Difference between revisions of "Part:BBa K4229020"

Latest revision as of 23:24, 13 October 2022

Encapsulin

Usage and Biology

Encapsulins are nanocompartments, which similar to microcompartments, are self-assembled protein compartments, natively found in some bacteria and archaea [1]. They can be distinguished from microcompartments through the size of the compartments (20-42 nm) [1]. The encapsulins from Thermotoga maritima and Mycobacterium tuberculosis have outer diameters of 20–24 nm and are composed of 60 identical encapsulin protein subunits. The largest encapsulin compartment discovered to date is represented by that of Quasibacillus thermotolerans with a 42 nm outer diameter and 240 identical subunits [2]. Structural experiments showed that encapsulins are icosahedral shell-like protein compartments resembling viral capsids (Hong Kong 97‐like fold) [2][3]. The pore size of ~5 Å allows channelling small molecular substrates through the shell. Multiple encapsulins encapsulate cargo protein based on a short C-terminal peptide sequence, called the targeting peptide (TP) [1]. TPs often include a specific anchoring sequence, such as the Gly–Ser–Leu singlet or doublet motif and binding is mediated by hydrophobic and ionic interactions [4][6]. Encapsulins have attracted the attention of the synthetic biology community for the possibility of engineering small protein nanocages e.g. for drug delivery [5]. The encapsulins are highly suitable for such purposes given their high stability at high temperatures and various pH levels [8]. For our project, we decided to use an encapsulin derived from M. xanthus which is composed of the protein EncA, forming the shell [3][7]. In M. xanthus, the encapsulin is known to encapsulate three different cargo proteins, which play a role in iron storage [7]. This specific encapsulin was deemed a great fit for our team, as it has previously been engineered to encapsulate non-native enzymes in yeast [9]. For experimental data please refer to Biobrick BBa_K4229070.

Encapsulin of the organism M. xanthus, which is composed of the protein EncA. Encapsulin compartments can provide stabilization and co-localization of cargo proteins and can also be engineered to encapsulate non-native enzymes, as previously shown in yeast (structure from PDB: 4PT2). Figure created with PyMOL.

References:

[1] T. W. Giessen, “Encapsulins: Microbial nanocompartments with applications in biomedicine, nanobiotechnology and materials science,” Curr. Opin. Chem. Biol., vol. 34, pp. 1–10, 2016, doi: 10.1016/j.cbpa.2016.05.013.

[2]J. A. Jones and T. W. Giessen, “Advances in encapsulin nanocompartment biology and engineering,” Biotechnol. Bioeng., vol. 118, no. 1, pp. 491–505, 2021, doi: 10.1002/bit.27564.

[3] J. Fontana et al., “Phage capsid-like structure of Myxococcus xanthus encapsulin, a protein shell that stores iron,” Microsc. Microanal., vol. 20, no. 3, pp. 1244–1245, 2014, doi: 10.1017/S1431927614007958.

[4] M. Sutter et al., “Structural basis of enzyme encapsulation into a bacterial nanocompartment,” Nat. Struct. Mol. Biol., vol. 15, no. 9, pp. 939–947, 2008, doi: 10.1038/nsmb.1473.

[5] A. Van de Steen et al., “Bioengineering bacterial encapsulin nanocompartments as targeted drug delivery system,” Synth. Syst. Biotechnol., vol. 6, no. 3, pp. 231–241, 2021, doi: 10.1016/j.synbio.2021.09.001.

[6] W. J. Altenburg, N. Rollins, P. A. Silver, and T. W. Giessen, “Exploring targeting peptide-shell interactions in encapsulin nanocompartments,” Sci. Rep., vol. 11, no. 1, pp. 1–9, 2021, doi: 10.1038/s41598-021-84329-z.

[7] C. A. McHugh et al., “A virus capsid‐like nanocompartment that stores iron and protects bacteria from oxidative stress,” EMBO J., vol. 33, no. 17, pp. 1896–1911, 2014, doi: 10.15252/embj.201488566.

[8] I. Boyton, S. C. Goodchild, D. Diaz, A. Elbourne, L. Collins-Praino, and A. Care, “Exploring the Self-Assembly of Encapsulin Protein Nanocages from Different Structural Classes,” bioRxiv, 2021, doi: 10.1101/2021.06.06.447285.

[9] Y. H. Lau, T. W. Giessen, W. J. Altenburg, and P. A. Silver, “Prokaryotic nanocompartments form synthetic organelles in a eukaryote,” Nat. Commun., vol. 9, no. 1, 2018, doi: 10.1038/s41467-018-03768-x.

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
COMPATIBLE WITH RFC[21]
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
COMPATIBLE WITH RFC[1000]

@@ Line 3: / Line 3: @@
 <partinfo>BBa_K4229020 short</partinfo>
-Encapsulins  are nanocompartments, which similar to microcompartments, are self-assembled protein compartments, natively found in some bacteria and archaea [1]. They can be distinguished from microcompartments through the size of the compartments (20-42 nm) [1]. The encapsulins from Thermotoga maritima and <i>Mycobacterium tuberculosis</i> have outer diameters of 20–24 nm and are composed of 60 identical encapsulin protein subunits. The largest encapsulin compartment discovered to date is represented by that of <i>Quasibacillus thermotolerans</i> with a 42 nm outer diameter and 240 identical subunits [2]. Structural experiments showed that encapsulins are icosahedral shell-like protein compartments resembling viral capsids (Hong Kong 97‐like fold) [2][3]. The pore size of ~5 Å allows channelling small molecular substrates through the shell. Multiple encapsulins encapsulate cargo protein based on a short C-terminal peptide sequence, called the targeting peptide (TP) [1]. TPs often include a specific anchoring sequence, such as the Gly–Ser–Leu singlet or doublet motif and binding is mediated by hydrophobic and ionic interactions [4][6]. Encapsulins have attracted the attention of the synthetic biology community for the possibility of engineering small protein nanocages e.g. for drug delivery [5]. The encapsulins are highly suitable for such purposes given their high stability at high temperatures and various pH levels [8]. For our project, we decided to use an encapsulin derived from M. xanthus which is composed of the protein EncA, forming the shell [3][7]. In M. xanthus, the encapsulin is known to encapsulate three different cargo proteins, which play a role in iron storage [7]. This specific encapsulin was deemed a great fit for our team, as it has previously been engineered to encapsulate non-native enzymes in yeast [9]. For exmperimental data please refer to Biobrick BBa_K4229070.
+===Usage and Biology===
+Encapsulins  are nanocompartments, which similar to microcompartments, are self-assembled protein compartments, natively found in some bacteria and archaea [1]. They can be distinguished from microcompartments through the size of the compartments (20-42 nm) [1]. The encapsulins from <i>Thermotoga maritima</i> and <i>Mycobacterium tuberculosis</i> have outer diameters of 20–24 nm and are composed of 60 identical encapsulin protein subunits. The largest encapsulin compartment discovered to date is represented by that of <i>Quasibacillus thermotolerans</i> with a 42 nm outer diameter and 240 identical subunits [2]. Structural experiments showed that encapsulins are icosahedral shell-like protein compartments resembling viral capsids (Hong Kong 97‐like fold) [2][3]. The pore size of ~5 Å allows channelling small molecular substrates through the shell. Multiple encapsulins encapsulate cargo protein based on a short C-terminal peptide sequence, called the targeting peptide (TP) [1]. TPs often include a specific anchoring sequence, such as the Gly–Ser–Leu singlet or doublet motif and binding is mediated by hydrophobic and ionic interactions [4][6]. Encapsulins have attracted the attention of the synthetic biology community for the possibility of engineering small protein nanocages e.g. for drug delivery [5]. The encapsulins are highly suitable for such purposes given their high stability at high temperatures and various pH levels [8]. For our project, we decided to use an encapsulin derived from <i>M. xanthus</i> which is composed of the protein EncA, forming the shell [3][7]. In <i>M. xanthus</i>, the encapsulin is known to encapsulate three different cargo proteins, which play a role in iron storage [7]. This specific encapsulin was deemed a great fit for our team, as it has previously been engineered to encapsulate non-native enzymes in yeast [9]. For experimental data please refer to Biobrick BBa_K4229070.
-[[File:Encapsulines.png|200px|thumb|left|Encapsulin of the organism M. xanthus, which is composed of the protein EncA. Encapsulin compartments can provide stabilization and co-localization of cargo proteins and can also be engineered to encapsulate non-native enzymes, as previously shown in yeast (structure from PDB: 4PT2). Figure created with PyMOL.]]
+[[File:Encapsulines.png|200px|thumb|left|Encapsulin of the organism <i>M. xanthus</i>, which is composed of the protein EncA. Encapsulin compartments can provide stabilization and co-localization of cargo proteins and can also be engineered to encapsulate non-native enzymes, as previously shown in yeast (structure from PDB: 4PT2). Figure created with PyMOL.]]
+References:
 [1] T. W. Giessen, “Encapsulins: Microbial nanocompartments with applications in biomedicine, nanobiotechnology and materials science,” Curr. Opin. Chem. Biol., vol. 34, pp. 1–10, 2016, doi: 10.1016/j.cbpa.2016.05.013.