Encapsulins: molecular biology of the shell

References

• Ahmad, M., et al., 2010. Development of novel assays for lignin degradation: comparative analysis of bacterial and fungal lignin degraders. Molecular biosystems, 6 (5), 815–821.
   PubMed Web of Science ®Google Scholar
• Ahmad, M., et al., 2011. Identification of DypB from Rhodococcus jostii RHA1 as a lignin peroxidase. Biochemistry, 50 (23), 5096–5107.
   PubMed Web of Science ®Google Scholar
• Akita, F., et al., 2007. The crystal structure of a virus-like particle from the hyperthermophilic archaeon Pyrococcus furiosus provides insight into the evolution of viruses. Journal of molecular biology, 368 (5), 1469–1483.
   PubMed Web of Science ®Google Scholar
• Andrews, S.C., 1998. Iron storage in bacteria. In: R.K. Poole, ed. Advances in microbial physiology. San Diego, CA: Academic Press, 281–351.
   Google Scholar
• Axen, S.D., Erbilgin, O., and Kerfeld, C.A., 2014. A taxonomy of bacterial microcompartment loci constructed by a novel scoring method. PLoS computational biology, 10 (10), e1003898.
   PubMed Web of Science ®Google Scholar
• Bobik, T.A., Lehman, B.P., and Yeates, T.O., 2015. Bacterial microcompartments: widespread prokaryotic organelles for isolation and optimization of metabolic pathways. Molecular microbiology, 98 (2), 193–207.
   PubMed Web of Science ®Google Scholar
• Caspar, D.L. and Klug, A., 1962. Physical principles in the construction of regular viruses. Cold spring harbor symposia on quantitative biology, 27, 1–24.
   PubMedGoogle Scholar
• Cassidy-Amstutz, C., et al., 2016. Identification of a minimal peptide tag for in vivo and in vitro loading of encapsulin. Biochemistry, 55 (24), 3461–3468.
   PubMed Web of Science ®Google Scholar
• Choi, B., et al., 2016. Effective delivery of antigen–encapsulin nanoparticle fusions to dendritic cells leads to antigen-specific cytotoxic T cell activation and tumor rejection. ACS nano, 10 (8), 7339–7350.
   PubMed Web of Science ®Google Scholar
• Chow, E.D., et al., 2007. Exploration of whole-genome responses of the human AIDS-associated yeast pathogen Cryptococcus neoformans var grubii: nitric oxide stress and body temperature. Current genetics, 52 (3–4), 137–148.
   PubMed Web of Science ®Google Scholar
• Chowdhury, C., et al., 2014. Diverse bacterial microcompartment organelles. Microbiology and molecular biology reviews: MMBR, 78 (3), 438–468.
   PubMed Web of Science ®Google Scholar
• Contreras, H., et al., 2014. Characterization of a Mycobacterium tuberculosis nanocompartment and its potential cargo proteins. The journal of biological chemistry, 289 (26), 18279–18289.
   PubMed Web of Science ®Google Scholar
• Cornejo, E., Abreu, N., and Komeili, A., 2014. Compartmentalization and organelle formation in bacteria. Current opinion in cell biology, 26, 132–138.
   PubMed Web of Science ®Google Scholar
• Diekmann, Y. and Pereira-Leal, J.B., 2013. Evolution of intracellular compartmentalization. Biochemical journal, 449 (2), 319–331.
   PubMed Web of Science ®Google Scholar
• Giessen, T.W., 2016. Encapsulins: microbial nanocompartments with applications in biomedicine, nanobiotechnology and materials science. Current opinion in chemical biology, 34, 1–10.
   PubMed Web of Science ®Google Scholar
• Giessen, T.W. and Silver, P.A., 2016. Converting a natural protein compartment into a nanofactory for the size-constrained synthesis of antimicrobial silver nanoparticles. ACS synthetic biology, 5 (12), 1497–1504.
   PubMed Web of Science ®Google Scholar
• Giessen, T.W. and Silver, P.A., 2017. Widespread distribution of encapsulin nanocompartments reveals functional diversity. Nature microbiology, 2, 17029.
   PubMed Web of Science ®Google Scholar
• Goulding, C.W., et al., 2005. Regulation by oligomerization in a mycobacterial folate biosynthetic enzyme. Journal of molecular biology, 349 (1), 61–72.
   PubMed Web of Science ®Google Scholar
• Green, E.R. and Mecsas, J., 2016. Bacterial secretion systems: an overview. Microbiology spectrum, 4 (1), 215–239.
   Web of Science ®Google Scholar
• He, D., et al., 2016. Structural characterization of encapsulated ferritin provides insight into iron storage in bacterial nanocompartments. eLife, 5, e18972.
   PubMed Web of Science ®Google Scholar
• Heinemann, J., et al., 2011. Fossil record of an archaeal HK97-like provirus. Virology, 417 (2), 362–368.
   PubMed Web of Science ®Google Scholar
• Hicks, P.M., et al., 1998. Homomultimeric protease in the hyperthermophilic bacterium Thermotoga maritima has structural and amino acid sequence homology to bacteriocins in mesophilic bacteria. FEBS letters, 440 (3), 393–398.
   PubMed Web of Science ®Google Scholar
• Imlay, J.A., Chin, S.M., and Linn, S., 1988. Toxic DNA damage by hydrogen peroxide through the Fenton reaction in vivo and in vitro. Science, 240 (4852), 640–642.
   PubMed Web of Science ®Google Scholar
• Kartal, B., et al., 2013. How to make a living from anaerobic ammonium oxidation. FEMS microbiology reviews, 37 (3), 428–461.
   PubMed Web of Science ®Google Scholar
• Kawamoto, S., et al., 2001. Molecular and functional analyses of the gene (eshA) encoding the 52-kilodalton protein of Streptomyces coelicolor A3 (2) required for antibiotic production. Journal of bacteriology, 183 (20), 6009–6016.
   PubMed Web of Science ®Google Scholar
• Kendall, J.J., et al., 2014. Hemerythrins in the microaerophilic bacterium Campylobacter jejuni help protect key iron–sulphur cluster enzymes from oxidative damage. Environmental microbiology, 16 (4), 1105–1121.
   PubMed Web of Science ®Google Scholar
• Kerfeld, C.A., Heinhorst, S., and Cannon, G.C., 2010. Bacterial microcompartments. Annual review of microbiology, 64, 391–408.
   PubMed Web of Science ®Google Scholar
• Kim, D., et al., 2009. Operon required for fruiting body development in Myxococcus xanthus. Journal of microbiology and biotechnology, 19 (11), 1288–1294.
   PubMed Web of Science ®Google Scholar
• Kwak, J., et al., 2001. Identification and characterization of a developmentally regulated protein, EshA, required for sporogenic hyphal branches in Streptomyces griseus. Journal of bacteriology, 183 (10), 3004–3015.
   PubMed Web of Science ®Google Scholar
• Li, X., et al., 2014. A bacterial hemerythrin-like protein MsmHr inhibits the SigF-dependent hydrogen peroxide response in mycobacteria. Frontiers in microbiology, 5, 800.
   PubMed Web of Science ®Google Scholar
• Manca, C., et al., 1999. Mycobacterium tuberculosis catalase and peroxidase activities and resistance to oxidative killing in human monocytes in vitro. Infection and immunity, 67 (1), 74–79.
   PubMed Web of Science ®Google Scholar
• Mangan, N.M., et al., 2016. pH determines the energetic efficiency of the cyanobacterial CO2 concentrating mechanism. Proceedings of the National Academy of Sciences, 113 (36), E5354–E5362.
   PubMed Web of Science ®Google Scholar
• McHugh, C.A., et al., 2014. A virus capsid-like nanocompartment that stores iron and protects bacteria from oxidative stress. The Embo journal, 33 (17), 1896–1911.
   PubMed Web of Science ®Google Scholar
• Moon, H., et al., 2014. Developing genetically engineered encapsulin protein cage nanoparticles as a targeted delivery nanoplatform. Biomacromolecules, 15 (10), 3794–3801.
   PubMed Web of Science ®Google Scholar
• Namba, K., et al., 2005. Expression and molecular characterization of spherical particles derived from the genome of the hyperthermophilic euryarchaeote Pyrococcus furiosus. Journal of biochemistry, 138 (2), 193–199.
   PubMed Web of Science ®Google Scholar
• Niklowitz, W. and Drews, G., 1956. Beitrage zur cytologie der blaualgen. 1. Untersuchungen zur substruktur von phormidium uncinatum gom. Archiv für mikrobiologie, 24 (2), 134–146.
   PubMedGoogle Scholar
• Pandey, R. and Rodriguez, G.M., 2012. A ferritin mutant of Mycobacterium tuberculosis is highly susceptible to killing by antibiotics and is unable to establish a chronic infection in mice. Infection and immunity, 80 (10), 3650–3659.
   PubMed Web of Science ®Google Scholar
• Penrod, J.T. and Roth, J.R., 2006. Conserving a volatile metabolite: a role for carboxysome-like organelles in Salmonella enterica. Journal of bacteriology, 188 (8), 2865–2874.
   PubMed Web of Science ®Google Scholar
• Radford, D., 2015. Understanding the encapsulins: prediction and characterization of phage capsid-like nanocompartments in prokaryotes. University of Toronto (Canada). Available from: http://gradworks.umi.com/37/20/3720094.html [Accessed 1 February 2017].
   Google Scholar
• Rahmanpour, R. and Bugg, T.D.H., 2013. Assembly in vitro of Rhodococcus jostii RHA1 encapsulin and peroxidase DypB to form a nanocompartment. The FEBS Journal, 280 (9), 2097–2104.
   PubMed Web of Science ®Google Scholar
• Reddy, P.V., et al., 2012. Iron storage proteins are essential for the survival and pathogenesis of Mycobacterium tuberculosis in THP-1 macrophages and the guinea pig model of infection. Journal of bacteriology, 194 (3), 567–575.
   PubMed Web of Science ®Google Scholar
• Rosenkrands, I., et al., 1998. Identification and characterization of a 29-kilodalton protein from Mycobacterium tuberculosis culture filtrate recognized by mouse memory effector cells. Infection and immunity, 66 (6), 2728–2735.
   PubMed Web of Science ®Google Scholar
• Rurup, W.F., et al., 2014. Self-sorting of foreign proteins in a bacterial nanocompartment. Journal of the American Chemical Society, 136 (10), 3828–3832.
   PubMed Web of Science ®Google Scholar
• Saito, N., et al., 2003. Genetic and biochemical characterization of EshA, a protein that forms large multimers and affects developmental processes in Streptomyces griseus. The journal of biological chemistry, 278 (8), 5902–5911.
   PubMed Web of Science ®Google Scholar
• Sampson, E.M. and Bobik, T.A., 2008. Microcompartments for B12-dependent 1,2-propanediol degradation provide protection from DNA and cellular damage by a reactive metabolic intermediate. Journal of bacteriology, 190 (8), 2966–2971.
   PubMed Web of Science ®Google Scholar
• Shively, J.M., 1974. Inclusion bodies of prokaryotes. Annual review of microbiology, 28, 167–187.
   PubMed Web of Science ®Google Scholar
• Slauch, J.M., 2011. How does the oxidative burst of macrophages kill bacteria? Still an open question. Molecular microbiology, 80 (3), 580–583.
   PubMed Web of Science ®Google Scholar
• Snijder, J., et al., 2014. Defining the stoichiometry and cargo load of viral and bacterial nanoparticles by Orbitrap mass spectrometry. Journal of the American Chemical Society, 136 (20), 7295–7299.
   PubMed Web of Science ®Google Scholar
• Snijder, J., et al., 2016. Assembly and mechanical properties of the cargo-free and cargo-loaded bacterial nanocompartment encapsulin. Biomacromolecules, 17 (8), 2522–2529.
   PubMed Web of Science ®Google Scholar
• Sonotaki, S., et al., 2017. Successful PEGylation of hollow encapsulin nanoparticles from Rhodococcus erythropolis N771 without affecting their disassembly and reassembly properties. Biomaterials science, 5, 1082–1089.
   PubMed Web of Science ®Google Scholar
• Sugano, Y., et al., 2007. DyP, a unique dye-decolorizing peroxidase, represents a novel heme peroxidase family: ASP171 replaces the distal histidine of classical peroxidases. The journal of biological chemistry, 282 (50), 36652–36658.
   PubMed Web of Science ®Google Scholar
• Sutter, M., et al., 2008. Structural basis of enzyme encapsulation into a bacterial nanocompartment. Nature structural & molecular biology, 15 (9), 939–947.
   PubMed Web of Science ®Google Scholar
• Tamura, A., et al., 2015. Packaging guest proteins into the encapsulin nanocompartment from Rhodococcus erythropolis N771. Biotechnology and bioengineering, 112 (1), 13–20.
   PubMed Web of Science ®Google Scholar
• Triccas, J.A., et al., 1996. A 35-kilodalton protein is a major target of the human immune response to Mycobacterium leprae. Infection and immunity, 64 (12), 5171–5177.
   PubMed Web of Science ®Google Scholar
• Valdés-Stauber, N. and Scherer, S., 1994. Isolation and characterization of Linocin M18, a bacteriocin produced by Brevibacterium linens. Applied and environmental microbiology, 60 (10), 3809–3814.
   PubMed Web of Science ®Google Scholar
• Wang, P., et al., 2010. Robust growth of Escherichia coli. Current biology, 20 (12), 1099–1103.
   PubMed Web of Science ®Google Scholar
• Wikoff, W.R., et al., 2000. Topologically linked protein rings in the bacteriophage HK97 capsid. Science, 289 (5487), 2129–2133.
   PubMed Web of Science ®Google Scholar
• Winter, N., et al., 1995. Characterization of the gene encoding the immunodominant 35 kDa protein of Mycobacterium leprae. Molecular microbiology, 16 (5), 865–876.
   PubMed Web of Science ®Google Scholar
• Yeates, T.O., Crowley, C.S., and Tanaka, S., 2010. Bacterial microcompartment organelles: protein shell structure and evolution. Annual review of biophysics, 39, 185–205.
   PubMed Web of Science ®Google Scholar
• Yeates, T.O., Thompson, M.C., and Bobik, T.A., 2011. The protein shells of bacterial microcompartment organelles. Current opinion in structural biology, 21 (2), 223–231.
   PubMed Web of Science ®Google Scholar
• Zubieta, C., et al., 2007. Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif. Proteins, 69 (2), 223–233.
   PubMed Web of Science ®Google Scholar