Constraint-Based Modeling of Diatoms Metabolism and Quantitative Biology Approaches

Kumar, Manish; Zuñiga, Cristal; Tibocha‐Bonilla, Juan D.; Smith, Sarah R.; Coker, Joanna; Allen, Andrew E.; Zengler, Karsten

doi:10.1007/978-3-030-92499-7_26

Cited by 3 publications

(2 citation statements)

References 166 publications

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“…The rigorous reconstruction process allowed capturing a detailed metabolic network that can be used as a reference/template model for other model reconstructions of yet unexplored diatoms to investigate the metabolic diversity of diatoms (62).…”

Section: Discussionmentioning

confidence: 99%

Mixotrophic growth of a ubiquitous marine diatom

Kumar,

Tibocha-Bonilla,

Füssy

et al. 2024

Sci. Adv.

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Diatoms are major players in the global carbon cycle, and their metabolism is affected by ocean conditions. Understanding the impact of changing inorganic nutrients in the oceans on diatoms is crucial, given the changes in global carbon dioxide levels. Here, we present a genome-scale metabolic model ( i MK1961) for Cylindrotheca closterium , an in silico resource to understand uncharacterized metabolic functions in this ubiquitous diatom. i MK1961 represents the largest diatom metabolic model to date, comprising 1961 open reading frames and 6718 reactions. With i MK1961, we identified the metabolic response signature to cope with drastic changes in growth conditions. Comparing model predictions with Tara Oceans transcriptomics data unraveled C. closterium ’s metabolism in situ. Unexpectedly, the diatom only grows photoautotrophically in 21% of the sunlit ocean samples, while the majority of the samples indicate a mixotrophic (71%) or, in some cases, even a heterotrophic (8%) lifestyle in the light. Our findings highlight C. closterium’ s metabolic flexibility and its potential role in global carbon cycling.

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Section: Discussionmentioning

confidence: 99%

Mixotrophic growth of a ubiquitous marine diatom

Kumar,

Tibocha-Bonilla,

Füssy

et al. 2024

Sci. Adv.

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“…Integration of experimental data and mathematical models to predict metabolic behavior and optimize product yield (Zeng et al, 2021;Kumar M. et al, 2022) Dynamic metabolic flux analysis Simulation of dynamic metabolic behavior and metabolic pathway regulation (Tibocha-Bonilla et al, 2018) Flux balance analysis Estimation of metabolic flux distribution and identification of metabolic pathways (Parichehreh et al, 2019) Genome-scale metabolic model…”

Section: Constraint-based Modelingmentioning

confidence: 99%

Emerging technologies for advancing microalgal photosynthesis and metabolism toward sustainable production

Hu,

Meng,

et al. 2023

Front. Mar. Sci.

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Microalgae are unicellular photosynthetic microorganisms that play a vital role in primary production and have diverse applications in various industries. They have high photosynthetic and metabolic capacities and can produce a variety of valuable metabolites, such as lipids, carbohydrates, pigments, and proteins. However, practical applications of microalgae are limited to high-value products due to the high production costs. Algal biotechnology faces challenges such as low energy utilization efficiency and product yield that are currently inadequate to fulfill commercial production. To overcome these challenges, emerging technologies have shown promise to achieve higher production efficiency, including molecular manipulation of photosynthetic efficiency and metabolic activities. Here, we provided an overview of the importance, diversity, and photosynthesis of microalgae, as well as strategies for enhancing their photosynthetic efficiency. We discussed various approaches for improving microalgal photosynthesis, including strain selection and optimization, rational genetic modification, and innovative technologies such as spectral recomposition of light, nanomaterials, advanced cultivation systems, and symbiotic systems. Additionally, we summarized metabolic engineering strategies that focus on optimizing the synthesis of value-added metabolites, such as pigments, long-chain polyunsaturated fatty acids, starch, proteins, and hydrogen in microalgae. By concentrating on improving photosynthetic efficiency and the synthesis of bioactive metabolites, this review provided valuable insights into enhancing microalgae production yields. Overcoming limitations in microalgae production costs can lead to broader applications in various industries. Furthermore, we highlight the potential of these strategies in increasing the efficiency of microalgae as a sustainable source for high-value products.

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DiatOmicBase, a gene-centered platform to mine functional omics data across diatom genomes

Villar,

Zweig,

Vincens

et al. 2024

Preprint

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Diatoms are prominent microalgae found in all aquatic environments. Over the last 20 years, thanks to the availability of genomic and genetic resources, diatom species such asPhaeodactylum tricornutumhave emerged as valuable experimental model systems for exploring topics ranging from evolution to cell biology, (eco)physiology and biotechnology. Since the first genome sequencing in 2008, numerous genome-enabled datasets have been generated, based on RNA-Seq and proteomics, epigenomes, and ecotype variant analysis. Unfortunately, these resources, generated by various laboratories, are often in disparate formats and challenging to access and analyze. Here we present DiatOmicBase, a genome portal gathering comprehensive omics resources fromP. tricornutumand two other diatoms to facilitate the exploration of dispersed public datasets and the design of new experiments based on the prior-art.DiatOmicBase provides gene annotations, transcriptomic profiles and a genome browser with ecotype variants, histone and methylation marks, transposable elements, non-coding RNAs, and read densities from RNA-Seq experiments. We developed a semi-automatically updated transcriptomic module to explore both publicly available RNA-Seq experiments and users’ private datasets. Using gene-level expression data, users can perform exploratory data analysis, differential expression, pathway analysis, biclustering, and co-expression network analysis. Users can create heatmaps to visualize precomputed comparisons for selected gene subsets. Automatic access to other bioinformatic resources and tools for diatom comparative and functional genomics is also provided. Focusing on the resources currently centralized forP. tricornutum, we showcase several examples of how DiatOmicBase strengthens molecular research on diatoms, making these organisms accessible to a broad research community.Significance statementIn recent years, diatoms have become the subject of increasing interest because of their ecological importance and their biotechnological potential for natural products such as pigments and polyunsaturated fatty acids. Here, we present an interactive web-based server that integrates public diatom ‘omics data (genomics, transcriptomics, epigenomics, proteomics, sequence variants) to connect individual diatom genes to broader-scale functional processes.

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Constraint-Based Modeling of Diatoms Metabolism and Quantitative Biology Approaches

Cited by 3 publications

References 166 publications

Mixotrophic growth of a ubiquitous marine diatom

Mixotrophic growth of a ubiquitous marine diatom

Emerging technologies for advancing microalgal photosynthesis and metabolism toward sustainable production

DiatOmicBase, a gene-centered platform to mine functional omics data across diatom genomes

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