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Revision as of 20:25, 27 October 2010

An Integrated Platform Based on Bacterial Microcompartment for de novo Proteinaceous Artificial Organelles


Known Conditions

This table illustrate some basic information of pdu shell protein family.[1]


USTC2010_known_conditions_table_1.jpg

Table 1| Basic information of pdu shell protein family.


USTC2010_known_conditions_figure_1.jpg

Figure 1| 3-dimension structure of the known shell proteins from Salmonella enterica . UPPER: pduU. [2] MIDDLE: pduA. [3] DOWN:pduT. [3]


Hypothesis

I)Pdu N is the vertex and its pentametic structuresfor its identity with a proved vertex pentametic protein---CcmL. [4]

II) Hexamers forms the facets, which comprises the building blocks of bacterial microcompartment shells. [5]

USTC2010_hypothesis_N_vertex.jpg USTC2010_Hypothesis_Hexamer.jpg

Figure 2| LEFT: A diagram showing the construction of a large icosahedron from many smaller hexagons and 12 pentagons at the vertices. The figure shown has a triangulation number (T) of 75 (29). RIGHT: Individual CsoS1A molecules, typical shell proteins, are differently in each hexamer.

III) Similarity of the shell proteins to the carboxysome [6] and carboxysome is believed to be in icosohedral shape.


Results

From the paper data of EM observation:

USTC2010_model_a_result_Equation_1.jpg


Then we decide to count the molecular copies of each structural basic element.

Relative abundance [6]

pdu -J:-A:-B':-B:-K:-T:-U=15:10:7:6:1:1:2

  • the diameter of a hexamer is 7 nm
  • the edge is 3.5 nm
  • the area of a hexamer is 31.8255 nm2
  • then the number of hexamer is 23936.353 nm2/31.8255 nm2=752.11

So. in total 752 hexamers

Because B, B' and T have two BMC domains, so they form trimer instead

(15t+10t+t+2t)/6+(7t+6t+t)/3=752 => t=77.8

USTC2010_model_1_Result_of_composition.jpg

USTC2010_model_a_Result_of_composition.jpg

Table 2| The distribution of shell proteins in microcompartment.


Conclusion

Explanation about the size.

  • Typical size of a prokaryotes is 1~10 µm
  • Diameter of a Pdu Microcompartment is 100nm=0.1 µm
  • Volume of a Pdu Microcompartment is 317018.839 nm3 ~=320000 nm3=3.2*105 nm3=3.2*10-4 µm3
  • Bacterium, are about 2 µm long and 0.5 µm in diameter, with a cell volume of 0.6 - 0.7 µm3

=> Conclusion: about 1875 Pdu microcompartments can fill a bacterial cell!


Reference

[1] Martin J. Warren, et al. 2010. Synthesis of empty bacterial microcompartments, directed organelle protein incorporation, and evidence of filament-associated organelle movement. Molecular Cell. 2010 Apr 38 (2), 305–315

[2] Structure of the PduU shell protein from the Pdu microcompartment of Salmonella. Structure. 2008 Sep 16(9):1324-32

[3] Structural insights into the mechanisms of transport across the Salmonella enterica Pdu microcompartment shell. J Biol Chem. 2010 Sep: [Epub ahead of print]

[4] Atomic-level models of the bacterial carboxysome shell. Science. 2008 Feb, 319(5866):1083-6

[5] Structural analysis of CsoS1A and the protein shell of the Halothiobacillus neapolitanus carboxysome. PLoS Biol. 2007 Jun;5(6):e144.

[6] Protein content of polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol in Salmonella enterica serovar Typhimurium LT2. J Bacteriol. 2003 Sep;185(17):5086-95