Search for pyrrolysine synthesizing gene before predicting PylProt

[keuv-grvl]

Few proteins are know to be necessary for pyrrolysine synthesis. Searching for these proteins may prevent the predition of PylProt in genome which are not able to synthesize pyrrolysine.

• [ ] List known proteins/genes
• [ ] Choose between Diamond and Hmmer approach
• [x] Investigate tRNA prediction to locate pylT
• [ ] Search them in the input genomes

[keuv-grvl]

Use of tRNA prediction

tRNAscan-SE (http://lowelab.ucsc.edu/tRNAscan-SE/) can predict the tRNA with the CTA anticodon (TAG codon) using the following parameters:

• Input : https://www.ncbi.nlm.nih.gov/nuccore/AY064401.1?report=fasta
• Sequence source: mixed (general tRNA model)
• Search mode : default

Here is the pyl genes description : https://www.ncbi.nlm.nih.gov/pubmed/12029131 Here is the associated pyl gene sequences : https://www.ncbi.nlm.nih.gov/nuccore/AY064401 Here is the visualization of the predicted tRNA: http://lowelab.ucsc.edu/tRNAscan-SE/structs/drwtrna19409.gif

I propose the following strategy:

1. Search for tRNA with CTA anticodon
2. If found (probably), search for the mandatory pylS (a.k.a. pylRS) (it charges the tRNA with a Pyl)
3. If found, confirm by searching for pylB, pylC and pylD (involved in Pyl synthesis)
4. If "confirmed enough", predict Pyl-containing proteins as usual

• Pros:
  • tRNA prediction is easy
  • It may reduce the pyl genes search space (around 10kb around the tRNA)
• Cons:
  • Another dependency
  • It may be faster to simply search for PylS, PylB, PylC and PylD in the whole genome

In all cases, finding a gene cluster with pylT, pylS and pylB/C/D would strongly suggest the possibility of Pyl-containing proteins.