Difference between revisions of "Part:BBa K4088890"
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<partinfo>BBa_K4088890 short</partinfo> | <partinfo>BBa_K4088890 short</partinfo> | ||
| + | <br/><br/> | ||
| + | С-terminal fragment of β-lactamase fused with dCas13a and C-terminal intein. | ||
| + | <br/><br/> | ||
| + | <!-- --> | ||
| + | <span class='h3bb'>Sequence and Features</span> | ||
| + | <partinfo>BBa_K4088890 SequenceAndFeatures</partinfo> | ||
| + | |||
| + | <br/><br/><br/><br/> | ||
| + | ==Usage and Biology== | ||
| + | '''β-Lactamase'''<br/> | ||
| + | β-Lactamase (AmpR) - the gene encoding beta-lactamase is a protein known for providing antibiotic resistance of bacteria to ampicillin because it is able to destroy the beta-lactam ring. This ability allows beta-lactamase to be used as a reporter protein (reaction with nitrocefin, which changes color when the beta-lactam ring is destroyed). Simple, reliable, readily available, it is not difficult to express in cells. These advantages have led us to use this particular reporter protein. | ||
| + | <br/> | ||
| + | N_lac and C_lac are genes encoding N and C fragments of beta-lactamase, respectively. We selected their sequence in a special way, taking into account the mechanism of protein splicing <ref> Perler FB. Protein splicing mechanisms and applications. IUBMB Life. 2005 Jul;57(7):469-76. https://doi.org/10.1080/15216540500163343</ref> . For this, we purposefully divided the ampR sequence in front of cysteine (you can also use threonine, the main thing is that they carry nucleophiles in the radical). | ||
| + | <br/><br/> | ||
| + | '''Linker'''<br/> | ||
| + | Usually, researchers use neutral amino acids like glycine and alanine as part of the linkers: it is desirable to make the linker neutral. Hydrophobic amino acids can be added, e.g. serine. Aliphatic amino acids may also be added. The length of linkers is usually 6-8 amino acids, primarily less than 10 amino acids. We use GGGGGG because it meets these criteria. | ||
| + | <br/><br/> | ||
| + | '''dCas13a'''<br/> | ||
| + | Cas13a is a classic RNA-targeting nuclease that is widely used in a variety of diagnostics methods. It is one enzyme of Cas13 family which contains at least 4 subtypes, including Cas13a, used as our Parts BioBrick. We took LwaCas13a, identified from Leptotrichia wadei (Lwa).<br/> | ||
| + | |||
| + | dCas13a is a catalytically dead lwaCas13a enzyme (formerly C2c2) with R407A and R1046A mutations in HEPN-domain. dCas13a interacts with gRNA about 65 nucleotides in length. dCas13a-gRNA complex detects complementary RNA in the sample. dCas13a is a very specific variant of RNA detection, it can be customized to recognize single nucleotides on the target RNA.<br/> | ||
| + | |||
| + | LwaCas13a has been reported to mediate more robust RNA-targeting activity than other Cas13 systems like LshCas13, but it requires a stabilizer fusion, for example, msfGFP for efficient interference activity <ref> Mahas, A., Aman, R. & Mahfouz, M. CRISPR-Cas13d mediates robust RNA virus interference in plants. Genome Biol 20, 263 (2019). https://doi.org/10.1186/s13059-019-1881-2</ref>. As a stabilizer fusion we use fragments of beta-lactamase thus improving targeting activity.<br/> | ||
| + | <br/><br/> | ||
| + | '''Intein'''<br/> | ||
| + | Intein is a segment of a protein that can self-catalytically excised out and ligate the remaining parts of the protein (N- and C-exteins) with a peptide bond <ref>Anraku, Y., Mizutani, R. and Satow, Y. (2005), Protein Splicing: Its Discovery and Structural Insight into Novel Chemical Mechanisms. IUBMB Life, 57: 563-574. https://doi.org/10.1080/15216540500215499</ref>. | ||
| + | <br/> | ||
| + | For this part, we used the DnaE intein. DnaE - alpha subunit of the DNA polymerase III intein. This intein is identified as a naturally occurring split intein in Nostoc punctiforme <ref>Oeemig JS, Aranko AS, Djupsjöbacka J, Heinämäki K, Iwaï H. Solution structure of DnaE intein from Nostoc punctiforme: structural basis for the design of a new split intein suitable for site-specific chemical modification. FEBS Lett. 2009 May 6;583(9):1451-6. https://doi.org/10.1016/j.febslet.2009.03.058</ref>. Split inteins can also be created artificially by separating the inteins' primary sequence into two pieces on the genetic level<ref>Zettler, Joachim, Schütz, Vivien and Mootz, Henning D.(2009), The naturally split Npu DnaE intein exhibits an extraordinarily high rate in the protein trans-splicing reaction, FEBS Letters, 583, doi: 10.1016/j.febslet.2009.02.003</ref>.<br/> | ||
| + | The rates for protein trans-splicing of the Npu DnaE intein that are 5.5-fold higher (at 37 °C) than the rate reported for the split Sce VMA intein and up to about 33 to 170-fold higher than found for the Ssp DnaE intein. The splice product yields obtained with the Npu intein were nearly unaffected in the temperature range: 6°, 12°, 25°, 37° with the highest rate observed at 37 °C. Split inteins can also be created artificially by separating the inteins’ primary sequence into two pieces on the genetic level. <br/> | ||
| + | The most important properties of the split intein tools are [5]: <br/> | ||
| + | 1. the yield of the protein trans-splicing reaction <br/> | ||
| + | 2. its rate constant <br/> | ||
| + | 3. the solubility of the intein fragments <br/> | ||
| + | 4. their tolerance towards different fused “substrate” exteins. <br/> | ||
| + | |||
| + | For this part we used the C fragment of the Npu DnaE intein (<partinfo>BBa_K4088893</partinfo>). | ||
| + | <br/><br/> | ||
| + | |||
| + | ==How our system would work== | ||
| + | When the two proteins (this one and <partinfo>BBa_K4088891</partinfo>) come together due to landing on RNA, trans-splicing occurs, this process needs to be stimulated with DTT or 2-mercaptoethanol. The result of trans-splicing is a peptide bond between the beta-lactamase fragments to form the active enzyme. It cleaves nitrocefin and the appearance of red coloration indicates the presence of the RNA in solution. | ||
| + | <br/><br/> | ||
| + | <br/><br/> | ||
| + | |||
| + | ==References== | ||
| + | |||
| + | |||
| + | |||
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Latest revision as of 02:08, 22 October 2021
dCas13a-Clact-int
С-terminal fragment of β-lactamase fused with dCas13a and C-terminal intein.
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal BglII site found at 1907
Illegal BglII site found at 2117
Illegal BglII site found at 2384
Illegal BglII site found at 3149
Illegal XhoI site found at 4078 - 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
Usage and Biology
β-Lactamase
β-Lactamase (AmpR) - the gene encoding beta-lactamase is a protein known for providing antibiotic resistance of bacteria to ampicillin because it is able to destroy the beta-lactam ring. This ability allows beta-lactamase to be used as a reporter protein (reaction with nitrocefin, which changes color when the beta-lactam ring is destroyed). Simple, reliable, readily available, it is not difficult to express in cells. These advantages have led us to use this particular reporter protein.
N_lac and C_lac are genes encoding N and C fragments of beta-lactamase, respectively. We selected their sequence in a special way, taking into account the mechanism of protein splicing [1] . For this, we purposefully divided the ampR sequence in front of cysteine (you can also use threonine, the main thing is that they carry nucleophiles in the radical).
Linker
Usually, researchers use neutral amino acids like glycine and alanine as part of the linkers: it is desirable to make the linker neutral. Hydrophobic amino acids can be added, e.g. serine. Aliphatic amino acids may also be added. The length of linkers is usually 6-8 amino acids, primarily less than 10 amino acids. We use GGGGGG because it meets these criteria.
dCas13a
Cas13a is a classic RNA-targeting nuclease that is widely used in a variety of diagnostics methods. It is one enzyme of Cas13 family which contains at least 4 subtypes, including Cas13a, used as our Parts BioBrick. We took LwaCas13a, identified from Leptotrichia wadei (Lwa).
dCas13a is a catalytically dead lwaCas13a enzyme (formerly C2c2) with R407A and R1046A mutations in HEPN-domain. dCas13a interacts with gRNA about 65 nucleotides in length. dCas13a-gRNA complex detects complementary RNA in the sample. dCas13a is a very specific variant of RNA detection, it can be customized to recognize single nucleotides on the target RNA.
LwaCas13a has been reported to mediate more robust RNA-targeting activity than other Cas13 systems like LshCas13, but it requires a stabilizer fusion, for example, msfGFP for efficient interference activity [2]. As a stabilizer fusion we use fragments of beta-lactamase thus improving targeting activity.
Intein
Intein is a segment of a protein that can self-catalytically excised out and ligate the remaining parts of the protein (N- and C-exteins) with a peptide bond [3].
For this part, we used the DnaE intein. DnaE - alpha subunit of the DNA polymerase III intein. This intein is identified as a naturally occurring split intein in Nostoc punctiforme [4]. Split inteins can also be created artificially by separating the inteins' primary sequence into two pieces on the genetic level[5].
The rates for protein trans-splicing of the Npu DnaE intein that are 5.5-fold higher (at 37 °C) than the rate reported for the split Sce VMA intein and up to about 33 to 170-fold higher than found for the Ssp DnaE intein. The splice product yields obtained with the Npu intein were nearly unaffected in the temperature range: 6°, 12°, 25°, 37° with the highest rate observed at 37 °C. Split inteins can also be created artificially by separating the inteins’ primary sequence into two pieces on the genetic level.
The most important properties of the split intein tools are [5]:
1. the yield of the protein trans-splicing reaction
2. its rate constant
3. the solubility of the intein fragments
4. their tolerance towards different fused “substrate” exteins.
For this part we used the C fragment of the Npu DnaE intein (BBa_K4088893).
How our system would work
When the two proteins (this one and BBa_K4088891) come together due to landing on RNA, trans-splicing occurs, this process needs to be stimulated with DTT or 2-mercaptoethanol. The result of trans-splicing is a peptide bond between the beta-lactamase fragments to form the active enzyme. It cleaves nitrocefin and the appearance of red coloration indicates the presence of the RNA in solution.
References
- ↑ Perler FB. Protein splicing mechanisms and applications. IUBMB Life. 2005 Jul;57(7):469-76. https://doi.org/10.1080/15216540500163343
- ↑ Mahas, A., Aman, R. & Mahfouz, M. CRISPR-Cas13d mediates robust RNA virus interference in plants. Genome Biol 20, 263 (2019). https://doi.org/10.1186/s13059-019-1881-2
- ↑ Anraku, Y., Mizutani, R. and Satow, Y. (2005), Protein Splicing: Its Discovery and Structural Insight into Novel Chemical Mechanisms. IUBMB Life, 57: 563-574. https://doi.org/10.1080/15216540500215499
- ↑ Oeemig JS, Aranko AS, Djupsjöbacka J, Heinämäki K, Iwaï H. Solution structure of DnaE intein from Nostoc punctiforme: structural basis for the design of a new split intein suitable for site-specific chemical modification. FEBS Lett. 2009 May 6;583(9):1451-6. https://doi.org/10.1016/j.febslet.2009.03.058
- ↑ Zettler, Joachim, Schütz, Vivien and Mootz, Henning D.(2009), The naturally split Npu DnaE intein exhibits an extraordinarily high rate in the protein trans-splicing reaction, FEBS Letters, 583, doi: 10.1016/j.febslet.2009.02.003