Effects of LPS from Rhodobacter sphaeroides , a Purple Non-Sulfur Bacterium (PNSB), on the Gene Expression of Rice Root

• Published in: Microorganisms (Basel) 2023-06, Vol.11 (7), p.1676
• Main Authors: Iwai, Ranko, Uchida, Shunta, Yamaguchi, Sayaka, Nagata, Daiki, Koga, Aoi, Hayashi, Shuhei, Yamamoto, Shinjiro, Miyasaka, Hitoshi
• Format: Article
• Language: English
• Subjects: Bacteria; Cell culture; Chalcone synthase; Drought; Gene expression; Gene sequencing; Genes; Genomes; Germination; Gram-negative bacteria; Isoenzymes; Jasmonic acid; Lipopolysaccharides; LPS; Next-generation sequencing; Pathogenicity; Pathogens; Plant growth; PNSB; purple non-sulfur bacterium; Rhodobacter sphaeroides; Ribonucleic acid; Rice; RNA; RNA-seq; Seeds; Signal transduction; Software; Stresses; Sulfur
• ISSN: 2076-2607; 2076-2607
• DOI: 10.3390/microorganisms11071676

The effects of lipopolysaccharide (LPS) from , a purple non-sulfur bacterium (PNSB), on the gene expression of the root of rice ( ) were investigated by next generation sequencing (NGS) RNA-seq analysis. The rice seeds were germinated on agar plates containing 10 pg/mL of LPS from NBRC 12203 (type culture). Three days after germination, RNA samples were extracted from the roots and analyzed by RNA-seq. The effects of dead (killed) PNSB cells of NBRC 12203 at the concentration of 10 cfu/mL (ca. 50 pg cell dry weight/mL) were also examined. Clean reads of NGS were mapped to rice genome (number of transcript ID: 44785), and differentially expressed genes were analyzed by DEGs. As a result of DEG analysis, 300 and 128 genes, and 86 and 8 genes were significantly up- and down-regulated by LPS and dead cells of PNSB, respectively. The plot of logFC (fold change) values of the up-regulated genes of LPS and PNSB dead cells showed a significant positive relationship (r = 0.6333, < 0.0001), indicating that most of the effects of dead cell were attributed to those of LPS. Many genes related to tolerance against biotic (fungal and bacterial pathogens) and abiotic (cold, drought, and high salinity) stresses were up-regulated, and the most strikingly up-regulated genes were those involved in the jasmonate signaling pathway, and the genes of chalcone synthase isozymes, indicating that PNSB induced defense response against biotic and abiotic stresses via the jasmonate signaling pathway, despite the non-pathogenicity of PNSB.