Identification of Gene Candidates in Diterpenoid Biosynthesis of Curcuma longa: An mRNA Sequencing Approach
Identification of Gene Candidates in Diterpenoid
DOI:
https://doi.org/10.11594/jtls.14.03.08Keywords:
Curcuma longa, diterpenoid biosynthesis, gene expressionAbstract
Curcuma longa is a medicinal plant renowned for its therapeutic properties and potential treatment of cancer. This study focused on the biosynthesis of diterpenoids in the rhizome and leaves of C. longa. The genes responsible for producing these medicinal compounds were analyzed using BLASTx, Gene Ontology (GO) annotation, differential expression, and homology. The substantial dataset was obtained from the National Center for Biotechnology Information (NCBI), comprising 151,730,334 clean reads and 167,264 transcripts for the analysis. The results of the BLASTx analysis were as follows: NR yielded 65.93%, Swiss-Prot yielded 44.52%, and COG yielded 17.35%. Subsequently, GO annotation was performed using Blast2GO, resulting in an annotation rate of 56.79%. Differential expression analysis revealed a total of 636 genes that were significantly differentiated between the rhizome and leaves. The homology analysis resulted in 11 proteins associated with diterpenoid biosynthesis and nine proteins related to CYP450. Approximately three class I proteins were highly expressed in the rhizome. Additionally, seven CYP450 enzymes from the CYP71D and CYP726 subfamilies were identified; three were highly expressed in the rhizome. The expression patterns of these enzymes were similar to the aforementioned three class I diTPSs, indicating their potential involvement in macroditerpenoid biosynthesis in C. longa. These findings provide valuable genomic resources for future functional genomics research on C. longa, facilitating targeted efforts to enhance the production of bioactive compounds.
References
Chakraborty A, Mahajan S, Jaiswal SK, Sharma VK (2021) Genome sequencing of turmeric provides evolutionary insights into its medicinal properties. Communications Biology 4 (1): 1193. doi: 10.1038/s42003-021-02720-y.
Zahariah S, Winarsih S, Baktiyani SCW et al. (2017) The Effect of Turmeric Decoctum to the Angiogenic Molecules Expression on Chicken Embryo. Journal of Tropical Life Science 7 (1): 61–65. doi: 10.11594/jtls.07.01.10.
Suprihatin T, Widyarti S, Rifa’i M, Rahayu S (2019) Malondialdehyde (MDA) Ovary and Estradiol Blood Serum Levels of Premenopause White Rat (Rattus norvegicus) after Turmeric Powder (Curcuma longa L.) Treatment. Journal of Tropical Life Science 9 (3): 237–242.
Changxing L, Galani S, Hassan F, et al. (2020) Bio-technological approaches to the production of plant-derived promising anticancer agents: An update and overview. Biomedicine & Pharmacotherapy 132 110918. doi: 10.1016/j.biopha.2020.110918.
Imaningsih W, Ekowati N, Salamiah et al. (2023) An Overview of Stress-Tolerant Promoting Endophytic Fungal Isolates from Hiyung Chilli Grown in South Kalimantan: Endophytic Fungi of Hiyung Chilli Pep-pers. Journal of Tropical Life Science 13 (1): 183–192. doi: 10.11594/jtls.13.01.18.
Annadurai RS, Neethiraj R, Jayakumar V et al. (2013) De Novo Transcriptome Assembly (NGS) of Curcuma longa L. Rhizome Reveals Novel Transcripts Related to Anticancer and Antimalarial Terpenoids. PLOS ONE 8 (2): e56217. doi: 10.1371/journal.pone.0056217.
Chen R, Wei Q, Liu Y et al. (2021) Transcriptome sequencing and functional characterization of new sesquiterpene synthases from Curcuma wenyujin. Archives of Biochemistry and Biophysics 709 108986. doi: 10.1016/j.abb.2021.108986.
Chen R, Hu T, Wang M et al. (2022) Functional characterization of key polyketide synthases by inte-grated metabolome and transcriptome analysis on curcuminoid biosynthesis in Curcuma wenyujin. Syn-thetic and Systems Biotechnology 7 (3): 849–861. doi: 10.1016/j.synbio.2022.04.006.
Yin Y, Xie X, Zhou L, et al. (2022) A chromosome-scale genome assembly of turmeric provides insights into curcumin biosynthesis and tuber formation mechanism. Frontiers in Plant Science 13.
Dong Q, Zou Q-C, Mao L-H, et al. (2022) The Chromosome-Scale Assembly of the Curcuma alis-matifolia Genome Provides Insight Into Anthocyanin and Terpenoid Biosynthesis. Frontiers in Plant Sci-ence 13.
Gururani S, Gairola K, Kumar R, et al. (2022) Altitudinal and geographical variations in phyto-chemical composition and biological activities of Cur-cuma longa accession from Uttarakhand, the Himala-yan region. Journal of Food Processing and Preserva-tion 46 (3): e16384. doi: 10.1111/jfpp.16384.
Cao X, Zhang F, Yuan B, et al. (2017) De novo transcriptome sequencing and analysis of Euphorbia pekinensis Rupr. and identification of genes involved in diterpenoid biosynthesis. Plant Gene 12 33–42. doi: 10.1016/j.plgene.2017.07.001.
Zerbe P, Chiang A, Dullat H, et al. (2014) Diterpene synthases of the biosynthetic system of medicinally active diterpenoids in Marrubium vul-gare. The Plant Journal 79 (6): 914–927. doi: 10.1111/tpj.12589.
Inabuy FS, Fischedick JT, Lange I, et al. (2017) Biosynthesis of Diterpenoids in Tripterygium Adven-titious Root Cultures. Plant Physiology 175 (1): 92–103. doi: 10.1104/pp.17.00659.
Trikka FA, Nikolaidis A, Ignea C, et al. (2015) Combined metabolome and transcriptome profiling provides new insights into diterpene biosynthesis in S. pomifera glandular trichomes. BMC Genomics 16 (1): 935. doi: 10.1186/s12864-015-2147-3.
Rangan P, Furtado A, Henry R (2020) Tran-scriptome profiling of wheat genotypes under heat stress during grain-filling. Journal of Cereal Science 91:102895.
Jin J, Sun Y, Qu J, et al. (2017) Transcriptome and functional analysis reveals hybrid vigor for oil biosynthesis in oil palm. Scientific Reports 7 (1): 439. doi: 10.1038/s41598-017-00438-8.
Chu HD, Tran YTH, Pham CT, et al. (2024) Identification of Two Enzymes for Trehalose Synthe-sis and Their Potential Function in Growth and De-velopment in Peanut (Arachis hypogaea): Genome Analysis of the Encoding Trehalose Synthesis En-zymes in Peanut. Journal of Tropical Life Science 14 (1): 83–94. doi: 10.11594/jtls.14.01.10.
Matasci N, Hung L-H, Yan Z, et al. (2014) Data access for the 1,000 Plants (1KP) project. Gigasci-ence 3 (1): 2047–217X.
Wu X, Wafula E, Yan Z, et al. (2014) Data ac-cess for the 1,000 Plants (1KP) project.
Afgan E, Baker D, Batut B, et al. (2018) The Galaxy platform for accessible, reproducible and col-laborative biomedical analyses: 2018 update. Nucle-ic Acids Research 46 (W1): W537–W544. doi: 10.1093/nar/gky379.
Wickham H, Averick M, Bryan J, et al. (2019) Welcome to the Tidyverse. Journal of Open Source Software 4 (43): 1686. doi: 10.21105/joss.01686.
Bretaudeau A, Corguillé GL, Corre E, Liu X (2023) De novo transcriptome assembly, annota-tion, and differential expression analysis. https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/full-de-novo/tutorial.html. Accessed: December 2023.
Andrews S (2010) FastQC: a quality control tool for high throughput sequence data.
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina se-quence data. Bioinformatics 30 (15): 2114–2120.
Grabherr MG, Haas BJ, Yassour M, et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature biotech-nology 29 (7): 644–652.
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nature methods 9 (4): 357–359.
Li B, Dewey CN (2011) RSEM: accurate tran-script quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12 (1): 323. doi: 10.1186/1471-2105-12-323.
Cock PJA, Chilton JM, Grüning B, et al. (2015) NCBI BLAST+ integrated into Galaxy. Gigascience 4 (1): s13742-015.
Apweiler R, Bairoch A, Wu CH (2004) Protein sequence databases. Current opinion in chemical bi-ology 8 (1): 76–80.
Conesa A, Götz S, García-Gómez JM, et al. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics re-search. Bioinformatics 21 (18): 3674–3676.
Ashburner M, Ball CA, Blake JA et al. (2000) Gene ontology: tool for the unification of biology. Na-ture genetics 25 (1): 25–29.
Love MI, Huber W, Anders S (2014) Moderat-ed estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15 (12): 550. doi: 10.1186/s13059-014-0550-8.
Kolde R, Kolde MR (2018) Package ‘pheatmap.’ R Package 1
Blighe K, Rana S, Lewis M (2019) En-hancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling. R Package Version 1
Sievers F, Higgins DG (2014) Clustal omega, accurate alignment of very large numbers of se-quences. Methods in Molecular Biology. doi: 10.1007/978-1-62703-646-7_6
Tamura K, Stecher G, Kumar S (2021) MEGA11: molecular evolutionary genetics analysis version 11. Molecular biology and evolution 38 (7): 3022–3027.
Davis EM, Croteau R (2000) Cyclization En-zymes in the Biosynthesis of Monoterpenes, Sesquit-erpenes, and Diterpenes. In: Leeper FJ, Vederas JC eds Biosynthesis: Aromatic Polyketides, Isoprenoids, Alkaloids. Berlin, Heidelberg, Springer. pp 53–95.
Feng M, Chen C, Qu-Bie J, et al. (2022) Metab-olome and transcriptome associated analysis of ses-quiterpenoid metabolism in Nardostachys jatamansi. Frontiers in Plant Science 13. doi: 10.3389/fpls.2022.1041321.
Ayer DK, Modha K, Parekh V, et al. (2020) Associating gene expressions with curcuminoid bio-synthesis in turmeric. Journal of Genetic Engineering and Biotechnology 18 (1): 83. doi: 10.1186/s43141-020-00101-2.
Zhu F, Sun H, Wang J et al. (2022) Differential expression involved in starch synthesis pathway genes reveal various starch characteristics of seed and rhizome in lotus (Nelumbo Nucifera). Journal of Food Science 87 (9): 4250–4263. doi: 10.1111/1750-3841.16283.
Chen L, Xu S, Liu Y et al. (2022) Identification of key gene networks controlling polysaccharide ac-cumulation in different tissues of Polygonatum cyr-tonema Hua by integrating metabolic phenotypes and gene expression profiles. Frontiers in Plant Sci-ence 13. doi: 10.3389/fpls.2022.1012231.
Barrero RA, Chapman B, Yang Y, et al. (2011) De novo assembly of Euphorbia fischeriana root tran-scriptome identifies prostratin pathway related genes. BMC Genomics 12 (1): 600. doi: 10.1186/1471-2164-12-600.
Pandit S, Shitiz K, Sood H, et al. (2013) Ex-pression pattern of fifteen genes of non-mevalonate (MEP) and mevalonate (MVA) pathways in different tissues of endangered medicinal herb Picrorhiza kur-roa with respect to picrosides content. Molecular Bi-ology Reports 40 (2): 1053–1063. doi: 10.1007/s11033-012-2147-1.
He M, Wang Y, Hua W, et al. (2012) De Novo Sequencing of Hypericum perforatum Transcriptome to Identify Potential Genes Involved in the Biosyn-thesis of Active Metabolites. PLoS ONE 7 (7): e42081. doi: 10.1371/journal.pone.0042081.
Davis EM, Croteau R (2000) Cyclization En-zymes in the Biosynthesis of Monoterpenes, Sesquit-erpenes, and Diterpenes. In: Leeper FJ, Vederas JC eds Biosynthesis. Berlin, Heidelberg, Springer Berlin Heidelberg. pp 53–95.
Wang K, Yu H, Wu H, et al. (2015) A new cas-bane diterpene from Euphorbia pekinensis. Natural Product Research 29 (15): 1456–1460. doi: 10.1080/14786419.2015.1027704.
Mau CJ, West CA (1994) Cloning of casbene synthase cDNA: evidence for conserved structural features among terpenoid cyclases in plants. Pro-ceedings of the National Academy of Sciences 91 (18): 8497–8501. doi: 10.1073/pnas.91.18.8497.
Kirby J, Nishimoto M, Park JG, et al. (2010) Cloning of casbene and neocembrene synthases from Euphorbiaceae plants and expression in Sac-charomyces cerevisiae. Phytochemistry 71 (13): 1466–1473. doi: 10.1016/j.phytochem.2010.06.001.
Luo D, Callari R, Hamberger B, et al. (2016) Oxidation and cyclization of casbene in the biosyn-thesis of Euphorbia factors from mature seeds of Eu-phorbia lathyris L. Proc Natl Acad Sci USA. doi: 10.1073/pnas.1607504113
Zerbe P, Bohlmann J (2015) Plant diterpene synthases: exploring modularity and metabolic di-versity for bioengineering. Trends in Biotechnology 33 (7): 419–428. doi: 10.1016/j.tibtech.2015.04.006
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