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Department of Biochemistry


Structural and functional studies of assemblies of riboregulation and transport

We are studying multi­component assemblies involved in the regulation of the expression of genetic information through controlling the fate of messenger RNA. We hope to understand how such post-transcriptional regulation enables rapid and specific response to developmental or environmental stimuli. In the bacterium, Escherichia coli, RNA turnover and processing is mediated by a multi-enzyme assembly, known as the RNA degradosome. We are exploring the structure and function of the RNA degradosome assembly from E. coli and other bacteria, to understand their multifaceted regulatory functions. The degradosome assembly can target specific transcripts by interacting with non-coding regulatory RNAs, and our structural and biochemical studies are providing insight into the mechanism of this targeted gene silencing. The structure of the catalytic domain in complex with RNA substrate and other structural information has enabled us to propose models for substrate recognition and allosteric activation of components of the degradosome assembly.

We have also undertaken a study of bacterial systems which transport proteins and antibiotics outside of the cell. We have obtained the structure of tripartite assemblies that span the cell envelope of Gram-negative bacteria. A structural view of these systems has helped to understand the molecular bases of bacterial virulence and drug resistance.

We directly visualise the individual components and their complexes at an atomic level using X-­ray diffraction and cryo-EM to reveal the intricate and subtle structures which underlie these complexes. We also use a number of other complementary techniques such as non­dissociating mass spectrometry, neutron and X-ray solution scattering, and calorimetry to analyse macromolecular complexes. Through international collaborations, we are studying genetic regulation in vivo, and have obtained evidence for a linkage between RNA metabolism and metabolic state of the cell.


Lab members: Dr Kasia Bandyra, Dr Steven Hardwick, Dr Xue Yuan Pei, Dr Dijun Du, Dr Miao Ma, Dr Jamie Blaza, Dr Md. Saiful Islam, Dr Kotryna Bloznelyte, Mr Tom Dendooven, Ms Laura Shen, Mr Tai Yang, Mr Arthur Neuberger

Lab visitors: Mr Manuel Wagner


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Recent publications:

Huang, P.-S., Oberdorfer, G., Xu, C., Pei, X.Y., Nannenga, B.L., Rogers, J.M., DiMaio, F., Gonen, T., Luisi, B.F. and Baker, D. (2014) High thermodynamic stability of parametrically designed helical bundles. Science 346, 481-485. Doi; 10.1126/science.1257481

Voss J.E., Luisi B.F., Hardwick S. W. (2014) Molecular recognition of RhlB and RNase D in the Caulobacter crescentus RNA degradosome. Nucleic Acids Research. PMID:25389270.

Du, D., Wang, Z., James, N.R., Voss, J.E., Klimont, E., Ohene-Agyei, T., Venter, H., Chiu, W., Luisi, B.F. (2014) Structure of the AcrAB-TolC multidrug efflux pump. Nature 509, 512-515.

Ayub, M., Hardwick, S.W., Luisi, B.F., Bayley, H. (2013) Nanopore-based identification of individual nucleotides for direct RNA sequencing. Nano Lett. PMID 24171554.

Short, F.L., Pei, X.Y., Blower, T.R., Ong, S.L., Fineran, P.C., Luisi, B.F., Salmond, G.P. (2013) Selectivity and self-assembly in the control of a bacterial toxin by an antitoxic noncoding RNA pseudo knot. Proc. Natl. Acad. Sci. U.S.A. 110, E241-9. 

Bandyra, K.J., Said, N., Pfeiffer, V., Gorna, M.W., Vogel, J., Luisi, B.F. (2012) The seed region of a small RNA drives the controlled destruction of the target mRNA by the endoribonuclease RNase E. Mol. Cell 47, 943-953.

Hardwick, S.W., Gubbey, T., Hug, I., Jenal, U., Luisi, B.F. (2012) Crystal structure of Caulobacter crescentus polynucleotide phosphorylase reveals a mechanism of RNA substrate channelling and RNA degradosome assembly. Open Biol 2, 120028.