Regulatory transcription factor (CooA)-driven carbon monoxide partial pressure sensing whole-cell biosensor

We designed and constructed a whole-cell biosensor capable of detecting the presence and quantity of carbon monoxide (CO) using the CO regulatory transcription factor. This biosensor utilizes CooA, a CO-sensing transcription regulator that activates the expression of carbon monoxide dehydrogenase (CODH), to detect the presence of CO and respond by triggering the expression of a GUS reporter protein (β-glucuronidase). The GUS reporter protein is expressed from a CO-induced CooA-binding promoter (P_cooF) by CooA and enables the effective colorimetric detection of CO. An Escherichia coli strain used to validate the biosensor showed growth and GUS activity under anaerobic conditions; this study used the inert gas (Ar) to create anaerobic conditions. The pBRCO biosensor could successfully detect the presence of CO in the headspace. Moreover, the GUS-specific activity of pBRCO according to the CO strength as partial pressure followed Michaelis-Menten kinetics (R² = 0.98). It was confirmed that the GUS-specific activity of pBRCO increased linearly up to 30.39 kPa (R² = 0.98), and thus, a quantitative analysis of CO concentration (i.e., partial pressure) was possible.

Tinkering Cis Motifs Jigsaw Puzzle Led to Root-Specific Drought-Inducible Novel Synthetic Promoters

Following an in-depth transcriptomics-based approach, we first screened out and analyzed (in silico) cis motifs in a group of 63 drought-inducible genes (in soybean). Six novel synthetic promoters (SynP14-SynP19) were designed by concatenating 11 cis motifs, ABF, ABRE, ABRE-Like, CBF, E2F-VARIANT, G-box, GCC-Box, MYB1, MYB4, RAV1-A, and RAV1-B (in multiple copies and various combination) with a minimal 35s core promoter and a 222 bp synthetic intron sequence. In order to validate their drought-inducibility and root-specificity, the designed synthetic assemblies were transformed in soybean hairy roots to drive GUS gene using pCAMBIA3301. Through GUS histochemical assay (after a 72 h 6% PEG6000 treatment), we noticed higher glucuronidase activity in transgenic hairy roots harboring SynP15, SynP16, and SynP18. Further screening through GUS fluorometric assay flaunted SynP16 as the most appropriate combination of efficient drought-responsive cis motifs. Afterwards, we stably transformed SynP15, SynP16, and SynP18 in Arabidopsis and carried out GUS staining as well as fluorometric assays of the transgenic plants treated with simulated drought stress. Consistently, SynP16 retained higher transcriptional activity in Arabidopsis roots in response to drought. Thus the root-specific drought-inducible synthetic promoters designed using stimulus-specific cis motifs in a definite fashion could be exploited in developing drought tolerance in soybean and other crops as well. Moreover, the rationale of design extends our knowledge of trial-and-error based cis engineering to construct synthetic promoters for transcriptional upgradation against other stresses.

Gold nanoparticle biosensors, a novel application in gene transformation and expression

The conventional techniques of PCR, Southern blot, northern blot, in situ hybridization, and RNase protection assay have long been used to investigate transformation and expression of genes, but most of them are time-consuming and have relatively low sensitivity. In recent years, applying biosensors for molecular identification of biomolecules has been expanding significantly. Hence in this study, Zabol melon was used as a model plant to introduce new DNA and RNA-based biosensors for confirming gene transformation and expression. First, the melon seeds were grown in vivo and Agrobacterium tumefaciens LBA4404 was used to introduce GUS reporter gene to the plant. In order to analyze GUS gene transformation and expression, probes were designed based on DNA, RNA, and cDNA of GUS gene sequence. Then, the analysis was performed using probes attached to gold nanoparticles to observe color change of the solution in presence of the target biomolecules. Hybridization of the probes with target molecules was evaluated at a wavelength of 400-700 nm and maximum change was observed in the wavelength range of 550-650 nm. In addition, lower detection limit of the assay was 0.25 ng/μL and linear regression showed the relationship between different concentrations of the genomic DNA and absorbance. Consequently, results showed that application of detectors attached to gold nanoparticles for investigation on gene transformation and expression is more rapid, specific and economic compared to the biochemical and molecular techniques. These tests can be carried out with initial optimization at research centers using the least facilities; hence there will be no need for special equipment.

Establishment of transgenic Rhazya stricta hairy roots to modulate terpenoid indole alkaloid production

Transgenic hairy roots of R. stricta were developed for investigation of alkaloid accumulations. The contents of five identified alkaloids, including serpentine as a new compound, increased compared to non-transformed roots. Rhazya stricta Decne. is a rich source of pharmacologically active terpenoid indole alkaloids (TIAs). In order to study TIA production and enable metabolic engineering, we established hairy root cultures of R. stricta by co-cultivating cotyledon, hypocotyl, leaf, and shoot explants with wild-type Agrobacterium rhizogenes strain LBA 9402 and A. rhizogenes carrying the pK2WG7-gusA binary vector. Hairy roots initiated from the leaf explants 2 to 8 weeks. Transformation was confirmed by polymerase chain reaction and in case of GUS clones with GUS staining assay. Transformation efficiency was 74 and 83% for wild-type and GUS hairy root clones, respectively. Alkaloid accumulation was monitored by HPLC, and identification was achieved by UPLC-MS analysis. The influence of light (16 h photoperiod versus total darkness) and media composition (modified Gamborg B5 medium versus Woody Plant Medium) on the production of TIAs were investigated. Compared to non-transformed roots, wild-type hairy roots accumulated significantly higher amounts of five alkaloids. GUS hairy roots contained higher amounts two of alkaloids compared to non-transformed roots. Light conditions had a marked effect on the accumulation of five alkaloids whereas the composition of media only affected the accumulation of two alkaloids. By successfully establishing R. stricta hairy root clones, the potential of transgenic hairy root systems in modulating TIA production was confirmed.

A cis-element containing PAL-box functions in the expression of the wound-inducible peroxidase gene of horseradish

 In an attempt to understand the molecular basis of plant responses to wounding, we have investigated the transcriptional regulation of the wound-inducible prxC2 gene, which encodes horseradish peroxidase. In the previous work, 5'-deletion analysis revealed that a cis-element involved in the expression of the prxC2 gene is located at a position between -296 and -283 bp from the translation start site and contains a G-box sequence. We have also reported that a trans-acting factor, TFHP-1, can bind to the G-box sequence in this cis-element. Although the antisense RNA of TFHP-1 suppressed the expression of a prxC2 promoter-GUS chimeric gene in tobacco protoplasts, the sense RNA of TFHP-1 could not enhance this expression. These results suggested that other elements function in the expression of the prxC2 gene, and therefore additional deletion analysis of the promoter was performed with a transient expression system in cultured tobacco cells. Consequently, the second cis-element was found at a position between -177 and -134 bp from the translation start site of prxC2. This second cis-element contains a sequence similar to a PAL-box, and a nuclear protein possibly binds to it through the PAL-box sequence.