Part:BBa_K1484319:Design

P_Ni1, marchantia promoter

Assembly Compatibility:

• 10
  INCOMPATIBLE WITH RFC[10]

  Illegal XbaI site found at 1012
  Illegal XbaI site found at 1330
  Illegal XbaI site found at 1426
  
• 12
  COMPATIBLE WITH RFC[12]
• 21
  INCOMPATIBLE WITH RFC[21]

  Illegal XhoI site found at 412
  Illegal XhoI site found at 790
  
• 23
  INCOMPATIBLE WITH RFC[23]

  Illegal XbaI site found at 1012
  Illegal XbaI site found at 1330
  Illegal XbaI site found at 1426
  
• 25
  INCOMPATIBLE WITH RFC[25]

  Illegal XbaI site found at 1012
  Illegal XbaI site found at 1330
  Illegal XbaI site found at 1426
  
• 1000
  COMPATIBLE WITH RFC[1000]

Design Notes

The removal of illegal restriction sites was considered but not completed due to direct interaction of the DNA with regulatory proteins. Also, it was ensured that the region selected for this part was directly upstream of the first ATG of the gene used to identify the promoter sequence. This was so that the 5' UTR, that is vital in plants, was maintained.

Source

This part was found by screening the genome of the Marchantia polymorpha Cam strain maintained by the Haseloff lab for homologues to a Nitrate Transporter protein in A. Thaliana known as AtNRT2.2 or ACH2. Transcription is thought to be induced by nitrate (NO-3). Matches to the protein CDS sequence were found using Geneious to perform a tblastn search on the genome scaffolds. Predicted genes that contained hits graded above 30% and with at least 40% congruence to mRNA transcript sequences were shortlisted. The best gene candidates (judged according to number and distribution of hits along its length, and supporting mRNA sequence) formed the basis for our predicted promoters. This part was identified as a 2kb region upstream of the first ATG of such a gene.

References

Forde BG. 2000. Nitrate transporters in plants: structure, function and regulation. (BBA) – Biomembranes 1465(1-2):219-235. GenBank, NIH. Accession no: AF019749.1