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A novel folate binding protein in Arabidopsis expressed during salicylic acid-induced folate accumulation Bijesh Puthusseri, Peethambaran Divya, Veeresh Lokesh, Gyanendra Kumar, Mohammed Azharuddin Savanur, and Bhagyalakshmi Neelwarne J. Agric. Food Chem., Just Accepted Manuscript • DOI: 10.1021/acs.jafc.7b04236 • Publication Date (Web): 12 Dec 2017 Downloaded from http://pubs.acs.org on December 12, 2017
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A novel folate binding protein in Arabidopsis expressed during salicylic
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acid-induced folate accumulation
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Bijesh Puthusseri,1 Peethambaran Divya,1,# Veeresh Lokesh,1 Gyanendra Kumar,1
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Mohammed Azharuddin Savanur,2,# and Bhagyalakshmi Neelwarne1,* 1
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CSIR-Central Food Technological Research Institute, Mysore-570020, India
6
2
7 #
8 9 10 11
Plant Cell Biotechnology Department
Department of Biochemistry, Karnatak University, Dharwad, India
Present address: Indian Institute of Science, Banaglore-560012, India
Running Title: A novel folate binding protein in Arabidopsis *
Corresponding author: E-mail:
[email protected];
[email protected] Telephone: 91-821-2516501
Telefax: 91-821-2517233
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ABSTRACT: Increasing the quantity of natural folates in plant foods is recently
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gaining significant interest, owing to their acute deficiencies in various populations. This
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study observed that foliar salicylic acid treatment enhanced the accumulation of folates
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in Arabidopsis, which correlated with the increase in a folate binding protein (FBP) and
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the expression of mRNA of a putative folate binding protein At5G27830. A protein band
18
corresponding to ~43 kDa was observed after resolving the affinity-purified protein on
19
SDS-PAGE, and the partial amino acid sequence indicated that the protein is indeed
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At5G27830. Docking studies performed with At5G27830, confirmed specific binding of
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folic acid to predicted site. Heterologous expression of At5G27830 in the yeast resulted
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in significant uptake and accumulation of folic acid in cells. This novel study of a plant
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FBP will be useful for folate metabolic engineering of a wide range of crops.
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KEYWORDS: Folate binding protein · Folate receptor · At5G27830 · Plant folate ·
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Metabolic engineering
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1. INTRODUCTION
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Importance of folates in nutrition and health has received newer dimensions ever since
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the discovery of the key roles played by folates as mobile co-factors in intracellular
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transfer and utilization of one-carbon moieties, transfer of methyl groups, in the
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synthesis of nucleic acids, methionine replenishment and as co-substrates.1 Folate
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deficiency is linked to anaemia, poor health and infant mortality in several populations
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globally. Therefore, efforts are being made to find novel approaches that ensure the
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delivery of adequate levels of natural folates through plant foods. In plant cells, folate
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turnover rate is very high owing to a number of key roles in various metabolic
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processes, in addition to those stated above. This means that folate is utilised very
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rapidly and needs to be replenished in the same pace. Increasing the quantity of folates
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by metabolic engineering of folate biosynthetic genes has discreetly been successful in
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tomato, fruits2,3 and in rice seeds.4 Transgenic expression of a bovine FBP gene resulted
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in 150-fold folate increase in rice,5 implying the need to understand the genes involved
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in folate enhancement in plants and to target them for folate metabolic engineering.
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Researchers have pointed at the need for better understanding of the regulation of the
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folate biosynthetic pathway in order to explore an engineering strategy applicable to a
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wide range of crops.6–8 In addition to over-expressing biosynthetic genes, folate
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enhancement can also be strategically achieved by improving the stability of the
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synthesised folate via :1) down-regulating folate catabolic enzymes, 2) transforming
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folates into stable derivatives, 3) increasing the abundance of folate binding protein
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(FBP), 4) enhancing cellular antioxidants, and 5) promoting folate sequestration into the
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vacuole.6,9 In a previous study we have shown that treatment of coriander with aqueous
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solution of salicylic acid (SA, 250 µM) resulted in two-fold increase in total folates
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(from 1330 in
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methyltetrahydrofolate (5-MTHF) was the folate derivative present in abundance (60%).
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SA treatment also imparted better folate stability in coriander foliage during post-harvest
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storage,10 indicating that stabilizing factors might be playing a major role in enhancing
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the accumulation of folates. Other than the biosynthetic genes, the folate binding
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proteins (FBPs) are vital gene-targets for folate metabolic engineering. The
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tetrahydrofolates, which are the highly recommended form of the folate derivatives, are
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significantly stabilised by the presence of the FBPs in milk.11 Transgenic expression of a
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bovine FBP gene in Arabidopsis resulted in the enhancement folates in rice, implying
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that FBPs are indeed present in plant foliage.12 The folate levels were positively
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correlated with the upregulation in levels of FBPs, indicating the importance of FBPs in
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folate enhancement.12 The present study was undertaken to identify and characterize
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FBP at functional level, employing affinity purification, amino acid sequencing, in silico
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modelling and docking, and heterologous expression of the novel FBP identified in
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Arabidopsis.
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2. MATERIALS AND METHODS
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Extraction and purification of folate binding proteins from foliage
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Extraction and purification of folate binding proteins (FBPs) involves the principle of
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affinity chromatography, where methotrexate or folic acid bound to a gel matrix acts as
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ligand for binding and retaining the FBPs present in the sample. Such bound FBPs may
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be eluted by changing the buffer to acidic pH. Experiments were conducted at 4 °C
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unless otherwise stated. For the preparation of the protein samples, an earlier reported
control to 2867 µg/100g DW in SA-treated), where 5-
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method with minor modifications was followed.13 Foliage of the Arabidopsis plants (3
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g) was extracted in 0.05 M mannitol (10 mL), in the presence of protease inhibitor
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phenylmethylsulfonyl fluoride (PMSF). The homogenates were centrifuged at 10000 × g
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for 10 min, and the supernatant was saved. The protein was precipitated with the
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addition of solid CaCl2 to a final concentration of 10 mM, stirred for 20 min and
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centrifuged at 10000 × g for 15 min. To remove the folates that remain bound tightly
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with FBPs and are co-extracted along with the proteins, the pellet was solubilised in 30
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mL 0.05 M mannitol, and acidified with acetic acid to a final pH of 3.5. The proteins
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were precipitated and clarified with CaCl2 method as described above. The final protein
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pellet obtained was suspended in 30 mL 0.05 mannitol and the pH was adjusted to 7.4
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with 5 N NaOH. To this solution, triton-X 100 was added dropwise to a final
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concentration of 2%. The mixture was stirred for 48 h and pelleted by centrifugation at
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10000 × g and the supernatant was collected in a separate tube.
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Methotrexate-sepharose 4B affinity columns were used for the purification of FBPs.14
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CNBr-activated sepharose 4B gel was washed with cold 0.1 M NaHCO3 (3 L), and re-
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suspended in 400 mL of 0.1 M NaHCO3 containing 1.8 g of 1,6-diaminohexane (pH 9).
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The suspension was stirred for 48 h, and then washed with 2 L of 0.1 M NaHCO3. The
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gel was re-suspended in equal volume of 0.1 M NaHCO3 containing 2.4 g methotrexate,
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and the pH was adjusted to 8.5. To this suspension, 2.4 g of 1-ethyl-3(3-
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dimethylaminopropyl) carbodiimide-HCl was added over a time of 30 min. The
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suspension was stirred for 2 h at room temperature, and then at 4 °C for 24 h. The gel
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was transferred into a coarse sintered glass funnel, and was washed with 3 L of 2 M
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NaCl in 0.05 M potassium phosphate buffer, pH 7, followed by 2 L of water, 2 L of 1 M
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acetic acid, and then by 2 L of water. The gel was stored at 4 °C after mixing with
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0.03% sodium azide.
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For purification of the FBPs, the total protein extract was dissolved in phosphate
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buffer (final pH 6.4 and 0.5 M). The column with the activated methotrexate-sepharose
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4B gel was washed with 0.5 M phosphate buffer (pH 6.4). The protein solution was
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passed through the column, followed by washing with 2 M NaCl in 0.05 M sodium
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borate buffer (pH 8). Further washing was done with 0.01 M sodium borate buffer (pH
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8). The FBPs retained in the column were eluted with 0.05 M acetic acid and the acidic
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fraction was collected as eluent. The FBP fraction was precipitated by adding equal
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quantity of 80% ice-cold acetone. After overnight-storage at -20 °C, the solution was
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centrifuged at 10000 × g for 10 min to recover the protein pellet, which was re-dissolved
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in 0.05 M mannitol solution for protein quantification. For the quantification of protein,
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Qubit® protein assay kit and Qubit® fluorometer (Life technologies, Gaithersburg, MD)
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were used. To obtain internal sequence data, the purified FBP fraction was run on 10%
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SDS-PAGE, and protein bands were detected with Coomassie Brilliant Blue R-250.
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The~43 kDa band was excised from the SDS-PAGE gel, homogenized in 100 mM Tris,
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pH 8.0, and digested with trypsin at an estimated enzyme:substrate ratio of 1:20 for 16 h
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at 37 °C. The purified samples were sequenced by an automatic peptide sequencer (ABI
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491, Procise, Applied Biosystems). Protein with similar sequences in Arabidopsis was
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searched in GenBank databank using the BLAST program. The search returned a
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putative folate binding protein At5G27830.
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In silico analysis of the putative folate binding protein AtFBP1 (At5G27830)
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Search for the conserved domains present in the putative folate binding protein was
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conducted
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(http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi).15 The best fit protein template,
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human folate receptor alpha (4km7.A) identified by the Swiss-Model template search
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(http://swissmodel.expasy.org/)16
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(https://www.ebi.ac.uk/Tools/msa/clustalw2/).17
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conducted using the AtFBP1 amino acid sequences in NCBI BLAST interface,18 and the
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filtered results were used for generating an unrooted phylogenetic tree by MEGA 6
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software,19 using neighbour joining algorithm. The significantly related proteins were
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further analysed by ClustalW2.
using
NCBI
was
conserved
aligned
with A
domain
AtFBP1
protein
database
using
BLAST
ClustalW2 search
was
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Protein secondary structure prediction was done in the ITASSER server
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(http://zhanglab.ccmb.med.umich.edu/I-TASSER/)20 using the default parameters.
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Ligand
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(http://zhanglab.ccmb.med.umich.edu/COACH/).21
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structure of the folic acid molecule (zinc_18456289) was obtained from the Zinc
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database (http://zinc.docking.org/).22 The molecules were prepared for docking using
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Autodock Tools (http://autodock.scripps.edu/resources/adt), where polar hydrogens
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were added and the files were saved as PDBQT. Docking simulation was conducted
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using Autodock Vina23 using PyRx interface.24 The docking results were analysed using
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the molecular visualization tool UCSF Chimera (https://www.cgl.ucsf.edu/chimera/).25
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LigPlot+26 was employed for the generation of 2D plots of the result and to find the
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interaction of surrounding molecules with the ligand.
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Functional analysis of the putative folate binding protein AtFBP1 (At5G27830)
binding
sites
were
predicted
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COACH
server
For docking studies, crystal
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Full-length cDNA of the At5G27830 gene was amplified using the cDNA prepared from
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Arabidopsis mRNA. Previous researchers have cloned and overexpressed the AtRBP1 in
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Arabidopsis plants in a study that meant to identify proteins protecting Arabidopsis from
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oxidative stress.27 Out of the 23 proteins with obscure features analysed in this work,
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AtFBP1 did not show a significant protection during oxidative stress when compared
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with many other proteins. An open reading frame was used, leaving 51 bases of the
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coding sequences (CDS) in the TAIR database at the 5’ end to clone as the full-length
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gene. BLAST search, followed by CLUSTAL alignment of the At5G27830 mRNA in
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the NCBI database pointed towards fact that the initial 51 bases reported in the TAIR
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database might be of non-coding region as it was absent in the other mRNA sequences
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(Figure 1). PCR reactions for the amplification of the full length CDS with the start
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codon as provided in the TAIR database also failed repeatedly even after trials with
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different primers, which indicate that the 51 bases at the 5’ end might not be even part of
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the mRNA generated. Hence, the same gene specific-primer sequences used for full
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length cloning27 were used for the present study as well.
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A forward primer (CGGGGTACCAGATGGGAAGATGTTTAACG) with an added
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restriction
site
for
Kpn1
and
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(CCGCTCGAGTTAATCAGAGCTTGTTCTTCT) with an added restriction site for
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Xho1, in frame with the N-terminal 6His-tag of the pYES2/NTA plasmid were
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designed. The gene was amplified from the cDNA by PCR reaction with the mixture
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consisting of 100 ng template, 10 pmol primer, 0.2 mM dNTPs and 1 U of Taq DNA
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polymerase in 1× reaction buffer. The gene amplification was carried out under the
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following conditions: initial denaturation of the template at 95 °C for 4 min followed by
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35 cycles at 95 °C for 1 min (denaturation), 60 °C for 1 min (annealing) and 72 °C for 1
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min (extension). The final extension was done at 72 °C for 10 min. Both the amplified
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DNA and the pYES2/NTA vector were cut using restriction enzymes. The DNA and
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plasmid (1 µg), and restriction enzymes (Kpn1 and Xho1 1 unit each) were digested in
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1× Cut Smart buffer at 37 °C overnight. The digested DNA and plasmid were purified
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by gel extraction kit (Sigma-Aldrich, St. Louis, USA) as per the manufacturer’s
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instructions. The DNA and the plasmid (50 ng each) were ligated using T4 DNA ligase
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(1 U) in 1× reaction buffer at room temperature for 15 min and chilled on ice. For
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amplifying the ligated plasmid, the Escherichia coli (E. coli) strain DH5α was used.
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The transformed cells were selected by growing on SOB agar containing nalidixic acid
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(15 µg/mL) and ampicillin (50 µg/mL). The plates were incubated at 37 °C for 12–16 h.
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The plasmids were isolated by Mini plasmid preparation kit (Sigma-Aldrich, St. Louis,
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USA) and the restriction enzyme-digested plasmids were run on 0.8% agarose for the
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confirmation of the presence of insert. The presence of the AtFBP1 gene in frame with
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the 6His tag was confirmed by sequencing with a T7 forward primer.
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The Saccharomyces cerevisiae wild type (BY4741; Mat a; his3D1; leu2D0;
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met15D0; ura3D0; YPL268w::kanMX4) strain was used for the protein expression.
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Lithium acetate (LiAc) method28 was used for the yeast transformation. After
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transformation, cells (100 µL) were seeded on the selective media, synthetic defined
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(SD) agar media lacking uracil (SD/−Ura) for the selection of the transformants. The
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presence of the AtFBP1-gene insert in transformants was confirmed by colony PCR and
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sequencing of the isolated plasmid.
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The yeast cultures with the AtFBP1 insert were grown overnight in SD/−Urabroth
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with dextrose as the carbon source at 30 °C. For the protein induction, the pellets of
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cultures were transferred into SD/−Ura broth with the protein-inducing agent,
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galactose, for 32 h. A yeast-lysis buffer was prepared with Tris (pH 8, 100 mM),
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MgCl2, NaCl (300 mM), PMSF (1 mM) and glycerol along with appropriate quantity of
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protein inhibitor cocktail. The pellet obtained after centrifugation (3000 × g, 5 min) was
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re-suspended in 500 µL of lysis buffer in a 2 mL microfuge tube and 50 µL of glass
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beads were added. A vortexing cycle with 30 s vortex followed by 1 min incubation on
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ice for 30 cycles was done to lyse the cells. The cells were pelleted by centrifuging at
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10000 × g for 5 min, and the supernatant was separated from the pellet. The extracted
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proteins were analysed by sodium dodecyl sulfate polyacrylamide gel electrophoresis
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(SDS-PAGE).29 The expressed protein was analysed for the presence the 6His tag by
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Western blotting using the monoclonal anti-polyHistidine antibody. For the Western
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blotting, the proteins were transferred from the gel to a nitrocellulose membrane using
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semi-dry
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California). The transfer to the membrane was carried out at 15 V for 30 min. For the
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detection of the expressed protein, the procedure provided with the monoclonal anti-
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polyHistidine antibody produced in mice (Sigma-Aldrich, St. Louis, USA) was
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followed. After treatment with the primary antibody, followed by washing, the
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membrane was treated with anti-mouse IgG-alkaline phosphatase as the secondary
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antibody (Sigma-Aldrich, St. Louis, USA). The membrane was treated with BCIP/NBT
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until the bands developed to optimum intensity. The membrane was washed with
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distilled water for three times, air dried and documented.
electrophoretic
transfer
instrument
(Transblot,
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Uptake of FA-EDA-FITC conjugate by AtFBP1-transformed yeast
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For determining the binding affinity of the AtFBP1 to the folate, the yeast, expressing
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the AtFBP1 were grown in the presence of the folate tagged with the fluorescent
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molecule fluorescein isothiocyanate (FA-EDA-FITC). In brief, the wild type and the
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transformant were grown overnight in a 1 mL culture at 200 g and 30 °C. The wild type
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was supplied with a complete SD medium with glucose as the carbon source, and
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transformant was supplied with SD/-Ura medium with galactose as the carbon source.
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The cells were centrifuged at 3000 × g for 5 min, and to the pellet fresh medium was
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added. FA-EDA-FITC was added at 0.5 mg/mL to the culture, vortexed thoroughly to
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mix, and incubated for 6 h at 100 × g and 30 °C. The cells were pelleted by
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centrifugation at 3000 × g for 5 min and the pellet was washed twice with distilled water
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and analysed under a fluorescent microscope (Olympus BX51) having a dichroic mirror
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DM500 with excitation filter BP450-480, where a barrier filter BA515 was used for
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observing the FA-EDA-FITC fluorescence. Relative quantitation of folate uptake was
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analysed by ImageJ software (W.S. Rasband, ImageJ, NIH, Bethesda, MD). For
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estimating the actual folate uptake by the transformed yeast cells, the yeast cells were
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harvested and subjected for vortex extraction using glass beads for 3 min in ice cold
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extraction buffer. The folate content in the samples were determined by microbiological
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assay using Lactobacillus rhamnosus (ATCC 7469), as reported previously.12
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Statistical analysis
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Treatment values in triplicate were compared with the control values to arrive at
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significantly different values by Student's t-test using SPSS 17 software (SPSS Inc.,
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Chicago, USA).
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3. Results and discussion
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Presence of folate binding proteins in the Arabidopsis foliage
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Affinity purification of FBPs showed three protein bands upon silver staining. The
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prominent band was observed at ~43 kDa (Figure 2a). The other two faint bands were of
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~90 kDa and ~29 kDa. Partial sequences obtained from the amino acid sequencing of
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the tryptic digested ~43 kDa (Figure 2b) were used to conduct a blast search in NCBI
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for matches in Arabidopsis genome (taxid:3701). The search tallied with At5G27830, a
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protein with a folate receptor domain. Although FBPs are known to play a major role in
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folate enhancement in plants,5,9 hitherto no FBP has been functionally characterized
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from plants.
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In silico analysis of the putative folate binding protein AtFBP1 (At5G27830)
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Conserved domain search revealed that the AtFBP1 does in fact contain the folate-
244
binding domain pfam03024. This domain is characterised by the presence of disulphide
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bonds, where sixteen cysteine residues have been identified to contribute in many
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characterised folate binding proteins. Pfam03024 domain is present in the well-studied
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folate receptors such as α, β, γ and δ forms in humans. This domain search confirmed
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that ten conserved cysteines from AtFBP1 align perfectly with the Pfam03024 domain
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(Figure 3a). The template search showed that the PDB structure of the α-folate receptor
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of humans is structurally the most related one with the AtFBP1. Clustal alignment of
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AtFBP1 with 4km7.A indicated the alignment of six cysteines (Figure 3b). Since normal
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folate binding proteins, so far characterised only in animals, have sixteen cysteines, the
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absence of one cysteine in Arabidopsis may be an evolutionary change. For further
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insights into this, the phylogenetic analysis of this protein was conducted with BLAST
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results of flowering plant protein sequences (showing query coverage >75 and identity
256
>50), sequences of those excluding flowering plants (query coverage >45 and identity
257
>45) and of the four forms of human folate receptors. All the proteins retrieved by
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BLAST search were uncharacterised. The phylogenetic tree (Figure 3c) constructed with
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neighbour joining algorithm and with boot strapping (2000 replicates) clearly depicted
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two proteins with significant similarity (>80 bootstrap value) with AtFBP1 in one
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cluster (Figure 3c, indicated by red arrow). Further, all the three proteins (of Capsella
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rubella, Eutrema salsagineum and AtFBP1) have only fifteen cysteines and the clustal
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alignment of these three proteins clearly depicted that the cysteine residues are
264
conserved (Figure 3d).
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The model of the AtFBP1 was predicted using the ITASSER server, and was
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downloaded as PDB file (C-Score = −2.88, TM-Score = 0.39, RMSD = 13.3 Å). The
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TM-score was in the median range of reliability, which ranged between 0.17 and 0.5.
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Binding site prediction by COACH server showed the region with amino acids at 128,
269
131, 168, 172 and 201 may constitute a possible folic acid binding site. This has brought
270
forth a protein receptor model with folic acid as a ligand (C-score 0.01), which was
271
obtained by comparing with the human folate binding protein FOLR1 (4LRHA). The
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locations of the conserved cysteines in the model were compared with that of 4km7.A,
273
because in case of folate binding proteins the reliability of a predicted structure is
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largely influenced by the prevalence of cysteine-cysteine interactions.30 Out of the
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fifteen cysteines in AtFBP1, fourteen were found to contribute towards the formation of
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the binding site (Figure 4a). The bovine FBP DN512948, which is used to increase
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folate content in Arabidopsis by heterologous expression, was also found to have similar
278
sequence and structural characteristics of the AtFBP1. The bovine FBP had the same
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folate binding pfam03024 as the conserved domain. However, DN512948 have
280
seventeen cysteines instead of fifteen cysteines present in AtFBP1. Structural
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overlapping of the 4km7.A (Figure 4b) on AtFBP1 showed that the binding sites do
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align with each other (Figure 4c). The folic acid molecule was docked on the predicted
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binding site of the AtFBP1 (Figure 4d) with a free energy change (∆G) of −9.3. Whereas
284
docking of the folic acid with the human folate binding protein FOLR1 crystal structure
285
4km7.A showed a free energy change of (∆G) of −8. The 2D plot of the docked PDB
286
structure was generated with the LigPlot+, which revealed the formation of five
287
hydrogen bonds between the folic acid molecule and the amino acid residues (Gly 71,
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Asn 134, Leu 168 and Arg 170) of the protein (Figure 4e).
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Uptake and accumulation of the FA-EDA-FITC conjugates by AtFBP1 expressing
290
yeast cells
291
Microscopic observations revealed that the yeast cells expressing the AtFBP1 gene had
292
taken up significantly higher quantities FA-EDA-FITC, resulting in emitting bright
293
cellular fluorescence (Figure 5). The intense fluorescence of the transformed cells also
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indicates significantly higher quantity (relative fold change of 81) of the folate
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accumulation by the yeast cells over-expressing the AtFBP (Figure 5g). Actual
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estimation in transformed yeast cells showed a 352 fold increase in total folates,
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confirming high folate binding ability of the AtFBP1 protein.
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Since our earlier studies10,31 demonstrated that the accumulation of higher levels of
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folates in foliage after SA treatment is by folate stabilising factors rather than folate
300
biosynthesis factors, it appears feasible to target genes of folate-binding protein for
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folate metabolic engineering. As in the human counterparts, the AtFBP1 might be
302
actively expressed by cells undergoing rapid cell division. The AtFBP1 might be playing
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a role in the transport of the folates from the site of production (leaves) to the site of
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storage (fruits and seeds) and utilization (roots) as well.
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The present study demonstrates for the first time that the genes coding for proteins
306
that help in binding of folates, render higher stability to folates in plant foods. This
307
study also provides a new gene-target for folate metabolic engineering, and the over
308
expression of this gene (AtFBP1) not only increase folate contents but may also
309
enhance the post-harvest stability of this vitamin. Therefore, this approach of targeting
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folate-binding proteins appears more important for folate-metabolic engineering in
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leafy vegetables rather than targeting the folate biosynthetic pathway. The major
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problem with the folate-rich crops is the post-harvest degradation of the folates,
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resulting in inadequate dietary supply of folate even after consuming large quantity of
314
the food materials.6 Other studies also demonstrate that FBPs render stability to folates
315
present in food sources such as milk11,32 and that the transgenic expression of bovine
316
FBP is known to increase folate content in Arabidopsis,5 which may be applicable to
317
other plants as well.
318
ABBREVIATIONS USED
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SA, salicylic acid; FBP, Folate binding protein; 5-MTHF, 5-methyltetrahydrofolate; FA-
320
EDA-FITC, Folic acid conjugated with fluorescein isothiocyanate; DW, Dry weight
321
AUTHOR CONTRIBUTION STATEMENT
322
BP and BN conceived the study. BP, PD, LV, GK, MAS and BN designed, conducted
323
the experiments and analysed the data. BP, MAS and BN wrote the manuscript. The
324
authors have no competing financial interests to declare.
325
ACKNOWLEDGMENTS
326
We thank Mr. Avinash Kumar of Plant Cell Biotechnology Department, CSIR-CFTRI,
327
for providing the Arabidopsis seeds, as well as for assisting in conducting PCR analyses.
328
REFERENCES
329
(1)
Nutr. 2008, 87 (3), 517–533.
330 331
Smith, A. D.; Kim, Y.-I.; Refsum, H. Is folic acid good for everyone? Am. J. Clin.
(2)
Garza, R. I. D. de la; Quinlivan, E. P.; Klaus, S. M. J.; Basset, G. J. C.; Gregory,
332
J. F.; Hanson, A. D. Folate biofortification in tomatoes by engineering the
333
pteridine branch of folate synthesis. Proc. Natl. Acad. Sci. U. S. A. 2004, 101
334
(38), 13720–13725.
335
(3)
tomato fruit. Proc. Natl. Acad. Sci. 2007, 104 (10), 4218–4222.
336 337
Garza, R. I. D. de la; Gregory, J. F.; Hanson, A. D. Folate biofortification of
(4)
Storozhenko, S.; De Brouwer, V.; Volckaert, M.; Navarrete, O.; Blancquaert, D.;
338
Zhang, G.-F.; Lambert, W.; Van Der Straeten, D. Folate fortification of rice by
339
metabolic engineering. Nat. Biotechnol. 2007, 25 (11), 1277–1279.
340
(5)
Blancquaert, D.; Van Daele, J.; Strobbe, S.; Kiekens, F.; Storozhenko, S.; De
341
Steur, H.; Gellynck, X.; Lambert, W.; Stove, C.; Van Der Straeten, D. Improving
342
folate (vitamin B9) stability in biofortified rice through metabolic engineering.
343
Nat. Biotechnol. 2015, 33 (10), 1076–1078.
344 345
(6)
Scott, J.; Rébeillé, F.; Fletcher, J. Folic acid and folates: the feasibility for nutritional enhancement in plant foods. J. Sci. Food Agric. 2000, 80 (7), 795–824.
ACS Paragon Plus Environment
Page 16 of 27
Page 17 of 27
Journal of Agricultural and Food Chemistry
346
(7)
Blancquaert, D.; Storozhenko, S.; Daele, J. V.; Stove, C.; Visser, R. G. F.;
347
Lambert, W.; Straeten, D. V. D. Enhancing pterin and para-aminobenzoate
348
content is not sufficient to successfully biofortify potato tubers and Arabidopsis
349
thaliana plants with folate. J. Exp. Bot. 2013, 64 (12), 3899–3909.
350
(8)
Opin. Biotechnol. 2017, 44, 202–211.
351 352
Strobbe, S.; Van Der Straeten, D. Folate biofortification in food crops. Curr.
(9)
Blancquaert, D.; Storozhenko, S.; Loizeau, K.; De Steur, H.; De Brouwer, V.;
353
Viaene, J.; Ravanel, S.; Rébeillé, F.; Lambert, W.; Van Der Straeten, D. Folates
354
and Folic Acid: From Fundamental Research Toward Sustainable Health. Crit.
355
Rev. Plant Sci. 2010, 29 (1), 14–35.
356
(10) Puthusseri, B.; Divya, P.; Lokesh, V.; Neelwarne, B. Salicylic acid-induced
357
elicitation of folates in coriander (Coriandrum sativum L.) improves
358
bioaccessibility and reduces pro-oxidant status. Food Chem. 2013, 136 (2), 569–
359
575.
360 361
(11) Jones, M. L.; Nixon, P. F. Tetrahydrofolates Are Greatly Stabilized by Binding to Bovine Milk Folate-Binding Protein. J. Nutr. 2002, 132 (9), 2690–2694.
362
(12) Puthusseri, B.; Divya, P.; Veeresh, L.; Kumar, G.; Neelwarne, B. Evaluation of
363
folate-binding proteins and stability of folates in plant foliages. Food Chem. 2018,
364
242 (Supplement C), 555–559.
365 366
(13) Selhub, J.; Franklin, W. A. The folate-binding protein of rat kidney. Purification, properties, and cellular distribution. J. Biol. Chem. 1984, 259 (10), 6601–6606.
367
(14) Selhub, J.; Ahmad, O.; Rosenberg, I. H. Preparation and use of affinity columns
368
with bovine milk folate-binding protein (FBP) covalently linked to Sepharose 4B.
369
Methods Enzymol. 1980, 66, 686–690.
370
(15) Marchler-Bauer, A.; Panchenko, A. R.; Shoemaker, B. A.; Thiessen, P. A.; Geer,
371
L. Y.; Bryant, S. H. CDD: a database of conserved domain alignments with links
372
to domain three-dimensional structure. Nucleic Acids Res. 2002, 30 (1), 281–283.
373
(16) Arnold, K.; Bordoli, L.; Kopp, J.; Schwede, T. The SWISS-MODEL workspace:
374
a
web-based
environment
for
protein
375
Bioinformatics 2006, 22 (2), 195–201.
ACS Paragon Plus Environment
structure
homology
modelling.
Journal of Agricultural and Food Chemistry
376
(17) Larkin, M. A.; Blackshields, G.; Brown, N. P.; Chenna, R.; McGettigan, P. A.;
377
McWilliam, H.; Valentin, F.; Wallace, I. M.; Wilm, A.; Lopez, R.; et al. Clustal
378
W and Clustal X version 2.0. Bioinformatics 2007, 23 (21), 2947–2948.
379 380
(18) Altschul, S. F.; Gish, W.; Miller, W.; Myers, E. W.; Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 1990, 215 (3), 403–410.
381
(19) Tamura, K.; Stecher, G.; Peterson, D.; Filipski, A.; Kumar, S. MEGA6:
382
Molecular Evolutionary Genetics Analysis Version 6.0. Mol. Biol. Evol. 2013, 30
383
(12), 2725–2729.
384
(20) Roy, A.; Kucukural, A.; Zhang, Y. I-TASSER: a unified platform for automated
385
protein structure and function prediction. Nat. Protoc. 2010, 5 (4), 725–738.
386
(21) Yang, J.; Roy, A.; Zhang, Y. Protein–ligand binding site recognition using
387
complementary binding-specific substructure comparison and sequence profile
388
alignment. Bioinformatics 2013, 29 (20), 2588–2595.
389
(22) Irwin, J. J.; Sterling, T.; Mysinger, M. M.; Bolstad, E. S.; Coleman, R. G. ZINC:
390
A Free Tool to Discover Chemistry for Biology. J. Chem. Inf. Model. 2012, 52
391
(7), 1757–1768.
392
(23) Trott, O.; Olson, A. J. AutoDock Vina: Improving the speed and accuracy of
393
docking with a new scoring function, efficient optimization, and multithreading.
394
J. Comput. Chem. 2010, 31 (2), 455–461.
395 396
(24) Wolf, L. K. New software and websites for the chemical enterprise. Chem Eng News 2009, 87, 31.
397
(25) Pettersen, E. F.; Goddard, T. D.; Huang, C. C.; Couch, G. S.; Greenblatt, D. M.;
398
Meng, E. C.; Ferrin, T. E. UCSF Chimera—A visualization system for
399
exploratory research and analysis. J. Comput. Chem. 2004, 25 (13), 1605–1612.
400
(26) Laskowski, R. A.; Swindells, M. B. LigPlot+: Multiple Ligand–Protein
401
Interaction Diagrams for Drug Discovery. J. Chem. Inf. Model. 2011, 51 (10),
402
2778–2786.
403
(27) Luhua, S.; Ciftci-Yilmaz, S.; Harper, J.; Cushman, J.; Mittler, R. Enhanced
404
Tolerance to Oxidative Stress in Transgenic Arabidopsis Plants Expressing
405
Proteins of Unknown Function. Plant Physiol. 2008, 148 (1), 280–292.
ACS Paragon Plus Environment
Page 18 of 27
Page 19 of 27
Journal of Agricultural and Food Chemistry
406
(28) Gietz, D.; St Jean, A.; Woods, R. A.; Schiestl, R. H. Improved method for high
407
efficiency transformation of intact yeast cells. Nucleic Acids Res. 1992, 20 (6),
408
1425.
409
(29) Schägger, H.; von Jagow, G. Tricine-sodium dodecyl sulfate-polyacrylamide gel
410
electrophoresis for the separation of proteins in the range from 1 to 100 kDa.
411
Anal. Biochem. 1987, 166 (2), 368–379.
412
(30) Della-Longa, S.; Arcovito, A. Structural and functional insights on folate receptor
413
α (FRα) by homology modeling, ligand docking and molecular dynamics. J. Mol.
414
Graph. Model. 2013, 44, 197–207.
415
(31) Puthusseri, B.; Divya, P.; Lokesh, V.; Neelwarne, B. Enhancement of Folate
416
Content and Its Stability Using Food Grade Elicitors in Coriander (Coriandrum
417
sativum L.). Plant Foods Hum. Nutr. 2012, 67 (2), 162–170.
418 419
(32) Ford, J. E.; Salter, D. N.; Scott, K. J. The folate-binding protein in milk. J. Dairy Res. 2009, 36 (03), 435.
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Figure legends
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Figure 1 Clustal alignment of the 5’ end of complete AtFBP1 mRNAs available in the
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NCBI database. The first-highlighted ATG is that of the reported start codon in TAIR
425
database for AtFBP1 gene. The second-highlighted ATG is the perfectly aligning one
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and was used as the start codon by previous workers for the AtFBP1 full-length gene
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cloning (Luhua et al. 2008), which is also used as the start codon for the present study.
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Figure 2 Folate binding proteins (FBPs) in Arabidopsis foliage. The FBPs were
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obtained from total protein extract by affinity purification through methotrexate-FBP
430
binding column. The FBPs were separated ona 10% SDS-PAGE gel, followed by
431
detection with silver staining. a A major band of the size ~43 kDa was observed and is
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denoted with arrow mark. b Amino acid sequences obtained after digestion of protein
433
band ~43 kDa with trypsin.
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Figure 3 Sequence and Phylogenetic analysis of the AtFBP1 protein. a Conserved
435
domain analysis, using the NCBI conserved domain search interface of AtFBP1protein.
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Conserved cysteines are blocked and 10 cysteines are shown conserved in this domain
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search output. b Clustal alignment of AtFBP1 against 4km7.A (human folate receptor
438
alpha).Six cysteines are conserved and are shown in blocks. c An un-rooted neighbour
439
joining-phylogenetic tree constructed with 2000 bootstrap replicates. AtFBP1 is
440
indicated as AraFBP1 (red arrow) and is clustered with the uncharacterised proteins of
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Capsella rubella and Eutrema salsugineum. d Clustal alignment of proteins from
442
Capsella rubella and Eutrema salsugineum with AtFBP1 showing the alignment of 15
443
conserved cysteines (bracketed).
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Figure 4 Modelling and docking analysis of AtFBP1 protein. a Homology model of
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AtFBP1 protein modelled using the I-TASSER server, based on multiple-threading
446
alignments and iterative template fragment assembly simulations, showing cysteines in
447
red colour. b Structure of 4km7.A (human folate receptor alpha) obtained from PDB
448
protein data bank showing cysteines in red colour. c Superposition of AtFBP1 on
449
4km7.A showing the overlapping of folate binding domains of the two proteins. d
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AtFBP1 with a folic acid molecule docked at the predicted binding site (amino acid
451
residues 128,131,168,172 and 201). e 2D plot of the folic acid docked region of the
452
AtFBP1 with hydrogen bonding shown in dotted lines.
453
Figure 5 Uptake of the fluorescent-tagged folic acid (FA-EDA-FITC) by the yeast cells
454
expressing the AtFBP1 gene analysed by confocal microscopy. Figures a–c are those of
455
the wild type yeast cells and d–f are of the yeast cells expressing the AtFBP1 gene under
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the galactose inducible promoter. Figure e shows the fluorescent image of the yeast cells
457
expressing the AtFBP1 gene upon transfer to the galactose containing medium
458
supplemented with FITC tagged folates and are brightly fluorescing upon the uptake and
459
accumulation of the FA-EDA-FITC molecules as these cells are expressing AtFBP1
460
gene that binds to the folates, resulting in increased uptake and accumulation of folates.
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Figure g shows the relative quantification of folates up taken by the yeast cells
462
transformed with AtFBP1 in relation to the wild type. Significances of the mean values
463
were estimated by Student’s t-test.
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Figure 1
NM_001203483.1 NM_122665.3 AY039962.1 BT000985.1 AT5G27830 NM_001203484.1
---------------------TCGTCTTTGTCTTTTGTCATTTTTTGCTTCGAGCTAAGA ---------------------TCGTCTTTGTCTTTTGTCATTTTTTGCTTCGAGCTAAGA ----------------------TTTTTTTGTCTTTTGTCATTTTTTGCTTCGAGCTAAGA --------------------------------------------------------------------------------------ATGCAATTGGGTAATC---GGGTCGACCCA--GTTCTAAAACCATAATTGACGGAGTCTATGCAATTGGGTAATC---GGGTCGACCCA---
39 39 38
NM_001203483.1 NM_122665.3 AY039962.1 BT000985.1 AT5G27830 NM_001203484.1
TCAGTGAAGAGAAAAGATGGGAAGATGTTTAACGAAGAAGGTGTTTTTGATTCAGAGTCC TCAGTGAAGAGAAAAGATGGGAAGATGTTTAACGAAGAAGGTGTTTTTGATTCAGAGTCC TCAGTGAAGAGAAAAGATGGGAAGATGTTTAACGAAGAAGGTGTTTTTGATTCAGAGTCC ----------------ATGGGAAGATGTTTAACGAAGAAGGTGTTTTTGATTCAGAGTCC TCAGTGAAGAGAAAAGATGGGAAGATGTTTAACGAAGAAGGTGTTTTTGATTCAGAGTCC TCAGTGAAGAGAAAAGATGGGAAGATGTTTAACGAAGAAGGTGTTTTTGATTCAGAGTCC ********************************************
99 99 98 44 87 114
NM_001203483.1 NM_122665.3 AY039962.1 BT000985.1 AT5G27830 NM_001203484.1
GATCTTGTTTCTTCATCTCCTGATCTCTTTATCGTCCG--------------GTGCAGTG GATCTTGTTTCTTCATCTCCTGATCTCTTTATCGTCCG--------------GTGCAGTG GATCTTGTTTCTTCATCTCCTGATCTCTTTATCGTCCG--------------GTGCAGTG GATCTTGTTTCTTCATCTCCTGATCTCTTTATCGTCCG--------------GTGCAGTG GATCTTGTTTCTTCATCTCCTGATCTCTTTATCGTCCGAACAATGTTTTCAGGTGCAGTG GATCTTGTTTCTTCATCTCCTGATCTCTTTATCGTCCGAACAATGTTTTCAGGTGCAGTG ************************************** ********
145 145 144 90 147 174
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Figure 2 a Ruler
FBP fraction
kDa 97.4 66 43 29 20.1
14.3
b
KASNWESN ELLECSIC KTCCSSV
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Figure 3 a c
AtFBP1 Cdd: pfam03024
Populus trichocarpa
97 43
Ricinus communis
29
Citrus sinensis
9
Glycine max
9
Cucumis sativus Vitis vinifera
28
AtFBP1 Cdd: pfam03024
Theobroma cacao Prunus persica
9643 99 40
AtFBP1 Cdd: pfam03024
Fragaria vesca Solanum lycopersicum
100
56
Solanum tuberosum Picea sitchensis Selaginella moellendorffii
Eutrema salsugineum
b
AraFBP1
99
Capsella rubella
81
4km7A AtFBP1
FOLRd FOLR1
100
FOLR2
95 76
4km7A AtFBP1
0.2
d
Capsella rubella Eutrema salsugineum AtFBP1
4km7A AtFBP1
Capsella rubella Eutrema salsugineum AtFBP1
4km7A AtFBP1
Capsella rubella Eutrema salsugineum AtFBP1
4km7A AtFBP1
Capsella rubella Eutrema salsugineum AtFBP1 Capsella rubella Eutrema salsugineum AtFBP1
4km7A AtFBP1
Capsella rubella Eutrema salsugineum AtFBP1
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Figure 4 a
b
e c
d Folic acid
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Figure 5 DIC
Fluorescent B
A
Merged C
G
10 µm
D
10 µm
10 µm
10 µm
60 20 0.10 0.08 0.05 0.03
Wild type
Transformant 10 µm
P