Investigating the links between N2 fixation and metabolism in rhizobia
<p>In this thesis the metabolic flow of carbon and electrons enabling N2 fixation in the agriculturally relevant model organisms <em>Rhizobium leguminosarum</em> and <em>Azorhizobium caulinodans</em> was investigated. Building upon functional genomic data-sets including...
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| Format: | Thesis |
| Language: | English |
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2019
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| _version_ | 1797066440274083840 |
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| author | Crang, N |
| author2 | Poole, P |
| author_facet | Poole, P Crang, N |
| author_sort | Crang, N |
| collection | OXFORD |
| description | <p>In this thesis the metabolic flow of carbon and electrons enabling N2 fixation in the agriculturally relevant model organisms <em>Rhizobium leguminosarum</em> and <em>Azorhizobium caulinodans</em> was investigated. Building upon functional genomic data-sets including transcriptomics, metabolomics and mutagenic screens, the core metabolic reactions needed for dicarboxylate ORS571 and RL3841. Isocitrate dehydrogenase was found to be essential for N2-fixation and operation of the TCA-cycle in RL3841, contradicting previously published INSeq data. This was due to TA insertions in gene termini misleading the Hidden Markov Model used to asses INSeq data. As a result of this, new bioinformatic pipelines have been developed to avoid such errors. The redox sink poly-3-hydroxy butyrate (PHB) was shown to be non-essential for N<sub>2</sub> fixation in ORS571. Previously published results showing PHB synthesis to be essential are actually due to missregulation of <em>phaR</em> translation in <em>phaC</em> mutants used to block PHB synthesis, rather than the loss of PHB as a redox store. This bring ORS571 in line with other species of rhizobia, where PHB defective mutants retained their ability to fix N<sub>2</sub>. Two alternative metabolic pathways, the malonate shunt in ORS571 and the isocitrate shunt in RL3841 have both been investigated and shown to be inoperative at biologically relevant levels in their respective organisms. In ORS571, the entirety of the carbon flux between succinate and acetyl-CoA has been demonstrated to proceed via NAD+ dependent malic enzyme (DME) and phosphoenolpyruvate carboxykinase, allowing existing models of carbon flux to be revised to remove the erroneous malonate shunt. In addition, DME has been demonstrated to be essential for N<sub>2</sub> fixation, but dispensable for growth on succinate, indicating a disconnect between the requirements of N<sub>2</sub> fixation and dicarboxylate metabolism. </p> |
| first_indexed | 2024-03-06T21:42:06Z |
| format | Thesis |
| id | oxford-uuid:4847d2ec-5525-45a2-a4ad-313811a0b5e1 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T21:42:06Z |
| publishDate | 2019 |
| record_format | dspace |
| spelling | oxford-uuid:4847d2ec-5525-45a2-a4ad-313811a0b5e12022-03-26T15:24:51ZInvestigating the links between N2 fixation and metabolism in rhizobiaThesishttp://purl.org/coar/resource_type/c_db06uuid:4847d2ec-5525-45a2-a4ad-313811a0b5e1MicrobiologyEnglishORA Deposit2019Crang, NPoole, P<p>In this thesis the metabolic flow of carbon and electrons enabling N2 fixation in the agriculturally relevant model organisms <em>Rhizobium leguminosarum</em> and <em>Azorhizobium caulinodans</em> was investigated. Building upon functional genomic data-sets including transcriptomics, metabolomics and mutagenic screens, the core metabolic reactions needed for dicarboxylate ORS571 and RL3841. Isocitrate dehydrogenase was found to be essential for N2-fixation and operation of the TCA-cycle in RL3841, contradicting previously published INSeq data. This was due to TA insertions in gene termini misleading the Hidden Markov Model used to asses INSeq data. As a result of this, new bioinformatic pipelines have been developed to avoid such errors. The redox sink poly-3-hydroxy butyrate (PHB) was shown to be non-essential for N<sub>2</sub> fixation in ORS571. Previously published results showing PHB synthesis to be essential are actually due to missregulation of <em>phaR</em> translation in <em>phaC</em> mutants used to block PHB synthesis, rather than the loss of PHB as a redox store. This bring ORS571 in line with other species of rhizobia, where PHB defective mutants retained their ability to fix N<sub>2</sub>. Two alternative metabolic pathways, the malonate shunt in ORS571 and the isocitrate shunt in RL3841 have both been investigated and shown to be inoperative at biologically relevant levels in their respective organisms. In ORS571, the entirety of the carbon flux between succinate and acetyl-CoA has been demonstrated to proceed via NAD+ dependent malic enzyme (DME) and phosphoenolpyruvate carboxykinase, allowing existing models of carbon flux to be revised to remove the erroneous malonate shunt. In addition, DME has been demonstrated to be essential for N<sub>2</sub> fixation, but dispensable for growth on succinate, indicating a disconnect between the requirements of N<sub>2</sub> fixation and dicarboxylate metabolism. </p> |
| spellingShingle | Microbiology Crang, N Investigating the links between N2 fixation and metabolism in rhizobia |
| title | Investigating the links between N2 fixation and metabolism in rhizobia |
| title_full | Investigating the links between N2 fixation and metabolism in rhizobia |
| title_fullStr | Investigating the links between N2 fixation and metabolism in rhizobia |
| title_full_unstemmed | Investigating the links between N2 fixation and metabolism in rhizobia |
| title_short | Investigating the links between N2 fixation and metabolism in rhizobia |
| title_sort | investigating the links between n2 fixation and metabolism in rhizobia |
| topic | Microbiology |
| work_keys_str_mv | AT crangn investigatingthelinksbetweenn2fixationandmetabolisminrhizobia |