OmpR Indirectly Regulates Biosynthesis of Xenocoumacin 1 in <i>Xenorhabdus nematophila</i>
<i>Xenorhabdus nematophila</i> has excellent potential for application in both medicine and agriculture due to its various active secondary metabolites. The transcriptional regulator OmpR negatively regulates Xenocoumacin 1 (Xcn1), which has wide antimicrobial activity. Here, we expresse...
Saved in:
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-06-01
|
| Series: | Microorganisms |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-2607/13/6/1360 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849705897027174400 |
|---|---|
| author | Yunfei Han Xintong Zhao Mengru He Shujing Zhang Gaijuan Tang Yonghong Wang |
| author_facet | Yunfei Han Xintong Zhao Mengru He Shujing Zhang Gaijuan Tang Yonghong Wang |
| author_sort | Yunfei Han |
| collection | DOAJ |
| description | <i>Xenorhabdus nematophila</i> has excellent potential for application in both medicine and agriculture due to its various active secondary metabolites. The transcriptional regulator OmpR negatively regulates Xenocoumacin 1 (Xcn1), which has wide antimicrobial activity. Here, we expressed and purified OmpR and verified its binding activities to promoters via an electrophoretic mobility shift assay. RNA sequencing was used to analyze the relevance and difference of differentially expressed genes between <i>X. nematophila</i> and its mutant <i>ΔompR</i>. Compared with the WT, 1127 differentially expressed genes were found in <i>ΔompR</i>, while 4150 co-expressed genes were detected. RT-qPCR data validated the RNA-seq results with 20 randomly selected genes. OmpR positively regulates the process of porphyrin metabolism, quorum sensing, β-Lactam resistance and glyoxylate and dicarboxylate metabolism, while negatively regulating the phosphotransferase system, two-component system and bacterial chemotaxis. OmpR indirectly regulates the biosynthesis of Xcn1 by positively regulating the process of glyoxylate metabolism, which consumes energy and precursors, and negatively regulates biomacromolecules biosynthesis, which provides energy and precursors. Overall, this work revealed the indirect effects of OmpR on the biosynthesis of Xcn1, serving as a foundation for future research into the intricate regulatory network of <i>X. nematophila</i>. |
| format | Article |
| id | doaj-art-3623eee61bc84f238ee7bd809a332000 |
| institution | DOAJ |
| issn | 2076-2607 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj-art-3623eee61bc84f238ee7bd809a3320002025-08-20T03:16:21ZengMDPI AGMicroorganisms2076-26072025-06-01136136010.3390/microorganisms13061360OmpR Indirectly Regulates Biosynthesis of Xenocoumacin 1 in <i>Xenorhabdus nematophila</i>Yunfei Han0Xintong Zhao1Mengru He2Shujing Zhang3Gaijuan Tang4Yonghong Wang5Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Shaanxi Biopesticide Engineering & Technology Research Center, College of Plant Protection, Northwest A&F University, Yangling 712100, ChinaKey Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Shaanxi Biopesticide Engineering & Technology Research Center, College of Plant Protection, Northwest A&F University, Yangling 712100, ChinaKey Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Shaanxi Biopesticide Engineering & Technology Research Center, College of Plant Protection, Northwest A&F University, Yangling 712100, ChinaKey Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, School of Tropical Agriculture and Forestry (School of Agricultural and Rural Affairs, School of Rural Revitalization), Hainan University, Haikou 570228, ChinaKey Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Shaanxi Biopesticide Engineering & Technology Research Center, College of Plant Protection, Northwest A&F University, Yangling 712100, ChinaKey Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Shaanxi Biopesticide Engineering & Technology Research Center, College of Plant Protection, Northwest A&F University, Yangling 712100, China<i>Xenorhabdus nematophila</i> has excellent potential for application in both medicine and agriculture due to its various active secondary metabolites. The transcriptional regulator OmpR negatively regulates Xenocoumacin 1 (Xcn1), which has wide antimicrobial activity. Here, we expressed and purified OmpR and verified its binding activities to promoters via an electrophoretic mobility shift assay. RNA sequencing was used to analyze the relevance and difference of differentially expressed genes between <i>X. nematophila</i> and its mutant <i>ΔompR</i>. Compared with the WT, 1127 differentially expressed genes were found in <i>ΔompR</i>, while 4150 co-expressed genes were detected. RT-qPCR data validated the RNA-seq results with 20 randomly selected genes. OmpR positively regulates the process of porphyrin metabolism, quorum sensing, β-Lactam resistance and glyoxylate and dicarboxylate metabolism, while negatively regulating the phosphotransferase system, two-component system and bacterial chemotaxis. OmpR indirectly regulates the biosynthesis of Xcn1 by positively regulating the process of glyoxylate metabolism, which consumes energy and precursors, and negatively regulates biomacromolecules biosynthesis, which provides energy and precursors. Overall, this work revealed the indirect effects of OmpR on the biosynthesis of Xcn1, serving as a foundation for future research into the intricate regulatory network of <i>X. nematophila</i>.https://www.mdpi.com/2076-2607/13/6/1360<i>Xenorhabdus nematophila</i>transcriptomexenocoumacin 1OmpREMSA |
| spellingShingle | Yunfei Han Xintong Zhao Mengru He Shujing Zhang Gaijuan Tang Yonghong Wang OmpR Indirectly Regulates Biosynthesis of Xenocoumacin 1 in <i>Xenorhabdus nematophila</i> Microorganisms <i>Xenorhabdus nematophila</i> transcriptome xenocoumacin 1 OmpR EMSA |
| title | OmpR Indirectly Regulates Biosynthesis of Xenocoumacin 1 in <i>Xenorhabdus nematophila</i> |
| title_full | OmpR Indirectly Regulates Biosynthesis of Xenocoumacin 1 in <i>Xenorhabdus nematophila</i> |
| title_fullStr | OmpR Indirectly Regulates Biosynthesis of Xenocoumacin 1 in <i>Xenorhabdus nematophila</i> |
| title_full_unstemmed | OmpR Indirectly Regulates Biosynthesis of Xenocoumacin 1 in <i>Xenorhabdus nematophila</i> |
| title_short | OmpR Indirectly Regulates Biosynthesis of Xenocoumacin 1 in <i>Xenorhabdus nematophila</i> |
| title_sort | ompr indirectly regulates biosynthesis of xenocoumacin 1 in i xenorhabdus nematophila i |
| topic | <i>Xenorhabdus nematophila</i> transcriptome xenocoumacin 1 OmpR EMSA |
| url | https://www.mdpi.com/2076-2607/13/6/1360 |
| work_keys_str_mv | AT yunfeihan omprindirectlyregulatesbiosynthesisofxenocoumacin1inixenorhabdusnematophilai AT xintongzhao omprindirectlyregulatesbiosynthesisofxenocoumacin1inixenorhabdusnematophilai AT mengruhe omprindirectlyregulatesbiosynthesisofxenocoumacin1inixenorhabdusnematophilai AT shujingzhang omprindirectlyregulatesbiosynthesisofxenocoumacin1inixenorhabdusnematophilai AT gaijuantang omprindirectlyregulatesbiosynthesisofxenocoumacin1inixenorhabdusnematophilai AT yonghongwang omprindirectlyregulatesbiosynthesisofxenocoumacin1inixenorhabdusnematophilai |