Difference between revisions of "Part:BBa K538001:Design"
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__NOTOC__ | __NOTOC__ | ||
| − | + | ===Cpn60 (''O. antarctica'')=== | |
| − | <partinfo>BBa_K538001 | + | <partinfo>BBa_K538001 DeepComponents</partinfo> |
| − | + | ''Cpn60'' was used by team [http://2011.igem.org/Team:Amsterdam Amsterdam 2011] to create CryoBricks; cold resistance BioBricks. It encodes ''chaperonin 60'', a part of the ''Cpn60/10'' chaperone system of ''Oleispira antarctica'', and thus needs to be coexpressed with ''Cpn10'' ([[Part:BBa_K538000|BBa_K538000]]) to be functional. See also the [[Part:BBa_K538001 | Main Page]], or the team's [http://2011.igem.org/Team:Amsterdam/Project/Description Project Description] for further information. | |
| − | + | ||
| + | ===Design Notes=== | ||
| + | This protein's structure and function have been studied extensively by Ferrer ''et al.''[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2004.04077.x/full], also including its functionality in ''E. coli''[http://aem.asm.org/cgi/content/abstract/70/8/4499][http://www.nature.com/nbt/journal/v21/n11/full/nbt1103-1266b.html][http://onlinelibrary.wiley.com/doi/10.1002/pmic.200500031/abstract], and as such its [http://www.ncbi.nlm.nih.gov/nuccore/22266159?from=458&to=751&report=gbwithparts sequence] is publicly available. Pre- and suffixes were added to this as clarified in OpenWetWare's [http://openwetware.org/wiki/Biobrick_standard BioBrick standards] and, as is recommended, the TAA stop codon was replaced with TAATAA. The sequence's conformity with [https://parts.igem.org/Help:Assembly_standard_10 Assembly standard 10] and putative future standards was ensured using the [http://bioweb2.pasteur.fr/docs/EMBOSS/recoder.html EMBOSS recoder], by recoding restriction sites of ''EcoRI'', ''XbaI'', ''SpeI'', ''PstI'', ''NotI'', ''PvuII'', ''XhoI'', ''AvrII'', ''NheI'' and ''SapI''. Note that to ensure compatibility with [http://dspace.mit.edu/handle/1721.1/46747 RFC 21] and [http://dspace.mit.edu/handle/1721.1/45140 RFC 25], an additional 4 restriction sites must be recoded. For RFC 21 compatibility, no ''BamHI'' or ''BglII'' sites may be present in the sequence. Likewise, for RFC 25, no ''AgeI'' or ''NgoMIV'' sites may occur. | ||
| + | |||
| + | [http://bioweb2.pasteur.fr/docs/EMBOSS/recoder.html EMBOSS recoder] detected and silently mutated 1 SapI restriction site. Positions 907 through 913 matched SapI's target sequence: GAAGAGC. The site was recoded by changing the A on position 909 to a G. | ||
===Source=== | ===Source=== | ||
| + | ''De novo'' synthesis by [http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Cloning/gene-synthesis/GeneArt-Gene-Synthesis.html GeneArt] | ||
| − | |||
===References=== | ===References=== | ||
| + | # '''Ferrer ''et al.''''' Functional consequences of single:double ring transitions in chaperonins: life in the cold, ''Mol. Microbiol. 53 (1), 167-182'' (2004) | ||
| + | # '''Ferrer ''et al.''''' Expression of a Temperature-Sensitive Esterase in a Novel Chaperone-Based ''Escherichia coli'' Strain, ''App. Env. Microbiol. 70 (8), 4499-4504'' (2004) | ||
| + | # '''Ferrer ''et al.''''' Chaperonins govern growth of ''Escherichia coli'' at low temperatures, ''Nat. Biotech. 21, 1266 - 1267'' (2003) | ||
| + | # '''Strocchi, Ferrer, Timmis & Golyshin''' Low temperature-induced systems failure in ''Escherichia coli'': Insights from rescue by cold-adapted chaperones, ''Proteomics 6 (1), 193-206'' (2005) | ||
| + | |||
| + | |||
| + | ===Patents=== | ||
| + | # '''Ferrer ''et al.''''' Transgenic organisms with lower growth temperature, ''US Patent Number 7,811,784'' (2004) [http://www.google.com/patents/about?id=cGDXAAAAEBAJ (View in Google Patents)] | ||
| + | |||
| + | |||
| + | ===Sequence and Features=== | ||
| + | <partinfo>BBa_K538001 SequenceAndFeatures</partinfo> | ||
Latest revision as of 12:34, 15 September 2011
Cpn60 (O. antarctica)
| Cpn60 K538001 | |
 |
Cpn60 was used by team [http://2011.igem.org/Team:Amsterdam Amsterdam 2011] to create CryoBricks; cold resistance BioBricks. It encodes chaperonin 60, a part of the Cpn60/10 chaperone system of Oleispira antarctica, and thus needs to be coexpressed with Cpn10 (BBa_K538000) to be functional. See also the Main Page, or the team's [http://2011.igem.org/Team:Amsterdam/Project/Description Project Description] for further information.
Design Notes
This protein's structure and function have been studied extensively by Ferrer et al.[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2004.04077.x/full], also including its functionality in E. coli[http://aem.asm.org/cgi/content/abstract/70/8/4499][http://www.nature.com/nbt/journal/v21/n11/full/nbt1103-1266b.html][http://onlinelibrary.wiley.com/doi/10.1002/pmic.200500031/abstract], and as such its [http://www.ncbi.nlm.nih.gov/nuccore/22266159?from=458&to=751&report=gbwithparts sequence] is publicly available. Pre- and suffixes were added to this as clarified in OpenWetWare's [http://openwetware.org/wiki/Biobrick_standard BioBrick standards] and, as is recommended, the TAA stop codon was replaced with TAATAA. The sequence's conformity with Assembly standard 10 and putative future standards was ensured using the [http://bioweb2.pasteur.fr/docs/EMBOSS/recoder.html EMBOSS recoder], by recoding restriction sites of EcoRI, XbaI, SpeI, PstI, NotI, PvuII, XhoI, AvrII, NheI and SapI. Note that to ensure compatibility with [http://dspace.mit.edu/handle/1721.1/46747 RFC 21] and [http://dspace.mit.edu/handle/1721.1/45140 RFC 25], an additional 4 restriction sites must be recoded. For RFC 21 compatibility, no BamHI or BglII sites may be present in the sequence. Likewise, for RFC 25, no AgeI or NgoMIV sites may occur.
[http://bioweb2.pasteur.fr/docs/EMBOSS/recoder.html EMBOSS recoder] detected and silently mutated 1 SapI restriction site. Positions 907 through 913 matched SapI's target sequence: GAAGAGC. The site was recoded by changing the A on position 909 to a G.
Source
De novo synthesis by [http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Cloning/gene-synthesis/GeneArt-Gene-Synthesis.html GeneArt]
References
- Ferrer et al. Functional consequences of single:double ring transitions in chaperonins: life in the cold, Mol. Microbiol. 53 (1), 167-182 (2004)
- Ferrer et al. Expression of a Temperature-Sensitive Esterase in a Novel Chaperone-Based Escherichia coli Strain, App. Env. Microbiol. 70 (8), 4499-4504 (2004)
- Ferrer et al. Chaperonins govern growth of Escherichia coli at low temperatures, Nat. Biotech. 21, 1266 - 1267 (2003)
- Strocchi, Ferrer, Timmis & Golyshin Low temperature-induced systems failure in Escherichia coli: Insights from rescue by cold-adapted chaperones, Proteomics 6 (1), 193-206 (2005)
Patents
- Ferrer et al. Transgenic organisms with lower growth temperature, US Patent Number 7,811,784 (2004) [http://www.google.com/patents/about?id=cGDXAAAAEBAJ (View in Google Patents)]
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal BglII site found at 870
Illegal BamHI site found at 936 - 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]