Rationale

Today we will finish data collection and complete our final abstract for the independent research project.

Procedure

• Each AM specific gene in NapoleonB’s genome was BLASTed on NCBI
• Results were recorded if it hit was of low %GC content
• Our abstract was edited and revised to account for the comments made previously. The results presented in the abstract were updated to match the data collection conducted today.
• Slides for the final presentation were created.

Results

Abstract: Arthrobacter is a gram-positive soil bacteria that has a guanine and cytosine nucleotide composition (%GC) of 63.41% in its genome. NapoleonB and other Arthrobacter AM phages have a comparatively lower %GC of 45.3% and 45.2%, respectively. This is interesting because phages tend to have similar %GC compositions relative to their host bacteria. This project tests the hypothesis that lateral gene transfer is responsible for this discrepancy in %GC. %GC3 analyzes the GC content of the third codon, which is significant in the analysis of codon usage. In order to test this hypothesis, phams were used to separate NapoleonB’s genes into AM specific genes and genes shared with phages outside of the AM cluster. The percent GC and GC3 were analyzed for each gene and compared using Student’s T-test. AM specific genes were compared using NCBI BLAST, to search for matches from host or viruses with low %GC. The %GC of AM-specific genes was significantly lower than non-AM specific genes (P= 0.0029). However, no significant difference was seen between the GC3 values. 51 AM specific genes were checked for BLAST hits with low %GC species, and 12 genes had matches. The evidence indicates that lateral gene transfer from low percent GC bacteria is a potential cause of low %GC content in AM cluster phages, compared to their host. Future analysis of other sequenced genomes could help to strengthen this hypothesis.

An example of results for a single AM-specific gene is shown below:

• Gene 6
  • Clostridium
    • Hypothetical Protein
    • E value: 3 x 10^-7
    • Identity: 34.34
  • Candidatus Moranbacteria bacterium
    • Hypothetical Protein
    • E value 3 x 10^-14
    • Identity: 42.70

Conclusion/Next Steps

It was concluded that lateral gene transfer could be a probable cause for the exceptionally low %GC content in AM cluster phages and genes. Next, we will continue working on our final presentation.