Difference between revisions of "Part:BBa K2918011"

Revision as of 13:19, 6 October 2019

P_BHR sp1 promoter

Broad host range promoter with a binding site for TALE (Transcriptional Activator like Effector) repressor protein.

Sequence and Features

Usage and Biology

The (<a target=”_blank” href=”https://parts.igem.org/Part:BBa_K2918006”>broad host range promoter </a>) has been designed by combining promoter regions of E.coli , B.subtilis and S.cerevisiae . The promoter is based on the Pmin minimal promoter of S.cerevisiae. It was found that the conserved -35 and -10 regions (5′-TTGACA-3′ and 5′-TATAAT-3′ respectively) were the same in E.coli and B.subtilis . Therefore, to make the Pmin promoter broad host range, the 5′-TTGAAA-3′ sequence in the UAS region of the Pmin promoter was changed to 5′-TTGACA-3′ and the 5′-TTAAT-3′ in the AT rich region was changed to 5′-TATAAT-3′.
The (<a target=”_blank” href=”https://parts.igem.org/Part:BBa_K2918006”>broad host range promoter </a>) was engineered to contain a binding site for a Transcriptional Activator like Effector protein (TALE). The 17bp spacer between the -35 and -10 conserved sequences (5′-TTGACA-3′ and 5′-TATAAT-3′ respectively) was replaced with a binding site for TALE protein. TALE proteins consist of repeats where 12th and 13th amino acids can vary, the repeats are called the repeat variable diresidue (RVD). These RVDs have been shown to bind to DNA in a simple one-to-one binding code. A unique 18bp binding site was incorporated into the promoter, this binding site recruits a specific TALE protein called TALEsp1 that acts as a repressor (source). The TALEsp1 protein was designed to bind protein specifically at the binding site and are predicted not be bind anywhere in the genome (source). The position of the binding site can be readjusted to alter the extent of repression by the TALE protein.

Strain Construction

Strain construction: Aim: To clone the promoter in a level 0 MoClo backbone (pICH41233) . Procedure: The DNA sequence of the part was synthesized by IDT with flanking BpiI sites and respective MoClo compatible promoter overhangs. The cloning protocol can be found in the MoClo section below.

Modular Cloning

Modular Cloning (MoClo) is a system which allows for efficient one pot assembly of multiple DNA fragments. The MoClo system consists of Type IIS restriction enzymes that cleave DNA 4 to 8 base pairs away from the recognition sites. Cleavage outside of the recognition site allows for customization of the overhangs generated. The MoClo system is hierarchical. First, basic parts (promoters, UTRs, CDS and terminators) are assembled in level 0 plasmids in the kit. In a single reaction, the individual parts can be assembled into vectors containing transcriptional units (level 1). Furthermore, MoClo allows for directional assembly of multiple transcriptional units. Successful assembly of constructs using MoClo can be confirmed by visual readouts (blue/white or red/white screening). Click here for the protocol.

Note: The basic parts sequences of the Sci-Phi 29 collection in the registry contain only the part sequence and therefore contain no overhangs or restriction sites. For synthesizing MoClo compatible parts, refer to table 2. The complete sequence of our parts including backbone can be found here.

Table 1: Overview of different level in MoClo

For synthesizing basic parts, the part of interest should be flanked by a BpiI site and its specific type overhang. These parts can then be cloned into the respective level 0 MoClo parts. For level 1, where individual transcriptional units are cloned, the overhangs come from the backbone you choose. The restriction sites for level 1 are BsaI. However, any type IIS restriction enzyme could be used.

Table 2: Type specific overhangs and backbones for MoClo. Green indicates the restriction enzyme recognition site. Blue indicates the specific overhangs for the basic parts