Molecular dissection and an in-silico approach of a novel gibberellin 20-oxidase gene of Hibiscus cannabinus l.
Kenaf (Hibiscus cannabinus L) is widely grown for its fibre. The Gibberellin 20-oxidase (HcGA20ox) gene is responsible for the improvement in quality of kenaf fibre. The two transcripts designated as HcGA20ox1 (KY399834) and HcGA20ox1 (KY399835) were isolated from the shoot tissue of three-week-old...
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| Format: | Article |
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Pakistan Botanical Society
2022
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| author | Ab Shukor, Nor Aini Yu Lok, Yusuf Chong Kumar, Sures M Abiri, Rambod Abdullah, Mohd Puad |
| author_facet | Ab Shukor, Nor Aini Yu Lok, Yusuf Chong Kumar, Sures M Abiri, Rambod Abdullah, Mohd Puad |
| author_sort | Ab Shukor, Nor Aini |
| collection | UPM |
| description | Kenaf (Hibiscus cannabinus L) is widely grown for its fibre. The Gibberellin 20-oxidase (HcGA20ox) gene is responsible for the improvement in quality of kenaf fibre. The two transcripts designated as HcGA20ox1 (KY399834) and HcGA20ox1 (KY399835) were isolated from the shoot tissue of three-week-old seedlings using the Rapid Amplification of cDNA Ends PCR (RACE), and PCR walking approaches, which encoded the polypeptides of 430 and 345 amino acids, respectively. Therefore, HcGA20ox1b was presumed as a pseudogene and only HcGA20ox1 was focused in downstream works. A high level of similarity has been observed between amino acid sequence of HcGA20ox1 and the GA20ox of other species. In addition, substrate binding site “LPWKET” and two histidine residues which serve as Fe2+ binding domains were found in the sequence. The BLAST results showed that HcGA20ox1 shared high identity with the GA20ox from other species including Gossypium hirsutum, Citrus sinensis, Populus trichocarpa, Jatropha curcas, etc. The highest identity was attributed to the GA20ox of Gossypium hirsutum (accession no.: XP016668427) at 83 identity. Using the Conserved Domain Database (CDD) available in NCBI, the non-heme dioxygenase superfamily, 2OG-Fe (II) oxygenase superfamily and gibberellin 20-oxidase domains were detected in HcGA20ox1. The molecular weight of the protein was 122224.45 with 4.97 theoretical pI. |
| first_indexed | 2024-09-25T03:43:15Z |
| format | Article |
| id | upm.eprints-110530 |
| institution | Universiti Putra Malaysia |
| last_indexed | 2024-09-25T03:43:15Z |
| publishDate | 2022 |
| publisher | Pakistan Botanical Society |
| record_format | dspace |
| spelling | upm.eprints-1105302024-06-16T03:02:48Z http://psasir.upm.edu.my/id/eprint/110530/ Molecular dissection and an in-silico approach of a novel gibberellin 20-oxidase gene of Hibiscus cannabinus l. Ab Shukor, Nor Aini Yu Lok, Yusuf Chong Kumar, Sures M Abiri, Rambod Abdullah, Mohd Puad Kenaf (Hibiscus cannabinus L) is widely grown for its fibre. The Gibberellin 20-oxidase (HcGA20ox) gene is responsible for the improvement in quality of kenaf fibre. The two transcripts designated as HcGA20ox1 (KY399834) and HcGA20ox1 (KY399835) were isolated from the shoot tissue of three-week-old seedlings using the Rapid Amplification of cDNA Ends PCR (RACE), and PCR walking approaches, which encoded the polypeptides of 430 and 345 amino acids, respectively. Therefore, HcGA20ox1b was presumed as a pseudogene and only HcGA20ox1 was focused in downstream works. A high level of similarity has been observed between amino acid sequence of HcGA20ox1 and the GA20ox of other species. In addition, substrate binding site “LPWKET” and two histidine residues which serve as Fe2+ binding domains were found in the sequence. The BLAST results showed that HcGA20ox1 shared high identity with the GA20ox from other species including Gossypium hirsutum, Citrus sinensis, Populus trichocarpa, Jatropha curcas, etc. The highest identity was attributed to the GA20ox of Gossypium hirsutum (accession no.: XP016668427) at 83 identity. Using the Conserved Domain Database (CDD) available in NCBI, the non-heme dioxygenase superfamily, 2OG-Fe (II) oxygenase superfamily and gibberellin 20-oxidase domains were detected in HcGA20ox1. The molecular weight of the protein was 122224.45 with 4.97 theoretical pI. Pakistan Botanical Society 2022 Article PeerReviewed Ab Shukor, Nor Aini and Yu Lok, Yusuf Chong and Kumar, Sures M and Abiri, Rambod and Abdullah, Mohd Puad (2022) Molecular dissection and an in-silico approach of a novel gibberellin 20-oxidase gene of Hibiscus cannabinus l. Pakistan Journal of Botany, 55 (2). pp. 489-500. ISSN 0556-3321; ESSN: 2070-3368 https://www.pakbs.org/pjbot/papers/1676459707.pdf 10.30848/PJB2023-2(11) |
| spellingShingle | Ab Shukor, Nor Aini Yu Lok, Yusuf Chong Kumar, Sures M Abiri, Rambod Abdullah, Mohd Puad Molecular dissection and an in-silico approach of a novel gibberellin 20-oxidase gene of Hibiscus cannabinus l. |
| title | Molecular dissection and an in-silico approach of a novel gibberellin 20-oxidase gene of Hibiscus cannabinus l. |
| title_full | Molecular dissection and an in-silico approach of a novel gibberellin 20-oxidase gene of Hibiscus cannabinus l. |
| title_fullStr | Molecular dissection and an in-silico approach of a novel gibberellin 20-oxidase gene of Hibiscus cannabinus l. |
| title_full_unstemmed | Molecular dissection and an in-silico approach of a novel gibberellin 20-oxidase gene of Hibiscus cannabinus l. |
| title_short | Molecular dissection and an in-silico approach of a novel gibberellin 20-oxidase gene of Hibiscus cannabinus l. |
| title_sort | molecular dissection and an in silico approach of a novel gibberellin 20 oxidase gene of hibiscus cannabinus l |
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