Feruloyl esterase B (faeB) from A. niger is composed of 521 amino acids. Among them, 18 amino acids in the N-terminus function as a signal peptide that aides in the secretion of faeB. To target the expression of faeB to specific plant organelles, we cleaved the N-terminal signal peptide coding region, and replaced it with PR1b to target the proteins to the endoplasmic reticulum  and Rubisco leading the peptide to target expression to the chloroplast . Endoplasmic reticulum retention signal KEDL  and vacuole retention signal CTPP (from R Menassa, Agriculture and Agri-Food Canada, London, ON, Canada) were fused immediately after the protein to target the protein to the endoplasmic reticulum and vacuole, respectively. The c-Myc tag was used for protein purification and StrepII was used for detection. The schematic maps of the four faeB constructs are shown in Additional file 9. The codon usage of the faeB gene was optimized based on alfalfa codon usage preference with faeB synthesized at GenScript (Township, NJ, USA). The sequences of synthetic faeB genes are shown in Additional file 10.
The transformation vector pPZP100  was obtained from P Maliga (Rutgers University, New Brunswick, NJ, USA), and modified. In the pPZP100 vector, the CmR selectable marker gene was replaced with NPTII for selection of bacteria on kanamycin. The CmR gene generated instability in the vector, whereas it was stable with kanamycin (data not shown). In pEACH the non-mutated form of the NPTII gene  was inserted into the CmR gene, leaving the interrupted CmR gene sequence in the vector (Additional files 11 and 12). The MYB recognition sequence  allowed the excision of all sequences cloned into the multicloning site and acted as filler DNA to provide distance from the transfer DNA (T-DNA) borders , thereby minimizing interactions with elements at the insertion sites.
The plant selectable marker gene for kanamycin resistance was regulated by the enhanced tCUP4 promoter and ARBC terminator with the terminator adjacent to the left T-DNA border. Any deletions occurring at the left border would be selected against during plant tissue culture in the presence of kanamycin.
Genes regulated by the enhanced tCUP4 promoter and the PIN terminator were inserted in the same orientation as the selectable marker gene. The position of the enhanced tCUP4 promoter at the right border reduced the likelihood of promoter interactions with sequences within the adjacent insertion site. Enhanced tCUP4 has been shown to have no effect on the expression of adjacent genes, whereas the commonly used 35S promoter and super-promoter have been shown to interact with elements at the insertion site over large distances .
The EcoR I-Hind III fragment from the pEACH vector was released from pEACH 5,103 and subcloned into pUC18. In the resulting pUC18 vector, the synthetic faeB genes with protein signaling peptides were inserted between BamH I and Xba I sites. Finally, the EcoR I-Hind III fragment from pUC18 vector was cloned back into pEACH 5,103, resulting in faeB-apoplast, faeB-chloroplast, faeB-ER and faeB-vacuole constructs, respectively. All inserts were sequenced to confirm identity to original sequences.
The schematic map of the four faeB constructs is shown in Additional file 9.
faeBtransient expression in tobacco
The four faeB expression constructs were integrated into Agrobacterium tumefaciens strain LBA4401 using electroporation and were transiently expressed in 5- to 6-week-old Nicotiana benthamiana as described by Joensuu et al. . Total proteins were extracted from tobacco leaves infected with LBA4404 Agrobacterium, LBA4404 transformed with pEACH 5,103 (GUS-intron), faeB-apoplast, faeB-chloroplast, faeB-ER and faeB-vacuole vectors, respectively, and 25 μg of each protein was run on SDS-PAGE gel. Expressed faeB proteins were detected using the primary antibody anti-c-Myc (GenScript; 1,500 ×) and the secondary antibody, goat anti-mouse immunoglobulin G (IgG) with horseradish peroxidase (Bio-Rad; 3,000 ×).
Tissue culture and plant transformation
Donor plants of alfalfa (Medicago sativa L.) genotype N.4.4.2 were propagated in vitro by subculturing individual nodes in 10 cm magenta containers containing 0.5 × Murashige and Skoog medium (MSO) . The standard conditions for maintaining the cultures in a growth chamber were 25°C (day/night) with a photoperiod of 16 h at approximately 3,500 lux.
For alfalfa tissue culture and transformation, the procedures were performed as outlined in Han et al. . Briefly, the petioles were cut to 1 cm lengths and pre-cultured on SH2K medium  for 48 h at 25°C with a photoperiod of 16 h. After pre-culture, explants were immersed (shortly for 2 to 5 seconds) in a suspension of Agrobacterium cells cultured overnight (OD600 = 0.6 to 0.8). After immersion, petioles were blotted onto filter paper and placed on SH2K medium and co-cultivated for 5 days in the dark. The petioles were then transferred to the medium used for co-cultivation containing 300 mg/l timentin, and incubated for 2 weeks. When callus formation was observed, calli were transferred onto SH2K medium containing 50 mg/l kanamycin and 300 mg/l timentin. Calli surviving 1 week on this selection medium were moved to medium containing 75 mg/l kanamycin and 300 mg/l timentin, and incubated for another 2 weeks. The calli were then transferred to the embryo induction medium BOi2Y [45, 46] containing 300 mg/l timentin and 75 mg/l kanamycin, and incubated for 3 weeks in the light with a photoperiod of 16:8. Green elongated mature embryos with well-formed cotyledons were collected and transferred to 0.5 × MSO medium with 300 mg/l timentin and 75 mg/l kanamycin for 2 to 3 weeks. Germinated embryos were transferred to MSO containing 300 mg/l timentin and 25 mg/l kanamycin in magenta boxes. Well-established plants were transferred to soil. As a negative control, non-transformed explants were placed in SH2K medium with kanamycin (75 mg/l) to ensure effective selection of transformants (Additional file 13).
The control (non-transformed) and regenerated transgenic lines were multiplied in a greenhouse using cuttings of actively growing young shoots rooted in a moist sand bed, transferred to a soilless potting mixture (Pro-Mix, Premier Tech Horticulture, Rivière-du-Loup, QC, Canada) and grown in 200 cm plastic pots under seasonal greenhouse conditions, with daily watering and weekly fertilization (20 N:20P:20 K). Actively growing shoots were collected from all lines at the pre-bud vegetative stage, freeze-dried and stored at -20°C.
Validation by PCR and southern hybridization
Genomic DNA was extracted from leaves of putative transformed and non-transformed alfalfa plants using a commercially available kit (REDExtract-N-Amp™ Plant PCR Kit; Sigma-Aldrich, St Louis, MO, USA). The integration of transgenes into the alfalfa genome was confirmed by PCR with primers targeting the nptII and faeB genes. Additionally, a common tCUP4 promoter forward primer was used in combination with transgene specific reverse primers for faeB-apoplast, faeB-chloroplast, faeB-ER and faeB-vacuole. For amplification of the nptII gene, a 699 bp fragment was amplified using the forward primer (5’GAGGCTATTCGGCTATGACTG3’) and the reverse primer (5’ATCGGGAGCGGCGATACCGTA3’). The primers for amplification of faeB gene fragments of four constructs were as follows. For the faeB-apoplast construct, the forward primer was (5’ACGGTGGAGAGGCTGATA3’) and the reverse primer was (5’GGATGACTCCAAAGATCCTC3’), generating a product of 652 bp. For the faeB-chloroplast construct, the forward primer was (5’CTGCTGCTGTTGCAACAAGG3’) and the reverse primer was (5’GGAAAGCACCCCATGA3’), generating a product of 765 bp. For the faeB-vacuole construct, the forward primer was (5’ACGGTGGAGAGGCTGATA3’) and the reverse primer was (5’CCTTACATAGTAACAAGCAAACCG3’), generating a product of 695 bp. For the faeB-ER construct, the forward primer was (5’ACGGTGGAGGCTGATA3’) and the reverse primer was (5’GGATCCTTAAAGTTCATCTT3’), with PCR product size of 680 bp. The conditions of PCR were set as follows: 94°C, 5 min; 30 cycles at 94°C, 30 sec; 58°C, 30 sec; 72°C, 30 sec; and a final extension at 72°C, 5 min. The primers used for amplification of the tCUP4 promoter and transgene specific reverse primers for faeB-apoplast, faeB-chloroplast, faeB-ER and faeB-vacuole were used. The forward primer flanking tCUP4 promoter was (5’CGGCAGAATTTCCCTATATATATTTTTAATTCCCAAA3’) and the transgene specific reverse primers were as follows: faeB-apoplast reverse primer was (5’GGATGACTCCAAAGATCCTC3’), the size of PCR product was 1,809 bp; faeB- chloroplast reverse primer was (5’GGAAAGCACCCCATGA3’), generating a PCR product of 956 bp; faeB-ER reverse primer was (5’GGATCCTTAAAGTTCATCTT3’), the size of PCR product was 1,842 bp; and faeB-vacuole reverse primer was (5’CCTTACATAGTAACAAGCAAACCG3’), generating a PCR product of 1,695 bp. PCR conditions were as follows: 94°C, 5 min; 35 cycles at 94°C, 30 sec; 55°C, 30 sec; 72°C, 1 min 45 sec; and the final extension at 72°C, 5 min.
For Southern analysis, total genomic DNA was isolated from selected transgenic and control plants, then digested overnight with HindIII (New England Biolabs, Ipswich, MA, USA), with 10 μg of digested DNA being separated by agarose electrophoresis. DNA was transferred onto a Hybond-N membrane (GE Healthcare Life Sciences, Mississauga, ON, Canada) by capillary blotting. DNA was fixed to the membrane by UV crosslinking and probed with digoxigenin-labeled faeB prepared by PCR of plasmid DNA.
In situ immunolocalization of transgenic protein in the different organelles was performed on young alfalfa leaf tissue from transgenic and control plants, according to the protocol described by Sauer et al. . A 1:1,000 dilution of the 0.5 mg/ml stock of c-Myc anti-mouse antibody was used as the primary antibody and a 1:30 dilution of donkey anti-mouse IgG antibody stock (Molecular Probes, catalogue number A21202) labeled with Alexa Fluor 488 (Life Technologies, Carlsbad, CA, USA) was used as the secondary antibody.
Feruloyl esterase activity screening
Enzyme was extracted by grinding 3 g of stem and leaf tissue in liquid nitrogen, followed by suspension in 10 ml of extraction buffer (0.1% PBS Tween-20, 2% PVPP, 1 mM EDTA, 1 mM PMSF, 1 μg leupeptin, 100 mM ascorbic acid, pH 7.4). Crude protein extract was recovered by centrifugation and concentrated using centrifugal filters (Centriprep YM-10; EMD Millipore, Billerica, MA, USA). The concentrate was resuspended in 3 ml of 2.5 mM 3-(N-morpholino)propanesulfonic acid (MOPS) buffer (pH 7.2) and reisolated by centrifugation into a final volume of less than 1 ml. For preliminary assessment of feruloyl esterase activity in transgenic lines, enzyme was qualitatively estimated using a microplate screening assay  by measuring the hydrolysis of ethyl ferulate (50 mM ethyl ferulate, 5 mM of p-nitrophenol in isopropanol, diluted in nine volumes of 2.5 mM MOPS, pH 7.2). To test the samples, 10 mg (in triplicate) of concentrated plant protein extracts in 20 μl of 2.5 mM MOPS (pH 7.2) were placed in each microplate well, and 100 μl of substrate was added immediately before readings. Decrease in absorbance at 415 nm at 30°C was recorded (from triplicates) every 5 min for 1 h. Relative enzyme activity was determined by linear regression of the decrease in absorbance versus time and slope of the regression equation (Figure 2A).
In vitroruminal incubation
In vitro ruminal incubations were performed in 125 ml serum vials fitted with rubber stoppers. Whole alfalfa plants were ground to pass a 1.0 mm screen, and weighed into filter bags (F57; Ankom, Macedon, NY, USA; 0.5 g per bag) and loaded into vials prior to addition of ruminal inoculum. Six cows with permanent rumen cannula, fed an alfalfa hay diet were used as rumen fluid donors. Cattle used in this study were cared for in accordance with standards of the Canadian Council on Animal Care (CCAC, 1993). Rumen fluid was collected 2 h after feeding from five different locations in the rumen-reticulum and strained through four layers of cheese cloth. Equal amounts of rumen fluid from each cow were combined, mixed with a mineral buffer  in a ratio of 1:2 to serve as inoculum. Incubations were initiated by dispensing 20 ml of inoculum under a stream of CO2 into vials containing each substrate in F57 filter bags. The vials were immediately sealed and affixed to a rotary shaking platform (125 rpm) in a 39°C incubator (model 39419-1; Forma Scientific, Marietta, OH, USA). Triplicate vials for each sample and blank were retrieved from the incubator after 6 h and 72 h of incubation and processed for determination of VFAs, ammonia and IVDMD as previously described .
Residue remaining in the filter bag was rinsed thrice with phosphate buffer (pH 7.0), dried at 55°C and weighed to estimate the IVDMD. Two subsamples of the liquid culture were taken (1.5 ml each) from each vial immediately after retrieval of the filter bags. One sample was transferred to a 2 ml microcentrifuge tube containing 126 μl of trichloroacetic acid (TCA; 65% w/v) and centrifuged at 14,000 × g for 10 min to precipitate particulate. The supernatant was transferred into 2.0 ml microcentrifuge tubes and stored at -20°C until analysis for ammonia by the phenyl-hypochlorite method . Another sample was mixed with 0.3 ml of metaphosphoric acid (25% w/v), centrifuged at 14,000 × g for 10 min and the supernatant was analyzed for VFA as described by Wang et al. .
Attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR)
Ground samples and residues from in vitro digestion of transgenic (43A, 41A, 1A, 28ER, 24ER, 61 V, 15 V and 2 V) and control plants were subjected to FTIR spectroscopy using ALPHA FT-IR spectrometer (Bruker Optics, Ettlingen, Germany) equipped with a platinum diamond attenuated total reflectance (ATR) attachment. Spectra were collected over 4,000 to 600 cm-1 with resolution of 4 cm-1 and 32 repetitious scans were averaged for each spectrum. The sample contact area was circular with a diameter of approximately 1.5 mm as the samples were pressed against the diamond crystal of the ATR device. Spectra were baseline corrected and area normalized manually using Opus software (Opus Software Limited, Grantham, UK). Averages of 43A, 41A and 1A spectra were used to represent apoplast lines, while representative spectra for endoplasmic reticulum and vacuole targeted lines were computed by averaging data from lines 28ER and 24ER and 61 V, 15 V and 2 V, respectively. Spectra were subject to PCA and digital subtraction data analysis (XLSTAT 2013.4 statistical software; Addinsoft, New York, NY, USA).
Cell wall analysis
For each line, 50 to 60 whole plants were pooled and ground as described above. Ground samples (60 to 70 mg) were used to prepare alcohol insoluble residue (AIR) as described previously . Briefly, ground material was sequentially extracted over a sintered glass funnel under vacuum with two volumes of 100 ml of ice cold 80% ethanol, 100% ethanol, chloroform:methanol (1:1) and 100% acetone. Starch was removed by treatment with Type II-A Bacillus α-amylase (Sigma-Aldrich; approximately 1,000 units/100 mg cell wall AIR) in 50 mM sodium phosphate buffer (pH 7.0) at 25°C in a shaking incubator for 48 h. De-starched samples were centrifuged (3,660 × g for 10 min at 25°C) and the pellet was subsequently washed thrice with deionized water and recovered by centrifugation (3,660 × g for 10 min at 25°C). The resulting pellets were suspended in 500 μl of acetone and evaporated with a stream of air at 36°C until dry. For total sugar analysis, triplicate AIR samples (5 mg) of each line (43A, 41A, 1A, 28ER, 24ER, 61 V, 15 V, 2 V and C) were hydrolyzed with 72% H2SO4 and the released sugars were quantitated by a combination gas chromatography - mass spectroscopy (GC-MS) of alditol acetate derivatives. The remains after trifluoroacetic acid (TFA) treatment were hydrolyzed in Updegraff reagent (acetic acid:nitric acid:water, 8:1:2 v/v) and used in an anthrone assay to quantify crystalline cellulose . Uronic acid content in triplicate AIR samples of each representative line (43A, 41A, 1A, 28ER, 24ER, 61 V, 15 V, 2 V and C) were quantified by adapting the micro-assay of van den Hoogen et al.  and using galacturonic acid as a standard. An average of 43A, 41A and 1A, 28ER and 24ER and 61 V, 15 V and 2 V were used to represent apoplast lines (A), endoplasmic reticulum (ER) and vacuole (V) targeted lines, respectively.
To determine lignin content , approximately 1 mg of AIR samples (three replicates for each line, that is, 43A, 41A, 1A, 28ER, 24ER, 61 V, 15 V, 2 V and C) were solubilized in freshly prepared acetyl bromide solution (100 μl of 25% (v/v) acetyl bromide in glacial acetic acid) for 3 h at 50°C, with 2 M sodium hydroxide (400 μl) and 0.5 M hydroxylamine hydrochloride (70 μl) being added to stop the reaction. Absorbance at 280 nm was measured using Synergy HT multi-detection microplate reader (Biotek Instruments, Inc., Winooski, VT, USA). Cell wall phenolics were extracted according to Buanafina et al.  with minor modifications. Briefly, following the extraction of chlorophyll pigments with aqueous methanol, ester bound compounds were extracted from ground plant material (50 mg, three repeats) with 1 M NaOH (5 ml) followed by incubation at 25°C for 24 h in the dark. Aliquots of the mixture were combined with a 1.2 volume of 100 mM HCl and centrifuged (1,000 × g, 20 min). The supernatant was diluted with four volumes of methanol and UV spectrum was recorded between 200 to 400 nm.
Enzyme saccharification assay
Alkaline peroxide pretreatment was performed as described by Banerjee et al. . Briefly, 50 ml of 1% H2O2 was adjusted to pH 11.5 with 5 M NaOH and mixed with 1 g of ground AIR plant material (as prepared above) in a 250 ml Erlenmeyer flask. Final concentrations were 1% H2O2 (300 mM), 0.8% NaOH (200 mM) and 2% biomass. The flasks were incubated at 24°C with shaking at 90 rpm for 24 h. The slurries were neutralized to pH 7 by the addition of 12 N HCl. Residual H2O2 was inactivated by addition of 59 μl of catalase (28 mg protein/ml; Sigma-Aldrich). After inactivation of catalase by heating at 90°C for 15 min, the flask contents were centrifuged and dried at 55°C. Alkaline peroxide treated material from transgenic lines 43A, 41A, 1A, 28ER, 24ER, 61 V, 15 V, 2 V and control were suspended at a final concentration of 0.5% (w/v) in 50 mM sodium citrate buffer (pH 5.0) containing 5 μg/ml tetracycline, 5 μg/ml cycloheximide and 0.02% sodium azide. The slurry was kept in suspension using a paddle reservoir designed for dispensing pharmaceutical beads on the Biomek FXP (model VP 756C-1P100; V&P Scientific, Inc., San Diego, CA, USA). A total of 200 μl of substrate slurry was then dispensed into mini-Eppendorf tubes, followed by addition of commercial enzymes (Accellerase 1500) at a final concentration of 15 mg protein per g of cellulose and the mixture was incubated at 50°C for 48 h. The tubes were centrifuged at 1,500 × g for 5 min to separate solid residue from hydrolyzed biomass. The supernatants (100 μl) were transferred into a Costar 96-well plate and heated at 100°C for 10 min to inactivate the enzymes. Each reaction mixture was run in duplicate, sampled twice, and the supernatants were assayed twice for released glucose using a K-GLUC kit (Megazyme, Bray, Ireland). Sugar assays were conducted in 96-well plates using 194 μl of assay reagent and 12 μl of sample. The plates were incubated at 50°C for 20 min before reading absorbance at 510 nm using the Synergy HT multi-detection microplate reader (Biotek Instruments, Inc.).