| تعداد نشریات | 285 |
| تعداد نشریات سازمان | 83 |
| تعداد شماره‌ها | 3,086 |
| تعداد مقالات | 34,441 |
| تعداد مشاهده مقاله | 48,883,956 |
| تعداد دریافت فایل اصل مقاله | 79,338,093 |
The phylogenetic reconstruction of biosynthesizing genes from Cyanobacteria isolated from Ziarat waterfall of Golestan Province | ||
| The Iranian Journal of Botany | ||
| مقاله 10، دوره 29، شماره 2، اسفند 2023، صفحه 187-200 اصل مقاله (1.48 M) | ||
| نوع مقاله: Research Paper | ||
| شناسه دیجیتال (DOI): 10.22092/ijb.2023.362834.1418 | ||
| نویسندگان | ||
| Bahareh Nowruzi* ؛ Samaneh Jafari Porzani | ||
| Department of Biotechnology, Faculty of Converging Sciences and Technologies, Islamic Azad University, Science and Research, Tehran, Iran | ||
| چکیده | ||
| Cyanobacteria are anaerobic and photosynthesizing prokaryotes. In the past, the classification of cyanobacteria was only based on morphological characteristics. Today, advanced techniques such as molecular markers are used to achieve more accurate and reliable classification. In this research, sampling was done from the Ziarat waterfall in Golestan province. After cultivation and purification in solid culture medium BG-11, molecular identification of natural compounds’ biosynthesizing genes (hassallidins synthetase (hasN) and geosmin A (geoA) along with divergence analyses were performed using the amplification of the chloroplast genes RNA polymerase C1 (rpoC1). Then, the strain containing the above genes was identified by amplification of 16S rRNA and internal transcribed spacer (ITS) genes. Phylogenetic trees were built using the Maximum Likelihood method and the appropriate model with the help of a web server on the IQ-Tree server. The secondary structure of ITS was drawn in different parts of helix D1-D1′, D2, D3, tRNAIle, tRNAAla, BOX B, BOX A, and V3 using the Mfold program. The results showed that only the Nodosilinea sp. 1359 (Leptolyngbyaceae, Synechococcales) strain has the genes mentioned above. In addition, the results of calculating the KA/KS of hasN and geoA genes and the phylogenetic incongruence of 16S rRNA and rpoC1 genes showed that natural selection by creating positive mutations has led to diversity in the studied strain. This study is among the first research conducted on the molecular phylogeny of cyanobacteria producing natural compounds in Ziarat waterfall. | ||
| کلیدواژه‌ها | ||
| Nodosilinea sp. 1359؛ 16S rRNA؛ ITS؛ hasN, geoA, rpoC1, biosynthesizing genes؛ natural compounds | ||
| عنوان مقاله [English] | ||
| بازسازی فیلوژنتیک ژنهای بیوسنتزکننده سیانوباکتری‌های جدا شده از آبشار زیارت استان گلستان | ||
| نویسندگان [English] | ||
| بهاره نوروزی؛ سمانه جعفری پرزانی | ||
| گروه بیوتکنولوژی، دانشکده علوم و فناوری‌های همگرا، واحد علوم و تحقیقات، دانشگاه آزاد اسلامی، تهران | ||
| چکیده [English] | ||
| سیانوباکتری‌ها، پروکاریوت‌های بی‌هوازی و فتوسنتز کننده هستند. در گذشته رده‌بندی سیانوباکتری‌ها تنها براساس صفات مورفولوژیکی استوار بود. اما امروزه از تکنیک‌های پیشرفته مانند نشانگرهای مولکولی برای دستیابی به رده‌بندی دقیق‌تر و قابل اعتمادتر استفاده می‌شود. در این تحقیق نمونه‌برداری از آبشار زیارت استان گلستان انجام شد. پس از کشت و خالص‌سازی در محیط کشت جامد BG-11، شناسایی مولکولی ژنهای بیوسنتزکننده ترکیبات طبیعی (hasN، و geoA) به همراه آنالیزهای واگرایی با تکثیر ژنهای rpoC1 انجام گردید. سپس سویه حاوی ژنهای فوق با تکثیر ژنهای 16S rRNA و ITS شناسایی گردید. درختان فیلوژنتیک با استفاده از روش بیشینه درست‌نمایی و مدل مناسب به کمک وب سرور IQ-Tree ساخته شد. ساختار ثانویه ITS، در بخش‌های مختلف هلیکس D1-D1′، D2، D3، tRNAIle، tRNAAla، BOX B، BOX A و V3 به کمک برنامه M-fold رسم شد. نتایج نشان داد که تنها سویه Nodosilinea sp. 1359 دارای ژنهای فوق بوده و متعلق به تیره Leptolyngbyaceae و راسته Synechococcales است. علاوه بر آن، نتایج حاصل از محاسبه میزان KA/KS ژنهای hasN و geoA و ناسازگاری داده‌های ژنتیکی 16S rRNA و rpo C1 نشان داد که انتخاب طبیعی با ایجاد جهش‌های مثبت منجر به ایجاد تنوع در سویه مورد مطالعه شده است. این مطالعه، جزو نخستین تحقیقات انجام شده روی فیلوژنی مولکولی سیانوباکتریوم تولیدکننده ترکیبات طبیعی در آبشار زیارت است. | ||
| کلیدواژه‌ها [English] | ||
| Nodosilinea sp. 1359, 16S rRNA, ITS, hasN, geoA, rpoC1, ژنهای بیوسنتز کننده ترکیبات طبیعی | ||
| مراجع | ||
|
Abed, R.M., Garcia-Pichel, F. & Hernández-Mariné, M. 2002: Polyphasic characterization of benthic, moderately halophilic, moderately thermophilic cyanobacteria with very thin trichomes and the proposal of Halomicronema excentricum gen. nov., sp. nov. -Arch. Microbiol. 177: 361–370.
DOI: 10.1007/s00203-001-0390-2
Bohunická, M., Pietrasiak, N., Johansen, J., Berrendero-Gomez, E., Hauer, T., Gaysina, L. & Lukešová, A. 2015: Roholtiella, gen. nov. (Nostocales, Cyanobacteria)- a tapering and branching member of the Nostocaceae (Cyanobacteria). -Phytotaxa 197(2): 84–103.
DOI: 10.11646/phytotaxa.197.2.2
Boyer, S.L., Flechtner, V.R. & Johansen, J.R. 2001: Is the 16S–23S rRNA internal transcribed spacer region a good tool for use in molecular systematics and population genetics; A case study in cyanobacteria. -Mol. Biol. Evol. 18(6): 1057–1069. DOI: 10.1093/oxfordjournals.molbev.a003877
Cai, F., Li, X., Yang, Y., Jia, N., Huo, D. & Li, R. 2019: Compactonostoc shennongjiaensis gen. & sp. nov.(Nostocales, Cyanobacteria) from a wet rocky wall in China. -Phycologia 58(2): 200–210.
DOI: 10.1080/00318884.2018.1541270
Dvořák, P., Poulíčková, A., Hašler, P., Belli, M., Casamatta D. A. & Papini, A. 2015: Species concepts and speciation factors in cyanobacteria, with connection to the problems of diversity and classification. Biodivers. -Conserv. 24: 739–757. DOI: 10.1007/s10531-015-0888-6
Chlipala, G. E., Mo, S. & Orjala, J. 2011: Chemodiversity in freshwater and terrestrial cyanobacteria- a source for drug discovery. -Curr. Drug Targets. 12(11): 1654–1673.
Hall, T.A. 1999: BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. -Nucleic acids symposium series 41: 95–98. London.
Iteman, I., Rippka, R., Tandeau de Marsac, N. & Herdman, M. 2000: Comparison of conserved structural and regulatory domains within divergent 16S rRNA–23S rRNA spacer sequences of cyanobacteria. -Microbiology. 146(6): 1275–1286. DOI: 10.1099/00221287-146-6-1275
Johansen, J.R., Kovacik, L., Casamatta, D.A., Iková, K.F. & Kastovský, J. 2011: Utility of 16S-23S ITS sequence and secondary structure for recognition of intrageneric and intergeneric limits within cyanobacterial taxa: Leptolyngbya corticola sp. nov. (Pseudanabaenaceae, Cyanobacteria). -Nova Hedwigia 92(3): 283.
DOI: 10.1127/0029-5035/2011/0092-0283
Katoh, H., Furukawa, J., Tomita-Yokotani, K. & Nishi, Y. 2012: Isolation and purification of an axenic diazotrophic drought-tolerant cyanobacterium, Nostoc commune, from natural cyanobacterial crusts and its utilization for field research on soils polluted with radioisotopes. -Biochim Biophys Acta Bioenerg. 1817(8): 1499–1505.
Katoh, K. & Standley, D.M. 2013: MAFFT multiple sequence alignment software version 7: improvements in performance and usability. -Mol. Biol. Evol. 30(4): 772–780. DOI: 10.1093/molbev/mst010
Kim, O.S., Cho, Y.J., Lee, K., Yoon, S.H., Kim, M., Na, H., Park, S.C., Jeon, Y. S., Lee, J.H. & Yi, H. 2012: Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. -IJSEM. 62(3): 716–721. DOI: 10.1099/ijs.0.038075-0
Komárek, J. 2016: A polyphasic approach for the taxonomy of cyanobacteria: principles and applications. -Eur. J. Phycol. 51(3): 346–353.
DOI: 10.1080/09670262.2016.1163738
Miscoe, L.H., Johansen, J.R., Kociolek, J.P., Lowe, R.L., Vaccarino, M.A., Pietrasiak, N. & Sherwood, A.R. 2016: The diatom flora and cyanobacteria from caves on Kauai, Hawaii. -Acta Bot. Hung. 58: 3–4.
Neilan, B.A., Jacobs, D. & Goodman, A.E. 1995: Genetic diversity and phylogeny of toxic cyanobacteria determined by DNA polymorphisms within the phycocyanin locus. -AEM. 61(11): 3875–3883.
DOI: 10.1128/aem.61.11.3875-3883.1995
Nguyen, L.T., Schmidt, H.A., Von Haeseler, A. & Minh, B.Q. 2015: IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. -Mol. Biol. Evol. 32(1): 268–274. DOI: 10.1093/molbev/msu300
Nowruzi, B. 2022: Cyanobacteria Natural Products as Sources for Future Directions in Antibiotic Drug Discovery. -Recent Advances and New Perspectives 1: 1–19. DOI: 10.5772/intechopen.106364
Nowruzi, B. & Afshari, G. 2023: In silico Analysis of Molecular Phylogeny of Genes Involved in the Synthesis of Bioactive Compounds in Cyanobacteria Strains Located in Tehran Cascade. -JJCMB. 14(1). DOI: 10.5812/jjcmb-132400
Nowruzi, B. & Becerra-Absalón, I. 2022: A Novel Potentially Toxic Cyanobacterial Species From the Genus Desmonostoc, Desmonostoc Alborizicum sp. nov., Iisolated From a Water Supply System of IranA. -Res. Sq. 1: 1–19.
Nowruzi, B., Hutarova, L. 2023: Structural and functional genes, and highly repetitive sequences commonly used in the phylogeny and species concept of the phylum Cyanobacteria. -Cryptogamie, Algologie. 44(3): 59–84.
DOI: 10.5252/cryptogamiealogie2023v44a3
Nowruzi, B., Hutárová, L., Absalón, I.B. & Liu, L. 2022: A new strain of Neowestiellopsis (Hapalosiphonaceae): first observation of toxic soil cyanobacteria from agricultural fields in Iran. -BMC Microbiol. 22(1): 1–13. DOI: 10.1186/s12866-022-02525-x
Nowruzi, B. & Lorenzi, A.S. 2023: Molecular phylogeny of two Aliinostoc isolates from a paddy field. -Plant Syst. Evol. 309(2): 11.
DOI: 10.1007/s00606-023-01848-0
Nowruzi, B. & Porzani, S.J. 2021: Toxic compounds produced by cyanobacteria belonging to several species of the order Nostocales: A review. -J. Appl. Toxicol. 41(4): 510–548. DOI: 10.1002/jat.4088
Nowruzi, B. & Shalygin, S. 2021: Multiple phylogenies reveal a true taxonomic position of Dulcicalothrix alborzica sp. nov. (Nostocales, Cyanobacteria). -Fottea 21(2): 235–246. Prabha, R. & Singh, D.P. 2019: Cyanobacterial phylogenetic analysis based on phylogenomics approaches render evolutionary diversification and adaptation: an overview of representative orders. -3 Biotech. 9: 1–16. DOI:10.1007/s13205-019-1635-6
Premanandh, J., Priya, B., Teneva, I., Dzhambazov, B., Prabaharan, D. & Uma, L. 2006: Molecular characterization of marine cyanobacteria from the Indian subcontinent deduced from sequence analysis of the phycocyanin operon (cpcB-IGS-cpcA) and 16S-23S ITS region. -J. Microbiol. 44(6): 607–616.
Rantala, A., Fewer, D.P., Hisbergues, M., Rouhiainen, L., Vaitomaa, J., Börner, T. & Sivonen, K. 2004: Phylogenetic evidence for the early evolution of microcystin synthesis. -PNAS. 101(2): 568–573. DOI: 10.1073/pnas.0304489101
Rastogi, R.P., Singh, S.P., Häder, D.P. & Sinha, R.P. 2010: Detection of reactive oxygen species (ROS) by the oxidant-sensing probe 2′, 7′-dichlorodihydrofluorescein diacetate in the cyanobacterium Anabaena variabilis PCC 7937. -BBRC. 397(3): 603–607.
Řeháková, K., Johansen, J.R., Casamatta, D.A., Xuesong, L. & Vincent, J. 2007: Morphological and molecular characterization of selected desert soil cyanobacteria: three species new to science including Mojavia pulchra gen. et sp. nov. -Phycologia 46: 481–502. Rippka, R., Deruelles, J., Waterbury, J.B., Herdman, M. & Stanier, R.Y. 1979: Generic assignments, strain histories and properties of pure cultures of cyanobacteria. -Microbiology. 111(1): 1–61.
Rivandi, M., Nowruzi, B. & Fahimi, H. 2021: Molecular phylogenetic study of toxic cyanobacterium Anabaena sp. strain B3 isolated from Lavasan Lake, Tehran (Iran). -Rostaniha 22(1): 120–133.
Sciuto, K., Andreoli, C., Rascio, N., La Rocca, N. & Moro, I. 2012: Polyphasic approach and typification of selected Phormidium strains (Cyanobacteria). -Cladistics 28(4): 357–374.
Seo, P.S. & Yokota, A. 2003: The phylogenetic relationships of cyanobacteria inferred from 16S rRNA, gyrB, rpoC1 and rpoD1 gene sequences. -J. Gen. Appl. Microbiol. 49(3): 191–203.
Shardlow, T. 2021: Identification and characterization of toxic cyanobacteria in two forested maritime watersheds in North America, University of Waterloo. -UWSpace. DOI: hdl.handle.net/10012/17055
Tan, L.T. 2007: Bioactive natural products from marine cyanobacteria for drug discovery. -Phytochemistry. 68(7): 954–979.
Taton, A., Grubisic, S., Brambilla, E., De Wit, R. & Wilmotte, A. 2003: Cyanobacterial diversity in natural and artificial microbial mats of Lake Fryxell (McMurdo Dry Valleys, Antarctica): a morphological and molecular approach. -AEM. 69(9): 5157–5169.
DOI: 10.1128/AEM.69.9.5157-5169.2003
Tawong, W., Pongcharoen, P. & Saijuntha, W. 2022: "Neocylindrospermum variakineticum gen. & sp. nov.(Nostocales, Cyanobacteria), a novel genus separated from Cylindrospermum using a polyphasic method. -Phycologia. 61(6): 653–668. DOI: 10.1080/00318884.2022.2130829
Vestola, J., Shishido, T.K., Jokela, J., Fewer, D.P., Aitio, O., Permi, P., Wahlsten, M., Wang, H., Rouhiainen, L. & Sivonen, K. 2014: Hassallidins, antifungal glycolipopeptides, are widespread among cyanobacteria and are the end-product of a nonribosomal pathway. -Proceedings of the National Academy of Sciences 111(18): E1909–E1917. DOI: 10.1073/pnas.1320913111
Yarza, P., Yilmaz, P., Pruesse, E., Glöckner, F.O., Ludwig, W., Schleifer, K.H., Whitman, W.B., Euzéby, J., Amann, R. & Rosselló-Móra, R. 2014: Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. -Nat. Rev. Microbiol. 12(9): 63645. DOI: 10.1038/nrmicro3330 | ||
|
آمار تعداد مشاهده مقاله: 640 تعداد دریافت فایل اصل مقاله: 671 |
||