Dataset Information

Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom.

ABSTRACT: Diatoms outcompete other phytoplankton for nitrate, yet little is known about the mechanisms underpinning this ability. Genomes and genome-enabled studies have shown that diatoms possess unique features of nitrogen metabolism however, the implications for nutrient utilization and growth are poorly understood. Using a combination of transcriptomics, proteomics, metabolomics, fluxomics, and flux balance analysis to examine short-term shifts in nitrogen utilization in the model pennate diatom in Phaeodactylum tricornutum, we obtained a systems-level understanding of assimilation and intracellular distribution of nitrogen. Chloroplasts and mitochondria are energetically integrated at the critical intersection of carbon and nitrogen metabolism in diatoms. Pathways involved in this integration are organelle-localized GS-GOGAT cycles, aspartate and alanine systems for amino moiety exchange, and a split-organelle arginine biosynthesis pathway that clarifies the role of the diatom urea cycle. This unique configuration allows diatoms to efficiently adjust to changing nitrogen status, conferring an ecological advantage over other phytoplankton taxa.

SUBMITTER: Smith SR

PROVIDER: S-EPMC6779911 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom.

Smith Sarah R SR Dupont Chris L CL McCarthy James K JK Broddrick Jared T JT Oborník Miroslav M Horák Aleš A Füssy Zoltán Z Cihlář Jaromír J Kleessen Sabrina S Zheng Hong H McCrow John P JP Hixson Kim K KK Hixson Kim K KK Araújo Wagner L WL Nunes-Nesi Adriano A Fernie Alisdair A Nikoloski Zoran Z Palsson Bernhard O BO Allen Andrew E AE

Nature communications 20191007 1

Diatoms outcompete other phytoplankton for nitrate, yet little is known about the mechanisms underpinning this ability. Genomes and genome-enabled studies have shown that diatoms possess unique features of nitrogen metabolism however, the implications for nutrient utilization and growth are poorly understood. Using a combination of transcriptomics, proteomics, metabolomics, fluxomics, and flux balance analysis to examine short-term shifts in nitrogen utilization in the model pennate diatom in Ph ...[more]

PMID: 31591397

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Project description:BackgroundIt has been reported that the modularity of metabolic networks of bacteria is closely related to the variability of their living habitats. However, given the dependency of the modularity score on the community structure, it remains unknown whether organisms achieve certain modularity via similar or different community structures.ResultsIn this work, we studied the relationship between similarities in modularity scores and similarities in community structures of the metabolic networks of 1021 species. Both similarities are then compared against the genetic distances. We revisited the association between modularity and variability of the microbial living environments and extended the analysis to other aspects of their life style such as temperature and oxygen requirements. We also tested both topological and biological intuition of the community structures identified and investigated the extent of their conservation with respect to the taxonomy.ConclusionsWe find that similar modularities are realized by different community structures. We find that such convergent evolution of modularity is closely associated with the number of (distinct) enzymes in the organism's metabolome, a consequence of different life styles of the species. We find that the order of modularity is the same as the order of the number of the enzymes under the classification based on the temperature preference but not on the oxygen requirement. Besides, inspection of modularity-based communities reveals that these communities are graph-theoretically meaningful yet not reflective of specific biological functions. From an evolutionary perspective, we find that the community structures are conserved only at the level of kingdoms. Our results call for more investigation into the interplay between evolution and modularity: how evolution shapes modularity, and how modularity affects evolution (mainly in terms of fitness and evolvability). Further, our results call for exploring new measures of modularity and network communities that better correspond to functional categorizations.

Dataset Information

Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom.

Publications

Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom.

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