3-Hydroxyisobutyrate Dehydrogenase Is Involved in Both, Valine and Isoleucine Degradation in <i>Arabidopsis thaliana</i>

Schertl, Peter; Danne, Lennart; Braun, Hans‐Peter

doi:10.1104/pp.17.00649

Cited by 34 publications

(28 citation statements)

References 45 publications

(45 reference statements)

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“…We found that the amino acid metabolism ability of S. pogona overall was stronger than that of S. spinosa, indicating that S. pogona demonstrated a stronger synthetic ability to convert amino acids into acetyl-CoA and other key precursors compared with S. spinosa. For example, the abundance of enzymes (ilvE, bkdA, acdA-3, fadB, fadA, fadA4, pccB, and aldA) involved in the leucine to acetyl-CoA, valine to (R)-methylmalonyl-CoA, and isoleucine to (S)methylmalonyl-CoA pathways in S. pogona was remarkably higher than that in S. spinosa (Schertl et al, 2017). Meanwhile, leucine (0.36) and isoleucine (0.71) were detected at lower concentrations in S. pogona than in S. spinosa.…”

Section: Amino Acid Metabolismmentioning

confidence: 96%

Deciphering the Metabolic Pathway Difference Between Saccharopolyspora pogona and Saccharopolyspora spinosa by Comparative Proteomics and Metabonomics

Rang

Yuan

et al. 2020

Front. Microbiol.

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Butenyl-spinosyn, a secondary metabolite produced by Saccharopolyspora pogona, exhibits strong insecticidal activity than spinosyn. However, the low synthesis capacity and unknown metabolic characteristics of butenyl-spinosyn in wild-type S. pogona limit its broad application and metabolic engineering. Here, we showed that S. pogona exhibited increased glucose consumption ability and growth rate compared with S. spinosa, but the production of butenyl-spinosyn was much lower than that of spinosyn. To further elucidate the metabolic mechanism of these different phenotypes, we performed a comparative proteomic and metabolomic study on S. pogona and S. spinosa to identify the change in the abundance levels of proteins and metabolites. We found that the abundance of most proteins and metabolites associated with glucose transport, fatty acid metabolism, tricarboxylic acid cycle, amino acid metabolism, energy metabolism, purine and pyrimidine metabolism, and target product biosynthesis in S. pogona was higher than that in S. spinosa. However, the overall abundance of proteins involved in butenyl-spinosyn biosynthesis was much lower than that of the high-abundance protein chaperonin GroEL, such as the enzymes related to rhamnose synthesis. We speculated that these protein and metabolite abundance changes may be directly responsible for the above phenotypic changes in S. pogona and S. spinosa, especially affecting butenyl-spinosyn biosynthesis. Further studies revealed that the over-expression of the rhamnose synthetic genes and methionine adenosyltransferase gene could effectively improve the production of butenyl-spinosyn by 2.69-and 3.03fold, respectively, confirming the reliability of this conjecture. This work presents the first comparative proteomics and metabolomics study of S. pogona and S. spinosa, providing new insights into the novel links of phenotypic change and metabolic difference between two strains. The result will be valuable in designing strategies to promote the biosynthesis of butenyl-spinosyn by metabolic engineering.

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Section: Amino Acid Metabolismmentioning

confidence: 96%

Deciphering the Metabolic Pathway Difference Between Saccharopolyspora pogona and Saccharopolyspora spinosa by Comparative Proteomics and Metabonomics

Rang

Yuan

et al. 2020

Front. Microbiol.

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“…3-hydroxyisobutyrate dehydrogenase is essential for valine metabolism, and catalyzes a reversible oxidation of L-3-hydroxyisobutyrate to methylmalonate semialdehyde [26]. Leucine and valine concentrations increase under various stress conditions and their complete oxidation allows the generation of high amounts of ATP [27,28]. Furthermore, the protein expression profile showed that other differentially expressed proteins involved in amino acid metabolism were downregulated.…”

Section: Amino Acid Metabolism and Biosynthesismentioning

confidence: 99%

Proteomic Response of Pseudomonas putida KT2440 to Dual Carbon-Phosphorus Limitation during mcl-PHAs Synthesis

Możejko-Ciesielska

Serafim

2019

Biomolecules

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Pseudomonas putida KT2440, one of the best characterized pseudomonads, is a metabolically versatile producer of medium-chain-length polyhydroxyalkanoates (mcl-PHAs) that serves as a model bacterium for molecular studies. The synthesis of mcl-PHAs is of great interest due to their commercial potential. Carbon and phosphorus are the essential nutrients for growth and their limitation can trigger mcl-PHAs’ production in microorganisms. However, the specific molecular mechanisms that drive this synthesis in Pseudomonas species under unfavorable growth conditions remain poorly understood. Therefore, the proteomic responses of Pseudomonas putida KT2440 to the limited carbon and phosphorus levels in the different growth phases during mcl-PHAs synthesis were investigated. The data indicated that biopolymers’ production was associated with the cell growth of P. putida KT2440 under carbon- and phosphorus-limiting conditions. The protein expression pattern changed during mcl-PHAs synthesis and accumulation, and during the different physiological states of the microorganism. The data suggested that the majority of metabolic activities ceased under carbon and phosphorus limitation. The abundance of polyhydroxyalkanoate granule-associated protein (PhaF) involved in PHA synthesis increased significantly at 24 and 48 h of the cultivations. The activation of proteins belonging to the phosphate regulon was also detected. Moreover, these results indicated changes in the protein profiles related to amino acids metabolism, replication, transcription, translation, stress response mechanisms, transport or signal transduction. The presented data allowed the investigation of time-course proteome alterations in response to carbon and phosphorus limitation, and PHAs synthesis. This study provided information about proteins that can be potential targets in improving the efficiency of mcl-PHAs synthesis.

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“…It is also involved in degradation of branched-chain amino acids. Knockdown of this gene have reduced degradation of valine and isoleucine the root growth under presence of valine and isoleucine [60]. It seems apparent that these subgenomic biases are instrumental in shaping phenotypes and future plasticity of E. coracana no matter the driving mechanism.…”

Section: Discussionmentioning

confidence: 99%

Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet)

Hall

Patel

McElroy

et al. 2020

Preprint

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Background: Finger millet (Eleusine coracana 2n=4x=36 ) is a hardy, nutraceutical, climate change tolerant, orphan crop that is consumed throughout eastern Africa and India. Its genome has been sequenced multiple times, but A and B subgenomes could not be separated because no published genome for E. indica existed. The classification of A and B subgenomes is important for understanding the evolution of this crop and provide a means to improve current and future breeding programs. Results:We produced subgenome calls for 704 syntenic blocks and inferred A or B subgenomic identity for 59,377 genes 81% of the annotated genes. Phylogenetic analysis of a super matrix containing 455 genes shows high support for A and B divergence within the Eleusine genus. Synonymous substitution rates between A and B genes supports A and B calls. The repetitive contenton highly supported B contigs is higher than that on similar A contigs. Analysis of syntenic singletons showed evidence of biased fractionation showed a pattern of A genome dominance, with 61% A , 37% B and 1% unassigned, and was further supported by the pattern of loss observed among cyto-nuclear interacting genes. Examination of expression within the ciradian rhythm pathway suggests A subgenomic preference. Conclusion:The evidence of individual gene calls within each syntenic block, provides a powerful tool for inference for subgenome classification. Our results show the utility of a draft genome in resolving A and B subgenomes calls, primarily it allows for the proper polarization of A and B syntenic blocks. There have been multiple calls for the use of phylogenetic inference in subgenome classification, our use of synteny is a practical application in a system that has only one parental genome available. BackgroundEleusine coracana (finger millet) is an important small-seed cereal crop in its native Africa and South Asia [1,2]. It is believed to be the product of an allopolyploid hybridization between E. indica and another likely extinct species [3][4][5][6][7]. Eleusine indica is consistently identified as an A genome donor [3, 4], however, based on the strength plastid phylogenetic analysis, some have suggested that E. coracana is the result of multiple hybridization events, between the B genome donor, E. indica and E.

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3-Hydroxyisobutyrate Dehydrogenase Is Involved in Both, Valine and Isoleucine Degradation in Arabidopsis thaliana

Cited by 34 publications

References 45 publications

Deciphering the Metabolic Pathway Difference Between Saccharopolyspora pogona and Saccharopolyspora spinosa by Comparative Proteomics and Metabonomics

Deciphering the Metabolic Pathway Difference Between Saccharopolyspora pogona and Saccharopolyspora spinosa by Comparative Proteomics and Metabonomics

Proteomic Response of Pseudomonas putida KT2440 to Dual Carbon-Phosphorus Limitation during mcl-PHAs Synthesis

Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet)

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