AQ Data Collection and Project Outline

Date: 4-17-19

• Rationale
  • The rational for this lab is to continue gathering data to use for our independent research project as well as plan an outline for the project.
• Procedure
  1. DNAMaster was used to determine the start codon used for each gene by each phage in the AQ cluster.
  2. Findings were recorded on a Google Sheets page and tendencies were calculated.
  3. The group convened and discussed the parts of the project that needed to be worked on and an outline was formed.
• Results
  • The outline was made as follows:
  • Title:
    Subclustering of bacteriophage determined by start codon preference
    Guiding Question:
    Every phage has a different tendency to choose one of the following base pair sequences as start codons: ATG, GTG, or TTG. Given the percentage of each codon’s use in phages from clusters that infect Arthrobacter, can this preference be used to further cluster phages within existing clusters?
    Abstract:
    Start codons are nucleotide sequences that are found at the beginning of protein-coding genes of DNA. In bacteriophage specifically, they start with ATG, GTG or TTG start codons. In our experiment, we looked at the preferred start codons of bacteriophage that infect Arthrobacter in different clusters to examine the percentage of each start codon preferred in and between clusters. We found that within clusters, there were repeated patterns of preferred start codons that were unique to the cluster. In the AM cluster, the last four genes preferred the start codons GTG, GTG, ATG, and ATG in all 14 phages we looked at. With these discoveries, we can more easily characterize and group phages into their clusters based on their start codons as well as use these known patterns to reassure the clusterization of the phage.
    List of tools used:
    PhagesDB
    DNA Master
    Excel
    Splitstree
    Introduction (Background Information):
    In all DNA, genes start with specific three nucleotide sequences that promote transcription by a ribosome. These sequences are known as start codons and organisms can have specific preferences in start codons. Protein-coding genes of bacteriophages all start with either an ATG, GTG, or TTG start codon. On the Guiding Principles of Bacteriophage Genome Annotation, it mentions that, “… TTG is rarely used (about 7% of all genes). ATG and GTG are used at almost equivalent frequencies.”
    Types of Data Collected:
    Phage genomic sequences for clusters AM, AR, AQ
    Phylogenetic interrelatedness between phages within and between clusters
    Start codons for each gene of each phage within each cluster sampled
    Start codon usage percentage for the above phages
    Results (to date):
    Similarities of phages in each cluster were found. For example for all AM cluster phages the start codons for the last four genes were GTG ,GTG, ATG, and ATG. Phage Molivia, which belongs to AQ Cluster appears to be more closely related to AR and AM phages rather than to other AQ cluster phages. The average ATG, GTG, and TTG percentage within clusters don’t exactly align with the guiding principles mentioned by PhagesDB. The percentage of ATG and GTG were not similar; ATG was the most predominantly preferred start codon.
    Conclusions:
    No conclusions have been made to date
  • The following is an example of the start-codon preferences recorded for the AQ phage Anansi
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• Future Plans
  • The next step is to continue gathering data for the AU cluster and compare the start codon data to phylogenetic data for each cluster.