNA. Science 314: 1903-1908.
Wieruszeski JM, Landrieu I, Hanoulle X, Lippens G. 2006. ELISE NMR:Experimental liquid sealing of NMR samples. J Magn Reson 181: 199-202.
Xu QH, Wang S, Korystov D, Mikhailovsky A, Bazan GC, Moses D,Heeger AJ. 2005. The fluorescence resonance energy transfer (FRET) gate:A time-resolved study. P Natl Acad Sci USA 102: 530-535.
Xu YQ, Liu MH, Simpson PJ, Isaacson R, Cota E, Marchant J, Yang DW,Zhang XD, Freemont P, Matthews S. 2009. Automated Assignment inSelectively Methyl-Labeled Proteins. J Am Chem Soc 131: 9480-+.
Yagi H, Loscha KV, Su XC, Stanton-Cook M, Huber T, Otting G. 2010.Tunable paramagnetic relaxation enhancements by [Gd(DPA)(3)](3-) forprotein structure analysis. J Biomol Nmr 47: 143-153.
Yang DW, Zheng Y, Liu DJ, Wyss DF. 2004. Sequence-specificassignments of methyl groups in high-molecular weight proteins. J AmChem Soc 126: 3710-3711.
Arluison V, Folichon M, Marco S, Derreumaux P, Pellegrini O, Seguin J,Hajnsdorf E, Regnier P. 2004. The C-terminal domain of Escherichia coliHfq increases the stability of the hexamer. European Journal of Biochemistry271: 1258-1265.
Arluison V, Mutyam SK, Mura C, Marco S, Sukhodolets MV. 2007.Sm-like protein Hfq: Location of the ATP-binding site and the effect of ATPon Hfq-RNA complexes. Protein Science 16: 1830-1841.
Bailey S. 1994. The Ccp4 Suite - Programs for Protein Crystallography.Acta Crystallographica Section D-Biological Crystallography 50: 760-763.
Bartel DP. 2009. MicroRNAs: Target Recognition and RegulatoryFunctions. Cell 136: 215-233.
Battiste JL, Wagner G. 2000. Utilization of site-directed spin labelingand high-resolution heteronuclear nuclear magnetic resonance for globalfold determination of large proteins with limited nuclear overhauser effectdata. Biochemistry 39: 5355-5365.
Beich-Frandsen M, Vecerek B, Konarev PV, Sjoblom B, Kloiber K,Hammerle H, Rajkowitsch L, Miles AJ, Kontaxis G, Wallace BA et al. 2011.Structural insights into the dynamics and function of the C-terminus of the E.coli RNA chaperone Hfq. Nucleic Acids Res 39: 4900-4915.
Bochtler M, Hartmann C, Song HK, Bourenkov GP, Bartunik HD, HuberR. 2000. The structures of HslU and the ATP-dependent protease HslU-HslV.Nature 403: 800-805.
Boisbouvier J, Amero C, Dura MA, Noirclerc-Savoye M, Perollier A,Gallet B, Plevin MJ, Vernet T, Franzetti B. 2011. A systematicmutagenesis-driven strategy for site-resolved NMR studies ofsupramolecular assemblies. J Biomol Nmr 50: 229-236.
Brennan RG, Link TM. 2007. Hfq structure, function and ligand binding.Current Opinion in Microbiology 10: 125-133.
Brescia CC, Mikulecky PJ, Feig AL, Sledjeski DD. 2003. Identificationof the Hfq-binding site on DsrA RNA: Hfq binds without altering DsrAsecondary structure. Rna-a Publication of the Rna Society 9: 33-43.
Brown L, Elliott T. 1996. Efficient translation of the RpoS sigma factor inSalmonella typhimurium requires host factor I, an RNA-binding proteinencoded by the hfq gene. Journal of Bacteriology 178: 3763-3770.
Clore GM, Iwahara J. 2009. Theory, Practice, and Applications ofParamagnetic Relaxation Enhancement for the Characterization ofTransient Low-Population States of Biological Macromolecules and TheirComplexes. Chemical Reviews 109: 4108-4139.
Clore GM, Tang C, Iwahara J. 2007. Elucidating transientmacromolecular interactions using paramagnetic relaxation enhancement.Current Opinion in Structural Biology 17: 603-616.
Crick FH. 1958. On protein synthesis. Symp Soc Exp Biol 12: 138-163.
Croce CM, Volinia S, Calin GA, Liu CG, Ambs S, Cimmino A, PetroccaF, Visone R, Iorio M, Roldo C et al. 2006. A microRNA expression signatureof human solid tumors defines cancer gene targets. P Natl Acad Sci USA 103:2257-2261.
Eddy SR. 2001. Non-coding RNA genes and the modern RNA world.Nat Rev Genet 2: 919-929.
Fender A, Elf J, Hampel K, Zimmermann B, Wagner EG. 2010. RNAsactively cycle on the Sm-like protein Hfq. Genes Dev 24: 2621-2626.
Folichon M, Arluison V, Pellegrini O, Huntzinger E, Regnier P,Hajnsdorf E. 2003. The poly(A) binding protein Hfq protects RNA fromRNase E and exoribonucleolytic degradation. Nucleic Acids Research 31:7302-7310.
Geissmann TA, Touati D. 2004. Hfq, a new chaperoning role: bindingto messenger RNA determines access for small RNA regulator. EmboJournal 23: 396-405.
Gottesman S, McCullen CA, Guillier M, Vanderpool CK, Majdalani N,Benhammou J, Thompson KM, FitzGerald PC, Sowa NA, FitzGerald DJ. 2006.Small RNA regulators and the bacterial response to stress. Cold SpringHarbor Symposia on Quantitative Biology 71: 1-11.
Guo C, Tugarinov V. 2009. Identification of HN-methyl NOEs in largeproteins using simultaneous amide-methyl TROSY-based detection. JBiomol Nmr 43: 21-30.
Hengge-Aronis R. 2002. Signal transduction and regulatorymechanisms involved in control of the sigma(S) (RpoS) subunit of RNApolymerase. Microbiol Mol Biol Rev 66: 373-395.
Henzler-Wildman K, Kern D. 2007. Dynamic personalities of proteins.Nature 450: 964-972.
Hopkins JF, Panja S, Woodson SA. 2011. Rapid binding and release ofHfq from ternary complexes during RNA annealing. Nucleic Acids Research39: 5193-5202.
Huang TG, Hackney DD. 1994. Drosophila Kinesin Minimal MotorDomain Expressed in Escherichia-Coli - Purification and KineticCharacterization. J Biol Chem 269: 16493-16501.
Hussein R, Lim HN. 2011. Disruption of small RNA signaling caused bycompetition for Hfq. Proc Natl Acad Sci 108: 1110-1115.
Hwang W, Arluison V, Hohng S. 2011. Dynamic competition of DsrAand rpoS fragments for the proximal binding site of Hfq as a means forefficient annealing. Nucleic Acids Research 39: 5131-5139.
John C, Brothers WjF, Arthur G. Palmer I, Rance M, Nicholas JS. 2007.Protein NMR Spectroscopy. Elsevier, New York.
Jousselin A, Metzinger L, Felden B. 2009. On the facultativerequirement of the bacterial RNA chaperone, Hfq. Trends Microbiol 17:399-405.
Kolter R, Yanofsky C. 1982. Attenuation in Amino-Acid BiosyntheticOperons. Annu Rev Genet 16: 113-134.
Korzhnev DM, Kloiber K, Kanelis V, Tugarinov V, Kay LE. 2004.Probing slow dynamics in high molecular weight proteins bymethyl-TROSY NMR spectroscopy: Application to a 723-residue enzyme.Journal of the American Chemical Society 126: 3964-3973.
Lazar P, Kim S, Lee Y, Lee KW. 2010. Computational approach toensure the stability of the favorable ATP binding site in E. coli Hfq. J MolGraph Model 29: 573-580.
Lease RA, Belfort M. 2000. A trans-acting RNA as a control switch inEscherichia coli: DsrA modulates function by forming alternative structures.Proc Natl Acad Sci 97: 9919-9924.
Lease RA, Cusick ME, Belfort M. 1998. Riboregulation in Escherichiacoli: DsrA RNA acts by RNA : RNA interactions at multiple loci. Proc NatlAcad Sci 95: 12456-12461.
Lease RA, Woodson SA. 2004. Cycling of the Sm-like protein Hfq onthe DsrA small regulatory RNA. Journal of Molecular Biology 344:1211-1223.
Leslie AGW. 1992. Recent changes to the MOSFLM package forprocessing film and image plate data. Joint CCP4+ESF-EAMCB Newsletteron Protein Crystallography 26.
Link TM, Valentin-Hansen P, Brennan RG. 2009. Structure ofEscherichia coli Hfq bound to polyriboadenylate RNA. Proc Natl Acad Sci106: 19286-19291.
Liu JM, Camilli A. 2010. A broadening world of bacterial small RNAs.Current Opinion in Microbiology 13: 18-23.
Lundstrom P, Vallurupalli P, Religa TL, Dahlquist FW, Kay LE. 2007. Asingle-quantum methyl C-13-relaxation dispersion experiment withimproved sensitivity. Journal of Biomolecular Nmr 38: 79-88.
Majdalani N, Cunning C, Sledjeski D, Elliott T, Gottesman S. 1998.DsrA RNA regulates translation of RpoS message by an anti-antisensemechanism, independent of its action as an antisilencer of transcription.Proc Natl Acad Sci 95: 12462-12467.
Majdalani N, Vanderpool CK, Gottesman S. 2005. Bacterial small RNAregulators. Critical Reviews in Biochemistry and Molecular Biology 40:93-113.
McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC,Read RJ. 2007. Phaser crystallographic software. Journal of AppliedCrystallography 40: 658-674.
Mikulecky PJ, Kaw MK, Brescia CC, Takach JC, Sledjeski DD, Feig AL.2004. Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoSand poly(A) RNAs. Nature Structural & Molecular Biology 11: 1206-1214.
Moll I, Leitsch D, Steinhauser T, Blasi U. 2003. RNA chaperone activityof the Sm-like Hfq protein. Embo Reports 4: 284-289.
Muffler A, Fischer D, HenggeAronis R. 1996. The RNA-binding proteinHF-I, known as a host factor for phage Q beta RNA replication, is essentialfor rpoS translation in Escherichia coli. Genes & Development 10:1143-1151.
Nudler E, Mironov AS. 2004. The riboswitch control of bacterialmetabolism. Trends Biochem Sci 29: 11-17.
Opella SJ, Ma C. 2000. Lanthanide ions bind specifically to an added"EF-hand" and orient a membrane protein in micelles for solution NMRspectroscopy. J Magn Reson 146: 381-384.
Otting G. 2008. Prospects for lanthanides in structural biology by NMR.J Biomol Nmr 42: 1-9.
Palmer AG. 2004. NMR characterization of the dynamics ofbiomacromolecules. Chemical Reviews 104: 3623-3640.
Pelletier J, Sonenberg N. 1988. Internal initiation of translation ofeukaryotic mRNA directed by a sequence derived from poliovirus RNA.Nature 334: 320-325.
Pervushin K, Riek R, Wider G, Wuthrich K. 1997. Attenuated T2relaxation by mutual cancellation of dipole-dipole coupling and chemicalshift anisotropy indicates an avenue to NMR structures of very largebiological macromolecules in solution. Proc Natl Acad Sci U S A 94:12366-12371.
Piston DW, Rizzo MA. 2005. High-contrast imaging of fluorescentprotein FRET by fluorescence polarization microscopy. Biophysical Journal88: L14-L16.
Religa TL, Sprangers R, Kay LE. 2010. Dynamic Regulation of ArchaealProteasome Gate Opening As Studied by TROSY NMR. Science 328:98-102.
Riek R, Wider G, Pervushin K, Wuthrich K. 1999. Polarization transferby cross-correlated relaxation in solution NMR with very large molecules.P Natl Acad Sci USA 96: 4918-4923.
Rumpel S, Becker S, Zweckstetter M. 2008. High-resolution structuredetermination of the CylR2 homodimer using paramagnetic relaxationenhancement and structure-based prediction of molecular alignment. JBiomol Nmr 40: 1-13.
Runnels LW, Scarlata SF. 1995. Theory and Application ofFluorescence Homotransfer to Melittin Oligomerization. Biophysical Journal69: 1569-1583.
Ruschak AM, Kay LE. 2010. Methyl groups as probes ofsupra-molecular structure, dynamics and function. J Biomol Nmr 46: 75-87.
Salzmann M, Pervushin K, Wider G, Senn H, Wuthrich K. 1998. TROSYin triple-resonance experiments: New perspectives for sequential NMRassignment of large proteins. Proc Natl Acad Sci 95: 13585-13590.
Salzmann M, Wider G, Pervushin K, Senn H, Wuthrich K. 1999.TROSY-type triple-resonance experiments for sequential NMRassignments of large proteins. J Am Chem Soc 121: 844-848.
Sauer E, Weichenrieder O. 2011. Structural basis for RNA 3'-endrecognition by Hfq. Proc Natl Acad Sci 108: 13065-13070.
Sauter C, Basquin J, Suck D. 2003. Sm-like proteins in Eubacteria: thecrystal structure of the Hfq protein from Escherichia coli. Nucleic AcidsResearch 31: 4091-4098.
Schumacher MA, Pearson RF, Moller T, Valentin-Hansen P, BrennanRG. 2002. Structures of the pleiotropic translational regulator Hfq and anHfq-RNA complex: a bacterial Sm-like protein. Embo Journal 21: 3546-3556.
Sonnleitner E, Napetschnig J, Afonyushkin T, Ecker K, Vecerek B, MollI, Kaberdin VR, Blasi U. 2004. Functional effects of variants of the RNAchaperone Hfq. Biochemical and Biophysical Research Communications 323:1017-1023.
Soper T, Mandin P, Majdalani N, Gottesman S, Woodson SA. 2010.Positive regulation by small RNAs and the role of Hfq. P Natl Acad Sci USA107: 9602-9607.
Soper TJ, Woodson SA. 2008. The rpoS mRNA leader recruits Hfq tofacilitate annealing with DsrA sRNA. Rna-a Publication of the Rna Society 14:1907-1917.
Sprangers R, Velyvis A, Kay LE. 2007. Solution NMR of supramolecularcomplexes: providing new insights into function. Nature Methods 4:697-703.
Steward LE, Gilmore MG, M. A., Williams D, Okawa Y, Holguin B,James NG, Ross JA, Aoki KR, Jameson DM. 2011. Depolarization afterresonance energy transfer (DARET): A sensitive fluorescence-based assayfor botulinum neurotoxin protease activity. Analytical Biochemistry 413:36-42.
Su XC, Liang HB, Loscha KV, Otting G. 2009. [Ln(DPA)(3)](3-) Is aConvenient Paramagnetic Shift Reagent for Protein NMR Studies. J AmChem Soc 131: 10352-+.
Su XC, Man B, Beeren S, Liang H, Simonsen S, Schmitz C, Huber T,Messerle BA, Otting G. 2008. A dipicolinic acid tag for rigid lanthanidetagging of proteins and paramagnetic NMR spectroscopy. J Am Chem Soc130: 10486-+.
Sukhodolets MV, Garges S. 2003. Interaction of Escherichia coli RNApolymerase with the ribosomal protein S1 and the Sm-like ATPase Hfq.Biochemistry 42: 8022-8034.
Sun XG, Wartell RM. 2006. Escherichia coli Hfq binds A(18) and DsrAdomain II with similar 2 : 1 Hfq(6)/RNA stoichiometry using differentsurface sites. Biochemistry 45: 4875-4887.
Tugarinov V, Hwang PM, Ollerenshaw JE, Kay LE. 2003.Cross-correlated relaxation enhanced 1H[bond]13C NMR spectroscopy ofmethyl groups in very high molecular weight proteins and proteincomplexes. J Am Chem Soc 125: 10420-10428.
Tugarinov V, Kay LE. 2003. Ile, Leu, and Val methyl assignments of the723-residue malate synthase G using a new labeling strategy and novelNMR methods. J Am Chem Soc 125: 13868-13878.
Tugarinov V, Kay LE. 2004. An isotope labeling strategy for methylTROSY spectroscopy. Journal of Biomolecular Nmr 28: 165-172.
Updegrove TB, Correia JJ, Chen Y, Terry C, Wartell RM. 2011. Thestoichiometry of the Escherichia coli Hfq protein bound to RNA. Rna-aPublication of the Rna Society 17: 489-500.
Updegrove TB, Correia JJ, Galletto R, Bujalowski W, Wartell RM. 2010.E. coli DNA associated with isolated Hfq interacts with Hfq's distal surfaceand C-terminal domain. Biochimica Et Biophysica Acta-Gene RegulatoryMechanisms 1799: 588-596.
Vecerek B, Rajkowitsch L, Sonnleitner E, Schroeder R, Blasi U. 2008.The C-terminal domain of Escherichia coli Hfq is required for regulation.Nucleic Acids Research 36: 133-143.
Venditti V, Fawzi NL, Clore GM. 2011. Automated sequence- andstereo-specific assignment of methyl-labeled proteins by paramagneticrelaxation and methyl-methyl nuclear overhauser enhancementspectroscopy. J Biomol Nmr.
Vogel J, Luisi BF. 2011. Hfq and its constellation of RNA. Nature ReviewsMicrobiology 9: 578-589.
Walden WE, Selezneva AI, Dupuy J, Volbeda A, Fontecilla-Camps JC,Theil EC, Volz K. 2006. Structure of dual function iron regulatory protein 1complexed with ferritin IRE-RNA. Science 314: 1903-1908.
Wieruszeski JM, Landrieu I, Hanoulle X, Lippens G. 2006. ELISE NMR:Experimental liquid sealing of NMR samples. J Magn Reson 181: 199-202.
Xu QH, Wang S, Korystov D, Mikhailovsky A, Bazan GC, Moses D,Heeger AJ. 2005. The fluorescence resonance energy transfer (FRET) gate:A time-resolved study. P Natl Acad Sci USA 102: 530-535.
Xu YQ, Liu MH, Simpson PJ, Isaacson R, Cota E, Marchant J, Yang DW,Zhang XD, Freemont P, Matthews S. 2009. Automated Assignment inSelectively Methyl-Labeled Proteins. J Am Chem Soc 131: 9480-+.
Yagi H, Loscha KV, Su XC, Stanton-Cook M, Huber T, Otting G. 2010.Tunable paramagnetic relaxation enhancements by [Gd(DPA)(3)](3-) forprotein structure analysis. J Biomol Nmr 47: 143-153.
Yang DW, Zheng Y, Liu DJ, Wyss DF. 2004. Sequence-specificassignments of methyl groups in high-molecular weight proteins. J AmChem Soc 126: 3710-3711.