Summary
Bacterial Microcompartments (BMCs) are organelles composed of a polyhedral protein shell that encapsulates metabolically related enzymes. The best characterized BMC, the carboxysome, which functions to enhance CO2 fixation by D-ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), is found in all cyanobacteria. It is an essential part of the cyanobacterial CO2 concentrating mechanism. The shell of BMCs is composed of small (∼100 amino acids) proteins with a conserved primary structure known as the BMC domain. Proteins that contain BMC domains were shown to form hexamers that assemble in layers to form the facets of BMC shells. Previous structural models of the carboxysome shell were built from proteins which contain a single BMC domain. Recently, a new carboxysome shell protein was detected bioinformatically in Prochlorococcus and Synechococcus species. The crystal structure of this protein, CsoS1D, unexpectedly was the first tandem BMC domain protein structurally characterized. These data, together with the transcriptomic evidence suggested that CsoS1D is a novel alpha-carboxysome shell protein with unique functionally important features. Here we used bioinformatic and comparative structural modeling to show that a hypothetical protein found in all beta cyanobacterial genomes is the ortholog of CsoS1D. We also discuss observations of other tandem BMC domain proteins, and we propose the hypothesis that the carboxysome shell may be a dynamic structure that responds to the environmental conditions within the cell.
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Notes
- 1.
The exceptions are Bradyrhizobium sp. BTAi1 and three Acidithiobacillus ferrooxidans strains (ATCC 53993, ATCC 23270, and DSM 10331) sequenced to-date.
Abbreviations
- BMC:
-
bacterial microcompartment
- CA:
-
carbonic anhydrase
- CCM:
-
CO2 concentrating mechanism
- HL:
-
high light
- HMM:
-
hidden Markov model
- LL:
-
low light
- MSA:
-
multiple sequence alignment
- MV:
-
methyl viologen
- PG:
-
phosphoglycolate
- 3-PGA:
-
3-phosphoglyceric acid
- RMSD:
-
root mean square deviation
- RubisCO:
-
ribulose1,5-bisphosphate carboxylase/oxygenase
- RuBP:
-
ribulose 1,5-bisphosphate
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Acknowledgments
We thank Gordon C. Cannon, Sabine Heinhorst and Claire Ting for helpful discussions, Seth Axen for preparing Fig. 14.4, Phil Hugenholtz for providing a template for Fig. 14.5 and Edwin Kim for preparing Fig. 14.7c and d.
FC and CAK’s current carboxysome research is supported by NSF grant and MCB-085170. The work of CAK and GS is performed under the auspices of the US Department of Energy’s Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract number DE-AC02-05CH11231, and Lawrence Livermore National Laboratory under contract number DE-AC52-07NA27344.
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Cai, F., Kerfeld, C.A., Sandh, G. (2012). Bioinformatic Identification and Structural Characterization of a New Carboxysome Shell Protein. In: Burnap, R., Vermaas, W. (eds) Functional Genomics and Evolution of Photosynthetic Systems. Advances in Photosynthesis and Respiration, vol 33. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-1533-2_14
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