- Research article
- Open Access
Identification and use of the sugarcane bacilliform virus enhancer in transgenic maize
© Davies et al.; licensee BioMed Central. 2014
- Received: 22 August 2014
- Accepted: 27 November 2014
- Published: 19 December 2014
Transcriptional enhancers are able to increase transcription from heterologous promoters when placed upstream, downstream and in either orientation, relative to the promoter. Transcriptional enhancers have been used to enhance expression of specific promoters in transgenic plants and in activation tagging studies to help elucidate gene function.
A transcriptional enhancer from the Sugarcane Bacilliform Virus - Ireng Maleng isolate (SCBV-IM) that can cause increased transcription when integrated into the the genome near maize genes has been identified. In transgenic maize, the SCBV-IM promoter was shown to be comparable in strength to the maize ubiquitin 1 promoter in young leaf and root tissues. The promoter was dissected to identify sequences that confer high activity in transient assays. Enhancer sequences were identified and shown to increase the activity of a heterologous truncated promoter. These enhancer sequences were shown to be more active when arrayed in 4 copy arrays than in 1 or 2 copy arrays. When the enhancer array was transformed into maize plants it caused an increase in accumulation of transcripts of genes near the site of integration in the genome.
The SCBV-IM enhancer can activate transcription upstream or downstream of genes and in either orientation. It may be a useful tool to activate enhance from specific promoters or in activation tagging.
- Transgenic plant
- Transient assay
Enhancers are DNA elements that are able to increase transcription from other promoters whether they are placed upstream or downstream of transcription start sites and their promoter enhancing activity is independent of orientation relative to the transcription start site ,. Enhancers that are effective in plants have been isolated from genes of plants as well as from genes of viruses and bacteria that infect plants. These include enhancers from the tobacco tCUP ,, the pea plastocyanin , the Cauliflower mosaic virus 35S (CaMV 35S) ,, the Figwort mosaic virus  and the Agrobacterium tumefacians 780 , and ocs promoters .
Plant virus-derived promoters have been shown to be a rich source of strong constitutive promoters for use in plant biology and several have been shown to contain enhancer sequences ,. The CaMV 35S promoter has been used extensively in driving transgenes in transgenic plants. Many other viral promoters have also been shown to effectively drive expression of transgenes; CaMV 19S, Rice tungro bacilform virus (RTBV) , Soybean chlorotic mottle virus , Mirabilis mosaic virus ,, Figwort mosaic virus (FMV) ,, Peanut streak chlorotic virus , Banana streak badnavirus , Cestrum yellow leaf curling virus (CmYLCV)  and Sugarcane bacilliform badnavirus (SCBV) ,,. Among these, the CaMV 35S and the FMV promoters have been demonstrated to have enhancer sequences within the promoter ,.
The CaMV 35S enhancer  is the most common enhancer used in plant biology. Several studies have shown that the CaMV 35S promoter is not as active as other strong constitutive promoters in monocots -, raising the question whether the CaMV 35S enhancer sequences are as effective in monocots as they are in dicots. However, 2x and 4x arrays of the CaMV 35S enhancer have been shown to enhance transcription of heterologous promoters in stable transformants of rice as well as to cause increased transcript accumulation of endogenous genes -.
The Sugarcane bacilliform virus (SCBV), like the Cauliflower mosaic virus, is in the Caulimoviridae family of viruses. While the Cauliflower mosaic virus is in the Caulimovirus genus and mostly infects dicots, SCBV is in the Badnavirus genus along with Commelina yellow mottle virus (CoMV) and RTBV and infects monocots . Badnaviruses have circular genomes that produce a terminally redundant transcript ,. Like CoMV, SCBV has three large open reading frames on its plus strand . Promoters from several Badnaviruses have been shown to drive expression of heterologous genes in transgenic plants ,,,,. Because these viruses infect monocots, they may be useful sources of strong promoters for monocots. SCBV promoters from several isolates of the virus have been tested in transgenic plants and shown to be highly expressed in most tissues tested ,,.
We present a characterization of an 839 bp fragment of the Sugarcane Bacilliform Virus - Ireng Maleng isolate (SCBV-IM) promoter and demonstrate that it is comparable in strength to the strong maize ubiquitin 1 (ZmUBI1) promoter in transgenic maize. This work also presents a dissection of the SCBV-IM promoter and the identification of sequences that can enhance transcription when placed upstream of a truncated maize alcohol dehydrogenase (ZmADH1) promoter. Similar to what was seen with the CaMV 35S enhancer ,-, multiple tandem copies of the SCBV-IM enhancer are more effective in increasing transcription than a single copy. An activation tagging element containing four tandem copies of the enhancer element has been introduced into maize. Examination of events containing the activation tagging element indicates that the 4x SCBV-IM enhancer is capable of causing an increase in accumulation of transcripts of native maize genes near the site of insertion of the SCBV-IM enhancer.
The SCBV-IM promoter is a strong promoter in transgenic maize
SCBV-IM enhancer identification and characterization
SCBV-IM promoter fragments SCBV839, SCBV576 and SCBV333 (Figure 2) were cloned upstream of the luciferase (LUC) reporter gene. Transcriptional activities of these constructs were tested by transfecting maize Hi-II suspension cells and monitoring relative activities of the reporter genes.
Next, two upstream fragments of the SCBV-IM promoter were tested for their ability to enhance transcription from a truncated heterologous promoter. Two fragments of the SCBV-IM promoter (SCBV282 consisting of sequences −434 bp to −153 bp and SCBV537 consisting of sequences from −689 to −153, relative to the transcription start site) were cloned upstream of a truncated maize alcohol dehydrogenase 1 (ZmADH1) promoter (−100 to +106, relative to the transcription start site)  fused to the firefly luciferase gene. These constructs were designated SCBV282::ZmADH1::LUC and SCBV537::ZmADH1::LUC, respectively.
The results shown in Figure 4 indicate that the SCBV282 fragment (containing sequence from −434 bp to −153 bp) was able to enhance activity of the truncated ZmADH1 promoter more effectively than the larger SCBV537 fragment (containing sequences from −689 bp to −153 bp). These results indicate that these fragments of the SCBV-IM promoter cause an increase in activity of the reporter gene driven by a truncated heterologous promoter, and that most of this enhancing activity lies within the −434 bp to −153 bp region.
SCBV-enhancer activity in stable maize transformants
Transformants were examined for the location of the T-DNA insertion and the proximity of the enhancers to annotated genes in the maize genome that were reported to be expressed at moderate levels in leaf tissues . Determination of the site of integration of the construct was attempted for 223 events by a transgene border sequence identification method  and 107 of these events were mapped to locations in the maize B73 reference genome. To determine whether the enhancers within the T-DNA sequence are able to cause an increase in transcript accumulation of endogenous genes, these transformants were examined to identify T-DNA insertion sites within ~5.5 Kb of a gene. The CaMV 35S enhancer has been demonstrated to up-regulate genes within ~8 Kb of the enhancer sequences ,.
The promoter sequences that we define include significant portions of the SCBV ORF III gene. The SCBV839 sequence, which has the greatest activity in transient assays, overlaps with 525 protein coding nucleotides. The sequences overlapping the ORF III gene contain most of the promoter activity as demonstrated by the SCBV333 fragment containing only 20 bp of the ORF III gene and having just 10% of the promoter activity of the SCBV839 sequence (Figure 3). The SCBV282 enhancer fragment contains 189 bp of ORF III coding sequence. A similar situation is found in Arabidopsis where regulatory elements for the promoter of ZWICHEL (ZWI) gene are found in exon and intron sequences of the adjacent HYDROXYISOBUTYRL-CoA HYDROLASE 1 (CHY1) gene .
The enhancer sequences in the SCBV-IM promoter were able to increase the activity of the truncated ZmADH1 promoter (Figure 4), but these chimeric promoters were much weaker than the intact SCBV-IM promoter in the transient assays (Figure 3). This difference is so great it is unlikely to be the result of different cell preparations and may be the result of the SCBV-IM upstream activating sequences interacting differently with the heterologous core ZmADH1 promoter and the native SCBV-IM promoter. Similar results were seen when the CaMV 35S enhancer was placed upstream of the CaMV 19S core promoter .
Deletion analysis of the SCBV-IM promoter showed that removing sequences from −770 to −507 caused a 30% decline in promoter activity, while removing sequences from −770 to −264 caused a 90% decline in activity (Figure 3). It was, therefore, somewhat surprising to observe that the chimeric promoter SCBV537::ZmADH1 (containing SCBV-IM sequences −689 to −153) had less activity than the chimeric promoter SCBV282::ZmADH1 (containing SCBV-IM sequences −434 to −153) since the longer fragment in the promoter deletion analysis had the most activity. Surprising results are often obtained when portions of promoters are added or deleted and even small portions of promoters can have dramatic effects. For example, Dey and Matti  showed that removing 50 bp of the MMV promoter increased activity 10 fold and Simon et al.  showed that deleting 54 bp of the Inner No Outer promoter of Arabidopsis could reverse a silenced promoter.
Multiple copies of the SCBV-IM enhancer cause an increase in activity of the chimeric promoters in transient assays (Figure 5). This is consistent with what has been observed with the CaMV 35S and FMV ehancers ,- and may be due to multiple copies of the enhancer being more efficent in recruiting transcription factors to the promoter.
The SCBV282 fragment is capable of acting as a transcriptional enhancer when present in the maize genome in a 4x tandem array. In events containing the 4x SCBV-IM enhancer upstream and downstream of genes, and in either orientation with respect to these genes, increased transcript accumulation was observed (Figure 7). Furthermore, the element appeared to cause accumulation of transcripts that are not present, or present in very low levels, in non-transgenic lines. This demonstrates that the SCBV-IM enhancer may be used for activation tagging in maize. The SCBV-IM enhancers increased expression of 2 out of 8 genes that showed non-detectable expression in non-transgenic control plants. This is similar some studies that have reported ectopic expression of genes when the CaMV 35S enhancers integrate nearby ,.
In this work, we demonstrate that the SCBV-IM promoter is comparable in strength to the ZmUBI1 promoter in transgenic young maize leaves and roots and we identify sequences from the SCBV-IM promoter that can function as a transcriptional enhancer in maize plants. We used transient assays to identify promoter sequences that are responsible for most of the promoter activity and sequences of this promoter that enhance expression from a heterologous promoter. Finally, we generated stable transgenic plants containing 4x tandem arrays of the SCBV-IM enhancer and demonstrated that transcripts of genes near the insertion site are more abundant than in non-transgenic control plants.
Activation tagging by randomly inserting transcriptional enhancers in the genome is a powerful tool for identifying gene function. The CaMV 35S enhancer has been used to develop activation tagging systems for Arabidopsis, rice and barley. Using these activation tagging systems, researchers have identified a number of genes with novel functions ,-. To date, no activation tagging system has been developed for maize. As a first step in developing an activation tagging system for maize, we have identified a transcriptional enhancer from SCBV-IM and have shown it to be able to activate transcription from a truncated ZmADH1 promoter in transient assays and from endogenous promoters in transformed maize plants.
Leaf tissue was collected from seedlings of transgenic event 625–1 containing the SCBV-IM::AAD1 construct. Total RNA was prepared using NucleoSpin RNA Plant kit (Macherey-Nagel, Ref. 740949). 5′ RACE was performed with AAD1 gene specific primer (GACTTGGTCTTTCTTCCACCTCACA) and SMARTer RACE 5′/3′ kit (Clontech Labratories, CA. Cat# 634858) following the manufacture’s recommended methods. Sequeneces generated from the 5′ RACE were then aligned to the reference sequences of SCBV-IM promoter and AAD1 gene to determine the transcription start site.
The 839 bp SCBV-IM promoter sequence was synthesized by DNA2.0, Inc. The sequence is shown in Figure 2 (from GenBank accession AJ277091).
Two plant transformation vectors were constructed in the superbinary precursor plasmid pSB11. One of these contained the SCBV-IM promoter, aryloxyalkanoate dioxigenase herbicide resistance gene (AAD1)  and the maize Per5 3′ UTR, while the other contained the maize ubiquitin promoter , AAD1 and the maize Per5 3′ UTR. Between the T-DNA borders, these constructs also contained a ZmUBI promoter fused to the Phi Yellow Fluorescent Protein (PhiYFP) gene (Evrogen JSC, Moscow, Russia). These constructs were introduced into Agrobacterium tumefaciens strain LBA4404(pSB1) , to produce pDAB108625 and pDAB102110, respectively.
PCR primers used to amplify portions of the SCBV promoter
Putative SCBV-IM enhancer sequences (−434 to −153, SCBV282 and −689 to −153, SCBV537) were PCR amplified from the SCBV-IM promoter region. Chimeric promoters were made by fusing enhancer fragments from the SCBV-IM promoter and a truncated promoter fragment from the maize alcohol dehydrogenase 1 (ZmADH1) gene corresponding to positions from −100 to +106 relative to the transcription start site . The ZmADH1 promoter fragment was PCR amplified using genomic DNA from B73 using CGGGATCCGTATACCCACAGGCGGCCAAACCGC and CATGCCATGGTGCCCCCCTCCGCAAATCTT as the forward and reverse primers, respectively. The amplified PCR products were cloned upstream of the truncated ZmADH1 promoter fused to the luciferase gene. The promoter fragment was confirmed by sequencing. Two differences from the B73 reference sequence were observed; an “A” instead of a “G” at +44 bp and addition of “T” at residue +67 bp.
The 1x, 2x and 4x enhancer fragments of SCBV282 fragment were cloned in the BamHI and BstZ17I sites of pEPP1024, a plasmid containing the truncated ZmADH1 promoter fused to the LUC gene, for transient testing of the transcriptional enhancing activities. The 4x SCBV enhancer array was cloned into pSB11-derived plasmid pDAB3878 which also contains the rice actin1 gene promoter  driving the AAD1 selectable marker . Superbinary constructs were then constructed by in vivo recombination of pSB1 plasmid and the newly constructed pSB11 derivative plasmid in recombinant Agrobacterium tumefacians strain LBA4404/pSB1 to form superbinary construct pEPS1027.
Constructs were introduced into the maize inbred line B104 using Agrobacterium-mediated transformation based on the superbinary method of Ishida et al. . Maize plants (inbred B104) were grown in a greenhouse on a 16:8 hour Light:Dark photoperiod and hand pollinated using pollen from sibling plants. Immature embryos were isolated at 10 to 13 days after pollination when the embryos were 1.4 to 2.0 mm in size.
A suspension of Agrobacterium cells containing the superbinary vector pEPS1027 was prepared by transferring 1 or 2 loops of bacteria grown to solid medium containing 50 mg/L Spectinomycin, 10 mg/L Rifampicin, and 50 mg/L Streptomycin at 28° for 3 days and then a loop of this culture was used to innoculate 5 mL of liquid infection medium (MS salts, ISU Modified MS Vitamin stock (1000x, 2 g/L glycine, 0.5 g/L each of thiamine HCl and pyridoxine HCl, 0.05 g/L nicotinic acid, 3.3 mg/L Dicamba, 68.4 gm/L sucrose, 36 gm/L glucose, 700 mg/L L-proline, pH 5.2) containing 100 μM acetosyringone for 4 days at 25°C. This infection suspension was gently pipetted up and down using a sterile 5 mL pipette until a uniform suspension was achieved, and the concentration was adjusted to an optical density of 0.3 to 0.5 at 600 nm.
Prior to embryo excision and transformation, maize ears were surface sterilized. Immature embryos were then isolated and placed in 2 mL of infection medium. The medium was removed and replaced twice with 1 to 2 mL of fresh infection medium, which was then removed and replaced with 1.5 mL of the infection suspension and incubated for 5 minutes at room temperature. Then embryos were then transferred to co-cultivation medium and inubated for 3–4 day at 25°C in the dark. Co-cultivation medium contained MS salts, ISU Modified MS Vitamins, 3.3 mg/L Dicamba, 30 gm/L sucrose, 700 mg/L L-proline, 100 mg/L myo-inositol, 100 mg/L Casein Enzymatic Hydrolysate, 15 mg/L AgNO3, 100 μM acetosyringone, and 2.3 to 3 gm/L Gelzan™ (Sigma-Aldrich, St. Louis, MO), at pH 5.8.
After co-cultivation, the embryos were transferred to a MS-based resting medium containing MS salts, ISU Modified MS Vitamins, 3.3 mg/L Dicamba, 30 gm/L sucrose, 700 mg/L L-proline, 100 mg/L myo-inositol, 100 mg/L Casein Enzymatic Hydrolysate, 15 mg/L AgNO3, 0.5 gm/L MES (2-(N-morpholino)ethanesulfonic acid monohydrate; Fischer Scientific, Waltham, MA), 250 mg/L Carbenicillin, and 2.3 gm/L Gelzan™, at pH 5.8. Incubation continued for 7 days at 28°C in the dark. Following the 7 day resting period, the embryos were transferred to selection medium. MS-based resting medium (above) was used supplemented with Haloxyfop. The embryos were first transferred to selection medium containing 100 nM Haloxyfop and incubated at 28°C for 1 to 2 weeks, and then transferred to selection medium containing 500 nM Haloxyfop and incubated for an additional 2 to 4 weeks in the light (approximately 50 μEm−2 s−1). Transformed isolates were obtained in 5 to 8 weeks.
Following selection, cultures were transferred to an MS-based pre-regeneration medium containing MS salts, ISU Modified MS Vitamins, 45 gm/L sucrose, 350 mg/L L-proline, 100 mg/L myo-inositol, 50 mg/L Casein Enzymatic Hydrolysate, 1 mg/L AgNO3, 0.25 gm/L MES, 0.5 mg/L naphthaleneacetic acid, 2.5 mg/L abscisic acid, 1 mg/L 6-benzylaminopurine, 250 mg/L Carbenicillin, 2.5 gm/L Gelzan™, and 500 nM Haloxyfop, at pH 5.8 and incubated for 7 days at 28° under 24-hour white fluorescent light (approximately 50 μEm−2 s−1).
For regeneration, the cultures were transferred to an MS-based primary regeneration medium containing MS salts, ISU Modified MS Vitamins, 60 gm/L sucrose, 100 mg/L myo-inositol, 125 mg/L Carbenicillin, 2.5 gm/L Gelzan™, and 500 nM Haloxyfop, at pH 5.8 for 2 weeks at 28° in 24-hour white fluorescent light (approximately 50 μEm−2 s−1). Cultures were then transferred to an MS-based secondary regeneration medium composed of MS salts, ISU Modified MS Vitamins, 30 gm/L sucrose, 100 mg/L myo-inositol, 3 gm/L Gelzan™, at pH 5.8, with 500 nM Haloxyfop and regeneration continued for 2 weeks at 28°C under either 16-hour or 24-hour white fluorescent light conditions (approximately 50 μEm−2 s−1). When regenerated plants reached 3 to 5 cm in length, they were excised and transferred to secondary regeneration medium (as above, but without Haloxyfop) and incubated at 25° under 16-hour white fluorescent light conditions (approximately 50 μEm−2 s−1) to allow for further growth and development of the shoot and roots.
Regenerated plants were transplanted into Metro-Mix® 360 soilless growing medium (Sun Gro Horticulture) and placed a growth room. Plants were then transplanted into Sunshine Custom Blend 160 soil mixture and grown to flowering in the greenhouse. Controlled pollinations for seed production were conducted. In all cases, primary transformants were crossed with non-transformed B104.
Transcript accumulation in transgenic plants
Transgenic plants were identified by a quantitative PCR assay of the AAD1 gene. Approximately 30 mg of T1 tissue was harvested from each of the tissues. Tissue samples were maintained on ice until placed at 4°C for storage until processing for DNA extraction. DNA was purified using the BioSprint DNA 96 plant kit following the manufacturer’s instructions (Qiagen cat. No. 941558). Samples were normalized to 5 ng/μL for qPCR template. A Picogreen assay (Invitrogen, cat No. P11496) was performed to quantify DNA.
For transcript accumulation assays, samples were collected from leaves, roots and tassels at different times during development. For leaves, samples were collected at the V3 growth stage (14 days after planting) from the 3rd fully expanded leaf, at the V8 growth stage (41 days after planting) from the 8th fully expanded leaf and at the R1 growth stage (71 days after planting) from the leaf just below the ear. Samples from the root were collected at the V3 (14 days after planting) and V10 (51 days after planting) growth stages; one cm samples were collected from the tip of a root. Tassels were collected at the R1 growth stage by sampling an entire branch of the tassel. First strand cDNA was synthesized following manufacturer’s instructions using the High Capacity cDNA synthesis kit (Invitrogen, cat No. 4368813) in a 10 μL reaction containing 5 μL of total RNA. Following synthesis, cDNA was diluted 1:3 with nuclease free water. Quantitative PCR assays were set up using the Eppendorf epMotion5075 liquid handler. Each sample was assayed in triplicate for target gene (AAD1) and a reference gene TIP (GRMZM2G095185) for leaf and tassel tissues or MAZ95 (GRMZM2G053299) for root tissues. Each well contained 4 μL of assay mix (Roche Universal Probe Library (UPL)) and 1 μL of cDNA was added. Reference assay mix consisted of forward (AGCCAAGCCAGTGGTACTTC) and reverse (TCGCAGACAAAGTAGCAAATGT) primer at a final concentration of 0.25 μM and UPL probe at a final concentration of 0.1 μM with 1x Light Cycler480® Probes Master mix. AAD1 assay mix consisted of forward (AACCATGCAAGCCACCAT) and reverse (GGTAGAGGGAACCGAACACA) primer at a final concentration of 0.375 μM and UPL probe #53 at a final concentration of 0.1 μM with 1x Light Cycler480® Probes Master mix.
Detection was 6FAM channel in both assays. PCR cycling conditions were initially activated at 95°C for 10 minutes followed by 43 cycles of denaturation at 95°C for 10 seconds, annealing and extension at 60°C for 20 seconds and data acquisition for 1 second at 72°C. Assay plates were run on the Roche LC480II and analysis performed by relative quantification.
Transient assays in maize suspension cultures
Maize Hi-II suspension culture cells  were transfected by particle bombardment with plasmid DNA constructs harboring promoter or enhancer elements driving the LUC gene and a control plasmid DNA construct containing a ZmUBI1::GUS gene for normalization of transfection.
Bulk preparations of plasmid DNAs were prepared using QiAfilter™ Plasmid Maxi Kits (Qiagen, Germantown, Maryland) and the quantity and quality were analyzed using standard molecular methods. The Hi-II cells were grown by shaking at 125 rpm in H9CP+ medium (H9CP medium consists of MS salts 4.3 gm/L, sucrose 3%, Casamino acids 200 mg/L, myo-inositol 100 mg/L, 2,4-D 2 mg/L, NAA 2 mg/L, 1000X MS vitamins 1 mL/L, L-proline 700 mg/L, and coconut water (Sigma Aldrich, St. Louis, MO) 62.5 mL/L, pH 6.0) at 28°C in the dark. Prior to bombardment, the 2-day old Hi-II cultures were transferred to G-N6 medium (CHU N6 medium 3.98 g/L, CHU N6 vitamins 1 mL/L (both CHU components were from PhytoTechnology Laboratories®, Lenexa, KS), Myo-inositol 100 mg/L, 2,4-D 2 mg/L and sucrose 3%, pH 6.0) and allowed to grow for 24 hours. On the day of bombardment, 2.5 g of G-N6 grown cells were transferred to sterile Whatman No. 1 filter disks (55 mm) placed on G-N6 medium containing 0.5 M D-sorbitol and 0.5 M D-mannitol and incubated for 4 hours. The osmotically-adjusted cells were used for bombardment.
Gold particles (1 μm diameter, BioRad, Hercules, CA) were washed with 70% ethanol for 10 minutes, then three times with sterile water. The particles were dispensed in 50% glycerol at a concentration of 120 mg/mL. For a typical experiment, 150 μL (18 mg) of gold particles, approximately 5 μg of plasmid DNA, 150 μL of 2.5 M CaCl2 and 30 μL 0.2 M spermidine were combined. The reaction (total volume 375 μL) was incubated at room temperature for 10 minutes with occasional gentle vortexing. The DNA coated-gold particles were briefly centrifuged, washed with 420 μL of 70% ethanol and then with 420 μL of 100% ethanol. The final pellet was resuspended in 110 μL of 100% ethanol and subjected to a brief sonication (three bursts of 3 seconds each, with 1 minute between bursts) with a Branson 1450 sonicator.
Aliquots of 12.2 μL of the gold-particles coated with DNA were spread on each of nine macrocarriers (BioRad, Hercules, CA) and used in bombardment assays using a BioRad PDS1000/He system. The suspension culture cells were transfected at a target distance of 9 cm using 3510 psi disks and each plate was bombarded 3 times. Following bombardment, the cells were incubated in the dark at 28°, first for 12 hours on G-N6 containing D-sorbitol and D-mannitol medium, then on G-N6 plates for an additional 36 hours. Cells were collected from the plates, blotted to remove buffer and extracted with 300 μL of 2x CCLT LUC extraction buffer (Promega Corporation, Madison, WI). After centrifugation, about 600 μL of protein extract was collected. Protein concentrations were estimated using the Bradford assay.
LUC enzymatic activity (expressed in Luciferase Units (LU)/mg protein) and GUS enzymatic activity (expressed in GUS activity units (GU)/μg protein) were measured as previously described . Relative activities of the test promoters in SCBV:LUC constructs were compared by normalizing LUC levels to GUS levels as the ratio of LUC/mg protein:GUS/μg protein.
Analysis of activation tagging events
Primers for insertion site mapping confirmation
PCR primer information for gene expression assays
Availability of supporting data
The data sets supporting the results of this article are included within the article.
We would like to acknowledge Deka Smith, Suyan Wang and Wendy Matsumura for their assistance in generating constructs, analyzing transgenic plants, Nikolaus Matheis, Fira Negru and Morioara Tomuta for transformation of maize and Tyler Spurgeon, Michael Paruch and Cheryl Maahs for growing, caring for and harvesting transgenic plants and Kelli Gibson and Kristina Woodall for RNA isolation and first-strand cDNA synthesis.
- Blackwood EM, Kadonaga JT: Going the Distance: A Current View of Enhancer Action. Science. 1998, 281 (5373): 60-63. 10.1126/science.281.5373.60.View ArticlePubMedGoogle Scholar
- Struhl K: A Paradigm for Precision. Science. 2001, 293 (5532): 1054-1055. 10.1126/science.1064050.View ArticlePubMedGoogle Scholar
- Wu K, Hu M, Martin T, Wang C, Li X-Q, Tian L, Brown D, Miki B: The cryptic enhancer elements of the tCUP promoter. Plant Mol Biol. 2003, 51 (3): 351-362. 10.1023/A:1022087112152.View ArticlePubMedGoogle Scholar
- Wu K, Malik K, Tian L, Hu M, Martin T, Foster E, Brown D, Miki B: Enhancers and core promoter elements are essential for the activity of a cryptic gene activation sequence from tobacco, tCUP. Mol Gen Genomics. 2001, 265 (5): 763-770. 10.1007/s004380100478.View ArticleGoogle Scholar
- Sandhu J, Webster C, Gray J: A/T-rich sequences act as quantitative enhancers of gene expression in transgenic tobacco and potato plants. Plant Mol Biol. 1998, 37 (5): 885-896. 10.1023/A:1006051832213.View ArticlePubMedGoogle Scholar
- Benfey PN, Ren L, Chua NH: The CaMV 35S enhancer contains at least two domains which can confer different developmental and tissue-specific expression patterns. EMBO J. 1989, 8 (8): 2195-2202.PubMed CentralPubMedGoogle Scholar
- Odell JT, Nagy F, Chua N-H: Identification of DNA sequences required for activity of the cauliflower mosaic virus 35S promoter. Nature. 1985, 313 (6005): 810-812. 10.1038/313810a0.View ArticlePubMedGoogle Scholar
- Maiti IB, Gowda S, Kiernan J, Ghosh SK, Shepherd RJ: Promoter/leader deletion analysis and plant expression vectors with the figwort mosaic virus (FMV) full length transcript (FLt) promoter containing single or double enhancer domains. Transgenic Res. 1997, 6 (2): 143-156. 10.1023/A:1018477705019.View ArticlePubMedGoogle Scholar
- O’Grady K, Gurley WB: Site-directed mutagenesis of the enhancer region of the 780 gene promoter of T-DNA. Plant Mol Biol. 1995, 29 (1): 99-108. 10.1007/BF00019122.View ArticlePubMedGoogle Scholar
- Bruce WB, Bandyopadhyay R, Gurley WB: An enhancer-like element present in the promoter of a T-DNA gene from the Ti plasmid of Agrobacterium tumefaciens. Proc Natl Acad Sci. 1988, 85 (12): 4310-4314. 10.1073/pnas.85.12.4310.PubMed CentralView ArticlePubMedGoogle Scholar
- Ellis JG, Llewellyn DJ, Walker JC, Dennis ES, Peacock WJ: The ocs element: a 16 base pair palindrome essential for activity of the octopine synthase enhancer. EMBO J. 1987, 6 (11): 3203-3208.PubMed CentralPubMedGoogle Scholar
- Chen G, Müller M, Potrykus I, Hohn T, Fütterer J: Rice tungro bacilliform virus: transcription and translation in protoplasts. Virology. 1994, 204 (1): 91-100. 10.1006/viro.1994.1513.View ArticlePubMedGoogle Scholar
- Fukuoka H, Ogawa T, Mitsuhara I, Iwai T, Isuzugawa K, Nishizawa Y, Gotoh Y, Nishizawa Y, Tagiri A, Ugaki M: Agrobacterium-mediated transformation of monocot and dicot plants using the NCR promoter derived from soybean chlorotic mottle virus. Plant Cell Rep. 2000, 19 (8): 815-820. 10.1007/s002990000191.View ArticleGoogle Scholar
- Dey N, Maiti I: Structure and promoter/leader deletion analysis of mirabilis mosaic virus (MMV) full-length transcript promoter in transgenic plants. Plant Mol Biol. 1999, 40 (5): 771-782. 10.1023/A:1006285426523.View ArticlePubMedGoogle Scholar
- Dey N, Maiti I: Promoter deletion and comparative expression analysis of the Mirabilis mosaic caulimovirus (MMV) sub-genomic transcript (Sgt) promtoer in transgenic plants. Transgenics. 2003, 4: 35-53.Google Scholar
- Bhattacharyya S, Dey N, Maiti IB: Analysis of cis-sequence of subgenomic transcript promoter from the Figwort mosaic virus and comparison of promoter activity with the cauliflower mosaic virus promoters in monocot and dicot cells. Virus Res. 2002, 90 (1–2): 47-62. 10.1016/S0166-0934(02)00146-5.View ArticlePubMedGoogle Scholar
- Sanger M, Daubert S, Goodman R: Characteristics of a strong promoter from figwort mosaic virus: comparison with the analogous 35S promoter from cauliflower mosaic virus and the regulated mannopine synthase promoter. Plant Mol Biol. 1990, 14 (3): 433-443. 10.1007/BF00028779.View ArticlePubMedGoogle Scholar
- Maiti IB, Shepherd RJ: Isolation and Expression Analysis of Peanut Chlorotic Streak Caulimovirus (PClSV) Full-Length Transcript (FLt) Promoter in Transgenic Plants. Biochem Biophys Res Commun. 1998, 244 (2): 440-444. 10.1006/bbrc.1998.8287.View ArticlePubMedGoogle Scholar
- Schenk PM, Remans T, Sagi L, Elliott AR, Dietzgen RG, Swennen R, Ebert PR, Grof CP, Manners JM: Promoters for pregenomic RNA of banana streak badnavirus are active for transgene expression in monocot and dicot plants. Plant Mol Biol. 2001, 47 (3): 399-412. 10.1023/A:1011680008868.View ArticlePubMedGoogle Scholar
- Stavolone L, Kononova M, Pauli S, Ragozzino A, de Haan P, Milligan S, Lawton K, Hohn T: Cestrum yellow leaf curling virus (CmYLCV) promoter: a new strong constitutive promoter for heterologous gene expression in a wide variety of crops. Plant Mol Biol. 2003, 53 (5): 703-713. 10.1023/B:PLAN.0000019110.95420.bb.View ArticleGoogle Scholar
- Braithwaite KS, Geijskes RJ, Smith GR: A variable region of the Sugarcane Bacilliform Virus (SCBV) genome can be used to generate promoters for transgene expression in sugarcane. Plant Cell Rep. 2004, 23 (5): 319-326. 10.1007/s00299-004-0817-8.View ArticlePubMedGoogle Scholar
- Tzafrir I, Torbert K, Lockhart BL, Somers D, Olszewski N: The sugarcane bacilliform badnavirus promoter is active in both monocots and dicots. Plant Mol Biol. 1998, 38 (3): 347-356. 10.1023/A:1006075415686.View ArticlePubMedGoogle Scholar
- Cornejo M-J, Luth D, Blankenship K, Anderson O, Blechl A: Activity of a maize ubiquitin promoter in transgenic rice. Plant Mol Biol. 1993, 23 (3): 567-581. 10.1007/BF00019304.View ArticlePubMedGoogle Scholar
- Gallo-Meagher M, Irvine J: Effects of tissue type and promoter strength on transient GUS expression in sugarcane following particle bombardment. Plant Cell Rep. 1993, 12 (12): 666-670. 10.1007/BF00233416.View ArticlePubMedGoogle Scholar
- McElroy D, Blowers AD, Jenes B, Wu R: Construction of expression vectors based on the rice actin 1 (Act1) 5′ region for use in monocot transformation. Mol Gen Genet MGG. 1991, 231 (1): 150-160. 10.1007/BF00293832.View ArticlePubMedGoogle Scholar
- Christensen AH, Sharrock RA, Quail PH: Maize polyubiquitin genes: structure, thermal perturbation of expression and transcript splicing, and promoter activity following transfer to protoplasts by electroporation. Plant Mol Biol. 1992, 18 (4): 675-689. 10.1007/BF00020010.View ArticlePubMedGoogle Scholar
- Jeong DH, An S, Kang HG, Moon S, Han JJ, Park S, Lee HS, An K, An G: T-DNA insertional mutagenesis for activation tagging in rice. Plant Physiol. 2002, 130 (4): 1636-1644. 10.1104/pp.014357.PubMed CentralView ArticlePubMedGoogle Scholar
- Wan S, Wu J, Zhang Z, Sun X, Lv Y, Gao C, Ning Y, Ma J, Guo Y, Zhang Q, Zheng X, Zhang C, Ma Z, Lu T: Activation tagging, an efficient tool for functional analysis of the rice genome. Plant Mol Biol. 2009, 69 (1–2): 69-80. 10.1007/s11103-008-9406-5.View ArticlePubMedGoogle Scholar
- Jeong DH, An S, Park S, Kang HG, Park GG, Kim SR, Sim J, Kim YO, Kim MK, Kim SR, Kim J, Shin M, Jung M, An G: Generation of a flanking sequence-tag database for activation-tagging lines in japonica rice. Plant J. 2006, 45 (1): 123-132. 10.1111/j.1365-313X.2005.02610.x.View ArticlePubMedGoogle Scholar
- Qu S, Desai A, Wing R, Sundaresan V: A versatile transposon-based activation tag vector system for functional genomics in cereals and other monocot plants. Plant Physiol. 2008, 146 (1): 189-199. 10.1104/pp.107.111427.PubMed CentralView ArticlePubMedGoogle Scholar
- Medberry SL, Lockhart BEL, Olszewski NE: Properties of Commelina yellow mottle virus’s complete DNA sequence, genomic discontinuities and transcript suggest that it is a pararetrovirus. Nucleic Acids Res. 1990, 18 (18): 5505-5513. 10.1093/nar/18.18.5505.PubMed CentralView ArticlePubMedGoogle Scholar
- Qu R, Bhattacharyya M, Laco GS, De Kochko A, Subba Rao B, Kaniewska MB, Scott Elmer J, Rochester DE, Smith CE, Beachy RN: Characterization of the genome of rice tungro bacilliform virus: Comparison with < i > Commelina</i > yellow mottle virus and caulimoviruses. Virology. 1991, 185 (1): 354-364. 10.1016/0042-6822(91)90783-8.View ArticlePubMedGoogle Scholar
- Bouhida M, Lockhart B, Olszewski NE: An analysis of the complete sequence of a sugarcane bacilliform virus genome infectious to banana and rice. J Gen Virol. 1993, 74: 15-22. 10.1099/0022-1317-74-1-15.View ArticlePubMedGoogle Scholar
- Medberry SL, Lockhart B, Olszewski NE: The Commelina yellow mottle virus promoter is a strong promoter in vascular and reproductive tissues. Plant Cell Online. 1992, 4 (2): 185-192. 10.1105/tpc.4.2.185.View ArticleGoogle Scholar
- Yang IC, Iommarini JP, Becker DK, Hafner GJ, Dale JL, Harding RM: A promoter derived from taro bacilliform badnavirus drives strong expression in transgenic banana and tobacco plants. Plant Cell Rep. 2003, 21 (12): 1199-1206. 10.1007/s00299-003-0621-x.View ArticlePubMedGoogle Scholar
- Schenk PM, Sagi L, Remans T, Dietzgen RG, Bernard MJ, Graham MW, Manners JM: A promoter from sugarcane bacilliform badnavirus drives transgene expression in banana and other monocot and dicot plants. Plant Mol Biol. 1999, 39 (6): 1221-1230. 10.1023/A:1006125229477.View ArticlePubMedGoogle Scholar
- Kay R, Chan A, Daly M, McPherson J: Duplication of CaMV 35S Promoter Sequences Creates a Strong Enhancer for Plant Genes. Science (New York, NY). 1987, 236 (4806): 1299-1302. 10.1126/science.236.4806.1299.View ArticleGoogle Scholar
- Ow DW, Jacobs JD, Howell SH: Functional regions of the cauliflower mosaic virus 35S RNA promoter determined by use of the firefly luciferase gene as a reporter of promoter activity. Proc Natl Acad Sci. 1987, 84 (14): 4870-4874. 10.1073/pnas.84.14.4870.PubMed CentralView ArticlePubMedGoogle Scholar
- Fang RX, Nagy F, Sivasubramaniam S, Chua NH: Multiple cis regulatory elements for maximal expression of the cauliflower mosaic virus 35S promoter in transgenic plants. Plant Cell Online. 1989, 1 (1): 141-150. 10.1105/tpc.1.1.141.View ArticleGoogle Scholar
- Wright TR, Shan G, Walsh TA, Lira JM, Cui C, Song P, Zhuang M, Arnold NL, Lin G, Yau K, Russel SM, Cicchillo RM, Peterson MA, Simpson MD, Zhou N, Ponsamuel J, Zhang Z: Robust crop resistance to broadleaf and grass herbicides provided by aryloxyalkanoate dioxygenase transgenes. Proc Natl Acad Sci U S A. 2010, 107 (47): 20240-20245. 10.1073/pnas.1013154107.PubMed CentralView ArticlePubMedGoogle Scholar
- Ellis J, Llewellyn D, Dennis E, Peacock W: Maize Adh-1 promoter sequences control anaerobic regulation: addition of upstream promoter elements from constitutive genes is necessary for expression in tobacco. EMBO J. 1987, 6 (1): 11-PubMed CentralPubMedGoogle Scholar
- Leon P, Planckaert F, Walbot V: Transient gene expression in protoplasts of Phaseolus vulgaris isolated from a cell suspension culture. Plant Physiol. 1991, 95 (3): 968-972. 10.1104/pp.95.3.968.PubMed CentralView ArticlePubMedGoogle Scholar
- Cowen NM, Armstrong K, Smith KA: Use of regulatory sequences in transgenic plants. US Patent 7. 2007, 902-Google Scholar
- Sekhon RS, Lin H, Childs KL, Hansey CN, Buell CR, de Leon N, Kaeppler SM: Genome-wide atlas of transcription during maize development. Plant J. 2011, 66 (4): 553-563. 10.1111/j.1365-313X.2011.04527.x.View ArticlePubMedGoogle Scholar
- Cao Z, Novak S, Sastry-Dent L, Zhou N: High through-put analysis of transgene borders. vol. WO2013078318A1 World Intellectual Property Organization WO2013078318A1. 2013Google Scholar
- Ichikawa T, Nakazawa M, Kawashima M, Muto S, Gohda K, Suzuki K, Ishikawa A, Kobayashi H, Yoshizumi T, Tsumoto Y: Sequence database of 1172 T‐DNA insertion sites in Arabidopsis activation‐tagging lines that showed phenotypes in T1 generation. Plant J. 2003, 36 (3): 421-429. 10.1046/j.1365-313X.2003.01876.x.View ArticlePubMedGoogle Scholar
- Levine M, Tjian R: Transcription regulation and animal diversity. Nature. 2003, 424 (6945): 147-151. 10.1038/nature01763.View ArticlePubMedGoogle Scholar
- Banerji J, Rusconi S, Schaffner W: Expression of a β-globin gene is enhanced by remote SV40 DNA sequences. Cell. 1981, 27 (2): 299-308. 10.1016/0092-8674(81)90413-X.View ArticlePubMedGoogle Scholar
- Reddy VS, Reddy A: Developmental and cell-specific expression of ZWICHEL is regulated by the intron and exon sequences of its upstream protein-coding gene. Plant Mol Biol. 2004, 54 (2): 273-293. 10.1023/B:PLAN.0000028793.88757.8b.View ArticlePubMedGoogle Scholar
- Simon MK, Williams LA, Brady-Passerini K, Brown RH, Gasser CS: Positive-and negative-acting regulatory elements contribute to the tissue-specific expression of INNER NO OUTER, a YABBY-type transcription factor gene in Arabidopsis. BMC Plant Biol. 2012, 12 (1): 214-10.1186/1471-2229-12-214.PubMed CentralView ArticlePubMedGoogle Scholar
- Yoo SY, Bomblies K, Yoo SK, Yang JW, Choi MS, Lee JS, Weigel D, Ahn JH: The 35S promoter used in a selectable marker gene of a plant transformation vector affects the expression of the transgene. Planta. 2005, 221 (4): 523-530. 10.1007/s00425-004-1466-4.View ArticlePubMedGoogle Scholar
- Xu Y-Y, Wang X-M, Li J, Li J-H, Wu J-S, Walker JC, Xu Z-H, Chong K: Activation of the WUS gene induces ectopic initiation of floral meristems on mature stem surface in Arabidopsis thaliana. Plant Mol Biol. 2005, 57 (6): 773-784. 10.1007/s11103-005-0952-9.View ArticlePubMedGoogle Scholar
- van der Fits L, Memelink J: ORCA3, a jasmonate-responsive transcriptional regulator of plant primary and secondary metabolism. Science. 2000, 289 (5477): 295-297. 10.1126/science.289.5477.295.View ArticlePubMedGoogle Scholar
- Busov VB, Meilan R, Pearce DW, Ma C, Rood SB, Strauss SH: Activation tagging of a dominant gibberellin catabolism gene (GA 2-oxidase) from poplar that regulates tree stature. Plant Physiol. 2003, 132 (3): 1283-1291. 10.1104/pp.103.020354.PubMed CentralView ArticlePubMedGoogle Scholar
- Mathews H, Clendennen SK, Caldwell CG, Liu XL, Connors K, Matheis N, Schuster DK, Menasco DJ, Wagoner W, Lightner J, Wagner DR: Activation tagging in tomato identifies a transcriptional regulator of anthocyanin biosynthesis, modification, and transport. Plant Cell. 2003, 15 (8): 1689-1703. 10.1105/tpc.012963.PubMed CentralView ArticlePubMedGoogle Scholar
- Kakimoto T: CKI1, a histidine kinase homolog implicated in cytokinin signal transduction. Science. 1996, 274 (5289): 982-985. 10.1126/science.274.5289.982.View ArticlePubMedGoogle Scholar
- Ayliffe MA, Pallotta M, Langridge P, Pryor AJ: A barley activation tagging system. Plant Mol Biol. 2007, 64 (3): 329-347. 10.1007/s11103-007-9157-8.View ArticlePubMedGoogle Scholar
- Komari T, Takakura Y, Ueki J, Kato N, Ishida Y, Hiei Y: Binary vectors and super-binary vectors. Methods Mol Biol. 2006, 343: 15-41.PubMedGoogle Scholar
- Komori T, Imayama T, Kato N, Ishida Y, Ueki J, Komari T: Current status of binary vectors and superbinary vectors. Plant Physiol. 2007, 145 (4): 1155-1160. 10.1104/pp.107.105734.PubMed CentralView ArticlePubMedGoogle Scholar
- DeLuca M, McElroy W: Purification and properties of firefly luciferase. Methods Enzymol. 1978, 57: 3-15. 10.1016/0076-6879(78)57003-1.View ArticleGoogle Scholar
- McElroy D, Zhang W, Cao J, Wu R: Isolation of an efficient actin promoter for use in rice transformation. Plant Cell. 1990, 2 (2): 163-171. 10.1105/tpc.2.2.163.PubMed CentralView ArticlePubMedGoogle Scholar
- Ishida Y, Hiei Y, Komari T: Agrobacterium-mediated transformation of maize. Nat Protoc. 2007, 2 (7): 1614-1621. 10.1038/nprot.2007.241.View ArticlePubMedGoogle Scholar
- Armstrong C, Green C, Philips R: Development and availability of germplasm with high Type II culture formation response. Maize Genetics Coop Newsletter. 1991, 65: 92-93.Google Scholar
- Rosenkrans L, Vasil V, Vasil I, McCarty D: Functional analysis of a plant transcription factor using transient expression in maize protoplasts. In Edited by Maliga P, Klessig DF, Cashmore AR, Gruissem W; 1995:19–35.Google Scholar
- Sastry-Dent L, Sriram S, Elango N, Cao Z, Muthuranman KN: Data analysis of dna sequences. vol. WO2013119770A1 World Intellectual Property Organization WO2013119770A1. 2013Google Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.