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Crystallographic and functional studies of regulatory assemblies and molecular machines


Our aim is to understand how fundamental cellular processes are controlled through molecular interactions in multi-component assemblies. The expression of genetic information can be regulated by controlling the life time of mRNA to fine tune an organism's response to developmental or environmental stimuli. In the bacterium, Escherichia coli, this is regulated by an multi-enzyme assembly called the RNA degradosome. We are exploring the structure and function of the RNA degradosome assembly. The structure of the catalytic domain in complex with RNA substrate is shown in the figure below. We are studying thiamine-dependent, multi-enzyme assemblies from central metabolism. We have also undertaken a collaborative study of bacterial systems which transport proteins and antibiotics outside of the cell. A structural view of this system will help us to understand the molecular bases of virulence and drug resistance in the Gram-negative family of bacteria. We directly visualise the individual components and their complexes at an atomic level using X-ray diffraction to reveal the intricate and subtle structures which underlie these complexes. We also use a number of other techniques such as non-dissociating mass spectrometry, neutron and X-ray solution scattering, and calorimetry to analyse macromolecular complexes.

While RNase E forms a tetramer composed of a dimer of dimers, the selective advantage of this quaternary organization is not well understood. The large conformational changes we observe suggest that a highly flexible quaternary organization may play a role in the degradation of structured RNAs. Depicted here is a speculative model of the RNase E tetramer degrading a structured fragment of RNA that serves to illustrate the conformational changes. In the upper left is a view of a single dimer in which one of the S1/5’-sensing domain (blue) has closed down upon an RNA substrate (red) and holds it adjacent to a catalytic cleavage site on a DNase I domain. The complementary protomer within the dimer does not possess a substrate RNA and is in the open configuration. In the lower right, a second dimer plays a supporting role in the degradation of the RNA, interacting with the substrate via a S1 domain to further stabilize the complex. Figure prepared using PDB structures: 2BX2, 2VMK, and 2A64.

RNase E tetramer with RNA - model

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Group members

Katarzyna Bandyra, Vivian Chan, Dijun Du, Vasiliki E. Fadouloglou, Steven Hardwick, Xue Pei, Zbigniew Pietras, Yi-Chun Tsai, Jarrod Voss.

Visiting students: Laura Perez-Cano, Daniela Dimastrogiovanni

References

  • Hardwick SW, Chan VS, Broadhurst RW, Luisi BF. (2010) An RNA degradosome assembly in Caulobacter crescentus. Nucleic Acids Res.
  • Górna M.W., Pietras Z., Tsai Y.C., Callaghan A.J., Hernández H., Robinson C.V., Luisi B.F. (2010) The regulatory protein RraA modulates RNA-binding and helicase activities of the E. coli RNA degradosome. RNA. 16(3):553-62.
  • Bavro, V.N., Pietras, Z., Furnham, N., Perez-Cano, L., Fernandez-Recio, J., Pei, X.Y., Misra, R. and Luisi, B.F. (2008) Channel-opening and assembly in a bacterial drug efflux machine. Molecular Cell 30, 114-121.
  • Frank, R.A.W., Kay, C.W.M., Hirst, J. and Luisi, B.F. (2008) Off-pathway, oxygen-dependent thiamine radical in the Krebs cycle. J. Amer. Chem. Soc 130, 1662-1668.
  • Callaghan, A.J., Marcaida, M.J., Stead, J.A., McDowall, K.J., Scott, W.G. and Luisi, B.F. (2005) The structure of E. coli RNase E catalytic domain and implications for RNA turnover. Nature 437 1187-1191.
  • Frank, R.A.W., Titman, C., Pratap, V., Luisi, B.F. and Perham, R.N. (2004) A molecular switch and proton-wire synchronize the active-sites in thiamine-dependent enzymes. Science 306, 872-876
  • All publications

Former group members

Vidya Chandran
Anastasia Callaghan
Jonathan Worrall
Victor Hong-Ting Lin
Martyn Symmons
Venkatesh Pratap
Vassiliy Bavro
Fabien Walas
Maria Josefina Marcaida
Elliott Stollar
Daniel Koslover
Salima Nurmohamed
Rene Frank
Maria Górna
Marko Sustarsic

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