SummaryPlasmodium gene functions in mosquito and liver stages remain poorly characterized due to limitations in the throughput of phenotyping at these stages. To fill this gap, we followed more than 1,300 barcoded P. berghei mutants through the life cycle. We discover 461 genes required for efficient parasite transmission to mosquitoes through the liver stage and back into the bloodstream of mice. We analyze the screen in the context of genomic, transcriptomic, and metabolomic data by building a thermodynamic model of P. berghei liver-stage metabolism, which shows a major reprogramming of parasite metabolism to achieve rapid growth in the liver. We identify seven metabolic subsystems that become essential at the liver stages compared with asexual blood stages: type II fatty acid synthesis and elongation (FAE), tricarboxylic acid, amino sugar, heme, lipoate, and shikimate metabolism. Selected predictions from the model are individually validated in single mutants to provide future targets for drug development.

Non-alcoholic fatty liver disease (NAFLD) is a consequence of sedentary life style and high fat diets with an estimated prevalence of about 30% in western countries. It is associated with insulin resistance, obesity, glucose intolerance and drug toxicity. Additionally, polymorphisms within, e.g., APOC3, PNPLA3, NCAN, TM6SF2 and PPP1R3B, correlate with NAFLD. Several studies have already investigated later stages of the disease. This study explores the early steatosis stage of NAFLD with the aim of identifying molecular mechanisms underlying the etiology of NAFLD. We analyzed liver biopsies and serum samples from patients with high- and low-grade steatosis (also pre-disease states) employing transcriptomics, ELISA-based serum protein analyses and metabolomics. Here, we provide a detailed description of the various related datasets produced in the course of this study. These datasets may help other researchers find new clues for the etiology of NAFLD and the mechanisms underlying its progression to more severe disease states.

The ever-increasing availability of transcriptomic and metabolomic data can be used to deeply analyze and make ever-expanding predictions about biological processes, as changes in the reaction fluxes through genome-wide pathways can now be tracked. Currently, constraint-based metabolic modeling approaches, such as flux balance analysis (FBA), can quantify metabolic fluxes and make steady-state flux predictions on a genome-wide scale using optimization principles. However, relating the differential gene expression or differential metabolite abundances in different physiological states to the differential flux profiles remains a challenge. Here we present a novel method, named REMI ( R elative E xpression and M etabolomic I ntegrations), that employs genome-scale metabolic models (GEMs) to translate differential gene expression and metabolite abundance data obtained through genetic or environmental perturbations into differential fluxes to analyze the altered physiology for any given pair of conditions. REMI allows for gene-expression, metabolite abundance, and thermodynamic data to be integrated into a single framework, then uses optimization principles to maximize the consistency between the differential gene-expression levels and metabolite abundance data and the estimated differential fluxes and thermodynamic constraints. We applied REMI to integrate into the Escherichia coli GEM publicly available sets of expression and metabolomic data obtained from two independent studies and under wide-ranging conditions. The differential flux distributions obtained from REMI corresponding to the various perturbations better agreed with the measured fluxomic data, and thus better reflected the different physiological states, than a traditional model. Compared to the similar alternative method that provides one solution from the solution space, REMI was able to enumerate several alternative flux profiles using a mixed-integer linear programming approach. Using this important advantage, we performed a high-frequency analysis of common genes and their associated reactions in the obtained alternative solutions and identified the most commonly regulated genes across any two given conditions. We illustrate that this new implementation provides more robust and biologically relevant results for a better understanding of the system physiology.

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Understanding the adaptive responses of individual bacterial strains is crucial for microbiome engineering approaches that introduce new functionalities into complex microbiomes, such as xenobiotic compound metabolism for soil bioremediation. Adaptation requires metabolic reprogramming of the cell, which can be captured by multi-omics, but this data remains formidably challenging to interpret and predict. Here we present a new approach that combines genome-scale metabolic modeling with transcriptomics and exometabolomics, both of which are common tools for studying dynamic population behavior. As a realistic demonstration, we developed a genome-scale model of Pseudomonas veronii 1YdBTEX2, a candidate bioaugmentation agent for accelerated metabolism of mono-aromatic compounds in soil microbiomes, while simultaneously collecting experimental data of P. veronii metabolism during growth phase transitions. Predictions of the P. veronii growth rates and specific metabolic processes from the integrated model closely matched experimental observations. We conclude that integrative and network-based analysis can help build predictive models that accurately capture bacterial adaptation responses. Further development and testing of such models may considerably improve the successful establishment of bacterial inoculants in more complex systems.npj Systems Biology and Applications (2020) 6:1 ; https://doi.

The ever-increasing availability of transcriptomic and metabolomic data can be used to deeply analyze and make ever-expanding predictions about biological processes, as changes in the reaction fluxes through genome-wide pathways can now be tracked. Currently, constraint-based metabolic modeling approaches, such as flux balance analysis (FBA), can quantify metabolic fluxes and make steady-state flux predictions on a genome-wide scale using optimization principles. However, relating the differential gene expression or differential metabolite abundances in different physiological states to the differential flux profiles remains a challenge. Here we present a novel method, named REMI (Relative Expression and Metabolomic Integrations), that employs genome-scale metabolic models (GEMs) to translate differential gene expression and metabolite abundance data obtained through genetic or environmental perturbations into differential fluxes to analyze the altered physiology for any given pair of conditions. REMI is the first method that integrates thermodynamics together with relative gene-expression and metabolomic data as constraints for FBA. We applied REMI to integrate into the Escherichia coli GEM publicly available sets of expression and metabolomic data obtained from two independent studies and under wide-ranging conditions. The differential flux distributions obtained from REMI corresponding to the various perturbations better agreed with the measured fluxomic data, and thus better reflected the different physiological states, than a traditional model. Compared to the similar alternative method that provides one solution from the solution space, REMI was also able to enumerate several alternative flux profiles using a mixed-integer linear programming approach. Using this important advantage, we performed a high-frequency analysis of common genes and their associated reactions in the obtained alternative solutions and identified the most commonly regulated genes across any 2 two given conditions. We illustrate that this new implementation provides more robust and biologically relevant results for a better understanding of the system physiology. Author SummaryThe recent advances in omics technologies have provided us with an unprecedented abundance of data spanning genomes, global gene expression, and metabolomes. Though these advancements in highthroughput data collection offer an excellent opportunity for a more thorough understanding of metabolic capacities of a wide range of species, they have caused a considerable gap between "data generation" and "data integration." reconstructed model to predict the observed physiology, e.g., growth phase through omics data integration. In this study, we present a new method named REMI (Relative Expression and Metabolomic Integrations) that enables the co-integration of gene expression, metabolomics and thermodynamics data as constraints in genome-scale models. This not only allows the better understanding of how different phenotypes originate from a given genotype but also aid...

A large number of genome-scale models of cellular metabolism are available for various organisms. These models include all known metabolic reactions based on the genome annotation. However, the reactions that are active are dependent on the cellular metabolic function or environmental condition. Constraint-based methods that integrate condition-specific transcriptomics data into models have been used extensively to investigate condition-specific metabolism. Here, we present a method (TEX-FBA) for modeling condition-specific metabolism that combines transcriptomics and reaction thermodynamics data to generate a thermodynamically-feasible condition-specific metabolic model. TEX-FBA is an extension of thermodynamic-based flux balance analysis (TFA), which allows the simultaneous integration of different stages of experimental data (e.g., absolute gene expression, metabolite concentrations, thermodynamic data, and fluxomics) and the identification of alternative metabolic states that maximize consistency between gene expression levels and condition-specific reaction fluxes. We applied TEX-FBA to a genome-scale metabolic model of Escherichia coli by integrating available condition-specific experimental data and found a marked reduction in the flux solution space. Our analysis revealed a marked correlation between actual gene expression profile and experimental flux measurements compared to the one obtained from a randomly generated gene expression profile. We identified additional essential reactions from the membrane lipid and folate metabolism when we integrated transcriptomics data of the given condition on the top of metabolomics and thermodynamics data. These results show TEX-FBA is a promising new approach to study condition-specific metabolism when different types of experimental data are available.Author summaryCells utilize nutrients via biochemical reactions that are controlled by enzymes and synthesize required compounds for their survival and growth. Genome-scale models of metabolism representing these complex reaction networks have been reconstructed for a wide variety of organisms ranging from bacteria to human cells. These models comprise all possible biochemical reactions in a cell, but cells choose only a subset of reactions for their immediate needs and functions. Usually, these models allow for a large flux solution space and one can integrate experimental data in order to reduce it and potentially predict the physiology for a specific condition. We developed a method for integrating different types of omics data, such as fluxomics, transcriptomics, metabolomics into genome-scale metabolic models that reduces the flux solution space. Using gene expression data, the algorithm maximizes the consistency between the predicted and experimental flux for the reactions and predicts biologically relevant flux ranges for the remaining reactions in the network. This method is useful for determining fluxes of metabolic reactions with reduced uncertainty and suitable for performing context- and condition-specific analysis in metabolic models using different types of experimental data.

The transmission of malaria parasites from vertebrate host to mosquito vector requires a developmental switch in asexually dividing blood-stage parasites to sexual reproduction. In Plasmodium berghei the transcription factor AP2-G is required and sufficient for this switch, but how a particular sex is determined in a haploid parasite remains unknown. Using a global screen of barcoded mutants, we here identify ten genes essential for the formation of either male or female sexual forms and validate their importance for transmission. High-resolution single-cell transcriptomics of wild-type and mutant parasites portrays the developmental bifurcation and reveals a regulatory cascade of putative gene functions in determination and subsequent differentiation of each sex. A male-determining gene with a LOTUS/OST-HTH domain points towards unexpected conservation of molecular mechanisms of gametogenesis in animals and a distantly related eukaryotic parasite.