Difference between revisions of "Part:BBa K4432014"

Revision as of 22:01, 1 October 2022

Synthetic RBS designed for Pseudomonas aeruginosa PhzA1-G1 operon

This part is a synthetic RBS specifically designed for the Pseudomonas aeruginosa PhzA1-G1 operon (BBa_K4432040) using the Salis Lab RBS Library Calculator v2.0 [1-3].

Usage and Biology

This RBS was used to drive the expression of the PhzA1-G1 operon (BBa_K4432040) and its truncated version (BBa_I723028) under the control of the T5 promoter (BBa_K4432000) in the composite parts BBa_K4432140 and BBa_K4432142.

Using the Salis Lab RBS Library Calculator v2.0 [1-3], the predicted features of this RBS are:

Translation Initiation Rate (au)	:	1670.583702
dG_total (kcal/mol)	:	-0.674151476	
dG_mRNA_rRNA (kcal/mol)	:	-13.33135155
dG_spacing (kcal/mol)	:	0.288
dG_stacking (kcal/mol)	:	0
dG_standby (kcal/mol)	:	0
dG_start (kcal/mol)	:	-2.76
dG_mRNA (kcal/mol)	:	-15,42000008
Accuracy (warnings)	:	none

This RBS was selected fortuitously during the cloning process from a library of 108 RBSes (TAGHCACTAACDWAAGSAGGHAGTAGC) for which the estimated Translation Initiation Rates (TIR) range from 434.51 to 358600.92.

References

[1] Reis AC, Salis HM. An automated model test system for systematic development and improvement of gene expression models. ACS synthetic biology (2020) 9: 3145–3156.

[2] Farasat I, Kushwaha M, Collens J, Easterbrook M, Guido M, Salis HM. Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria. Molecular Systems Biology (2014) 10: 731.

[3] Ng CY, Farasat I, Maranas CD, Salis HM. Rational design of a synthetic Entner-Doudoroff pathway for improved and controllable NADPH regeneration. Metabolic Engineering (2015) 29: 86–96.

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_K4432014 short</partinfo>
-to do
+This part is a synthetic RBS specifically designed for the ''Pseudomonas aeruginosa'' PhzA1-G1 operon ([[Part:BBa_K4432040|BBa_K4432040]]) using the [https://www.denovodna.com/ Salis Lab RBS Library Calculator v2.0] [1-3].
-<!-- Add more about the biology of this part here
 ===Usage and Biology===
+This RBS was used to drive the expression of the PhzA1-G1 operon ([[Part:BBa_K4432040|BBa_K4432040]]) and its truncated version ([[Part:BBa_I723028|BBa_I723028]]) under the control of the T5 promoter ([[Part:BBa_K4432000|BBa_K4432000]]) in the composite parts [[Part:BBa_K4432140|BBa_K4432140]] and [[Part:BBa_K4432142|BBa_K4432142]].
+Using the Salis Lab RBS Library Calculator v2.0 [1-3], the predicted features of this RBS are:
+ Translation Initiation Rate (au)	:	1670.583702
+ dG_total (kcal/mol)	:	-0.674151476
+ dG_mRNA_rRNA (kcal/mol)	:	-13.33135155
+ dG_spacing (kcal/mol)	:	0.288
+ dG_stacking (kcal/mol)	:	0
+ dG_standby (kcal/mol)	:	0
+ dG_start (kcal/mol)	:	-2.76
+ dG_mRNA (kcal/mol)	:	-15,42000008
+ Accuracy (warnings)	:	none
+This RBS was selected fortuitously during the cloning process from a library of 108 RBSes (TAGHCACTAACDWAAGSAGGHAGTAGC) for which the estimated Translation Initiation Rates (TIR) range from 434.51 to 358600.92.
+===References===
+[1] Reis AC, Salis HM. An automated model test system for systematic development and improvement of gene expression models. ACS synthetic biology (2020) 9: 3145–3156.
+[2] Farasat I, Kushwaha M, Collens J, Easterbrook M, Guido M, Salis HM. Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria. Molecular Systems Biology (2014) 10: 731.
+[3] Ng CY, Farasat I, Maranas CD, Salis HM. Rational design of a synthetic Entner-Doudoroff pathway for improved and controllable NADPH regeneration. Metabolic Engineering (2015) 29: 86–96.
 <!-- -->