Bradyrhizobium diazoefficiens USDA110 PhaR functions for pleiotropic regulation of cellular processes besides PHB accumulation
Abstract Background Bradyrhizobium diazoefficiens USDA110 nodulates soybeans for nitrogen fixation. It accumulates poly-3-hydroxybutyrate (PHB), which is of physiological importance as a carbon/energy source for survival during starvation, infection, and nitrogen fixation conditions. PHB accumulatio...
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| Format: | Article |
| Language: | English |
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BMC
2018-10-01
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| Series: | BMC Microbiology |
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| Online Access: | http://link.springer.com/article/10.1186/s12866-018-1317-2 |
| _version_ | 1818672030513364992 |
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| author | Shogo Nishihata Takahiko Kondo Kosei Tanaka Shu Ishikawa Shinji Takenaka Choong-Min Kang Ken-ichi Yoshida |
| author_facet | Shogo Nishihata Takahiko Kondo Kosei Tanaka Shu Ishikawa Shinji Takenaka Choong-Min Kang Ken-ichi Yoshida |
| author_sort | Shogo Nishihata |
| collection | DOAJ |
| description | Abstract Background Bradyrhizobium diazoefficiens USDA110 nodulates soybeans for nitrogen fixation. It accumulates poly-3-hydroxybutyrate (PHB), which is of physiological importance as a carbon/energy source for survival during starvation, infection, and nitrogen fixation conditions. PHB accumulation is orchestrated by not only the enzymes for PHB synthesis but also PHB-binding phasin proteins (PhaPs) stabilizing the PHB granules. The transcription factor PhaR controls the phaP genes. Results Inactivation of phaR led to decreases in PHB accumulation, less cell yield, increases in exopolysaccharide (EPS) production, some improvement in heat stress tolerance, and slightly better growth under microaerobic conditions. Changes in the transcriptome upon phaR inactivation were analyzed. PhaR appeared to be involved in the repression of various target genes, including some PHB-degrading enzymes and others involved in EPS production. Furthermore, in vitro gel shift analysis demonstrated that PhaR bound to the promoter regions of representative targets. For the phaP1 and phaP4 promoter regions, PhaR-binding sites were determined by DNase I footprinting, allowing us to deduce a consensus sequence for PhaR-binding as TGCRNYGCASMA (R: A or G, Y: C or T, S: C or G, M: A or C). We searched for additional genes associated with a PhaR-binding sequence and found that some genes involved in central carbon metabolism, such as pdhA for pyruvate dehydrogenase and pckA for phosphoenolpyruvate carboxykinase, may be regulated positively and directly by PhaR. Conclusions These results suggest that PhaR could regulate various genes not only negatively but also positively to coordinate metabolism holistically in response to PHB accumulation. |
| first_indexed | 2024-12-17T07:33:25Z |
| format | Article |
| id | doaj.art-94bb951b7f9f444b986dda43a0620a0b |
| institution | Directory Open Access Journal |
| issn | 1471-2180 |
| language | English |
| last_indexed | 2024-12-17T07:33:25Z |
| publishDate | 2018-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Microbiology |
| spelling | doaj.art-94bb951b7f9f444b986dda43a0620a0b2022-12-21T21:58:24ZengBMCBMC Microbiology1471-21802018-10-0118111710.1186/s12866-018-1317-2Bradyrhizobium diazoefficiens USDA110 PhaR functions for pleiotropic regulation of cellular processes besides PHB accumulationShogo Nishihata0Takahiko Kondo1Kosei Tanaka2Shu Ishikawa3Shinji Takenaka4Choong-Min Kang5Ken-ichi Yoshida6Department of Agrobioscience, Kobe UniversityDepartment of Science, Technology and Innovation, Kobe UniversityDepartment of Science, Technology and Innovation, Kobe UniversityDepartment of Science, Technology and Innovation, Kobe UniversityDepartment of Agrobioscience, Kobe UniversityDepartment of Biological Science, California State UniversityDepartment of Science, Technology and Innovation, Kobe UniversityAbstract Background Bradyrhizobium diazoefficiens USDA110 nodulates soybeans for nitrogen fixation. It accumulates poly-3-hydroxybutyrate (PHB), which is of physiological importance as a carbon/energy source for survival during starvation, infection, and nitrogen fixation conditions. PHB accumulation is orchestrated by not only the enzymes for PHB synthesis but also PHB-binding phasin proteins (PhaPs) stabilizing the PHB granules. The transcription factor PhaR controls the phaP genes. Results Inactivation of phaR led to decreases in PHB accumulation, less cell yield, increases in exopolysaccharide (EPS) production, some improvement in heat stress tolerance, and slightly better growth under microaerobic conditions. Changes in the transcriptome upon phaR inactivation were analyzed. PhaR appeared to be involved in the repression of various target genes, including some PHB-degrading enzymes and others involved in EPS production. Furthermore, in vitro gel shift analysis demonstrated that PhaR bound to the promoter regions of representative targets. For the phaP1 and phaP4 promoter regions, PhaR-binding sites were determined by DNase I footprinting, allowing us to deduce a consensus sequence for PhaR-binding as TGCRNYGCASMA (R: A or G, Y: C or T, S: C or G, M: A or C). We searched for additional genes associated with a PhaR-binding sequence and found that some genes involved in central carbon metabolism, such as pdhA for pyruvate dehydrogenase and pckA for phosphoenolpyruvate carboxykinase, may be regulated positively and directly by PhaR. Conclusions These results suggest that PhaR could regulate various genes not only negatively but also positively to coordinate metabolism holistically in response to PHB accumulation.http://link.springer.com/article/10.1186/s12866-018-1317-2Bradyrhizobium diazoefficiensPoly-3-hydroxybutyrate (PHB)TranscriptomeTranscription factorDNA binding |
| spellingShingle | Shogo Nishihata Takahiko Kondo Kosei Tanaka Shu Ishikawa Shinji Takenaka Choong-Min Kang Ken-ichi Yoshida Bradyrhizobium diazoefficiens USDA110 PhaR functions for pleiotropic regulation of cellular processes besides PHB accumulation BMC Microbiology Bradyrhizobium diazoefficiens Poly-3-hydroxybutyrate (PHB) Transcriptome Transcription factor DNA binding |
| title | Bradyrhizobium diazoefficiens USDA110 PhaR functions for pleiotropic regulation of cellular processes besides PHB accumulation |
| title_full | Bradyrhizobium diazoefficiens USDA110 PhaR functions for pleiotropic regulation of cellular processes besides PHB accumulation |
| title_fullStr | Bradyrhizobium diazoefficiens USDA110 PhaR functions for pleiotropic regulation of cellular processes besides PHB accumulation |
| title_full_unstemmed | Bradyrhizobium diazoefficiens USDA110 PhaR functions for pleiotropic regulation of cellular processes besides PHB accumulation |
| title_short | Bradyrhizobium diazoefficiens USDA110 PhaR functions for pleiotropic regulation of cellular processes besides PHB accumulation |
| title_sort | bradyrhizobium diazoefficiens usda110 phar functions for pleiotropic regulation of cellular processes besides phb accumulation |
| topic | Bradyrhizobium diazoefficiens Poly-3-hydroxybutyrate (PHB) Transcriptome Transcription factor DNA binding |
| url | http://link.springer.com/article/10.1186/s12866-018-1317-2 |
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