Differential transcriptomic analysis by RNA-Seq of GSNO-responsive genes between Arabidopsis roots and leaves

Plant Cell Physiol. 2014 Jun;55(6):1080-95. doi: 10.1093/pcp/pcu044. Epub 2014 Mar 4.

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.

Keywords: Arabidopsis; Massively parallel sequencing; Methionine sulfoxide reductase; Nitric oxide; Plant signaling mechanisms; RNA-seq; S-nitrosoglutathione.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / drug effects
  • Arabidopsis / genetics*
  • Arabidopsis / physiology
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism
  • Base Sequence
  • Gene Expression Regulation, Plant*
  • High-Throughput Nucleotide Sequencing
  • Hydroponics
  • Methionine Sulfoxide Reductases / genetics*
  • Methionine Sulfoxide Reductases / metabolism
  • Nitric Oxide / metabolism
  • Nitric Oxide Donors / pharmacology*
  • Nucleotide Motifs
  • Organ Specificity
  • Plant Leaves / drug effects
  • Plant Leaves / genetics
  • Plant Leaves / physiology
  • Plant Roots / drug effects
  • Plant Roots / genetics
  • Plant Roots / physiology
  • Promoter Regions, Genetic / genetics
  • RNA, Plant / chemistry
  • RNA, Plant / genetics
  • S-Nitrosoglutathione / pharmacology*
  • Sequence Analysis, RNA
  • Signal Transduction*

Substances

  • Arabidopsis Proteins
  • Nitric Oxide Donors
  • RNA, Plant
  • Nitric Oxide
  • S-Nitrosoglutathione
  • Methionine Sulfoxide Reductases
  • methionine sulfoxide reductase