(r5) Barrick Lab :: ProtocolsAraMarker

---+ The Arabinose (Ara) Genetic Marker

---++ Background

The _Escherichia coli B_ strain REL606 has a mutation in the _araA_ gene that renders it unable to utilize the sugar L-arabinose. Strain REL607 is a spontaneous revertant of REL606 containing a single point mutation that restores the ability to metabolize L-arabinose. This marker is selectively neutral in a variety of conditions and can be used to determine the relative frequencies of Ara- (REL606-derived) and Ara+ (REL607-derived) cells in a mixture for competition assays or marker divergence experiments. Ara- and Ara+ cells form red and white colonies, respectively, on tetrazolium arabinose (TA) plates, because utilization of the sugar rather than only the tryptone and yeast extract components of this medium causes the excretion of acetic acid which acidifies the area surrounding the colony, changing the tetrazolium indicator color from red to white.

| *strain* | *marker* | *<i>araA</i> sequence* | 
| REL606 | Ara- | 92D (GAC) |
| REL607 | Ara+ | 92G (GGC) |

Selections for arabinose utilization from REL606 is known to also produce  Ara+ revertants that have an _araA_  92A (GCC) sequence.

---++ Selection of Ara+ Revertants from Ara- Strains Derived from REL606

For a non-mutator strain. Grow a 10 ml culture in LB or DM1000 media. Spin down to concentrate cells and plate them all on a minimal arabinose (MA) plate. Grow for 48 hours, pick an Ara+ colony. Streak on an MA plate to verify and purify clone. Grow an overnight culture in LB or DM1000 and freeze down.

---++ RFLP Assay for Verifying the REL607 Mutation

Perform a standard PCR reaction from whole cells with these two primers.

| *Primer* | *Coordinates* | *Sequence* |
| REL256 | REL606/70660-70683 | 5'-CCGATACGCTCATGGGCTTGTTTA-3' |
| REL257 | REL606/71177-71154 | 5'-CTGCCCAGGCCGTTGCGACTCTAT-3' |

Cut with _HaeII_ and run on a 3% agarose gel. Ara<sup>+</sup> with the REL607 reversion mutation will show a shift of the 226 bp band down into the composite ~200 bp band because this mutation recreates a restriction site.

| *Strain* | *Marker* | *RFLP Fragment Sizes* | 
| REL606 | Ara- | 226, 197, 72 (bp) |
| REL607 | Ara+ | 207, 197, 72, 19 (bp) |

Barrick Lab > ProtocolList > ProtocolsAraMarker

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JeffreyBarrick

Topic revision: r5 - 2010-06-10 - 18:13:56 - Main.JeffreyBarrick

Lab.ProtocolsAraMarker moved from Lab.ProceduresSelectingArabinoseMarkerRevertants on 2010-06-10 - 18:13 by Main.JeffreyBarrick -