Difference between revisions of "Part:BBa K3792000"

Latest revision as of 03:00, 22 October 2021

NodI

This part was lifted from the UniProt entry UniProtKB - P08720 [1]. This protein is from the Nodulation Operon (Nod) from Rhizobium leguminosarum bv. Viciae. This protein forms an ABC transporter cassette complex with Part BBa_K3792001 to transport Nodulation factors (Lipo-chito-oligomers or LCO’s) across the cell membrane to induce nodulation [2-5]. Nodulation is the process by which an organ is formed with a host plant to house the symbiotic bacterium.

The 2021 FSU iGEM team has experimented with BBa_K2380000 and BBa_K3792000 to try and express chito-oligomers efficiently outside the cell membrane of E. Coli. The predicted structure of the NodIJ complex is available for download at https://2021.igem.org/Team:FSU/Model

To test if the cells were secreting chitin, The FSU 2021 team used the Chitosan Assay Kit (XAN-5126) available from Cell Biolabs. The manual for this kit contains the protocols for converting chitin to chitosan, along with a protocol for detecting chitosan.

Chitin from the cells was converted into chitosan by reacting with 12.5M NaOH at 95°C for 24 hours. The solution was then neutralized with acetic acid. The assay was then performed on the supernatant of the cell culture.

[1] https://www.uniprot.org/uniprot/P08720

[2] Poinsot, Véréna, et al. “New Insights into Nod Factor Biosynthesis: Analyses of Chitooligomers and Lipo-Chitooligomers of Rhizobium Sp. IRBG74 Mutants.” Carbohydrate Research, vol. 434, 3 Nov. 2016, pp. 83–93., https://doi.org/10.1016/j.carres.2016.08.001.

[3] Spaink, H P, et al. “Rhizobium NodI and NodJ Proteins Play a Role in the Efficiency of Secretion of Lipochitin Oligosaccharides.” Journal of Bacteriology, vol. 177, no. 21, Nov. 1995, pp. 6276–6281., https://doi.org/10.1128/jb.177.21.6276-6281.1995.

[4] Mirdita, Milot, et al. “ColabFold - Making Protein Folding Accessible to All.” BioRxiv, Cold Spring Harbor Laboratory, 1 Jan. 2021, https://www.biorxiv.org/content/10.1101/2021.08.15.456425v1.

[5] Hollenstein, Kaspar, et al. “Structure and Mechanism of ABC Transporter Proteins.” Current Opinion in Structural Biology, Elsevier Current Trends, 27 Aug. 2007, https://www.sciencedirect.com/science/article/pii/S0959440X07001029.

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
INCOMPATIBLE WITH RFC[1000]
Illegal SapI.rc site found at 150

@@ Line 1: / Line 1: @@
+{{FSU/ChartsCSS}}
+<html>
+<style>
+#modular-promoter-library-chart.column {
+  height: 400px;
+  max-width: 100% !important;
+  margin: 0 auto;
+  --labels-size: 0.5rem;
+}
+#modular-promoter-library-chart tr {
+  transition-duration: 0.3s;
+}
+#modular-promoter-library-chart tr:hover {
+  background-color: rgba(0, 0, 0, 0.2);
+}
+#modular-promoter-library-chart tr:hover th {
+  background-color: rgba(0, 0, 0, 0.4);
+  color: #fff;
+}
+</style>
+</html>
 __NOTOC__
 <partinfo>BBa_K3792000 short</partinfo>
-Protein possibly involved in transporting chitin across the cell membrane. Expressed with nodC and nodJ by the 2021 FSU team.
+This part was lifted from the UniProt entry UniProtKB - P08720 [1]. This protein is from the Nodulation Operon (Nod) from Rhizobium leguminosarum bv. Viciae. This protein forms an ABC transporter cassette complex with Part BBa_K3792001 to transport Nodulation factors (Lipo-chito-oligomers or LCO’s) across the cell membrane to induce nodulation [2-5]. Nodulation is the process by which an organ is formed with a host plant to house the symbiotic bacterium.
+The 2021 FSU iGEM team has experimented with BBa_K2380000 and BBa_K3792000 to try and express chito-oligomers efficiently outside the cell membrane of E. Coli.
+The predicted structure of the NodIJ complex is available for download at https://2021.igem.org/Team:FSU/Model
 To test if the cells were secreting chitin, The FSU 2021 team used the Chitosan Assay Kit (XAN-5126) available from Cell Biolabs. The manual for this kit contains the protocols for converting chitin to chitosan, along with a protocol for detecting chitosan.
 Chitin from the cells was converted into chitosan by reacting with 12.5M NaOH at 95°C for 24 hours. The solution was then neutralized with acetic acid. The assay was then performed on the supernatant of the cell culture.
+[1] https://www.uniprot.org/uniprot/P08720
+[2] Poinsot, Véréna, et al. “New Insights into Nod Factor Biosynthesis: Analyses of Chitooligomers and Lipo-Chitooligomers of Rhizobium Sp. IRBG74 Mutants.” Carbohydrate Research, vol. 434, 3 Nov. 2016, pp. 83–93., https://doi.org/10.1016/j.carres.2016.08.001.
+[3] Spaink, H P, et al. “Rhizobium NodI and NodJ Proteins Play a Role in the Efficiency of Secretion of Lipochitin Oligosaccharides.” Journal of Bacteriology, vol. 177, no. 21, Nov. 1995, pp. 6276–6281., https://doi.org/10.1128/jb.177.21.6276-6281.1995.
+[4] Mirdita, Milot, et al. “ColabFold - Making Protein Folding Accessible to All.” BioRxiv, Cold Spring Harbor Laboratory, 1 Jan. 2021, https://www.biorxiv.org/content/10.1101/2021.08.15.456425v1.
+[5] Hollenstein, Kaspar, et al. “Structure and Mechanism of ABC Transporter Proteins.” Current Opinion in Structural Biology, Elsevier Current Trends, 27 Aug. 2007, https://www.sciencedirect.com/science/article/pii/S0959440X07001029.