Team:NEFU China/Project
Design
The major pathogens in spoiled yogurt include E. coli, Salmonella and Bacillus. If we can find a common feature among these bacteria, we may develop a method to detect them simultaneously. We searched literatures and discovered that a signal molecule, autoinducer 2 is a signaling molecule in quorum sensing, and also is common among these pathogenic bacteria.
Quorum sensing is a process of bacterial cell-to-cell communication involving the production and detection of extracellular signaling molecules called autoinducers. As the density of the bacterial population increases, so does the amount of secreted autoinducer molecules. When the concentration of the autoinducer reaches a critical threshold, it will be transported back into the cell and will activate or repress certain target genes. While most autoinducers are species specific, autoinducer 2(AI-2) is generated by many Gram-positive and Gram-negative bacteria and serves as a 'universal signal' for interspecies communication.
AI-2 is a byproduct of the Activated Methyl Cycle, which recycles S-Adenosyl-L-Methionine (SAM). As a main methyl donor in eubacteria, archeabacteria and eukaryotes, SAM is converted to S-Adenosyl-L-Homocysteine (SAH), which is subsequently detoxified by the Pfs enzyme (also called S-Adenosylhomocysteine Nucleosidase) to generate Adenine and S-Ribosyl-Homocysteine(SRH), the sole intracellular source of the substrate of LuxS. LuxS then produces the precursor of AI-2, 4,5-Dihydroxy-2,3-Pentanedione(DPD), during the conversion of SRH to Homocysteine (HCY).
Fig3. Activated Methyl Cycle
DPD can be converted from SRH by LuxS in the cytoplasm and then exported to culture medium, where DPD undergoes spontaneous cyclization to form AI-2. Depending on the bacteria, response to AI-2 can follow one of the two currently identified routes. In pathogens exemplified by Salmonella, AI-2 response involves ATP binding cassette transporter encoded by four LuxS-regulated (lsr) genes. lsrB encodes the periplasmic AI-2 binding protein, lsrC and lsrD encode two membrane channel proteins, and lsrA encodes the ATPase that provides energy for AI-2 transport. The extracellular AI-2 can bind LsrB to re-enter the cytoplasm and be phosphorylated by LsrK. Then the phosphorylated AI-2 can activate the lsr operon through binding the repressor protein LsrR and release it from the promoter. This will lead to the synthesis of LsrA,C,B, D and increase AI-2 entry.
Fig 4. AI-2 response in Salmonella typhimurium
AI-2 response pathway in Lactobacillus is different from that in pathogenic bacteria. So we will take the advantage of this difference and use the mechanism of AI-2 pathway in these pathogenic bacteria to build our detecting system. We choose Lactobacillus as our chassis. As beneficial bacteria, they are in food-grade and widely used in food fermentation. Lactobacillus bulgaricus can improve nutrient absorption and human gastrointestinal function, and inhibit the reproduction of pathogenic bacteria in guts. If fully developed into real products, our engineered Lactobacillus can be directly used in yogurt fermentation, which will make our detecting process even more convenient.
We cloned genes related to the AI-2 response in Salmonella and integrated these genes in Lactobacillus genomes. In our engineered bacteria, the lsrA, C, B, D genes will constitutively express to form the membrane transporter. We will clone the promoter sequence of the lsr operon and use it to drive the expression of the report gene. According to the previous studies, we have chosen an identified pigment in the Registry: the biobrick of amilCP (BBa_K592009). It encodes a blue pigment that can be recognized by naked eyes. Thus, when pathogenic bacteria express AI-2 molecules and secrete them extracellularly, these molecules can be transported into our engineered bacteria and trigger the expression of the report gene to produce the blue pigment.
Fig5. Working mechanism of our engineered bacteria
In our design, the PnisA promoters, which can be activated by nisin, are used to drive the expression of lsrA, C, B, D, R and K genes. Nisin is a anti-microbial peptide consisting of 34 amino acids. Because of its broad host spectrum, it is widely used as a food preservative.
The nisin-controlled gene expression (NICE) system is one of the most commonly used regulatory gene expression system of Gram-positive bacteria. In the natural situation, nisin binds to the receptor NisK, which activates NisR through phosphorylation. The activated NisR drives the nisA promoter. Sub-toxic amounts of nisin in the ng/mL range are sufficient to fully activate the otherwise tightly repressed promoter.
Fig6. Nisin induced regulation system
Previous studies indicate that the nisR and K are the only nis genes required for nisin-mediated signal transduction and PnisA promoter activation. However, our chassis, Lactobacillus bulgaricus Lb14, does not have nisR or nisK genes in its genome. In order to implement this strictly controlled expression system in such lactic acid bacteria, various nisR and K expression constructs were generated, and we picked pNZ9530 among them. Thus, apart from the plasmids for the expression of the essential parts in charge of AI-2 response, we also need to transform pNZ9530 into our engineered Lactobacillus.
This system for regulated gene expression shows many desirable characteristics: (1) nisin is an ideal molecule to be used as an inducer since it is already widely used in the food industry and can therefore be regarded as a food-grade inducer; (2) the protein expression levels are very high in this system; (3) the expression of the intergrated genes appears to be very tightly controlled, leading to undetectable protein expression in the uninduced state. So once our engineered bacteria are consumed as auxiliary starters in the yogurt fermentation, they will not express these genes modulated by PnisA, since the inducer nisin has been destroyed during digestion.
Plasmid construction
We have carefully considered the functions of these genes involved in AI-2 response, antibiotic resistance of expression vectors and plasmid incompatibility before transformation. In order to achieve the final goal of constructing the AI-2 response pathway of Salmonella in our engineered bacteria, we chose 3 types of plasmids with different replication origins and different antibiotics so that they can replicate in one host cell and provide convenience for screening post transformation. To visualize AI-2 existence, we chose a reporter gene, amilCP (BBa_K592009), from previous registered parts. This adds up to 7 plasmids for essential parts of AI-2 response system: (1) pNZ8148 is used to express lsrB, R and K; (2) pBBR1MCS-5 is used to express lsrA, C and D; (3) pHY300PLK is used to express the blue pigment, which is under the control of Plsr. We linearized these expression vectors and proceeded to stably integrating them into the genome of the host bacteria.
pNZ8148-lsrB, R, K
We chose pNZ8148 for the expression of those three genes. The replicon of the vector pNZ8148 is originally from the Lactococcus lactis plasmid pSH71. However, this replicon has a broad host range. Apart from Gram-positive bacteria, pNZ8148 can also replicate in E. coli, but require a recA+ strain like MC1061. It is chlorampenicol resistant.
pBBR1MCS-5 - lsrA, C, D
In Salmonella, AI-2 response involves an ATP binding cassette transporter. lsrC and lsrD encode the membrane channel proteins, and lsrA encodes the ATPase that provides energy for AI-2 transport.
Those three coding sequences were first inserted in pNZ8148. Afterwards, we used PCR to isolate them together with the upstream nisA promoters. And then we used double digestion and ligation to pBBR1MCS-5 to construct those three vectors.
pHY300PLK-plsr- amilCP
First, we isolated the promoter sequence of the plsr operon from the genomic DNA of Salmonella. Second, we isolated the coding sequence of amilCP together with the terminator from pET-14b, which was constructed by our iGEM team last year. After that, we spliced these two parts using SOE-PCR. Finally, the product was inserted to pHY300PLK using double digestion and ligation.
