Team:SDU-Denmark/Tour52

Characterization

“And by what, O Socrates, is the soul nourished?” - Hippocrates
“By knowledge, of course, I said.” - Socrates

Characterization of our biobricks is a chance for us to prove that our design works as intended. We invite you along on a journey through our attempts to obtain proof of concept; to show that Bacteriorganic Rubber is a true possibility. This page will slowly guide you through our results, but keep in mind that not everything is presented below. For all the details, consult our protocol page, where you will find a comprehensive picture of our project.

Characterization of LacI/Plac

Characterization of AraC/Para

Figure X. The HRT2 gene is under the control of the arabinose promoter (which is arabinose inducible). Therefore we assayed if we are in fact capable of inducing the expression by addition of arabinose, and that expression is shut down prior to induction. The assay was carried out by measuring the mRNA levels of HRT2 using the northern blotting technique.

To test if overexpression of AraC improved expression control, devices with and without the araC device was assayed. Duplicates of MG1655 strains carrying either pSB1C3-Para-HRT2 or pSB1C3-Pcon-araC-term-Para-HRT2 were grown to late-exponential phase: OD₆₀₀=0.8. At this OD the strains were induced with 0.2 % arabinose at time t=0 min, and samples were taken at times: -2 min, 15 min, and 30 min. Total RNA purified from the samples were run on a gel, blotted onto a membrane, and hybridized with probes specific for HRT2 mRNA and 5S rRNA (loading control), respectively.

The results proves that we are capable of inducing our HRT2 devices with arabinose. There is only little expression before induction and within the first 15 min the expression is at its maximum. Overexpression of AraC does not seem to have any effect on the expression levels after 15 min compared to natural levels of AraC, though we cannot conclude that it has no effect in the minutes prior to 15 min after induction (Fig. X).

Our obtained experience has been added to the experience of the part encoding the arabinose promoter on parts registry.

Characterization of dxs (B. subtilis)

Functionality assay
To optimize the flow through the MEP pathway, the dxs gene was overexpressed, and thus increased levels of IPP and DMAPP is expected. To examine if the overexpression led to an increase in substrate for rubber synthesis we attempted to assay the levels of DMAPP using a headspace gas chromatography (GC) approach.

DMAPP was first hydrolyzed in acid to the volatile hydrocarbon isoprene, and the gas was subsequently analyzed with headspace GC. A linear relationship between amount of detected isoprene and DMAPP concentration has previously been established. Source: Alison J. Fisher et. al; Nonradioactive Assay for Cellular Dimethyllyl Diphosphate We were capable of making a standard curve when reacting DMAPP with acid for only 2 min (instead of the 60 min as done in the previous study) (fig X). At this time point it seemed that we had optimal peak detection for standard solutions. We were, however, not capable of detecting isoprene in even high concentrations of bacterial samples treated with acid for either 2, 30, 60 or 90 min.

Figure 7. Optimization of the procedure needs to be done before a characterization of the dxs bricks can take place using this approach. We suspect that the complexity of the bacterial samples is too high, and thus the reaction does not take place as fast as might be necessary for detection in our setup. Sonication of bacterial samples with and without addition of standard DMAPP, and subsequent measurements might shed some light on this hypothesis. However, it should be noted that the GC wasn’t fully functional during the test period, consequently leading to broader peaks and thus lowered the sensitivity of the instrument. On the 3rd of October we received a mail from Professor Lars Porskjær Christensen, Department of Chemistry-, Bio- and Environmental Technology, University of Southern Denmark:

...The GC has now been repaired and the sensitivity has been improved considerably. The GC-peaks should be very sharp now. This may be the reason that you have not observed any release of isoprene from your samples...MailTranslated from danish”.

Unfortunately, with only 2 days left before wiki-freeze, there was no time for another round of testing.

(Growth Experiment
Carrying the dxs devices and expressing the gene could impair the growth, and hence be important in production purpose. To test if the growth of MG1655 bacteria is impaired when carrying and expressing our dxs devices, we measured the growth rate with OD₆₀₀ measurements.

2 triplicates of MG1655 carrying no vector, empty pSB1C3 vector, pSB1C3-Plac-dxs (B. subtilis), pSB1C3-Pcon-lacI-Plac-dxs (B. subtilis), or pSB1C3-Pcon-lacI:LVA-Plac-dxs (B. subtilis) were started from ONC at time 0 hours, OD₆₀₀=0.005, and grown at 37oC and at 180 rpm. OD₆₀₀ measurements were done every half hour, and 1 of each triplicate was induced at time 2.5 hours. All strains grew at the same pace and induction didn’t impair growth rate (Fig X).

Characterization of the Prenyltransferase