Team:Sorbonne U Paris/Basic-parts

Basic parts

Basic parts



This year, our team will be submitting 11 basic parts that are key component of two aspects of our project :

- The development of a kill-switch adapted to Chlamydomonas reinhardtii based on the principle of the one developed by the Munich 2013 iGEM team.
- The degradation of atrazine into cyanuric acid by three microbial enzymes found in the bacterium Pseudomonas sp. ADP . Cyanuric acid does not appear to be harmful to Chlamydomonas.

All these parts are standardized in a way that they can be integrated into the Chlamydomonas reinhardtii MoClo kit as basic parts by adding BbsI sites and the corresponding fusion sites (which depend on the desired position of the part) on both ends. By doing so, they can be integrated into a level 0 plasmid which is the backbone utilized for basic parts.

New parts submitted to the registry

Part name

BBa_K3373001

BBa_K3373002

BBa_K3373003

BBa_K3373004

BBa_K3373005

BBa_K3373007

BBa_K3373006

BBa_K3373011

BBa_K3373008

BBa_K3373009

BBa_K3373010

Type

Coding

Coding

Coding

Coding

Coding

Protein Domain

Protein Domain

Protein Domain

Coding

Protein Domain

Protein Domain

Position in the MoClo standard

B3-B4

B3-B4

B3-B4

B3

B3

B3

B4

B4

B5

B5

B5

Description

atA_B3-B4 MoClo C. reinhardtii

atB_B3-B4 MoClo C. reinhardtii

atC_B3-B4 MoClo C. reinhardtii

COP1_B3 MoClo C. reinhardtii

UVR8_B3 MoClo C. reinhardtii

TMD-HAP2_ B3 MoClo C. reinhardtii

GSAT_B4 MoClo C. reinhardtii

Linker+TEV-site_B4 MoClo C. reinhardtii

NucleaseA+SV40-NLS(x2)_B5 MoClo C. reinhardtii

Nter-TEV_B5 MoClo C. reinhardtii

Cter-TEV_B5 MoClo C. reinhardtii

ATZA_B3-B4 MOCLO C. REINHARDTII ( BBa_K3373001 )

Coding sequence of the Atrazine chlorohydrolase enzyme (P72156) encoded by the gene atzA from Pseudomonas sp. ADP and codon optimized for Chlamydomonas reinhardtii. It catalyses the hydrolytic dechlorination of the pesticide atrazine into hydroxyatrazine. 

The CDS is standardized in the Phytobrick standard for the C. reinhardtii MoClo Kit at the B3-B4 (CDS) position by adding BbsI sites and the corresponding fusion sites on both ends. The stop codon was removed to allow for tagging at the C-terminal position, the stop codon being provided by the part on the position B5.

ATZB_B3-B4 MOCLO C. REINHARDTII ( BBa_K3373002 )

Coding sequence of the Hydroxydechloroatrazine ethylaminohydrolase enzyme from Pseudomonas sp. ADP codon optimized for Chlamydomonas reinhardtii. Catalyzes the deamination reaction of hydroxyatrazine to N-isopropylammelide (dihydroxy-isopropyl-atrazine). 

The CDS is standardized in the Phytobrick standard for the C. reinhardtii MoClo Kit at the B3-B4 (CDS) position by adding BbsI sites and the corresponding fusion sites on both ends. The stop codon was removed to allow for tagging at the C-terminal position, the stop codon being provided by the part on the position B5.

ATZC_B3-B4 MOCLO C. REINHARDTII ( BBa_K3373003 )

Coding sequence of the N-isopropylammelide isopropyl amidohydrolase enzyme from Pseudomonas sp. ADP codon optimized for Chlamydomonas reinhardtii. Catalyzes the hydrolysis reaction of N-isopropylammelide (dihydroxy-isopropyl-atrazine) to cyanuric acid and isopropylamine.

The CDS is standardized in the Phytobrick standard for the C. reinhardtii MoClo Kit at the B3-B4 (CDS) position by adding BbsI sites and the corresponding fusion sites on both ends. The stop codon was removed to allow for tagging at the C-terminal position, the stop codon being provided by the part on the position B5.

COP1_B3 MOCLO C. REINHARDTII ( BBa_K3373004 )

Coding sequence of the E3 ubiquitin-protein ligase CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) encoded by the gene COP1 from Arabidopsis thaliana and codon optimized for Chlamydomonas reinhardtii. This enzyme is involved in the protein ubiquitination pathway. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin conjugating enzyme and then directly transfers the ubiquitin to targeted substrates for proteasomal degradation. COP1 is the interaction partner of ultraviolet B (UVB) light receptor UVR8.

The CDS is standardized in the Phytobrick standard for the C. reinhardtii MoClo Kit at the B3 (N-terminus coding region) position by adding BbsI sites and the corresponding fusion sites on both ends. The stop codon was removed to allow for fusion with another protein sequence and also tagging at the C-terminal position, the stop codon being provided by the part on the position B5.

UVR8_B3 MOCLO C. REINHARDTII ( BBa_K3373005 )

Coding sequence of the Ultraviolet-B receptor encoded by the gene UVR8 from Arabidopsis thaliana and codon optimized for Chlamydomonas reinhardtii. Upon UV-B irradiation, UVR8 undergoes an immediate switch from homodimer to monomer which leads to the interaction with the photomorphogenic repressor COP1.

The CDS is standardized in the Phytobrick standard for the C. reinhardtii MoClo Kit at the B3 (N-terminus coding region) position by adding BbsI sites and the corresponding fusion sites on both ends. The stop codon was removed to allow for fusion with another protein sequence and also tagging at the C-terminal position, the stop codon being provided by the part on the position B5.

TMD-HAP2_ B3 MOCLO C. REINHARDTII ( BBa_K3373007 )

Coding sequence of the transmembrane domain of the protein Hapless2 encoded by the gene HAP2 from Chlamydomonas reinhardtii.

The CDS is standardized in the Phytobrick standard for the C. reinhardtii MoClo Kit at the B3 (C-terminus coding region) position by adding BbsI sites and the corresponding fusion sites on both ends.

GSAT_B4 MOCLO C. REINHARDTII ( BBa_K3373006 )

Coding sequence of the GSAT-linker BBa_K404301 designed by Freiburg Bioware 2010 team and codon optimized for Chlamydomonas reinhardtii. This part is a peptide linker with a length of 36 amino acids which can be used to connect two protein parts / domains and add additional space between them. The GSAT linker was adapted to our chassis and used to connect our protein domains to a fusion construct. 

The peptide linker is standardized in the Phytobrick standard for the C. reinhardtii MoClo Kit at the B4 (Coding region) position by adding BbsI sites and the corresponding fusion sites on both ends.

LINKER+TEV-SITE_B4 MOCLO C. REINHARDTII ( BBa_K3373011 )

Coding sequence of a peptide linker fused to TEV protease recognition site from Tobacco etch virus codon optimized for Chlamydomonas reinhardtii.

The peptide linker is standardized in the Phytobrick standard for the C. reinhardtii MoClo Kit at the B4 (Coding region) position by adding BbsI sites and the corresponding fusion sites on both ends.

NUCLEASEA+SV40-NLS(x2)_B5 MOCLO C. REINHARDTII ( BBa_K3373008 )

Coding sequence of the micrococcal NucleaseA encoded by the gene nuc from Staphylococcus aureus and codon optimized for Chlamydomonas reinhardtii.

The CDS is standardized in the Phytobrick standard for the C. reinhardtii MoClo Kit at the B5 (C-terminus coding region) position by adding BbsI sites and the corresponding fusion sites on both ends. The stop codon was added after the NLS sequence.

NTER-TEV_B5 MOCLO C. REINHARDTII ( BBa_K3373009 )

Coding sequence of the N-terminus region of TEV protease from Tobacco etch virus codon optimized for Chlamydomonas reinhardtii.

The CDS is standardized in the Phytobrick standard for the C. reinhardtii MoClo Kit at the B5 (C-terminus coding region) position by adding BbsI sites and the corresponding fusion sites on both ends. The stop codon was added after the NLS sequence.

CTER-TEV_B5 MOCLO C. REINHARDTII ( BBa_K3373010 )

Coding sequence of the C-terminus region of TEV protease from Tobacco etch virus codon optimized for Chlamydomonas reinhardtii.

The CDS is standardized in the Phytobrick standard for the C. reinhardtii MoClo Kit at the B5 (C-terminus coding region) position by adding BbsI sites and the corresponding fusion sites on both ends. The stop codon was added after the NLS sequence.