Team:Uppsala University/Project

Team Uppsala University 2012 is dedicated to combating the rising antibiotic resistance in bacteria by means of synthetic biology. Old and well-known antibiotics are quickly becoming ineffective as resistance genes are spreading. Scientist around the world struggle with varying success to develop new antibacterial substances. But do we really have to abandon classic antibiotics? Team Uppsala University begs to differ, we believe new methods will allow us to combat the resistance itself, and make the bacteria once again sensitive to old drugs.

Working with real-world resistance genes isolated from ESBL outbreaks at Swedish hospitals, we are developing anti-resistance systems active at three different levels: DNA level, transcriptional level and translational level. Our systems will be delivered to the target bacteria using an engineered phage and/or a conjugative plasmid.

At DNA level, we will develop a method for permanent removal of plasmids from bacteria. Using TAL Effector Nucleases, we will be able to target and cut individual resistance genes.

At transcriptional level, we will use synthetic super-repressors to repress transcription of resistance genes and native defense mechanisms in bacteria.

At translational level, we will construct a modular large-scale screening system for sRNA:s and use it to find strongly silencing RNA sequences against three common resistance genes.

Antibiotic resistance genes are commonly carried on plasmids, which aid their spreading among bacteria. When a bacteria has acquired an resistance plasmid, it will have an evolutionary advantage over it's peers even at very low antibiotic concentrations. We are investigating methods to radically increase plasmid loss rate among bacteria by inducing plasmid-cutting enzymes in the bacteria. We are using TAL Effector Nucleases, a new fusion protein originating from a plant pathogen DNA binder and a FokI DNA cleavage domain

In the same was as infectious bacteria tries to make the human body a more habitable place for themselves, we can also employ methods to make bacteria more sensitive to antibiotic agents.

By targeting genetic networks and increasing transcription of genes that aid antibiotic influx to the cell, lower production of enzymes involved in metabolition of antibiotics and other similar functions, we will increase bacterial susceptibility to antibiotics.

The well-known use of RNAi in eukaryotes have a lesser known cousin in bacteria: small RNA (sRNA). It has been shown that sRNA:s can induce or repress transcription by binding to the RBS or ORF beginning of the mRNA. However, the behaviour of a sRNA against a given mRNA is far less predictable than in RNAi. It is generally not possible to design a silencing sRNA de novo.

We are building a high throughput screening-selection system to find strongly repressing sRNA:s. Using this, we will be able to screen random sequences at a hundredfold faster rate than in previous studies. We count on finding strong silencers for three clinically important resistance genes.

The screening system will be modular and can also be applied by other researchers to any gene of interest.