Biology subjects

Mahadevan, R.

Publications and source records attributed to Mahadevan, R..

40 records · Page 3Linked to original sources

bioRxiv2018

Interspecies malate-pyruvate shuttle drives amino acid exchange in organohalide-respiring microbial communities

Most microorganisms in the biosphere live in communities and develop coordinated metabolisms via trading metabolites. In this study, we sought to deconstruct the metabolic interdependency in organohalide-respiring microbial communities enriched with Dehalobacter restrictus (Dhb), using a complementary approach of computational metabolic modeling and experimental validation. Dhb possesses a complete set of genes for amino acid biosynthesis yet requires amino acid supplementation. We reconciled this discrepancy using Flux Balance Analysis with consideration for cofactor availability, enzyme promiscuity, and shared protein expression patterns of several Dhb strains. Experimentally, 13C incorporation assays, growth assays, and metabolite analysis of strain PER-K23 cultures were performed to validate the model predictions. The model resolved that Dhbs amino acid dependency results from restricted NADPH regeneration and diagnosed that malate supplementation can replenish intracellular NADPH using malic enzyme. Interestingly, we observed unexpected export of glutamate and pyruvate in parallel to malate consumption in the strain PER-K23 cultures. Further experiments on Dhb-enriched consortium ACT-3 suggested an interspecies malate-pyruvate shuttle between Dhb and a glutamate-auxotrophic Bacteroides sp., reminiscent of the mitochondrial malate shunt pathway in eukaryotic cells. Altogether, this study reveals that redox constraints and metabolic complementarity are important driving forces for amino acid exchange in anaerobic microbial communities.

microbiology↗

bioRxiv2018

Genome-scale metabolic network reconstruction of the chloroform-respiring Dehalobacter restrictus strain CF

BackgroundOrganohalide-respiring bacteria (OHRB) play an important role in the global halogen cycle and bioremediation of industrial sites contaminated with chlorinated organics. One notable OHRB is Dehalobacter restrictus strain CF, which is capable of respiring chloroform to dichloromethane. Improved bioremediation strategies could be employed with a greater understanding of D. restrictus metabolism in isolate and community cultures. To this end, we reconstructed the genome-scale metabolic network of D. restrictus to study its metabolism in future studies using flux balance analysis.\n\nMethodThe RAST annotation server and Model SEED framework were used to obtain a draft metabolic network reconstruction. Additional curation was required for its acetyl-CoA sources, the Wood-Ljungdahl pathway, TCA cycle, electron transport chain, hydrogenase complexes, and formate dehydrogenase complexes.\n\nResultsiHH623 is the first curated genome-scale metabolic model in the Peptococcaceae family. It spans 1087 reactions and 983 metabolites, covering 623 genes (21% of all ORFs). Its potential sources of acetyl-CoA are pyruvate ferredoxin oxidoreductase, pyruvate formate lyase, acetyl-CoA synthetase, phosphate acetyltransferase, and CO-methylating acetyl-CoA synthase. NADPH may be regenerated by isocitrate dehydrogenase, malic enzyme, NADP-reducing hydrogenase, cytosolic formate dehydrogenase, ferredoxin-dependent bifurcating transhydrogenase, 5-methyltetrahydrofolate dehydrogenase, and 5-10-methylenetetrahydrofolate. Additional reactions that were added or removed to the D. restrictus reconstruction are discussed.\n\nConclusionsWe reconstructed the genome-scale metabolic network of D. restricus by obtaining an initial draft with the RAST server and Model SEED framework. Curation was required for D. restricus acetyl-CoA sources, TCA cycle, electron transport chain, hydrogenase complexes, and formate dehydrogenase complexes. This metabolic model can be used to decipher D. restrictus metabolism in isolate and community cultures in future studies, or as a template to reconstruct the metabolic network of other Peptococcaceae species. The extensive curation of the draft metabolic network reconstruction highlights the need to be cautious of automated metabolic network reconstruction.

systems biology↗

bioRxiv2018

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

Several studies have shown that neither the formal representation nor the functional requirements of genome-scale metabolic models (GEMs) are precisely defined. Without a consistent standard, comparability, reproducibility, and interoperability of models across groups and software tools cannot be guaranteed.\n\nHere, we present memote (https://github.com/opencobra/memote) an open-source software containing a community-maintained, standardized set of metabolic model tests. The tests cover a range of aspects from annotations to conceptual integrity and can be extended to include experimental datasets for automatic model validation. In addition to testing a model once, memote can be configured to do so automatically, i.e., while building a GEM. A comprehensive report displays the models performance parameters, which supports informed model development and facilitates error detection.\n\nMemote provides a measure for model quality that is consistent across reconstruction platforms and analysis software and simplifies collaboration within the community by establishing workflows for publicly hosted and version controlled models.

systems biology↗

bioRxiv2017

Reconstructing the evolution of metabolism in budding yeasts

Budding yeasts inhabit a range of environments by exploiting various metabolic traits. The genetic bases for these traits are mostly unknown, preventing their addition or removal in a chassis organism for metabolic engineering. To help understand the molecular evolution of these traits in yeasts, we created Analyzing Yeasts by Reconstructing Ancestry of Homologs (AYbRAH), an open-source database of predicted and manually curated ortholog groups for 33 diverse fungi and yeasts in Dikarya, spanning 600 million years of evolution. OrthoMCL and OrthoDB were used to cluster protein sequence into ortholog and homolog groups, respectively; MAFFT and PhyML were used to reconstruct the phylogeny of all homolog groups. Ortholog assignments for enzymes and small metabolite transporters were compared to their phylogenetic reconstruction, and curated to resolve any discrepancies. Information on homolog and ortholog groups can be viewed in the AYbRAH web portal (https://kcorreia.github.io/aybrah/) to review ortholog groups, predictions for mitochondrial localization and transmembrane domains, literature references, and phylogenetic reconstructions. Ortholog groups in AYbRAH were compared to HOGENOM, KEGG Orthology, OMA, eggNOG, and PANTHER. PANTHER and OMA had the most congruent ortholog groups with AYbRAH, while the other phylogenomic databases had greater amounts of under-clustering, over-clustering, or no ortholog annotations for proteins. Future plans are discussed for AYbRAH, and recommendations are made for other research communities seeking to create curated ortholog databases.

evolutionary biology↗