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FLAVONOID PATHWAY GENE DISCOVERIES in Boesenbergia Rotunda THROUGH RNA-SEQ TRANSCRIPTOME PROFILING of CELL SUSPENSION CULTURES in RESPONSE to PHENYLALANINE

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FLAVONOID PATHWAY GENE DISCOVERIES in Boesenbergia Rotunda THROUGH RNA-SEQ TRANSCRIPTOME PROFILING of CELL SUSPENSION CULTURES in RESPONSE to PHENYLALANINE FLAVONOID PATHWAY GENE DISCOVERIES IN Boesenbergia rotunda THROUGH RNA-SEQ TRANSCRIPTOME PROFILING OF CELL SUSPENSION CULTURES IN RESPONSE TO PHENYLALANINE NOOR DIYANA BINTI MD MUSTAFAMalaya of FACULTY OF SCIENCE UNIVERSITY OF MALAYA KUALA LUMPUR University 2017 FLAVONOID PATHWAY GENE DISCOVERIES IN Boesenbergia rotunda THROUGH RNA-SEQ TRANSCRIPTOME PROFILING OF CELL SUSPENSION CULTURES IN RESPONSE TO PHENYLALANINE NOOR DIYANA BINTI MD MUSTAFA Malaya of THESIS SUBMITTED IN FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY INSTITUTE OF BIOLOGICAL SCIENCES FACULTY OF SCIENCE UNIVERSITY OF MALAYA KUALA LUMPUR University 2017 UNIVERSITY OF MALAYA ORIGINAL LITERARY WORK DECLARATION Name of Candidate: NOOR DIYANA BINTI MD MUSTAFA Registration/Matric No: SHC080079 Name of Degree: DOCTOR OF PHILOSOPHY Title of Project Paper/Research Report/Dissertation/Thesis (“this Work”): FLAVONOID PATHWAY GENE DISCOVERIES IN Boesenbergia rotunda THROUGH RNA-SEQ TRANSCRIPTOME PROFILING OF CELL SUSPENSION CULTURES IN RESPONSE TO PHENYLALANINE Field of Study: PLANT BIOTECHNOLOGY I do solemnly and sincerely declare that: (1) I am the sole author/writer of this Work; (2) This Work is original; (3) Any use of any work in which copyright exists was done by way of fair dealing and for permitted purposes and any excerpt or extract from, or reference to or reproduction of any copyright work has been disclosed expressly and sufficiently and the title of the Work and its authorship have been acknowledged in this Work; (4) I do not have any actual knowledge nor doMalaya I ought reasonably to know that the making of this work constitutes an infringement of any copyright work; (5) I hereby assign all and every rights in the copyright to this Work to the University of Malaya (“UM”), whoof henceforth shall be owner of the copyright in this Work and that any reproduction or use in any form or by any means whatsoever is prohibited without the written consent of UM having been first had and obtained; (6) I am fully aware that if in the course of making this Work I have infringed any copyright whether intentionally or otherwise, I may be subject to legal action or any other action as may be determined by UM. Candidate’s Signature Date: SubscUniversityribed and solemnly declared before, Witness’s Signature Date: Name: PROF. DR. ROFINA YASMIN BINTI OTHMAN Designation: ii FLAVONOID PATHWAY GENE DISCOVERIES IN Boesenbergia rotunda THROUGH RNA-SEQ TRANSCRIPTOME PROFILING OF CELL SUSPENSION CULTURES IN RESPONSE TO PHENYLALANINE ABSTRACT Panduratin A extracted from Boesenbergia rotunda is a flavonoid reported to possess a range of medicinal properties which include anti-dengue, anti-HIV, anti-cancer, antioxidant and anti-inflammatory activities. B. rotunda is a plant from the Zingiberaceae family commonly used as a food ingredient and traditional medicine in Southeast Asia and China. Reports on the health benefits of secondary metabolites extracted from B. rotunda over the last few years have increased demands for panduratin A. However, large scale extraction has been hindered by low abundance of the compound in nature and limited knowledge of its biosynthetic pathway. ExperimentsMalaya showed an increase in panduratin A production after 14 days post treatment with exogenous phenylalanine, an aromatic amino acid derived from the shikimicof acid pathway. Transcriptome sequencing and digital gene expression (DGE) analysis of untreated and phenylalanine treated B. rotunda cell suspension cultures were carried out to elucidate the key genes differentially expressed in the panduratin A biosynthetic pathway. Total RNA of untreated and 14 days post-phenylalanine treated cell suspension cultures were extracted and sequenced using next generation sequencing technology employing an Illumina-Solexa platform. The transcriptome data generated 101,043 unigenes with 50,932 (50.41%) successfully annotatedUniversity in the public protein databases; including 49.93% (50,447) in the non- redundant (NR) database, 34.63% (34,989) in Swiss-Prot, 24.07% (24,316) in Kyoto Encyclopedia of Genes and Genomes (KEGG) and 16.26% (16,426) in Clusters of Orthologous Groups (COG). Through DGE analysis, it was found that 14,644 unigenes were up-regulated and 14,379 unigenes down-regulated in response to exogenous phenylalanine treatment. In the flavonoid pathway leading to the proposed panduratin A iii production, 2 unigenes encoded for phenylalanine ammonia-lyase (PAL), 3 for 4- coumaroyl:coenzyme A ligase (4CL) and 1 for chalcone synthase (CHS) were found up- regulated. In this thesis, a flavonoid pathway leading to panduratin A biosynthesis was proposed. In addition, two enzymes, namely flavonoid O-methyltransferase and prenyltransferase, were suggested to be key enzymes for panduratin A biosynthesis. In the transcriptome data, Unigene891_All, Unigene21507_All were predicted to encode flavonoid O-methyltransferase whereas, Unigene31983_All was predicted to encode prenyltransferase. At the gene regulatory level, transcripts for MYB transcription factors in the transcriptome database were further analysed by transcriptome-wide R2R3 MYB transcription factor analysis. As a result, transcripts for three MYB transcription factors namely BrMYB1, BrMYB2 and BrMYB3 were successfully sequenced and characterized. To date, this is the first report of B. rotunda de novoMalaya transcriptome data that could serve as a reference for gene or enzyme functional studies in the Zingiberaceae family. Although enzymes that are directly involvedof in the panduratin A biosynthetic pathway were not completely elucidated, the data provide an overall picture of gene regulation patterns leading to panduratin A production. University iv ABSTRAK Panduratin A yang diekstrak daripada Boesenbergia rotunda adalah kompaun flavonoid yang dilaporkan mempunyai pelbagai faedah dari segi perubatan termasuk aktiviti anti-denggi, anti-HIV, anti-kanser, antioksida dan anti-radang. B. rotunda adalah tumbuhan dari keluarga Zingiberacea yang biasa digunakan sebagai makanan dan ubat- ubatan tradisional di Asia Tenggara dan China. Laporan mengenai manfaat kesihatan metabolit sekunder yang diekstrak daripada B. rotunda sejak beberapa tahun yang lalu telah menyebabkan permintaan yang semakin meningkat untuk panduratin A. Walau bagaimanapun pengeluaran berskala besar tidak berjaya dihasilkan kerana banyak faktor termasuk penghasilan panduratin A secara semulajadi yang sangat rendah dan pengetahuan laluan biosintesis panduratin A yang terhad. Berdasarkan kajian terdahulu, penghasilan panduratin A dapat ditingkatkan denganMalaya penambahan fenilalanin di dalam ampaian kultur selama 14 hari di mana fenilalanin adalah asid amino aromatik yang diperoleh melalui laluan asid shikimik. Penjujukanof seluruh transkrip dan analisis ekspresi gen secara digital ( DGE ) daripada ampaian kultur B. rotunda yang dirangsang dan tanpa rangsangan oleh fenilalanin telah dijalankan untuk mengenal pasti gen utama yang terlibat dalam penghasilan panduratin A. Seluruh RNA daripada ampaian kultur yg tidak dirangsang dan dirangsang oleh fenilalanin selama 14 hari telah diekstrak dan penjujukan transkrip telah dilakukan melalui kaedah teknologi penjujukan generasi baru yang menggunakan platform Illumina-Solexa. Keseluruhannya, data transkrip telah menjana 101,043University unigen dengan 50,932 (50.41 %) berjaya dipadankan dalam pangkalan data protein awam; termasuk 49,93 % (50,447) dalam pangkalan data yang tidak bertindih (NR), 34.63 % (34,989), di Swiss-Prot , 24.07 % (24 ,316), dalam Ensiklopedia Kyoto daripada Gen dan Genom (KEGG) dan 16.26 % (16,426) dalam Kelompok Kumpulan Orthologous (COG). Melalui analisis DGE, didapati bahawa ekspresi 14,644 unigenes meningkat dan ekspresi 14,379 unigenes menurun disebabkan oleh rangsangan daripada v fenilalanin. Dalam laluan secara langsung flavonoid yang membawa kepada penghasilan panduratin A, didapati bahawa ekspresi 2 unigen yang merekodkan fenilalanin ammonia- lyase (PAL), 3 unigen untuk coumaroyl:koenzim A ligase (4CL) menigkat dan 1 unigen untuk chalcone sintase (CHS) meningkat. Dalam tesis ini, laluan flavonoid dalam penghasilan panduratin A telah dicadangkan. Selain itu, terdapat dua jenis enzim penting iaitu flavonoid O-methyltransferase dan prenyltransferase yang turut dicadangkan terlibat dalam penghasilan panduratin A. Daripada data transcriptom ini, Unigene891_All dan Unigene21507_All telah diramalkan berfungsi sebagai flavonoid O-methyltransferase. Manakala Unigene31983_All pula diramalkan merekodkan prenyltransferase. Di peringkat pengawalaturan gen, analisis yang lebih mendalam terhadap transkrip untuk MYB faktor transkripsi telah dilakukan melalui transkripsi mendalam (transcriptome- wide) R2R3 MYB faktor transkripsi analisis. SelainMalaya daripada itu, penjujukan transkrip untuk tiga MYB faktor transkripsi telah berjaya dilakukan, iaitu BrMYB1, BrMYB2 and BrMYB3. Ini merupakan laporan pertama dataof transkrip B. rotunda yang boleh dijadikan sebagai rujukan untuk kajian masa depan yang berkenaan fungsi gen dan enzim dalam keluarga Zingiberaceae secara amnya. Walaupun enzim yang terlibat secara langsung dalam penghasilan panduratin A di laluan biosintesisnya tidak difahami sepenuhnya, data ini memberikan gambaran keseluruhan corak transkripsi gen yang terlibat secara tidak langsung ke arah penghasilan panduratin A. University vi ACKNOWLEDGEMENTS Alhamdulillah praise to Allah SWT, the Most Merciful and the Most Gracious for giving me the strength mentally and physically to complete the degree of
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