Compositions and methods for identifying the essential genome of an organism
Compositions and methods are provided for the rapid and highly accurate identification of the entire essential genome of any organism under a given selection condition at a resolution of a few base pairs. An engineered transposon bearing an adapter sequence for ultra high throughput adaptor-based sequencing is employed for hyper-saturated transposon mutagenesis. Transposon junctions are subsequently isolated and collectively amplified through a shared parallel PCR strategy such that a second adaptor sequence is further incorporated into template DNA so that the first adaptor sequence and the second adaptor sequence flank the 5′ and 3′ regions of the sample DNA, respectively. Sample DNA is then sequenced in an ultra high-throughput adaptor-based DNA sequencer using adaptor primers. Transposon insertion sites are mapped onto the organism's genome, allowing for the algorithmic identification of essential genetic elements based on genomic transposition frequency.
1. A method for determining genetic elements of an organism's genome, the method comprising:
performing hyper-saturated transposon mutagenesis to generate an engineered transposon comprising a Tn5 O-end insertion primer having the sequence of SEQ ID NO: 3, and a Tn5 I-end primer having the sequence of SEQ ID NO. 2;
said hyper-saturated transposon mutagenesis having a transposition density from about 8 to 100 bp;
selecting for viable mutants in the engineered transposon under a given selection condition;
pooling the selected viable mutants;
isolating transposon junctions through a shared parallel PCR strategy utilizing a first primer that is transposon specific, at least one semi-arbitrary primer, and at least one adaptor sequence primer, wherein the at least one semi-arbitrary primer is selected from the group consisting of SEQ ID NO. 4, SEQ ID NO. 5, and SEQ ID NO. 6;
sequencing the isolated transposon junctions in the ultra high-throughput adaptor based DNA sequencer;
mapping transposon insertion sites onto the organism's genome; and identifying the genetic elements based on frequency, locations and insertion orientation of the mapped transposon insertion sites.
2. The method of claim 1 , wherein the engineered transposon further comprises an inducible outward pointing promoter.
3. The method of claim 1 , wherein the engineered transposon further comprises a first ribosomal binding site and a start codon located between an outward pointing promoter and a transposon end.
4. The method of claim 3 , wherein the engineered transposon further comprises a second ribosomal binding site preceding the start codon.
5. The method of claim 1 , wherein the engineered transposon is compatible with a Tn5 transposase.
6. The method of claim 2 , wherein the outward pointing promoter is a Pxyl promoter.
7. The method of claim 1 , wherein said parallel PCR comprises a nested PCR approach.
8. The method of claim 1 , wherein the at least one adaptor sequence primer anneals to a first adaptor sequence of the engineered transposon to provide 5′ to 3′ amplification; and the at least one semi-arbitrary primer comprises a defined 3′ penta- nucleotide sequence, an interspacing 10 bp long arbitrary sequence, and the 5′ second adaptor sequence to provide 5′ to 3′ amplification.
9. The method of claim 8 , wherein the at least one semi-arbitrary primers anneal on average from every 1000 bp to 300 bp throughout the organism's genome.
10. The method of claim 8 , wherein the at least one semi-arbitrary primer employed following a first round of PCR amplification comprises a first semi-arbitrary primer which anneals to the first adaptor sequence and a second semi-arbitrary primer which anneals to the 5′ second adaptor sequence.
11. The method of claim 1 , wherein an algorithm maps transposon insertion sites onto the organism's genome and identifies genetic elements based on genomic transposition frequency.
12. The method of claim 11 , wherein the algorithm identifies non-disruptable noncoding genome elements of at least 90 bp in length.
13. The method of claim 11 , wherein the algorithm detects promoter regions of open reading frames (ORFs) by measuring the distance between an annotated start codon of the ORF and a first anti-sense upstream insertion.
14. The method of claim 13 , wherein the algorithm classifies ORFs harboring an essential promoter region fully including one or more upstream ORFs as essential operons.
15. The method of claim 11 , wherein the algorithm detects essential promoter regions of essential RNA elements by measuring a distance between an annotated transcriptional start of an RNA element and a first anti-sense upstream insertion.
16. The method of claim 11 , wherein the algorithm calculates p-values for essentiality.
17. The method of claim 11 , wherein the algorithm identifies cytotoxic genetic elements by identifying genomic regions with an insertional bias in an antisense orientation.
18. The method of claim 1 , wherein the at least one adaptor sequence primer is selected from the group consisting of SEQ ID NO. 7 and SEQ ID NO. 8.