Coat protein of alfalfa mosaic alfamovirus (AMV) from Türkiye: genetic inference and in silico docking analysis for potential antiphytoviral purposes
In 2021, a study was conducted in the Denizli region of Türkiye 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...
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AcademicPres
2024-03-01
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| Series: | Notulae Botanicae Horti Agrobotanici Cluj-Napoca |
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| Online Access: | https://www.notulaebotanicae.ro/index.php/nbha/article/view/13529 |
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| author | Serap DEMİREL Abdullah GÜLLER Mustafa USTA Zeynelabidin KURT Gülüstan KORKMAZ |
| author_facet | Serap DEMİREL Abdullah GÜLLER Mustafa USTA Zeynelabidin KURT Gülüstan KORKMAZ |
| author_sort | Serap DEMİREL |
| collection | DOAJ |
| description |
In 2021, a study was conducted in the Denizli region of Türkiye 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.
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| first_indexed | 2024-04-24T15:42:50Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 0255-965X 1842-4309 |
| language | English |
| last_indexed | 2024-04-24T15:42:50Z |
| publishDate | 2024-03-01 |
| publisher | AcademicPres |
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| series | Notulae Botanicae Horti Agrobotanici Cluj-Napoca |
| spelling | doaj.art-769466467bc348ec88753ce2a15c68692024-04-01T18:46:31ZengAcademicPresNotulae Botanicae Horti Agrobotanici Cluj-Napoca0255-965X1842-43092024-03-0152110.15835/nbha52113529Coat protein of alfalfa mosaic alfamovirus (AMV) from Türkiye: genetic inference and in silico docking analysis for potential antiphytoviral purposesSerap DEMİREL0Abdullah GÜLLER1Mustafa USTA2Zeynelabidin KURT3Gülüstan KORKMAZ4University of Van Yuzuncu Yil, Faculty of Science, Molecular Biology and Genetic Department, Bardakçı, Yüzüncü Yıl Üniversitesi Kampüsü, Tuşba, Van, PK: 65090, VanUniversity of Bingöl, Faculty of Agriculture, Plant Protection Department, Selahaddin-i Eyyubi Mah. Üniversite Cad. No 1, PK: 12000, BingölUniversity of Van Yuzuncu Yil, Faculty of Agriculture, Plant Protection Department, Bardakçı, Yüzüncü Yıl Üniversitesi Kampüsü, Tuşba, Van, PK: 65090, VanUniversity of Van Yuzuncu Yil, Faculty of Agriculture, Plant Protection Department, Bardakçı, Yüzüncü Yıl Üniversitesi Kampüsü, Tuşba, Van, PK: 65090, VanVan Agricultural Resarch Institute, Abdurrahman Gazi Mah. İskele Cad. Çalı Durağı Tuşba, Van In 2021, a study was conducted in the Denizli region of Türkiye 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. https://www.notulaebotanicae.ro/index.php/nbha/article/view/13529antiphytoviral compoundAMVin silico modellingmolecular dockingphylogeny |
| spellingShingle | Serap DEMİREL Abdullah GÜLLER Mustafa USTA Zeynelabidin KURT Gülüstan KORKMAZ Coat protein of alfalfa mosaic alfamovirus (AMV) from Türkiye: genetic inference and in silico docking analysis for potential antiphytoviral purposes Notulae Botanicae Horti Agrobotanici Cluj-Napoca antiphytoviral compound AMV in silico modelling molecular docking phylogeny |
| title | Coat protein of alfalfa mosaic alfamovirus (AMV) from Türkiye: genetic inference and in silico docking analysis for potential antiphytoviral purposes |
| title_full | Coat protein of alfalfa mosaic alfamovirus (AMV) from Türkiye: genetic inference and in silico docking analysis for potential antiphytoviral purposes |
| title_fullStr | Coat protein of alfalfa mosaic alfamovirus (AMV) from Türkiye: genetic inference and in silico docking analysis for potential antiphytoviral purposes |
| title_full_unstemmed | Coat protein of alfalfa mosaic alfamovirus (AMV) from Türkiye: genetic inference and in silico docking analysis for potential antiphytoviral purposes |
| title_short | Coat protein of alfalfa mosaic alfamovirus (AMV) from Türkiye: genetic inference and in silico docking analysis for potential antiphytoviral purposes |
| title_sort | coat protein of alfalfa mosaic alfamovirus amv from turkiye genetic inference and in silico docking analysis for potential antiphytoviral purposes |
| topic | antiphytoviral compound AMV in silico modelling molecular docking phylogeny |
| url | https://www.notulaebotanicae.ro/index.php/nbha/article/view/13529 |
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