Parts

Here you can find a table summarizing all of the parts which were used in our project. We have designed four composite parts - A, B, C and D to test out different aspects of our project and composite part Z combining composite parts A, C and D to form a functioning system which responds to the increase in phosphate levels by initiating production of BMCs. More information about how we have designed and picked our parts can be found on the page project design.

Basic parts

Part	Part no.	Type	Description	Designer	Length
BMC - PduA	BBa_K3831000	Coding	This is one of the BMC (bacterial microcompartment) shell proteins from the Pdu operon of the bacteria Parageobacillus thermoglucosidasius which is closely related to Bacillus subtilis.	Klára Odehnalová	285
BMC - PduB	BBa_K3831001	Coding	This is one of the BMC (bacterial microcompartment) shell proteins from the Pdu operon of the bacteria Parageobacillus thermoglucosidasius which is closely related to Bacillus subtilis.	Klára Odehnalová	783
BMC - PduJ	BBa_K3831002	Coding	This is one of the BMC (bacterial microcompartment) shell proteins from the Pdu operon of the bacteria Parageobacillus thermoglucosidasius which is closely related to Bacillus subtilis.	Klára Odehnalová	276
BMC - PduK	BBa_K3831003	Coding	This is one of the BMC (bacterial microcompartment) shell proteins from the Pdu operon of the bacteria Parageobacillus thermoglucosidasius which is closely related to Bacillus subtilis.	Klára Odehnalová	696
BMC - PduN	BBa_K3831004	Coding	This is one of the BMC (bacterial microcompartment) shell proteins from the Pdu operon of the bacteria Parageobacillus thermoglucosidasius which is closely related to Bacillus subtilis.	Klára Odehnalová	270
Synthetic RBS_a	BBa_K3831005	RBS	This is a synthetic ribosome binding site which our team designed using this RBS calculator : https://salislab.net/software/predict_rbs_calculator	Klára Odehnalová	22
Synthetic RBS_b	BBa_K3831006	RBS	This is a synthetic ribosome binding site which our team designed using this RBS calculator : https://salislab.net/software/predict_rbs_calculator	Klára Odehnalová	33
Native RBS R2	BBa_K3831007	RBS	This is a native ribosome binding site from Bacillus subtilis.	Klára Odehnalová	21
RBS R6	BBa_K3831008	RBS	This is a synthetic ribosome bing site which was designed by Guiziou et al. in a study from 2016.	Klára Odehnalová	22
Synthetic RBS_c	BBa_K3831009	RBS	This is a synthetic ribosome binding site which our team designed using this RBS calculator : https://salislab.net/software/predict_rbs_calculator	Klára Odehnalová	27
Spacer_0	BBa_K3831010	DNA	Spacer sequence was inserted between other biobricks to separate them. This sequence was designed by Giuziou et al. in a study from 2016 and was then modified by our team.	Klára Odehnalová	40
Spacer_1	BBa_K3831011	DNA	Spacer sequence was inserted between other biobricks to separate them. This sequence was designed by Giuziou et al. in a study from 2016 and was then modified by our team.	Klára Odehnalová	15
Spacer_5	BBa_K3831012	DNA	Spacer sequence was inserted between other biobricks to separate them. This sequence was designed by Giuziou et al. in a study from 2016 and was then modified by our team.	Tomáš Kotačka	40
Ggggs linker	BBa_K3831013	Coding	This glycine-serine linker was used to connect a localization tag and GFP protein to join them together without affecting their functions.	Tomáš Kotačka	15
Native RBS R1	BBa_K3831014	RBS	This is a native ribosome binding site from Bacillus subtilis.	Tomáš Kotačka	21
Spacer_7	BBa_K3831015	DNA	Spacer sequence was inserted between other biobricks to separate them. This sequence was designed by Giuziou et al. in a study from 2016 and was then modified by our team.	Tomáš Kotačka	15
sfGFP	BBa_K3831016	Coding	This Green Fluorescent Protein was found on FPbase and codon optimised for B. subtilis	Tomáš Kotačka	714
Localization tag for BMC encapsulation	BBa_K3831017	Coding	This localization tag was designed in a study by Wade Y. et al. in 2019 where it was taken from N-termial sequence of PduP protein of Parageobacillus thermoglucosidasius.	Tomáš Kotačka	24
Native RBS R0	BBa_K3831018	RBS	Native RBS R0 from Bacillus subtilis	Michaela Dušková	24
Degradation tag	BBa_K3831019	Coding	The degradation tag ensures the quick degradation of the tagged protein.	Barbora Hrnčířová	45
Artificial RBS R3	BBa_K3831020	RBS	This is an artificial ribosome binding site from Bacillus subtilis.	Michaela Dušková	22
mScarlet-I	BBa_K3831021	Coding	Red fluorescent protein	Michaela Dušková	696
Promoter region for phosphate response	BBa_K3831022	Regulatory	This promoter is able to react to phosphate concentrations in the surrounding area. The promoter is activated in low phosphate levels.	Michaela Dušková	489
Spacer 03	BBa_K3831023	DNA	Spacers were placed between terminators and the rest of the composite part at both ends and also around the bidirectional terminator in the middle of the composite part.	Michaela Dušková	15
cI repressor	BBa_K3831024	Coding	Phage lambda forms the repressor cI, which binds to the O1, O2 and O3 operators, forms multimers and bends DNA, preventing transcription initiation from the pR promoter. We added one of the operator sequences into the P_gracpromoter to create P_Grac-OcIwhich should then be turned off in the presence of the cI repressor.	Barbora Hrnčířová	711
P_{Grac OcI}promoter	BBa_K3831025	Regulatory	The P_Gracpromoter was created by combining the groE promoter, gsiBSD sequence and lacO operator to allow for IPTG induction. We took out the lacO sequence and we replaced it with cI operator. This design should allow the strong promoter to be repressed by cI repressor originating from Phage lambda.	Barbora Hrnčířová	99
Spacer 02	BBa_K3831026	DNA	Spacers were placed between terminators and the rest of the composite part at both ends and also around the bidirectional terminator in the middle of the composite part.	Filip Křivák	15
Spacer 06	BBa_K3831027	DNA	Spacers were placed between terminators and the rest of the composite part at both ends and also around the bidirectional terminator in the middle of the composite part.	Filip Křivák	15
Spacer 04	BBa_K3831028	DNA	Spacers were placed between terminators and the rest of the composite part at both ends and also around the bidirectional terminator in the middle of the composite part.	Filip Křivák	40
Green fluorescent protein	BBa_K3831029	Coding	The Green Fluorescent protein serves as a reporter of the expression of cI repressor. We found its protein sequence on FPbase, we rendered it back to DNA and codon-optimized it to be expressed in B. subtilis.	Tomáš Kotačka	714
P_Gracpromoter	BBa_K3831035	Regulatory	The P_Gracpromoter was created by combining the groE promoter, gsiBSD sequence and lacO operator to allow for IPTG induction.	Barbora Hrnčířová	103
Spacer_SP1	BBa_K3831038	DNA	Spacer sequence inserted between other biobricks to separate them. This sequence was designed by Giuziou et al. in a study from 2016 and was then modified by our team.	Barbora Hrnčířová	40
P_Hyperspank	BBa_K3831039	Regulatory	IPTG inducible promoter - a regulatory sequence for B. subtilis	Saša Zahornacká	95
SVN Tag	BBa_K3831040	Tag	A short sequence which signals for the cell to degrade the protein with which it is fused	Saša Zahornacká	48
SVN Tag	BBa_K3831041	Tag	A short sequence which signals for the cell to degrade the protein with which it is fused	Saša Zahornacká	48
GFP	BBa_K3831042	Coding	Green fluorescent protein	Saša Zahornacká	714
Reverse terminator	BBa_K3831044	Terminator	Terminator sequence defines the end of transcriptional unit and initiates the process of releasing the newly synthesized RNA	Saša Zahornacká	54
SVN tag	BBa_K3831045	Tag	A short sequence which signals for the cell to degrade the protein with which it is fused	Saša Zahornacká	45
PduN - reverse complement	BBa_K3831046	Coding	This is one of the BMC (bacterial microcompartment) shell proteins from the Pdu operon of the bacteria Parageobacillus thermoglucosidasius which is closely related to Bacillus subtilis.	Barbora Hrnčířová	270
Synthetic RBS_c - reversed	BBa_K3831047	RBS	Synthetic ribosome binding site designed using RBScalculator:	Barbora Hrnčířová	27
PduK - reverse complement	BBa_K3831048	Coding	This is one of the BMC (bacterial microcompartment) shell proteins from the Pdu operon of the bacteria Parageobacillus thermoglucosidasius which is closely related to Bacillus subtilis.	Barbora Hrnčířová	696
RBS R6 - reversed	BBa_K3831049	RBS	Synthetic ribosome bing site designed by Guiziou et al. in a study from 2016	Barbora Hrnčířová	22
PduJ - reverse complement	BBa_K3831050	Coding	This is one of the BMC (bacterial microcompartment) shell proteins from the Pdu operon of the bacteria Parageobacillus thermoglucosidasius which is closely related to Bacillus subtilis.	Barbora Hrnčířová	276
RBS R2 - reversed	BBa_K3831051	RBS	Native ribosome binding site from Bacillus subtilis	Barbora Hrnčířová	21
PduB - reverse complement	BBa_K3831052	Coding	This is one of the BMC (bacterial microcompartment) shell proteins from the Pdu operon of the bacteria Parageobacillus thermoglucosidasius which is closely related to Bacillus subtilis.	Barbora Hrnčířová	783
Synthetic RBS_b - reversed	BBa_K3831053	RBS	Synthetic ribosome binding site designed with RBS calculator:	Barbora Hrnčířová	33
PduA - reverse complement	BBa_K3831054	Coding	This is one of the BMC (bacterial microcompartment) shell proteins from the Pdu operon of the bacteria Parageobacillus thermoglucosidasius which is closely related to Bacillus subtilis.	Barbora Hrnčířová	285
Synthetic RBS_a - reversed	BBa_K3831055	RBS	Synthetic ribosome binding site designed with RBS calculator:	Barbora Hrnčířová	22

Composite parts

Part	Part no.	Type	Description	Designer	Length
Construct A	BBa_K3831030	Composite	This construct was designed from BMC production.	Klára Odehnalová	2853
Construct B	BBa_K3831031	Composite	This construct was designed to test the formation of BMCs and the encapsulation of proteins inside of them.	Tomáš Kotačka	1146
Construct C	BBa_K3831032	Composite	This construct was designed to verify production of cI repressor and test the P_Phopromoter and its response to changes in phosphate concentration.	Michaela Dušková	2311
Construct D	BBa_K3831033	Composite	This construct was designed to test the function of the modified P_Gracpromoter and the expression of cI repressor.	Barbora Hrnčířová	2909
Construct Z	BBa_K3831034	Composite	This construct combines constructs A, D, C. It was designed to respond to changes in phosphate concentrations by stopping or initiating BMC production.	Barbora Hrnčířová, Michaela Dušková	4993

Igem Team Brno, Czech Republic 2021

Team:Brno Czech Republic/Parts

Parts

Basic parts

Composite parts