Molecular Characterization and Bioinformatics Analysis of ACT-toxin Produced by Alternaria spp. Isolated from Corn and Rice in Saudi Arabia.
The aim of the current study is the molecular identification of toxigenic Alternaria contaminating some grains and protein structural analysis depicted from the gene(s) responsible for toxin biosynthesis.
MATERIALS AND METHODS
One hundred fifty grains corn (yellow and red corn grains) and rice (short and long white rice) were collected from different area of Saudi Arabia (Riyadh, Hail, Qasim, Asir, Tabuk, Jizan, Jouf, Jeddah and Dammam), where collected from storage markets and houses. The collected grains were randomly and its weight between 0.5-1 kg of each grain in cleans and dries packaging. Isolation of mycotoxigenic Alternaria spp.
Agar plate and blotter tests were used to isolate Alternaria spp. as described by Neergaard (1977). Grains were divided into two groups, the first group was disinfected with sodium hypochlorite 1% for 2 min and the second group was non-disinfected. All grains were washed several times by sterilized water, and then dried between sterilized filter papers. The half of each group was plated on potato dextrose agar (PDA). All dishes were incubated for 5 to 7 days at 25[degrees]C. Purification and identification of Alternaria spp.
Single colony was transferred and purified by hypha tip technique onto PDA medium in the presence of streptomycin (50 mg /ml). The developing fungi were prepared for molecular identification using primers specific for the ACTTS gene.
Molecular identification of ACTTS gene
The molecular identification of the A CTTS gene was carried out by PCR and sequencing of amplicons.
Isolation of DNA genome
The mycelium mass of Alternaria spp isolates grown on PDA broth medium was harvested by centrifugation at 6000 rpm for 10 min. The pellets were washed twice by PBS buffer and stored at 200 C. Total DNA of the three isolates was isolated using lysozyme - dodecyl sulfate lysis method as described by Leach, et al (1990).
Amplification and purification of ACTTS gene
Specific PCR reactions were conducted to assess the presence of ACTTS gene. The primers used in this study are provided in a supplementary table. The PCR amplification conditions included initial denaturation at 94[degrees]C for 5min then 35 cycles at 94[degrees] C for 30 s, 55[degrees] C for 60 s followed by extension step at 72[degrees] C for 90 s. and a final extension at 72[degrees] C for 7 min. The amplification reaction was performed by thermal cycler (COT Thermocycler model 1105). Purification of PCR product was detected by electrophoresis using agarose 1.5% in 1x TAE buffer and staining with ethidium bromide (Sambrook et al., 1989). The resultant fragment of ACTTS gene was excised from the gel and purified using a QIA quick gel extraction kit (Qiagen, Berlin, Germany).
The purified PCR products were prepared for Sanger sequencing technology using DNA sequencer technique (Sigma, central lab, PNU, KSA). DNA sequences of Alternaria isolates were aligned using Bio Edit software version 7(www. mbio-ncus. edu/bio. edit) and were compared of the often accessions of Alternaria spp. available in the NCBI data base using BLAST algorithm to identify closely related sequences (http/www.ncbi. nih.gov). Dendrogram were constructed by using un-weighed pair Group method with Arithmetic (UPGMA) on Gen bank.
Epitope prediction and antigenicity
The primary amino acids sequence of the ACTTS protein was evaluated from the corresponding nucleotide sequence using MEGA 6.0 software. The linear B-cell epitopes in the primary amino acid sequence of the coat protein was performed using BCPREDS server with default parameters (http://ailab.cs.iastate.edu/ bcpreds/) which implements a support vector machine (SVM) and the subsequence kernel method (El-Manzalawy et al., 2008a). Flexible length linear B-cell epitopes were predicted using FBCPred (El-Manzalawy et al., 2008b) method with a specificity cut-off; 75%.
The antigenicity of each amino acid residue in the primary protein sequence was determined using a semi-empirical method (Kolaskar and Tongaonkar, 1990) which makes use of physicochemical properties of each amino acid and their frequencies of occurrence in experimentally known segmental epitopes.
Three Alternaria isolated from tested grains by PDA method was purified by single spore and hypha tip on PDA slant medium. The Alternaria isolates were selected for molecular identification using ACTTS gene sequencing. Three Alternaria isolates represented grains from yellow corn, white rice and red corn and designated as Alternaria AYC, AWR and ARC, respectively.
Molecular characterization of ACTTS gene
Total DNA was extracted from Alternaria spp. AWR; AYC and ARC infected grains. ACTTS gene of three Alternaria spp isolate AWR; AYC and ARC was amplified from isolated DNA of mycelium using PCR reaction mixture and specific primer sets. PCR amplicons were allowed for sequencing reaction through cycle sequencing method. The DNA Amplicons returned as electropherogram Files. Electropherogram showed distinct peaks for each base cell as well as high Q values for each Cell. Sequences obtained for each primer for each isolate had sufficient overlap between them and used to form one continuous sequence (Coting). The nucleotide partial sequence of ACTTS gene in the three isolates was compared with published isolates on GenBank. The sequence homology revealed that the gene of interest was ACTTS gene (coding for enoyl reductase) and the test fungal isolates were A. alternata isolates. A multiple sequence alignment was constructed using Clustal W software between the three studied isolates. The alignment showed many conserved regions in all sequences as well as distinguished the heterogeneity positions among the aligned sequences. Phylogenetic analysis was performed by construction of phylogenetic tree using a neighbor joining method to unravel the relationships among all Alternaria isolates (Fig. 2). The phylogenetic tree resulted in two clades in which AYC (yellow corn isolate) and AWR (white rice isolate) were in the same cluster whilst ARC (red corn isolate) was separate in a different cluster. Thus, the molecular identification based on sequence homology of the ACTTS gene confirmed the identity and phylogeny of the studied three Alternaria isolates.
Detection of epitope sequences of the Alternaria ACTTS gene
For prediction of the linear B-cell epitopes in the ACTTS protein primary amino acids sequence, BCPREDS server was used. Five to six epitopes, whose sequence length was 14 residues, were retrieved in the amino acid sequences of the three Alternaria isolates (Table 1). The highest epitope according to specificity was AMGAKGGKYTALLP, LEKEKIKTHPVGVR and LEKEKIKTHPVGVR in the ACTTS in AWR, AYC and ARC, respectively. The epitope prediction analysis demonstrated that there were 5, 6 and 5 epitopes whose score were above 0.90 in AWR, AYC and ARC, respectively. Interestingly, there were great variations in the epitope sequences among the three isolates except for the epitope, VYGASTATGTLAVQ which was found to be conserved among all. The predicted epitopes were displayed and highlighted (in red) with their positions on the amino acids sequence as shown in Figure (2).
The antigenicity profile of the amino acid residues of the ACTTS protein demonstrated the residue of high frequency to be part in the genetic determinant (fig. 4). The highest residues above the threshold value were numerous such as Valine (V), Leucine (L), Isoleucine (I), serine (S), Cytosine (C), Aspartic acid (D) , glutamine (Q) and glutamic acid (E) with antigenicity score and spanning the region, 281- 293, 218-230, 280-290 in the primary protein sequence of ARC, AWR and AYC, respectively. These residues with high frequencies of occurrences in antigenic determinants were highlighted (yellow) in the antigenicity profile (fig. 3). Figure 3 also show the variability in the positions and types of amino acid residues with high antigenic frequency.
The emergence of toxigenic fungi on small grains has a negative impact on the safety and quality of feed and food. The genus Alternaria includes cosmopolitan and ubiquitous mold fungi in which saprobes and plant pathogens are many (Thomma, 2003). Alternaria species causes yield losses in processing and production (Vukovi, 2012). Being able to grow at low temperature, Alternaria spp. are responsible for spoilage of food commodities during transport and storage (Barkai-Golan, 2008; Dall'Asta et al., 2014). In addition, reduction in nutritive value, insipidness and discoloration are other problems resulted from contamination of grains by Alternaria (Kosiak et al., 2004). In addition to economic losses, many species are well known mycotoxins producers with various toxicological properties and high risks for human and animal health (Logrieco et al., 2009). Rapid and accurate identification of Alternaria and / or their metabolites are mandatory for the implementation of preventive measures in the whole food production system. The molecular characterization of the three Alternaria spp. isolated from small grains (yellow corn, white rice and red corn) using the mycotoxins gene was performed and the ACTTS gene sequence analysis allowed for coupled identification and mycotoxins screening in the three Alternaria isolates. Mycotoxins-producing fungi were isolated from sorghum grains from Saudia Arabia before (Mahmoud et al., 2013; Yassin et al., 2010). Following the molecular identification of Alternaria spp., B-cell epitopes in the ACTTS gene were predicted. The characterization of B-cell epitopes using computational tools is highly advantageous for the synthesis of specific antibodies for rapid detection of microbial pathogens in their environments. The epitopes prediction saves labor and time for validation experiments. The identification of epitopes plays a crucial role in the vaccine design, immunodiagnostic testing and antibody production (Sette and Fikes, 2003). In this study, BCPREDS server was used to predict epitopes found in the primary amino acids sequence of ACTTS protein. BCPREDS proved high efficiency to predict linear B-cell epitopes in SARS-CoV S protein (El-Manzalawy et al., 2008). There was variability in the sequence and numbers of epitopes among the three toxin proteins analyzed. Here, a fixed length of epitopes (14 residues) was observed. The epitope, VYGASTATGTLAVQ, was found to be common between all isolates suggesting its exploitation for design of a specific antibody to be used for rapid detection of different Alternaria species in small grains. The highly frequent residues with high antigenicity profiles such as Valine, Leucine, Isoleucine, Aspartic acid, Glutamine and Glutamic acid are mostly hydrophobic. The occurrence of hydrophobic residues in epitopes is frequent and do have a hierarchy signature (Aftabuddin and Kundu, 2007; Mine and Zhang, 2002). Epitope prediction has many implications in pathogen detection and differentiation applications.
The consideration of occurrence of Alternaria spp. on small grains is important in risk assessment of mycotoxins and setting up preventive measures proactively.
The authors are grateful to Deanship of Scientific Research; PNU for financial support. And thanks for all technicians in Research Labe, Biology department, PNU.
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Latifa A. Al-Husnan , Muneera D.F. Al-Kahtani , Ahmed G. Abdelhamid  and Randa M.A. Farag 
 Biology Department, Faculty of Science, Princess Nourah bint Abdulrahman University (PNU). Riyadh, Kingdom of Saudi Arabia (KSA).
 Botany Department, Faculty of Science, Benha University, Benha,
(Received: 29 July 2017; accepted: 23 September 2017)
* To whom all correspondence should be addressed.
Tel.: +966540672520; E-mail: email@example.com
Caption: Fig. 1. Phylogeny of the three studied Alternaria isolates (A. Alternata AYC, A. alternata AWR and A. alternata ARC) isolated from yellow corn, white rice and red corn
Caption: Fig. 2. Amino acid residues of ACTTS protein in ARC (A), AWR (B) and ARC (C) showing predicted as epitopes (Red) that are highlighted
Caption: Fig. 3. Kolaskar and Tongaonkar antigenicity scale for prediction of antigenic determinants in ACTTS protein in ARC (A), AWR (B) and AYC (C). Amino acid residues of high frequencies in epitopes are distinguished (yellow)
Table 1. Flexible length predictions of epitopes in the amino acids sequence of ACTTS protein of the three studied Alternaria isolates No. Epitope/AWR Score/ Epitope/AYC AWR 1 AMGAKGGKYTALLP 0.996 LEKEKIKTHPVGVR 2 GPHATPGSILGCDY 0.992 AMGAKGGKYTALLP 3 LEKERSMTHPVGVR 0.991 WKMLYGPHATPGSI 4 VYGASTATGTLAVQ 0.973 VYGASTATGTLAVQ 5 FAFRECPYNHDEGG 0.958 FDYRNPECGAKIRT 6 -- -- PANQKDFEFSAFWK No. Score/ Epitope/ ARC Score/ AYC ARC 1 1 LEKEKIKTHPVGVR 1 2 0.996 WPAAMGAKGGKYTA 0.999 3 0.977 GPHATPGSILGCDY 0.992 4 0.973 VYGASTATGTLAVQ 0.973 5 0.938 IKNFPRSDVKVTTI 0.911 6 0.901 -- --
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|Author:||Al-Husnan, Latifa A.; Al-Kahtani, Muneera D.F.; Abdelhamid, Ahmed G.; Farag, Randa M.A.|
|Publication:||Journal of Pure and Applied Microbiology|
|Date:||Sep 1, 2017|
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