title: Differential transcriptomic analysis by RNA-Seq of GSNO-responsive genes between Arabidopsis roots and leaves.
abstract: S-Nitrosoglutathione (GSNO) is a nitric oxide-derived molecule that can regulate protein function by a post-translational modification designated S-nitrosylation. GSNO has also been detected in different plant organs under physiological and stress conditions, and it can also modulate gene expression. Thirty-day-old Arabidopsis plants were grown under hydroponic conditions, and exogenous 1 mM GSNO was applied to the root systems for 3 h. Differential gene expression analyses were carried out both in roots and in leaves by RNA sequencing (RNA-seq). A total of 3,263 genes were identified as being modulated by GSNO. Most of the genes identified were associated with the mechanism of protection against stress situations, many of these having previously been identified as target genes of GSNO by array-based methods. However, new genes were identified, such as that for methionine sulfoxide reductase (MSR) in leaves or different miscellaneous RNA (miscRNA) genes in Arabidopsis roots. As a result, 1,945 GSNO-responsive genes expressed differently in leaves and roots were identified, and 114 of these corresponded exclusively to one of these organs. In summary, it is demonstrated that RNA-seq extends our knowledge of GSNO as a signaling molecule which differentially modulates gene expression in roots and leaves under non-stress conditions.
authors.affiliation: Group of Biochemistry and Cell Signalling in Nitric Oxide, Área de Bioquímica y Biología Molecular, Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Campus Universitario 'Las Lagunillas' s/n, Universidad de Jaén, E-23071 Jaén, Spain.
authors.forename: Juan C
authors.initials: JC
authors.lastname: Begara-Morales
authors.affiliation: Group of Biochemistry and Cell Signalling in Nitric Oxide, Área de Bioquímica y Biología Molecular, Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Campus Universitario 'Las Lagunillas' s/n, Universidad de Jaén, E-23071 Jaén, Spain.
authors.forename: Beatriz
authors.initials: B
authors.lastname: Sánchez-Calvo
authors.affiliation: Group of Biochemistry and Cell Signalling in Nitric Oxide, Área de Bioquímica y Biología Molecular, Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Campus Universitario 'Las Lagunillas' s/n, Universidad de Jaén, E-23071 Jaén, Spain.
authors.forename: Francisco
authors.initials: F
authors.lastname: Luque
authors.affiliation: Group of Biochemistry and Cell Signalling in Nitric Oxide, Área de Bioquímica y Biología Molecular, Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Campus Universitario 'Las Lagunillas' s/n, Universidad de Jaén, E-23071 Jaén, Spain.
authors.forename: María O
authors.initials: MO
authors.lastname: Leyva-Pérez
authors.affiliation: Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín (EEZ), Consejo Superior de Investigaciones Científicas, E-18080 Granada, Spain.
authors.forename: Marina
authors.initials: M
authors.lastname: Leterrier
authors.affiliation: Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín (EEZ), Consejo Superior de Investigaciones Científicas, E-18080 Granada, Spain javier.corpas@eez.csic.es.
authors.forename: Francisco J
authors.initials: FJ
authors.lastname: Corpas
authors.affiliation: Group of Biochemistry and Cell Signalling in Nitric Oxide, Área de Bioquímica y Biología Molecular, Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Campus Universitario 'Las Lagunillas' s/n, Universidad de Jaén, E-23071 Jaén, Spain.
authors.forename: Juan B
authors.initials: JB
authors.lastname: Barroso
mesh_terms: D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics* / Q000502:physiology; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing; D018527:Hydroponics; D051150:Methionine Sulfoxide Reductases / Q000235:genetics* / Q000378:metabolism; D009569:Nitric Oxide / Q000378:metabolism; D020030:Nitric Oxide Donors / Q000494:pharmacology*; D059372:Nucleotide Motifs; D009928:Organ Specificity; D018515:Plant Leaves / Q000187:drug effects / Q000235:genetics / Q000502:physiology; D018517:Plant Roots / Q000187:drug effects / Q000235:genetics / Q000502:physiology; D011401:Promoter Regions, Genetic / Q000235:genetics; D018749:RNA, Plant / Q000737:chemistry / Q000235:genetics; D026422:S-Nitrosoglutathione / Q000494:pharmacology*; D017423:Sequence Analysis, RNA; D015398:Signal Transduction
chemical_list: D029681:Arabidopsis Proteins; D020030:Nitric Oxide Donors; D018749:RNA, Plant; D009569:Nitric Oxide; D026422:S-Nitrosoglutathione; D051150:Methionine Sulfoxide Reductases; C027219:methionine sulfoxide reductase
keywords: Arabidopsis; Massively parallel sequencing; Methionine sulfoxide reductase; Nitric oxide; Plant signaling mechanisms; RNA-seq; S-nitrosoglutathione