author: Sofie Thijs ([email protected])
Two basic types of TEs are known in bacteria:
-Insertion Sequence (IS) elements
-transposons (composite and complex)
Insertion Sequences are short pieces of DNA that move about in the genome.
IS element insertion disrupts gene function.
All genes downstream from insertion in an operon will be disrupted.
The mutation is said to be polar.
All IS elements are flanked by inverted repeats.
In Japanese hospitals in the 1950's a strain of Shigella bacteria appeared that was resistant to a wide array of antibiotics. The multiple-drug resistance phenotype was inherited as a single package. Other bacterial species could obtain this resistance via transformation. The genes were being spread via a self-replicating episome that could replicate freely in the cytoplasm or insert into the bacterial chromosome (and replicate with it) It was later dubbed a transposon.
A bacterial transposon can:
- excise from a host gene without disrupting it (precise excision)
- excise and take some host DNA along with it (imprecise excision)
Imprecise excision is far more common than precise excision.
Use the NCBI database and search for transposons and insertion elements in:
- Pseudomonas putida F1
- Pseudomonas putida HS1
What is the size of the bacteria genome of Pseudomonas putida F1?
Compare with other bacterial strains?
Can you explain differences in genome size based on lifestyle? where was the bacteria isolated from? Soil, gut, plant rhizosphere?
Was your bacteria infected in the past with a phage? Use the Phaster database
Select a bacterium of interest, and search if it has CRISPRcas9 systems using this database? How many phage elements has the strain incorporated?