Transcriptomic Profiling Analysis of Arabidopsis Thaliana Treated with Exogenous Myo-Inositol

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2016 Sep 8

PMID 27603208

Citations 8

Authors

Wenxing Ye

Weibo Ren

Lingqi Kong

Wanjun Zhang

Tao Wang

Affiliations

Soon will be listed here.

Abstract

Myo-insositol (MI) is a crucial substance in the growth and developmental processes in plants. It is commonly added to the culture medium to promote adventitious shoot development. In our previous work, MI was found in influencing Agrobacterium-mediated transformation. In this report, a high-throughput RNA sequencing technique (RNA-Seq) was used to investigate differently expressed genes in one-month-old Arabidopsis seedling grown on MI free or MI supplemented culture medium. The results showed that 21,288 and 21,299 genes were detected with and without MI treatment, respectively. The detected genes included 184 new genes that were not annotated in the Arabidopsis thaliana reference genome. Additionally, 183 differentially expressed genes were identified (DEGs, FDR ≤0.05, log2 FC≥1), including 93 up-regulated genes and 90 down-regulated genes. The DEGs were involved in multiple pathways, such as cell wall biosynthesis, biotic and abiotic stress response, chromosome modification, and substrate transportation. Some significantly differently expressed genes provided us with valuable information for exploring the functions of exogenous MI. RNA-Seq results showed that exogenous MI could alter gene expression and signaling transduction in plant cells. These results provided a systematic understanding of the functions of exogenous MI in detail and provided a foundation for future studies.

Citing Articles

Characterization of -inositol oxygenase from rice (): influence of salinity stress in different rice cultivars.

Adak S, Agarwal T, Das P, Ray S, Majumder A Physiol Mol Biol Plants. 2023; 29(7):927-945.

PMID: 37649879 PMC: 10462604. DOI: 10.1007/s12298-023-01340-6.

Combined Transcriptomic and Metabolomic Analysis Reveals Insights into Resistance of Arabidopsis Mutant against the Phytopathogenic Fungus .

Kalogeropoulou E, Aliferis K, Tjamos S, Vloutoglou I, Paplomatas E Plants (Basel). 2022; 11(24).

PMID: 36559570 PMC: 9785915. DOI: 10.3390/plants11243457.

Foliar Application of an Inositol-Based Plant Biostimulant Boosts Zinc Accumulation in Wheat Grains: A μ-X-Ray Fluorescence Case Study.

Amaral D, Brown P Front Plant Sci. 2022; 13:837695.

PMID: 35463431 PMC: 9020830. DOI: 10.3389/fpls.2022.837695.

Genome-wide identification of the MIOX gene family and their expression profile in cotton development and response to abiotic stress.

Li Z, Liu Z, Wei Y, Liu Y, Xing L, Liu M PLoS One. 2021; 16(7):e0254111.

PMID: 34242283 PMC: 8270170. DOI: 10.1371/journal.pone.0254111.

A Transcriptional Analysis of the Genes Involved in the Ascorbic Acid Pathways Based on a Comparison of the Juice and Leaves of Navel and Anthocyanin-Rich Sweet Orange Varieties.

Caruso P, Russo M, Caruso M, Di Guardo M, Russo G, Fabroni S Plants (Basel). 2021; 10(7).

PMID: 34202884 PMC: 8309047. DOI: 10.3390/plants10071291.

References

Conesa A, Gotz S . Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics. 2008; 2008:619832. PMC: 2375974. DOI: 10.1155/2008/619832. View

de Jong F, Thodey K, Lejay L, Bevan M . Glucose elevates NITRATE TRANSPORTER2.1 protein levels and nitrate transport activity independently of its HEXOKINASE1-mediated stimulation of NITRATE TRANSPORTER2.1 expression. Plant Physiol. 2013; 164(1):308-20. PMC: 3875810. DOI: 10.1104/pp.113.230599. View

Huang D, Sherman B, Lempicki R . Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009; 4(1):44-57. DOI: 10.1038/nprot.2008.211. View

Rautengarten C, Ebert B, Herter T, Petzold C, Ishii T, Mukhopadhyay A . The interconversion of UDP-arabinopyranose and UDP-arabinofuranose is indispensable for plant development in Arabidopsis. Plant Cell. 2011; 23(4):1373-90. PMC: 3101560. DOI: 10.1105/tpc.111.083931. View

Wang Z, Gerstein M, Snyder M . RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2008; 10(1):57-63. PMC: 2949280. DOI: 10.1038/nrg2484. View

Monserrate J, York J . Inositol phosphate synthesis and the nuclear processes they affect. Curr Opin Cell Biol. 2010; 22(3):365-73. DOI: 10.1016/j.ceb.2010.03.006. View

Liang H, Yao N, Song J, Luo S, Lu H, Greenberg J . Ceramides modulate programmed cell death in plants. Genes Dev. 2003; 17(21):2636-41. PMC: 280613. DOI: 10.1101/gad.1140503. View

Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M . The KEGG resource for deciphering the genome. Nucleic Acids Res. 2003; 32(Database issue):D277-80. PMC: 308797. DOI: 10.1093/nar/gkh063. View

Chatterjee J, Majumder A . Salt-induced abnormalities on root tip mitotic cells of Allium cepa: prevention by inositol pretreatment. Protoplasma. 2010; 245(1-4):165-72. DOI: 10.1007/s00709-010-0170-4. View

10.

Donahue J, Alford S, Torabinejad J, Kerwin R, Nourbakhsh A, Ray W . The Arabidopsis thaliana Myo-inositol 1-phosphate synthase1 gene is required for Myo-inositol synthesis and suppression of cell death. Plant Cell. 2010; 22(3):888-903. PMC: 2861443. DOI: 10.1105/tpc.109.071779. View

11.

Kim C, Bove J, Assmann S . Overexpression of wound-responsive RNA-binding proteins induces leaf senescence and hypersensitive-like cell death. New Phytol. 2008; 180(1):57-70. DOI: 10.1111/j.1469-8137.2008.02557.x. View

12.

Klinghammer M, Tenhaken R . Genome-wide analysis of the UDP-glucose dehydrogenase gene family in Arabidopsis, a key enzyme for matrix polysaccharides in cell walls. J Exp Bot. 2007; 58(13):3609-21. DOI: 10.1093/jxb/erm209. View

13.

Ebbs M, Bender J . Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase. Plant Cell. 2006; 18(5):1166-76. PMC: 1456864. DOI: 10.1105/tpc.106.041400. View

14.

Gelvin S . Agrobacterium transformation of Arabidopsis thaliana roots: a quantitative assay. Methods Mol Biol. 2006; 343:105-13. DOI: 10.1385/1-59745-130-4:105. View

15.

Sancenon V, Puig S, Mira H, Thiele D, Penarrubia L . Identification of a copper transporter family in Arabidopsis thaliana. Plant Mol Biol. 2003; 51(4):577-87. DOI: 10.1023/a:1022345507112. View

16.

Hosmani P, Kamiya T, Danku J, Naseer S, Geldner N, Guerinot M . Dirigent domain-containing protein is part of the machinery required for formation of the lignin-based Casparian strip in the root. Proc Natl Acad Sci U S A. 2013; 110(35):14498-503. PMC: 3761638. DOI: 10.1073/pnas.1308412110. View

17.

Gamborg O, Miller R, Ojima K . Nutrient requirements of suspension cultures of soybean root cells. Exp Cell Res. 1968; 50(1):151-8. DOI: 10.1016/0014-4827(68)90403-5. View

18.

Naumann K, Fischer A, Hofmann I, Krauss V, Phalke S, Irmler K . Pivotal role of AtSUVH2 in heterochromatic histone methylation and gene silencing in Arabidopsis. EMBO J. 2005; 24(7):1418-29. PMC: 1142535. DOI: 10.1038/sj.emboj.7600604. View

19.

Alcazar-Roman A, Wente S . Inositol polyphosphates: a new frontier for regulating gene expression. Chromosoma. 2007; 117(1):1-13. DOI: 10.1007/s00412-007-0126-4. View

20.

Gillaspy G . The cellular language of myo-inositol signaling. New Phytol. 2011; 192(4):823-839. DOI: 10.1111/j.1469-8137.2011.03939.x. View