Stanford/BIOE44:Module3:Day2:atrazine

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Atrazine Sensor Project

Authors: Claire Durkin, Frank Li, Sanjay Saraf

We propose 4 new BioBrick parts compatible with Assembly Standard 10:

Project Description: Pseudomonas sp. ADP digests atrazine under nitrogen starvation conditions. atzABC are constitutively expressed and convert atrazine to cyanuric acid. atzDEF convert cyanuric acid to carbon dioxide and ammonia, which the cell digests. The atzDEF operon is regulated by atzR, a protein that autoregulates its production in the same region. GlnK is produced under nitrogen limitation conditions and induces expression of atzDEF.

Here we reproduce the parts of this system, with the intent of creating a general atrazine sensor. Because Pseudomonas sp. ADP is hard to manipulate, we will be working in Pseudomonas putida KT2440.

1. reverse complement of atzR from Pseudomonas sp. ADP (969 bp) 2. reverse complement of constitutive promoter BBa_J23101 (35 bp) 3. atzDEF operator region from Pseudomonas sp. ADP (96 bp) 4. glnK from Psuedomonas putida KT2440 (339 bp)

Part 1: 1. reverse complement of atzR (969 bp) (bp #99885..100853 on Psuedomonas sp. ADP http://www.ncbi.nlm.nih.gov/nuccore/13937422)

Short Description: Reverse complement of the coding sequence for atzR, the regulator protein in the atzDEF pathway, in accordance with BioBrick assembly 10.

Sequence: gaattcgcggccgcttctagagtcacgttgcattgtgggtcgtatcagcgagcttgccggcgacgaactccgcaaatgccgccgatgccacaggcagcaccctctcacgcaatgcgaccagtacga cgcgtccggaagccaggctgcgctcgtcgattggaattgcaacctcaccctccgtggaaccagcaccgatctcgatctgaaagctcaccccaccggtttcgcgggcaaaaccgcgcatcatttcgt aggaattactgaccagttgaggccgcggtcgagctgatgatttgtcgaataactcgtccaacacgttgcgcccggagagactgctgtccggtagcgcaagggggtagtccaggcaatctttcagac gcagactcgtacgcttcgcgagcggatggtcggaagcaacgacggcacagatgcgttgccgcgcttgtgcaatgacagtcaaaccgcgcaggtccgggggattgaagaccagcgccaggtcggccg cgaaatccgtcacggcgagaacagcacgctcgcggtccagcacctttacgtcgaaggcaatacctggacgttgggcctggaacgcgtgtattacgcggggcaggaactccggagccagcgcctggc tggctgccaatgtcacacggccgcgtttcatgccgctgagatcctggatctgtgactggacttgttccagatcggcattgcggcgacgagcgtaggcaacgaacagttcgcctgccgcagtcaggc gtacaccacgcggcagacgctcgaaaatcggcgtacctaactcgtattccagatcctggacgcggcgatttaccgctgatgcggcgacgtgcagctgttctgcggcggcccgaatggagccgcagc gagccacggcatcgatgtaatgaagaaagcgtaaatgttgcataggtggtcgaagtaaaaaggatggaatagagatggcctgtatcgctgacggccgctgtgcccgcattactagtagcggccgct gcag


Part 2: 2. reverse complement of constitutive promoter BBa_J23101 (35bp) (from http://partsregistry.org/Part:BBa_J23101:Design)

Short Description: Reverse complement that will be used for the reverse complement CDS of part 1.

Sequence: gaattcgcggccgcttctagaggctagcataatacctaggactgagctagctgtaaatactagtagcggccgctgcag

Part 3: 3. atzDEF operator region (96 bp) (bp #100851..100946 on Psuedomonas sp. ADP http://www.ncbi.nlm.nih.gov/nuccore/13937422)

Short Description:  ??

Sequence: gaattcgcggccgcttctagagcatgcgagtcaaagcaagatcggtgccggatcggcaccagttaggtcggaaaaaggcggcagtcaagtgcgcagggcggcgttaagcttgaacgaatactagta gcggccgctgcag

Part 4:

4. glnK from Pseudomonas putida KT2440 (339 bp) (bp #5967730..5968070 on Psuedomonas putida KT2440 http://www.ncbi.nlm.nih.gov/nuccore/NC_009512)

Short Description:  ??

Sequence: gaattcgcggccgcttctagatgaagctagtcacagccatcatcaagccgttcaagctggacgacgtgcgcgagtcgctgtcggaaatcggcgtgcagggcatcaccgtcaccgaagtcaaaggttt cggtcggcagaagggccacaccgagctgtatcgcggtgctgaatatgtggtcgatttcctgcccaaggtgaagatcgatgtcgccatcgatgacaaagaccttgatcgggtaatcgaagccatcacc aaggcagccaacaccggcaagatcggtgacggcaagattttcgtggtgaatctggagcaggcgatccgcatccgtaccggcgaaaccgataccgacgcgatctaatactagtagcggccgctgcag

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