Browsing by Author "Korkmaz, Gulustan"

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Coat Protein of Alfalfa Mosaic Alfamovirus (Amv) From Türkiye: Genetic Inference and in Silico Docking Analysis for Potential Antiphytoviral Purposes
(Univ Agr Sci & veterinary Med Cluj-napoca, 2024) Demirel, Serap; Guller, Abdullah; Usta, Mustafa; Kurt, Zeynelabidin; Korkmaz, Gulustan
In 2021, a study was conducted in the Denizli region of Turkiye to investigate the phylogenetic relationship and presence of alfalfa mosaic alfamovirus (AMV) infecting pepper plants exhibiting viral disease symptoms. A total of 57 samples were collected, of which twenty-four tested positive for AMV with reverse transcriptase polymerase chain reaction (RT-PCR) assays. Samples from pepper plants displaying virus symptoms gave positive bands on the agarose gel, while healthy plants yielded negative results. One of the positive samples was randomly selected, cloned and sequenced. This sequence of the Denizli AMV isolate (753 bp) was recorded in the GenBank database with accession number OQ845956. The nucleotide sequence showed a high nucleotide consensus of 97%-99% compared with the nucleotide sequences of the same variants from different origins in GenBank. According to the phylogenetic tree generated through the Neighbour Joining (NJ) method, this AMV isolate belongs to the same group as Iranian isolates from various of hosts. Furthermore, in silico docking analysis of the coat protein (CP) of the AMV isolate and promising 12 essential oil compounds was performed to enable potential antiviral drug development. Docking study showed that eucalyptol, eugenol and carvacrol can make important contributions to the advancement of drug -based strategies for the managing of plant viruses by interacting with the virus coat protein of high binding energies, -5.3, -5.2 and -5.0 kcal mol-1, respectively. Although the presence of AMV in Denizli province has been reported previously, this study reports the phylogenetic relationships and docking analysis of the new AMV isolate in pepper crops.
First Report of Natural Infection of Watermelon Mosaic Virus (Wmv) Infecting Bottle Gourd and Snake Melon
(Univ Namik Kemal, 2024) Guller, Abdullah; Usta, Mustafa; Korkmaz, Gulustan; Demirel, Serap
Cucurbitaceous crops, one of the main crops of agriculture, are sensitive to many plant viruses. In August 2019, virus-like symptoms were observed on some cucurbit plants grown in private home gardens in Antalya and Denizli provinces (Turkey). A total of 53 leaf samples were sampled from plants with the most symptoms (melon (Cucumis melo L.), watermelon (Citrullus lanatus L.), bottle gourd (Lagenaria siceraria (Molina) Standl.), and snake melon (Cucumis melo var. flexuosus) and tested by Reverse-Transcriptase Polymerase Chain Reaction (RT-PCR) against possible watermelon mosaic potyvirus (WMV) infection. The coat protein gene (CP) specific primer sets amplified a gene product of nearly 820 bp fragment from symptomatic plants. WMV infections were detected in 31 individual cucurbit plants, including 11 melons, 8 watermelons, 7 snake melons and 5 bottle gourds. The presence of viral infection was found only in ornamental squash plants in Antalya province and in all cucurbits sampled in Denizli province. To better comprehend the molecular characteristics of virus isolates, the amplified viral DNA fragments were cloned in a proper prokaryotic plasmid, sequenced by Next Generation Sequencing (NGS) and recorded to GenBank. Bioinformatic analyses using the Basic Local Alignment Search Tool (BLAST) showed that the identified CP gene sequences exhibited significant nucleotide homogeneity, supported by a high nucleotide similarity index with that of other isolates around the world. In addition, Turkish isolates isolated from Antalya and Denizli regions showed approximately 94% nucleotide similarity among themselves. For phylogenetic inference, WMV sequences were subjected to multiple alignments with isolates from different geographic origins of the same viruses. Molecular phylogeny showed that all WMV isolates are closely related to other world WMV isolates at variable rates. WMV is wide host range viruses in cucurbit crops, however, this work is the first scientific report of WMV isolates detected in bottle gourd and snake melon from the South and West Regions of Turkey all over the world.
Recombinant Tritin Protein Exhibits Antiviral Activity Against Zucchini Yellow Mosaic Virus
(BMC, 2025) Demirel, Serap; Usta, Mustafa; Korkmaz, Gulustan; Kurt, Zeynelabidin
BackgroundRibosome-inactivating proteins (RIPs) are a group of proteins known to inhibit protein synthesis and contribute to plant defense responses. Although the antiviral properties of various RIPs have been demonstrated, the antiviral potential of tritin, a type 1 RIP from bread wheat (Triticum aestivum L.), remains unexplored. This study aimed to investigate the antiviral activity of recombinant tritin against zucchini yellow mosaic virus (ZYMV) in zucchini (Cucurbita pepo L.) plants.MethodsThe tritin gene was isolated from the wheat cultivar Kutluk-94, cloned into the pETDuet-1 expression vector, and expressed in Escherichia coli BL21 (DE3) cells. Following induction, recombinant tritin was purified using Ni-NTA affinity chromatography. Antiviral activity was assessed by measuring morphological parameters, disease severity, and the expression levels of the ZYMV Coat Protein (CP) gene and the Pathogenesis-Related 1 (PR1) through quantitative real-time PCR.ResultsTritin-treated plants exhibited significantly lower ZYMV-CP gene expression compared to virus-inoculated controls at 3- and 15- days post-inoculation. Furthermore, PR1 gene expression was upregulated in response to tritin application, suggesting the activation of systemic defense pathways. Morphological assessments revealed dose-dependent phytotoxic effects, including reductions in chlorophyll content and plant growth at higher tritin concentrations.ConclusionThis study represents the first report in demonstrating that recombinant tritin exhibits antiviral activity against ZYMV, reducing viral replication and enhancing defense gene expression in zucchini plants. However, the phytotoxic effects observed at higher concentrations suggest the need for dose optimization before agricultural application. These findings provide a promising basis for the development of RIP-based antiviral strategies to improve crop tolerance.
Survey of Apple Mosaic Virus in Apple-Growing Provinces of East Anatolia (Malatya and Van) by Rna Probe Hybridization Assay and Rt-Pcr
(Tubitak Scientific & Technological Research Council Turkey, 2013) Korkmaz, Gulustan; Sipahioglu, Hikmet Murat; Usta, Mustafa
Two main apple growing provinces (Van and Malatya) of East Anatolia were surveyed for the presence of the Apple mosaic virus (ApMV). Dot-blot hybridization and RT-PCR tests were implemented to investigate the incidence of ApMV, testing a total of 481 samples collected from commercial apple orchards. Digoxigenin-labeled RNA probes of the ApMV were synthesized from the cloned PCR products and applied in dot-blot hybridization to detect the virus in RNA extracts isolated from fresh leaf tissues. A validated RNA probe (dot-blot) hybridization method was adopted to investigate the presence of ApMV infections in the apple orchards of East Anatolia. In order to determine the most suitable mass extraction methods and to ascertain the presence of virus, 3 RNA preparation procedures (QIAGEN RNA extraction kit, silica capture, and citric buffer) were tested. Among the tested extraction methods, silica capture was determined as the most suitable extraction method for dot-blot hybridization assays. ApMV was found in the surveyed locations with an average incidence of 0.8%. The infected trees showed apparent disease symptoms on the leaves of apple trees. The coat protein (CP) genes of 2 viral isolates selected from Malatya (ApMV-G and ApMV-M) were cloned and their complete nucleotide sequences and deduced amino acids were determined (GenBank acc. nos. JX155668 and JX155669). The CP cistron of the ApMV-G and M isolates contained 224 amino acid residues. Phylogenetic trees based on nucleic acid sequences were constructed by the neighbor-joining and the unweighted pair-group mean arithmetic methods with 100 bootstrap replicates. The CP sequence of ApMV-G and ApMV-M varied among the 21 isolates, with overall identity ranging from 88% to 99% and ranging from 91% to 99% at the nucleotide level.