Effects of LPS from <i>Rhodobacter sphaeroides</i>, a Purple Non-Sulfur Bacterium (PNSB), on the Gene Expression of Rice Root
The effects of lipopolysaccharide (LPS) from <i>Rhodobacter sphaeroides</i>, a purple non-sulfur bacterium (PNSB), on the gene expression of the root of rice (<i>Oryza sativa</i>) were investigated by next generation sequencing (NGS) RNA-seq analysis. The rice seeds were germ...
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MDPI AG
2023-06-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/11/7/1676 |
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| author | Ranko Iwai Shunta Uchida Sayaka Yamaguchi Daiki Nagata Aoi Koga Shuhei Hayashi Shinjiro Yamamoto Hitoshi Miyasaka |
| author_facet | Ranko Iwai Shunta Uchida Sayaka Yamaguchi Daiki Nagata Aoi Koga Shuhei Hayashi Shinjiro Yamamoto Hitoshi Miyasaka |
| author_sort | Ranko Iwai |
| collection | DOAJ |
| description | The effects of lipopolysaccharide (LPS) from <i>Rhodobacter sphaeroides</i>, a purple non-sulfur bacterium (PNSB), on the gene expression of the root of rice (<i>Oryza sativa</i>) 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 <i>Rhodobacter sphaeroides</i> 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 <i>R. sphaeroides</i> NBRC 12203<sup>T</sup> at the concentration of 10<sup>1</sup> 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<sup>2</sup> = 0.6333, <i>p</i> < 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. |
| first_indexed | 2024-03-11T00:49:25Z |
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| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-11T00:49:25Z |
| publishDate | 2023-06-01 |
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| spelling | doaj.art-fa43030709f24aae8fcc5f4918678e042023-11-18T20:34:53ZengMDPI AGMicroorganisms2076-26072023-06-01117167610.3390/microorganisms11071676Effects of LPS from <i>Rhodobacter sphaeroides</i>, a Purple Non-Sulfur Bacterium (PNSB), on the Gene Expression of Rice RootRanko Iwai0Shunta Uchida1Sayaka Yamaguchi2Daiki Nagata3Aoi Koga4Shuhei Hayashi5Shinjiro Yamamoto6Hitoshi Miyasaka7Department of Applied Life Science, Sojo University, 4-22-1 Ikeda, Nishiku, Kumamoto 860-0082, JapanDepartment of Applied Life Science, Sojo University, 4-22-1 Ikeda, Nishiku, Kumamoto 860-0082, JapanDepartment of Applied Life Science, Sojo University, 4-22-1 Ikeda, Nishiku, Kumamoto 860-0082, JapanDepartment of Applied Life Science, Sojo University, 4-22-1 Ikeda, Nishiku, Kumamoto 860-0082, JapanCiamo Co., Ltd., G-2F Sojo University, 4-22-1 Ikeda, Nishiku, Kumamoto 860-0082, JapanDepartment of Applied Life Science, Sojo University, 4-22-1 Ikeda, Nishiku, Kumamoto 860-0082, JapanDepartment of Applied Life Science, Sojo University, 4-22-1 Ikeda, Nishiku, Kumamoto 860-0082, JapanDepartment of Applied Life Science, Sojo University, 4-22-1 Ikeda, Nishiku, Kumamoto 860-0082, JapanThe effects of lipopolysaccharide (LPS) from <i>Rhodobacter sphaeroides</i>, a purple non-sulfur bacterium (PNSB), on the gene expression of the root of rice (<i>Oryza sativa</i>) 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 <i>Rhodobacter sphaeroides</i> 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 <i>R. sphaeroides</i> NBRC 12203<sup>T</sup> at the concentration of 10<sup>1</sup> 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<sup>2</sup> = 0.6333, <i>p</i> < 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.https://www.mdpi.com/2076-2607/11/7/1676purple non-sulfur bacteriumPNSBLPS<i>Rhodobacter sphaeroides</i>RNA-seq |
| spellingShingle | Ranko Iwai Shunta Uchida Sayaka Yamaguchi Daiki Nagata Aoi Koga Shuhei Hayashi Shinjiro Yamamoto Hitoshi Miyasaka Effects of LPS from <i>Rhodobacter sphaeroides</i>, a Purple Non-Sulfur Bacterium (PNSB), on the Gene Expression of Rice Root Microorganisms purple non-sulfur bacterium PNSB LPS <i>Rhodobacter sphaeroides</i> RNA-seq |
| title | Effects of LPS from <i>Rhodobacter sphaeroides</i>, a Purple Non-Sulfur Bacterium (PNSB), on the Gene Expression of Rice Root |
| title_full | Effects of LPS from <i>Rhodobacter sphaeroides</i>, a Purple Non-Sulfur Bacterium (PNSB), on the Gene Expression of Rice Root |
| title_fullStr | Effects of LPS from <i>Rhodobacter sphaeroides</i>, a Purple Non-Sulfur Bacterium (PNSB), on the Gene Expression of Rice Root |
| title_full_unstemmed | Effects of LPS from <i>Rhodobacter sphaeroides</i>, a Purple Non-Sulfur Bacterium (PNSB), on the Gene Expression of Rice Root |
| title_short | Effects of LPS from <i>Rhodobacter sphaeroides</i>, a Purple Non-Sulfur Bacterium (PNSB), on the Gene Expression of Rice Root |
| title_sort | effects of lps from i rhodobacter sphaeroides i a purple non sulfur bacterium pnsb on the gene expression of rice root |
| topic | purple non-sulfur bacterium PNSB LPS <i>Rhodobacter sphaeroides</i> RNA-seq |
| url | https://www.mdpi.com/2076-2607/11/7/1676 |
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