Probing the structure, self-assembly, and nanomechanics of bacterial microcompartments



Faulkner, M
(2018) Probing the structure, self-assembly, and nanomechanics of bacterial microcompartments. PhD thesis, University of Liverpool.

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Abstract

Bacterial carbon fixation activity accounts for a significant proportion of global carbon capture. Bacteria do not have the complex carbon concentrating mechanisms and membrane bound organelles of plants and yet they have incredibly high photosynthetic efficiency. This is, in part, because of the alternative carbon concentrating mechanism bacteria employ involving the carboxysome. Carboxysomes are a type of bacterial microcompartment, a proteinaceous structure comprised of an outer semi-permeable shell encapsulating an internal enzyme filled lumen. By encapsulating the enzyme Rubisco, that catalyses the often rate limiting step of carbon fixation, carboxysomes are able to boost catalytic efficiency. Carboxysomes therefore increase overall carbon fixation activity. Bacterial microcompartments are widespread amongst bacterial phyla and apply the same approach to many enzymatic reactions. Our knowledge of the structure of carboxysomes and other such compartments and how they self-assemble is limited. This is thereby preventing the successful use of recombinant compartments to boost enzymatic efficiency in synthetic systems, plants, and other organisms. In this work, a multifactorial approach is employed to study the carboxysome, from the initial self-assembly of monomeric protein building blocks to the structural and mechanical properties of the entire functional compartment. Novel observations include the first application of near-native high-speed atomic force microscopy to the study of a purified micro-compartment shell protein and the first purification and characterisation of intact carboxysomes, from the widely studied model organism Synechococcus elongatus PCC 7942. Also the first direct functional and structural comparison of two different kinds of carboxysome, α and β, from different model-bacteria. Previously unobserved protein dynamic events within tiled arrays of shell proteins were recorded. These data shed light on the mechanisms of the initial stages of micro-compartment self-assembly. These data also gave rise to the first clear evidence that manipulating the interactions between individual amino acids in bacterial microcompartment shell proteins can control self-assembly. The mechanical properties of carboxysomes were identified as potential biomarkers to evaluate future synthetic carboxysome constructs through atomic force microscopy and nanoindentation.

Item Type: Thesis (PhD)
Divisions: Fac of Health & Life Sciences > Faculty of Health and Life Sciences
Depositing User: Symplectic Admin
Date Deposited: 09 Aug 2018 14:26
Last Modified: 09 Jan 2021 15:54
DOI: 10.17638/03022574
Supervisors:
  • Liu, Lu-Ning
URI: https://livrepository.liverpool.ac.uk/id/eprint/3022574