متا-آنالیز ترانسکریپتوم ژن های مسیر موالونیک‌اسید و متیل‌اریتریتول‌فسفات برای بیوسنتز ایزوپرینوئیدها در گیاهان

نوع مقاله : علمی پژوهشی

نویسندگان

1 دانشجوی دکتری اصلاح نباتات، دانشکده علوم کشاورزی، دانشگاه گیلان، رشت، ایران

2 استاد، گروه اصلاح نباتات، دانشکده علوم کشاورزی، دانشگاه گیلان، رشت، ایران

3 دانشیار، گروه بیوتکنولوژی گیاهی، دانشکده علوم زیستی و زیست فناوری، دانشگاه شهید بهشتی، تهران، ایران

4 دانشیار، گروه کشاورزی، پژوهشکده گیاهان و مواد اولیه دارویی، دانشگاه شهید بهشتی، تهران، ایران

چکیده

ایزوپرینوئیدها و مشتقات آن ها بزرگترین گروه از ترکیبات طبیعی در گیاهان هستند که از واحدهای پنج کربنه ایزوپرینیل فسفات ساخته می‌شوند. این واحدهای پنچ کربنه در گیاهان از طریق دو مسیر بیوسنتزی مجزا شامل مسیر موالونات (MVA) در سیتوپلاسم و مسیر متیل اریتریتول فسفات (MEP) در پلاستید، تولید می شوند. به منظور انجام متا-آنالیز ژن‌های دو مسیر MVA و MEP از داده‌های بیانی آزمایشات ریزآرایه در بافت های مختلف، مراحل نموی، تنش های زیستی و غیرزیستی در گیاه مدل آرابیدوپسیس استفاده شد. متا-آنالیز ترانسکریپتوم با استفاده از ابزار Genevestigator به عنوان یک بانک اطلاعاتی بزرگ شامل داده‌های ترانسکریپتوم مخازن GEO در NCBI و ArrayExpress در EBI، انجام گرفت. نتایج حاصل از متا-آنالیز نشان داد که به طور کلی رونویسی ژن‌های کد کننده آنزیم‌های دو مسیر MVA و MEP گیاهی با هم هماهنگ نیست و در بافت‌ها، مراحل رشدی و شرایط مختلف الگوی بیانی متفاوتی دارند. ژن‌های مسیر MVA بیشترین بیان را در ریشه و اندام‌های زایشی نشان می‌دهند، درحالی‌که ژن‌های مسیر MEP بیشتر در بافت‌های فتوسنتزی بیان می‌شوند. این نتایج می‌تواند به درک چگونگی تولید پیش سازهای ایزوپرینوئیدها از طریق دو مسیر با جایگاه متفاوت کمک کرده و همچنین سازماندهی شبکه‌های ژنی و تنظیم آن‌ها در شرایط، بافت‌ها و مراحل نموی مختلف را آشکار می‌سازد.

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

Meta-analysis of Transcriptomics related to the genes of the mevalonate (MVA) and the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathways for isoprenoids biosynthesis in plants

نویسندگان [English]

  • Zahra Aminfar 1
  • Babak Rabiei 2
  • Masoud Tohidfar 3
  • Mohammad Hossein Mirjalili 4
1 Ph.D. Student of Plant Breeding, Faculty of Agriculture, University of Guilan, Rasht, Iran.
2 Professor, Department of Plant Breeding, Faculty of Agriculture, University of Guilan, Rasht, Iran
3 Associate Professor, Department of Biotechnology, Faculty of Life Science and Biotechnology, Shahid Beheshti University, G.C. Tehran, Iran.
4 Associate Professor, Department of Agriculture, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, G.C., Tehran, Iran.
چکیده [English]

Isoprenoids and their derivatives represent the largest group of natural compounds in plants that are biosynthesized from isoprenyl diphosphate C5 units. These C5 units generated by two distinctive biosynthetic pathways in plants including mevalonate (MVA) pathway in the cytoplasm and methylerthritol phosphate (MEP) pathway in plastids. To perform a meta-analysis of two pathways of MVA and MEP, expression data of the microarray experiments in different tissues, developmental stages, biotic and abiotic stresses were used in Arabidopsis thaliana as a model plant. The transcriptom meta-analysis was carried out using Genevestigator as a large database containing transcriptomics data of GEO in NCBI and ArrayExpress in EBI. The results of the meta-analysis showed that the transcription of genes encoding the enzymes of MVA and MEP pathway did not coordinate and they had different expression patterns in developmental stages, various tissues and conditions. MVA pathway genes show the highest expression in the roots and reproductive organs, while the MEP pathway genes are expressed in photosynthetic tissues. The results obtained here can help to understand how the underlying pathway gene networks are organized and regulated in different conditions, tissues and developmental stages.

کلیدواژه‌ها [English]

  • Genevestigator
  • Isoprenoids
  • Meta-analysis
  • Microarray
  • Transcriptome

مراجع

Aharoni A, Jongsma MA, Kim T-Y, Ri M-B, Giri AP, Verstappen FW, Schwab W, Bouwmeester HJ (2006) Metabolic engineering of terpenoid biosynthesis in plants. Phytochem. Rev. 5: 49-58.
Banerjee A, Sharkey T (2014) Methylerythritol 4-phosphate (MEP) pathway metabolic regulation. Nat. Prod. Rep. 31: 1043-1055.
Banerjee A, Wu Y, Banerjee R, Li Y, Yan H, Sharkey TD (2013) Feedback inhibition of deoxy-D-xylulose 5-phosphate synthase regulates the methyl erythritol 4-phosphate pathway. J. Biol. Chem.jbc. M113. 464636.
Bohlmann J, Keeling CI (2008) Terpenoid biomaterials. Plant J. 54: 656-669.
Chenge‐Espinosa M, Cordoba E, Romero‐Guido C, Toledo‐Ortiz G, León P (2018) Shedding light on the methylerythritol phosphate (MEP) ‐pathway: long hypocotyl 5 (HY 5)/phytochrome‐interacting factors (PIF s) transcription factors modulating key limiting steps. Plant J. 96: 828-841.
Closa M, Vranová E, Bortolotti C, Bigler L, Arró M, Ferrer A, Gruissem W (2010) The Arabidopsis thaliana FPP synthase isozymes have overlapping and specific functions in isoprenoid biosynthesis, and complete loss of FPP synthase activity causes early developmental arrest. Plant J. 63: 512-525.
Cordoba E, Salmi M, León P (2009) Unravelling the regulatory mechanisms that modulate the MEP pathway in higher plants. J. Exp. Bot. 60: 2933-2943.
Disch A, Rohmer M (1998) On the absence of the glyceraldehyde 3-phosphate/pyruvate pathway for isoprenoid biosynthesis in fungi and yeasts. FEMS Microbiol. Lett. 168: 201-208.
Disch A, Schwender J, Muller C, Lichtenthaler HK, Rohmer M (1998) Distribution of the mevalonate and glyceraldehyde phosphate/pyruvate pathways for isoprenoid biosynthesis in unicellular algae and the cyanobacterium Synechocystis PCC 6714. Biochem. J. 333: 381-388.
Dos Santos CV, Letousey P, Delavault P, Thalouarn P (2003) Defense gene expression analysis of Arabidopsis thaliana parasitized by Orobanche ramosa. Phytopathology. 93: 451-457.
Ghassemian M, Lutes J, Tepperman JM, Chang H-S, Zhu T, Wang X, Quail PH, Lange BM (2006) Integrative analysis of transcript and metabolite profiling data sets to evaluate the regulation of biochemical pathways during photomorphogenesis. Arch. Biochem. Biophys. 448: 45-59.
Hemmerlin A, Harwood JL, Bach TJ (2012) A raison d’être for two distinct pathways in the early steps of plant isoprenoid biosynthesis? Prog. Lipid Res. 51: 95-148.
Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem W, Zimmermann P (2008) Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. Adv. Bioinf. 2008.
Kovacs WJ, Olivier LM, Krisans SK (2002) Central role of peroxisomes in isoprenoid biosynthesis. Prog. Lipid Res. 41: 369-391.
Lange BM, Ghassemian M (2003) Genome organization in Arabidopsis thaliana: a survey for genes involved in isoprenoid and chlorophyll metabolism. Plant molecular biology. 51: 925-948.
Leivar P, Antolín-Llovera M, Ferrero S, Closa M, Arró M, Ferrer A, Boronat A, Campos N (2011) Multilevel control of Arabidopsis 3-hydroxy-3-methylglutaryl coenzyme A reductase by protein phosphatase 2A. Plant Cell.tpc. 110.074278.
Liang Y-F, Liu H, Li H, Gao W-Y (2019) Determination of the Activity of 1-Deoxy-d-Xylulose 5-Phosphate Synthase by Pre-column Derivatization-HPLC Using 1, 2-Diamino-4, 5-Methylenedioxybenzene as a Derivatizing Reagent. Protein J.1-7.
Lombard J, Moreira D (2010) Origins and early evolution of the mevalonate pathway of isoprenoid biosynthesis in the three domains of life. Molecular biology and evolution. 28: 87-99.
Lumbreras V, Campos N, Boronat A (1995) The use of an alternative promoter in the Arabidopsis thaliana HMG1 gene generates an mRNA that encodes a novel 3‐hydroxy‐3‐methylglutaryl coenzyme A reductase isoform with an extended N‐terminal region. Plant J. 8: 541-549.
Miziorko HM (2011) Enzymes of the mevalonate pathway of isoprenoid biosynthesis. Arch. Biochem. Biophys. 505: 131-143.
Okada K, Kasahara H, Yamaguchi S, Kawaide H, Kamiya Y, Nojiri H, Yamane H (2008) Genetic evidence for the role of isopentenyl diphosphate isomerases in the mevalonate pathway and plant development in Arabidopsis. Plant and Cell Physiology. 49: 604-616.
Okada K, Saito T, Nakagawa T, Kawamukai M, Kamiya Y (2000) Five geranylgeranyl diphosphate synthases expressed in different organs are localized into three subcellular compartments in Arabidopsis. Plant Physiol. 122: 1045-1056.
Phillips MA, D'Auria JC, Gershenzon J, Pichersky E (2008) The Arabidopsis thaliana type I isopentenyl diphosphate isomerases are targeted to multiple subcellular compartments and have overlapping functions in isoprenoid biosynthesis. Plant Cell. 20: 677-696.
Pontes B, Giráldez R, Aguilar-Ruiz JS (2015) Biclustering on expression data: A review. J Biomed Inform. 57: 163-180.
Prelić A, Bleuler S, Zimmermann P, Wille A, Bühlmann P, Gruissem W, Hennig L, Thiele L, Zitzler E (2006) A systematic comparison and evaluation of biclustering methods for gene expression data. Bioinformatics. 22: 1122-1129.
Proteau PJ (1998) Biosynthesis of phytol in the cyanobacterium Synechocystis sp. UTEX 2470: utilization of the non-mevalonate pathway. J. Nat. Prod. 61: 841-843.
Pulido P, Perello C, Rodriguez-Concepcion M (2012) New insights into plant isoprenoid metabolism. Mol Plant. 5: 964-967.
Robertlee J, Kobayashi K, Tang J, Suzuki M, Muranaka T (2018) Evidence that the Arabidopsis thaliana 3-hydroxy-3-methylglutaryl-CoA reductase 1 is phosphorylated at Ser577 in planta. Plant Biotechnol.17.1208 a.
Rodríguez-Concepción M (2006) Early steps in isoprenoid biosynthesis: multilevel regulation of the supply of common precursors in plant cells. Phytochem. Rev. 5: 1-15.
Rohmer M, Knani M, Simonin P, Sutter B, Sahm H (1993) Isoprenoid biosynthesis in bacteria: a novel pathway for the early steps leading to isopentenyl diphosphate. Biochem. J. 295: 517-524.
Sapir-Mir M, Mett A, Belausov E, Tal-Meshulam S, Frydman A, Gidoni D, Eyal Y (2008) Peroxisomal localization of Arabidopsis isopentenyl diphosphate isomerases suggest that part of the plant isoprenoid mevalonic acid pathway is compartmentalized to peroxisomes. Plant Physiol. 148: 1219-1228.
Sawai S, Saito K (2011) Triterpenoid biosynthesis and engineering in plants. Front Plant Sci. 2: 25.
Simkin AJ, Guirimand G, Papon N, Courdavault V, Thabet I, Ginis O, Bouzid S, Giglioli-Guivarc’h N, Clastre M (2011) Peroxisomal localisation of the final steps of the mevalonic acid pathway in planta. Planta. 234: 903.
Smit A, Mushegian A (2000) Biosynthesis of isoprenoids via mevalonate in Archaea: the lost pathway. Genome Res. 10: 1468-1484.
Suzuki M, Kamide Y, Nagata N, Seki H, Ohyama K, Kato H, Masuda K, Sato S, Kato T, Tabata S (2004) Loss of function of 3‐hydroxy‐3‐methylglutaryl coenzyme A reductase 1 (HMG1) in Arabidopsis leads to dwarfing, early senescence and male sterility, and reduced sterol levels. Plant J. 37: 750-761.
Suzuki M, Nakagawa S, Kamide Y, Kobayashi K, Ohyama K, Hashinokuchi H, Kiuchi R, Saito K, Muranaka T, Nagata N (2009) Complete blockage of the mevalonate pathway results in male gametophyte lethality. J. Exp. Bot. 60: 2055-2064.
Tholl D, Lee S (2011) Terpene specialized metabolism in Arabidopsis thaliana. Arabidopsis Book. 9.
Vandermoten S, Haubruge É, Cusson M (2009) New insights into short-chain prenyltransferases: structural features, evolutionary history and potential for selective inhibition. Cell. Mol. Life Sci. 66: 3685-3695.
Vranová E, Coman D, Gruissem W (2013) Network analysis of the MVA and MEP pathways for isoprenoid synthesis. Annu Rev Plant Biol. 64: 665-700.
Walter MH, Hans J, Strack D (2002) Two distantly related genes encoding 1‐deoxy‐d‐xylulose 5‐phosphate synthases: differential regulation in shoots and apocarotenoid‐accumulating mycorrhizal roots. Plant J. 31: 243-254.
Wang G, Dixon RA (2009) Heterodimeric geranyl (geranyl) diphosphate synthase from hop (Humulus lupulus) and the evolution of monoterpene biosynthesis. Proc. Natl. Acad. Sci. U.S.A. 106: 9914-9919.
Wilding EI, Brown JR, Bryant AP, Chalker AF, Holmes DJ, Ingraham KA, Iordanescu S, So CY, Rosenberg M, Gwynn MN (2000) Identification, evolution, and essentiality of the mevalonate pathway for isopentenyl diphosphate biosynthesis in gram-positive cocci. J. Bacteriol. 182: 4319-4327.
Xiang S, Usunow G, Lange G, Busch M, Tong L (2012) 1-Deoxy-D-xylulose 5-phosphate synthase (DXS), a crucial enzyme for isoprenoids biosynthesis. Isoprenoid Synthesis in Plants and Microorganisms (pp. 17-28): Springer.
Zhao L, Chang W-c, Xiao Y, Liu H-w, Liu P (2013) Methylerythritol phosphate pathway of isoprenoid biosynthesis. Annu. Rev. Biochem. 82: 497-530.
Zhou YJ (2018) Expanding the terpenoid kingdom. Nat. Chem. Biol. 14: 1069.

فایل ها

هم رسانی

ارجاع به این مقاله

آمار