These two authors contributed equally
A virus capsid-like nanocompartment that stores iron and protects bacteria from oxidative stress
Article first published online: 14 JUL 2014
© 2014 The Authors
The EMBO Journal
Volume 33, Issue 17, pages 1896–1911, 1 September 2014
How to Cite
The EMBO Journal (2014) 33: 1896–1911
- Issue published online: 1 SEP 2014
- Article first published online: 14 JUL 2014
- Manuscript Accepted: 27 MAY 2014
- Manuscript Revised: 9 MAY 2014
- Manuscript Received: 24 MAR 2014
- Intramural Research Program of the National Institute of Arthritis
- Musculoskeletal and Skin Diseases of the National Institutes of Health
- Ruth L. Kirschstein National Research Service. Grant Number: T32 ES07141
- National Institutes of Health
- National Institute of General Medical Sciences. Grant Number: R01 GM085024
- cryo-electron microscopy;
- HK97 fold;
- oxidative stress
Living cells compartmentalize materials and enzymatic reactions to increase metabolic efficiency. While eukaryotes use membrane-bound organelles, bacteria and archaea rely primarily on protein-bound nanocompartments. Encapsulins constitute a class of nanocompartments widespread in bacteria and archaea whose functions have hitherto been unclear. Here, we characterize the encapsulin nanocompartment from Myxococcus xanthus, which consists of a shell protein (EncA, 32.5 kDa) and three internal proteins (EncB, 17 kDa; EncC, 13 kDa; EncD, 11 kDa). Using cryo-electron microscopy, we determined that EncA self-assembles into an icosahedral shell 32 nm in diameter (26 nm internal diameter), built from 180 subunits with the fold first observed in bacteriophage HK97 capsid. The internal proteins, of which EncB and EncC have ferritin-like domains, attach to its inner surface. Native nanocompartments have dense iron-rich cores. Functionally, they resemble ferritins, cage-like iron storage proteins, but with a massively greater capacity (~30,000 iron atoms versus ~3,000 in ferritin). Physiological data reveal that few nanocompartments are assembled during vegetative growth, but they increase fivefold upon starvation, protecting cells from oxidative stress through iron sequestration.
Bacteria compartmentalize by sequestering components into protein shells. Here, such a nanocompartment is shown to structurally resemble virus capsids and to store large amounts of iron for protection under starvation conditions.
- Iron homeostasis in Myxococcus xanthus involves iron sequestration into large protein shells (encapsulin nanocompartments).
- The shell is lined with adaptor proteins with ferritin-like folds that nucleate iron-rich granules.
- The encapsulin system appears to complement a ferritin system.
- The encapsulin shell closely resembles capsids of bacteriophages and herpesvirus.
- Thus, phages may have arisen from cellular genes, or M. xanthus may have acquired the encapsulin shell gene from a bacteriophage.