Microcompartments are proteinaceous capsules that have only recently been recognised to exist in a wide range of bacteria. They contain enzymes required for a particular metabolic process. The carboxysome is a particularly well-studied example of a specialised microcompartment, and is shown here as a schematic diagram (S. Frank et al, 2013).

The Pdu microcompartment that we are using in our project is composed of several proteins encoded in an operon consisting of the genes pduA, -B, -T, -U, -N, -J, -K. These are expressed in various stoichiometries to form different polyhedral shapes with a diameter of 200-250 nm. The faces of the polyhedron are formed by the hexagonal shell proteins PduA, PduB, and PduJ, while PduN is thought to form the vertices (Joshua B. Parsons et al, 2010).

We are expressing the pdu-ABTUNJK codon in E. coli in the pUNI vector, shown below, which we received from the University of Dundee iGEM team.









Additionally, we are expressing pduABUTNJK in P. putida, which to our knowledge has not been done before. For this purpose, we transferred the ABTUNJK sequence into the pBBR1MCS vector, shown below:



Oxford iGEM 2014

The pdu-encoded microcompartments which we are introducing into our bacteria are very similar in shape and structure to carboxysomes, so we used their structure as a starting point for predicting the microcompartment structure. Thus, our initial carboxysome-based structure was a perfect icosahedron with diameter 120nm as established from literature. Following this, we further developed the model by noting that many of the images taken of pdu microcompartments suggest slight and random deviations from an icosahedron.

Taking this into consideration, we have developed a simulation which generates pdu microcompartment structures by starting with a regular icosahedron and randomly distorting the location of each co-ordinate by up to 5% of total edge length.

Given more time and information, this model could be further improved by studying as many microcompartments as possible and refining the size of the deviation from a perfect icosahedron. The magnitude of structural deformation likely follows a normal distribution for which a mean and standard deviation could be established.

An example microcompartment structure (blue) visualized alongside a perfect icosahedral structure (red).

The number of microcompartments in a given cell can vary broadly, from a few microsomes to numbers that occupy the vast amount of the cytosol. Because of their size and the number of protein components, microcompartments are an extensive strain on the metabolism of cells. We have placed the E. coli ABTUNJK codon under control of the T7 promoter, while that for P. putida is placed under control of the T3 promoter.

The aim of this model was to predict a theoretical maximum number of enzyme molecules that can be packed into a single microcompartment. To get a first estimate, without taking into consideration whether this volume of protein would interrupt the biological processes in the cell, we approached the problem volumetrically.

Due to the complexity of the enzyme movements and their interactions, we simplified their structures by approximating them as ellipsoids with axes lengths calculated through modelling the monomers and predicting the structures of the FdhA tetramer and DcmA hexamer respectively.





Oxford iGEM 2014