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Widespread distribution of encapsulin nanocompartments reveals functional diversity


Cells organize and regulate their metabolism via membrane- or protein-bound organelles. In this way, incompatible processes can be spatially separated and controlled. In prokaryotes, protein-based compartments are used to sequester harmful reactions and store useful compounds. These protein compartments play key roles in various metabolic and ecological processes, ranging from iron homeostasis to carbon fixation. One of the newest types of protein organelle are encapsulin nanocompartments. They are able to encapsulate specific protein cargo and are proposed to be involved in redox-related processes. We identified more than 900 putative encapsulin systems in bacterial and archaeal genomes. Encapsulins can be found in fifteen bacterial and two archaeal phyla. Our analysis reveals one new capsid type and nine previously unknown cargo proteins targeted to the interior of encapsulins. We experimentally characterize three newly identified encapsulin systems and illustrate their probable involvement in iron mineralization, oxidative and nitrosative stress resistance and anaerobic ammonium oxidation, a process responsible for 30% of the nitrogen lost from the oceans.

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Figure 1: Distribution, organization and diversity of encapsulin systems in prokaryotes.
Figure 2: Secondary cargo, associated components and diversity of Flp-like cargo in encapsulin systems.
Figure 3: Classification and characterization of encapsulin capsids.
Figure 4: Characterization of the Streptomyces sp. AA4 Haem encapsulin system involved in oxidative and nitrosative stress resistance.
Figure 5: Characterization of the Bacillaceae bacterium MTCC 10057 IMEF encapsulin system involved in iron mineralization.
Figure 6: Characterization of the encapsulin system in the anammox bacterium K. stuttgartiensis.


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This work was supported by a Leopoldina Research Fellowship (LPDS 2014-05) from the German National Academy of Sciences Leopoldina (T.W.G), the DARPA Living Foundries 1000 Molecules grant (award no. HR0011-14-C-0072, to P.A.S) and the Wyss Institute for Biologically Inspired Engineering at Harvard University (to T.W.G and P.A.S). The authors thank A. Chan and J. Hegemann for thoughtful comments on the manuscript.

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T.W.G. and P.A.S designed the research and wrote the paper. T.W.G. performed experiments.

Corresponding author

Correspondence to Pamela A. Silver.

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The authors declare no competing financial interests.

Supplementary information

Supplementary information

Supplementary Table 2, Supplementary Figures 1–9 (PDF 4071 kb)

Supplementary Table 1

List of identified encapsulin systems (XLSX 88 kb)

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Giessen, T., Silver, P. Widespread distribution of encapsulin nanocompartments reveals functional diversity. Nat Microbiol 2, 17029 (2017).

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