Presentation Information
[P01-064]A Genome-Scale metabolic modelling study shows the metabolic alterations caused the loss of the pSCL4 megaplasmid in Streptomyces clavuligerus
○Claudio Avignone Rossa1, Daniel Farkas1, Sepideh Mofidifar1 (1. School of Biosciences, University of Surrey (UK))
Keywords:
Streptomyces clavuligerus,metabolic modelling,anti biotic biosynthesis
Members of the genus Streptomyces are know for thier capability of synthesizing secondary metabolites, including antibiotics. Among them, S. clavuligerus is the producer of the beta-lactamase inhibitor clavulanic acid.
S. clavuligerus carries numerous biosynthetic gene clusters for secondary metabolism contained in the megaplasmid pSCL4 [1]. Interestingly, the metabolic consequences of losing this plasmid remain poorly understood.
We investigated the metabolic alterations associated to pSCL4, by reconstructing genome-scale metabolic models (GEMs) of the plasmid-carrying wild-type strain S. clavuligerus ATCC 27064 and of the pSCL4-deficient strain S. clavuligerus pSCL4. For the construction of the models, we used the latest version of S. clavuligerus GEM [2], complemented by the introduction of transcriptomics data. We manually curated the model by refining gene-protein-reaction (GPR) associations based on UniProt annotations, and generated strain-specific models using the Metabolic Adjustment by Differential Expression (MADE) approach [3].
The result of simulations showed that the loss of pSCL4 led to an approximately 50% reduction in clavulanic acid production, consistent with experimental observations [4]. Metabolic flux analysis indicated that energy metabolism (including NADH dehydrogenase, cytochrome oxidases, and ATP synthesis pathways) was constrained in the wild-type strain but exhibited greater variability in S. clavuligerus pSCL4. These findings are supported by shadow price analysis: Key metabolites (ATP, ADP, AMP, Pi, NADH/NAD, NADPH/NADP, FAD/FADH2) had lower shadow prices in the wild-type strain.
The shadow prices of glutamate and methionine were positive in the wild-type strain, but negative in the plasmid-less mutant, strongly suggesting that increasing their availability could enhance clavulanic acid production in the wild type. Consistent with this conclusion, Flux Variability Analysis showed that glutamate-related transport reactions present greater variability in the pSCL4-deficient strain, whereas they were more constrained in the wild type.
Our findings suggest that pSCL4 enhances metabolic efficiency by optimizing resource allocation and precursor supply for secondary metabolism.
References
[1] Medema et al. 2010. Genome Biology & Evolution 2: 212 to 214
[2] Gomez-Rios et al. 2020. Microorganisms 8(9): 1255
[3] Jensen et al 2011. BMC Systems Biology 5(1): 147
[4]. Alvarez-Alvarez et al. 2017. BMC Genomics 18(1): 907
S. clavuligerus carries numerous biosynthetic gene clusters for secondary metabolism contained in the megaplasmid pSCL4 [1]. Interestingly, the metabolic consequences of losing this plasmid remain poorly understood.
We investigated the metabolic alterations associated to pSCL4, by reconstructing genome-scale metabolic models (GEMs) of the plasmid-carrying wild-type strain S. clavuligerus ATCC 27064 and of the pSCL4-deficient strain S. clavuligerus pSCL4. For the construction of the models, we used the latest version of S. clavuligerus GEM [2], complemented by the introduction of transcriptomics data. We manually curated the model by refining gene-protein-reaction (GPR) associations based on UniProt annotations, and generated strain-specific models using the Metabolic Adjustment by Differential Expression (MADE) approach [3].
The result of simulations showed that the loss of pSCL4 led to an approximately 50% reduction in clavulanic acid production, consistent with experimental observations [4]. Metabolic flux analysis indicated that energy metabolism (including NADH dehydrogenase, cytochrome oxidases, and ATP synthesis pathways) was constrained in the wild-type strain but exhibited greater variability in S. clavuligerus pSCL4. These findings are supported by shadow price analysis: Key metabolites (ATP, ADP, AMP, Pi, NADH/NAD, NADPH/NADP, FAD/FADH2) had lower shadow prices in the wild-type strain.
The shadow prices of glutamate and methionine were positive in the wild-type strain, but negative in the plasmid-less mutant, strongly suggesting that increasing their availability could enhance clavulanic acid production in the wild type. Consistent with this conclusion, Flux Variability Analysis showed that glutamate-related transport reactions present greater variability in the pSCL4-deficient strain, whereas they were more constrained in the wild type.
Our findings suggest that pSCL4 enhances metabolic efficiency by optimizing resource allocation and precursor supply for secondary metabolism.
References
[1] Medema et al. 2010. Genome Biology & Evolution 2: 212 to 214
[2] Gomez-Rios et al. 2020. Microorganisms 8(9): 1255
[3] Jensen et al 2011. BMC Systems Biology 5(1): 147
[4]. Alvarez-Alvarez et al. 2017. BMC Genomics 18(1): 907
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