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Substrate Recognition and Autoinhibition in the Central Ribonuclease RNase E.

Bandyra KJ, Wandzik JM, Luisi BF.

Mol Cell. 2018 Oct 18;72(2):275-285.e4. doi: 10.1016/j.molcel.2018.08.039. Epub 2018 Sep 27.


Author Correction: Multidrug efflux pumps: structure, function and regulation.

Du D, Wang-Kan X, Neuberger A, van Veen HW, Pos KM, Piddock LJV, Luisi BF.

Nat Rev Microbiol. 2018 Sep;16(9):577. doi: 10.1038/s41579-018-0060-x.


Multidrug efflux pumps: structure, function and regulation.

Du D, Wang-Kan X, Neuberger A, van Veen HW, Pos KM, Piddock LJV, Luisi BF.

Nat Rev Microbiol. 2018 Sep;16(9):523-539. doi: 10.1038/s41579-018-0048-6. Review. Erratum in: Nat Rev Microbiol. 2018 Jul 18;:.


Structure and mechanism of bacterial tripartite efflux pumps.

Neuberger A, Du D, Luisi BF.

Res Microbiol. 2018 Sep - Oct;169(7-8):401-413. doi: 10.1016/j.resmic.2018.05.003. Epub 2018 May 19. Review.


RNase E and the High-Fidelity Orchestration of RNA Metabolism.

Bandyra KJ, Luisi BF.

Microbiol Spectr. 2018 Apr;6(2). doi: 10.1128/microbiolspec.RWR-0008-2017.


Interplay between the catabolite repression control protein Crc, Hfq and RNA in Hfq-dependent translational regulation in Pseudomonas aeruginosa.

Sonnleitner E, Wulf A, Campagne S, Pei XY, Wolfinger MT, Forlani G, Prindl K, Abdou L, Resch A, Allain FH, Luisi BF, Urlaub H, Bläsi U.

Nucleic Acids Res. 2018 Feb 16;46(3):1470-1485. doi: 10.1093/nar/gkx1245.


Purification of AcrAB-TolC Multidrug Efflux Pump for Cryo-EM Analysis.

Du D, Wang Z, Chiu W, Luisi BF.

Methods Mol Biol. 2018;1700:71-81. doi: 10.1007/978-1-4939-7454-2_5.


Analysis of the natively unstructured RNA/protein-recognition core in the Escherichia coli RNA degradosome and its interactions with regulatory RNA/Hfq complexes.

Bruce HA, Du D, Matak-Vinkovic D, Bandyra KJ, Broadhurst RW, Martin E, Sobott F, Shkumatov AV, Luisi BF.

Nucleic Acids Res. 2018 Jan 9;46(1):387-402. doi: 10.1093/nar/gkx1083.


Structural insights into RapZ-mediated regulation of bacterial amino-sugar metabolism.

Gonzalez GM, Durica-Mitic S, Hardwick SW, Moncrieffe MC, Resch M, Neumann P, Ficner R, Görke B, Luisi BF.

Nucleic Acids Res. 2017 Oct 13;45(18):10845-10860. doi: 10.1093/nar/gkx732.


RNA search engines empower the bacterial intranet.

Dendooven T, Luisi BF.

Biochem Soc Trans. 2017 Aug 15;45(4):987-997. doi: 10.1042/BST20160373. Epub 2017 Jul 14. Review.


1.8 Å resolution crystal structure of the carbapenem intrinsic resistance protein CarF.

Tichy EM, Hardwick SW, Luisi BF, Salmond GPC.

Acta Crystallogr D Struct Biol. 2017 Jul 1;73(Pt 7):549-556. doi: 10.1107/S2059798317002236. Epub 2017 Jun 22.


The self-inhibitory nature of metabolic networks and its alleviation through compartmentalization.

Alam MT, Olin-Sandoval V, Stincone A, Keller MA, Zelezniak A, Luisi BF, Ralser M.

Nat Commun. 2017 Jul 10;8:16018. doi: 10.1038/ncomms16018.


Structure of the MacAB-TolC ABC-type tripartite multidrug efflux pump.

Fitzpatrick AWP, Llabrés S, Neuberger A, Blaza JN, Bai XC, Okada U, Murakami S, van Veen HW, Zachariae U, Scheres SHW, Luisi BF, Du D.

Nat Microbiol. 2017 May 15;2:17070. doi: 10.1038/nmicrobiol.2017.70.


Association of the Cold Shock DEAD-Box RNA Helicase RhlE to the RNA Degradosome in Caulobacter crescentus.

Aguirre AA, Vicente AM, Hardwick SW, Alvelos DM, Mazzon RR, Luisi BF, Marques MV.

J Bacteriol. 2017 Jun 13;199(13). pii: e00135-17. doi: 10.1128/JB.00135-17. Print 2017 Jul 1.


An allosteric transport mechanism for the AcrAB-TolC multidrug efflux pump.

Wang Z, Fan G, Hryc CF, Blaza JN, Serysheva II, Schmid MF, Chiu W, Luisi BF, Du D.

Elife. 2017 Mar 29;6. pii: e24905. doi: 10.7554/eLife.24905.


Structure of the Escherichia coli ProQ RNA-binding protein.

Gonzalez GM, Hardwick SW, Maslen SL, Skehel JM, Holmqvist E, Vogel J, Bateman A, Luisi BF, Broadhurst RW.

RNA. 2017 May;23(5):696-711. doi: 10.1261/rna.060343.116. Epub 2017 Feb 13.


Evolution of Pectobacterium Bacteriophage ΦM1 To Escape Two Bifunctional Type III Toxin-Antitoxin and Abortive Infection Systems through Mutations in a Single Viral Gene.

Blower TR, Chai R, Przybilski R, Chindhy S, Fang X, Kidman SE, Tan H, Luisi BF, Fineran PC, Salmond GP.

Appl Environ Microbiol. 2017 Mar 31;83(8). pii: e03229-16. doi: 10.1128/AEM.03229-16. Print 2017 Apr 15.


In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways.

Chao Y, Li L, Girodat D, Förstner KU, Said N, Corcoran C, Śmiga M, Papenfort K, Reinhardt R, Wieden HJ, Luisi BF, Vogel J.

Mol Cell. 2017 Jan 5;65(1):39-51. doi: 10.1016/j.molcel.2016.11.002.


Viral interference of the bacterial RNA metabolism machinery.

Dendooven T, Van den Bossche A, Hendrix H, Ceyssens PJ, Voet M, Bandyra KJ, De Maeyer M, Aertsen A, Noben JP, Hardwick SW, Luisi BF, Lavigne R.

RNA Biol. 2017 Jan 2;14(1):6-10. doi: 10.1080/15476286.2016.1251003. Epub 2016 Nov 11. Review.


Structural elucidation of a novel mechanism for the bacteriophage-based inhibition of the RNA degradosome.

Van den Bossche A, Hardwick SW, Ceyssens PJ, Hendrix H, Voet M, Dendooven T, Bandyra KJ, De Maeyer M, Aertsen A, Noben JP, Luisi BF, Lavigne R.

Elife. 2016 Jul 22;5. pii: e16413. doi: 10.7554/eLife.16413.


The ribonuclease polynucleotide phosphorylase can interact with small regulatory RNAs in both protective and degradative modes.

Bandyra KJ, Sinha D, Syrjanen J, Luisi BF, De Lay NR.

RNA. 2016 Mar;22(3):360-72. doi: 10.1261/rna.052886.115. Epub 2016 Jan 12.


Direct observation of processive exoribonuclease motion using optical tweezers.

Fazal FM, Koslover DJ, Luisi BF, Block SM.

Proc Natl Acad Sci U S A. 2015 Dec 8;112(49):15101-6. doi: 10.1073/pnas.1514028112. Epub 2015 Nov 23.


Maturation of 6S regulatory RNA to a highly elongated structure.

Fadouloglou VE, Lin HT, Tria G, Hernández H, Robinson CV, Svergun DI, Luisi BF.

FEBS J. 2015 Dec;282(23):4548-64. doi: 10.1111/febs.13516. Epub 2015 Oct 13.


Co-evolution of quaternary organization and novel RNA tertiary interactions revealed in the crystal structure of a bacterial protein-RNA toxin-antitoxin system.

Rao F, Short FL, Voss JE, Blower TR, Orme AL, Whittaker TE, Luisi BF, Salmond GP.

Nucleic Acids Res. 2015 Oct 30;43(19):9529-40. doi: 10.1093/nar/gkv868. Epub 2015 Sep 8.


Structure, mechanism and cooperation of bacterial multidrug transporters.

Du D, van Veen HW, Murakami S, Pos KM, Luisi BF.

Curr Opin Struct Biol. 2015 Aug;33:76-91. doi: 10.1016/ Epub 2015 Aug 15. Review.


Linkage of catalysis and 5' end recognition in ribonuclease RNase J.

Pei XY, Bralley P, Jones GH, Luisi BF.

Nucleic Acids Res. 2015 Sep 18;43(16):8066-76. doi: 10.1093/nar/gkv732. Epub 2015 Aug 7.


The pseudo-atomic structure of an RND-type tripartite multidrug efflux pump.

Du D, Voss J, Wang Z, Chiu W, Luisi BF.

Biol Chem. 2015 Sep;396(9-10):1073-82. doi: 10.1515/hsz-2015-0118. Review.


Assembly and operation of bacterial tripartite multidrug efflux pumps.

Du D, van Veen HW, Luisi BF.

Trends Microbiol. 2015 May;23(5):311-9. doi: 10.1016/j.tim.2015.01.010. Epub 2015 Feb 24. Review.


Membrane recognition and dynamics of the RNA degradosome.

Strahl H, Turlan C, Khalid S, Bond PJ, Kebalo JM, Peyron P, Poljak L, Bouvier M, Hamoen L, Luisi BF, Carpousis AJ.

PLoS Genet. 2015 Feb 3;11(2):e1004961. doi: 10.1371/journal.pgen.1004961. eCollection 2015 Feb.


Recognition of the small regulatory RNA RydC by the bacterial Hfq protein.

Dimastrogiovanni D, Fröhlich KS, Bandyra KJ, Bruce HA, Hohensee S, Vogel J, Luisi BF.

Elife. 2014 Dec 31;3. doi: 10.7554/eLife.05375.


5-Formylcytosine alters the structure of the DNA double helix.

Raiber EA, Murat P, Chirgadze DY, Beraldi D, Luisi BF, Balasubramanian S.

Nat Struct Mol Biol. 2015 Jan;22(1):44-49. doi: 10.1038/nsmb.2936. Epub 2014 Dec 15.


Molecular recognition of RhlB and RNase D in the Caulobacter crescentus RNA degradosome.

Voss JE, Luisi BF, Hardwick SW.

Nucleic Acids Res. 2014 Dec 1;42(21):13294-305. doi: 10.1093/nar/gku1134. Epub 2014 Nov 11.


Structure of the AcrAB-TolC multidrug efflux pump.

Du D, Wang Z, James NR, Voss JE, Klimont E, Ohene-Agyei T, Venter H, Chiu W, Luisi BF.

Nature. 2014 May 22;509(7501):512-5. doi: 10.1038/nature13205. Epub 2014 Apr 20.


Inhibition of triosephosphate isomerase by phosphoenolpyruvate in the feedback-regulation of glycolysis.

Grüning NM, Du D, Keller MA, Luisi BF, Ralser M.

Open Biol. 2014 Mar 5;4:130232. doi: 10.1098/rsob.130232.


Crystal structure of the carbapenem intrinsic resistance protein CarG.

Tichy EM, Luisi BF, Salmond GP.

J Mol Biol. 2014 May 1;426(9):1958-70. doi: 10.1016/j.jmb.2014.02.016. Epub 2014 Feb 28.


Nanopore-based identification of individual nucleotides for direct RNA sequencing.

Ayub M, Hardwick SW, Luisi BF, Bayley H.

Nano Lett. 2013;13(12):6144-50. doi: 10.1021/nl403469r. Epub 2013 Nov 13.


Potential regulatory interactions of Escherichia coli RraA protein with DEAD-box helicases.

Pietras Z, Hardwick SW, Swiezewski S, Luisi BF.

J Biol Chem. 2013 Nov 1;288(44):31919-29. doi: 10.1074/jbc.M113.502146. Epub 2013 Sep 17.


The assembly and distribution in vivo of the Escherichia coli RNA degradosome.

Domínguez-Malfavón L, Islas LD, Luisi BF, García-Villegas R, García-Mena J.

Biochimie. 2013 Nov;95(11):2034-41. doi: 10.1016/j.biochi.2013.07.022. Epub 2013 Aug 6.


Geometric principles in the assembly of α-helical bundles.

Pratap JV, Luisi BF, Calladine CR.

Philos Trans A Math Phys Eng Sci. 2013 May 20;371(1993):20120369. doi: 10.1098/rsta.2012.0369. Print 2013 Jun 28.


Licensing and due process in the turnover of bacterial RNA.

Bandyra KJ, Luisi BF.

RNA Biol. 2013 Apr;10(4):627-35. doi: 10.4161/rna.24393. Epub 2013 Apr 1. Review.


The social fabric of the RNA degradosome.

Bandyra KJ, Bouvier M, Carpousis AJ, Luisi BF.

Biochim Biophys Acta. 2013 Jun-Jul;1829(6-7):514-22. doi: 10.1016/j.bbagrm.2013.02.011. Epub 2013 Feb 28. Review.


A "mechanistic" explanation of the multiple helical forms adopted by bacterial flagellar filaments.

Calladine CR, Luisi BF, Pratap JV.

J Mol Biol. 2013 Mar 11;425(5):914-28. doi: 10.1016/j.jmb.2012.12.007. Epub 2012 Dec 26.


Selectivity and self-assembly in the control of a bacterial toxin by an antitoxic noncoding RNA pseudoknot.

Short FL, Pei XY, Blower TR, Ong SL, Fineran PC, Luisi BF, Salmond GP.

Proc Natl Acad Sci U S A. 2013 Jan 15;110(3):E241-9. doi: 10.1073/pnas.1216039110. Epub 2012 Dec 24.


Rarely at rest: RNA helicases and their busy contributions to RNA degradation, regulation and quality control.

Hardwick SW, Luisi BF.

RNA Biol. 2013 Jan;10(1):56-70. doi: 10.4161/rna.22270. Epub 2012 Oct 12. Review.


Recognition of the 70S ribosome and polysome by the RNA degradosome in Escherichia coli.

Tsai YC, Du D, Domínguez-Malfavón L, Dimastrogiovanni D, Cross J, Callaghan AJ, García-Mena J, Luisi BF.

Nucleic Acids Res. 2012 Nov 1;40(20):10417-31. doi: 10.1093/nar/gks739. Epub 2012 Aug 25.


The seed region of a small RNA drives the controlled destruction of the target mRNA by the endoribonuclease RNase E.

Bandyra KJ, Said N, Pfeiffer V, Górna MW, Vogel J, Luisi BF.

Mol Cell. 2012 Sep 28;47(6):943-53. doi: 10.1016/j.molcel.2012.07.015. Epub 2012 Aug 16.


Crystal structure of Caulobacter crescentus polynucleotide phosphorylase reveals a mechanism of RNA substrate channelling and RNA degradosome assembly.

Hardwick SW, Gubbey T, Hug I, Jenal U, Luisi BF.

Open Biol. 2012 Apr;2(4):120028. doi: 10.1098/rsob.120028.


Allosteric mutants show that PrfA activation is dispensable for vacuole escape but required for efficient spread and Listeria survival in vivo.

Deshayes C, Bielecka MK, Cain RJ, Scortti M, de las Heras A, Pietras Z, Luisi BF, Núñez Miguel R, Vázquez-Boland JA.

Mol Microbiol. 2012 Aug;85(3):461-77. doi: 10.1111/j.1365-2958.2012.08121.x. Epub 2012 Jun 21.


From beads on a string to the pearls of regulation: the structure and dynamics of chromatin.

Bowater RP, Wood IC, Luisi BF.

Biochem Soc Trans. 2012 Apr;40(2):331-4. doi: 10.1042/BST20120011.


Identification and classification of bacterial Type III toxin-antitoxin systems encoded in chromosomal and plasmid genomes.

Blower TR, Short FL, Rao F, Mizuguchi K, Pei XY, Fineran PC, Luisi BF, Salmond GP.

Nucleic Acids Res. 2012 Jul;40(13):6158-73. doi: 10.1093/nar/gks231. Epub 2012 Mar 19.

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