Efficient searching and annotation of metabolic networks using chemical similarity

A tripartite microbial co-culture system for de novo biosynthesis of diverse plant phenylpropanoids

Plant-derived phenylpropanoids, in particular phenylpropenes, have diverse industrial applications ranging from flavors and fragrances to polymers and pharmaceuticals. Heterologous biosynthesis of these products has the potential to address low, seasonally dependent yields hindering ease of widespread manufacturing. However, previous efforts have been hindered by the inherent pathway promiscuity and the microbial toxicity of key pathway intermediates. Here, in this study, we establish the propensity of a tripartite microbial co-culture to overcome these limitations and demonstrate to our knowledge the first reported de novo phenylpropene production from simple sugar starting materials. After initially designing the system to accumulate eugenol, the platform modularity and downstream enzyme promiscuity was leveraged to quickly create avenues for hydroxychavicol and chavicol production. The consortia was found to be compatible with Engineered Living Material production platforms that allow for reusable, cold-chain-independent distributed manufacturing. This work lays the foundation for further deployment of modular microbial approaches to produce plant secondary metabolites.

Rank-ordering of known enzymes as starting points for re-engineering novel substrate activity using a convolutional neural network

Retro-biosynthetic approaches have made significant advances in predicting synthesis routes of target biofuel, bio-renewable or bio-active molecules. The use of only cataloged enzymatic activities limits the discovery of new production routes. Recent retro-biosynthetic algorithms increasingly use novel conversions that require altering the substrate or cofactor specificities of existing enzymes while connecting pathways leading to a target metabolite. However, identifying and re-engineering enzymes for desired novel conversions are currently the bottlenecks in implementing such designed pathways. Herein, we present EnzRank, a convolutional neural network (CNN) based approach, to rank-order existing enzymes in terms of their suitability to undergo successful protein engineering through directed evolution or de novo design towards a desired specific substrate activity. We train the CNN model on 11,800 known active enzyme-substrate pairs from the BRENDA database as positive samples and data generated by scrambling these pairs as negative samples using substrate dissimilarity between an enzyme's native substrate and all other molecules present in the dataset using Tanimoto similarity score. EnzRank achieves an average recovery rate of 80.72% and 73.08% for positive and negative pairs on test data after using a 10-fold holdout method for training and cross-validation. We further developed a web-based user interface (available at https://huggingface.co/spaces/vuu10/EnzRank) to predict enzyme-substrate activity using SMILES strings of substrates and enzyme sequence as input to allow convenient and easy-to-use access to EnzRank. In summary, this effort can aid de novo pathway design tools to prioritize starting enzyme re-engineering candidates for novel reactions as well as in predicting the potential secondary activity of enzymes in cell metabolism.

MetChem: a new pipeline to explore structural similarity across metabolite modules

Summary

Computational analysis and interpretation of metabolomic profiling data remains a major challenge in translational research. Exploring metabolic biomarkers and dysregulated metabolic pathways associated with a patient phenotype could offer new opportunities for targeted therapeutic intervention. Metabolite clustering based on structural similarity has the potential to uncover common underpinnings of biological processes. To address this need, we have developed the MetChem package. MetChem is a quick and simple tool that allows to classify metabolites in structurally related modules, thus revealing their functional information.

Availabilityand implementation

MetChem is freely available from the R archive CRAN (http://cran.r-project.org). The software is distributed under the GNU General Public License (version 3 or later).

Learning graph representations of biochemical networks and its application to enzymatic link prediction

Motivation

The complete characterization of enzymatic activities between molecules remains incomplete, hindering biological engineering and limiting biological discovery. We develop in this work a technique, enzymatic link prediction (ELP), for predicting the likelihood of an enzymatic transformation between two molecules. ELP models enzymatic reactions cataloged in the KEGG database as a graph. ELP is innovative over prior works in using graph embedding to learn molecular representations that capture not only molecular and enzymatic attributes but also graph connectivity.

Results

We explore transductive (test nodes included in the training graph) and inductive (test nodes not part of the training graph) learning models. We show that ELP achieves high AUC when learning node embeddings using both graph connectivity and node attributes. Further, we show that graph embedding improves link prediction by 30% in area under curve over fingerprint-based similarity approaches and by 8% over support vector machines. We compare ELP against rule-based methods. We also evaluate ELP for predicting links in pathway maps and for reconstruction of edges in reaction networks of four common gut microbiota phyla: actinobacteria, bacteroidetes, firmicutes and proteobacteria. To emphasize the importance of graph embedding in the context of biochemical networks, we illustrate how graph embedding can guide visualization.

Availability and implementation

The code and datasets are available through https://github.com/HassounLab/ELP.

Computationally Prospecting Potential Pathways from Lignin Monomers and Dimers toward Aromatic Compounds

The heterogeneity of the aromatic products originating from lignin catalytic depolymerization remains one of the major challenges associated with lignin valorization. Microbes have evolved catabolic pathways that can funnel heterogeneous intermediates to a few central aromatic products. These aromatic compounds can subsequently undergo intra- or extradiol ring opening to produce value-added chemicals. However, such funneling pathways are only partially characterized for a few organisms such as Sphingobium sp. SYK-6 and Pseudomonas putida KT2440. Herein, we apply the de novo pathway design tool (novoStoic) to computationally prospect possible ways of funneling lignin-derived mono- and biaryls. novoStoic employs reaction rules between molecular moieties to hypothesize de novo conversions by flagging known enzymes that carry out the same biotransformation on the most similar substrate. Both reaction rules and known reactions are then deployed by novoStoic to identify a mass-balanced biochemical network that converts a source to a target metabolite while minimizing the number of de novo steps. We demonstrate the application of novoStoic for (i) designing alternative pathways of funneling S, G, and H lignin monomers, and (ii) exploring cleavage pathways of β-1 and β-β dimers. By exploring the uncharted chemical space afforded by enzyme promiscuity, novoStoic can help predict previously unknown native pathways leveraging enzyme promiscuity and propose new carbon/energy efficient lignin funneling pathways with few heterologous enzymes.

Finding metabolic pathways in large networks through atom-conserving substrate-product pairs

Motivation

Finding biosynthetic pathways is essential for metabolic engineering of organisms to produce chemicals, biodegradation prediction of pollutants and drugs, and for the elucidation of bioproduction pathways of secondary metabolites. A key step in biosynthetic pathway design is the extraction of novel metabolic pathways from big networks that integrate known biological, as well as novel, predicted biotransformations. However, the efficient analysis and the navigation of big biochemical networks remain a challenge.

Results

Here, we propose the construction of searchable graph representations of metabolic networks. Each reaction is decomposed into pairs of reactants and products, and each pair is assigned a weight, which is calculated from the number of conserved atoms between the reactant and the product molecule. We test our method on a biochemical network that spans 6546 known enzymatic reactions to show how our approach elegantly extracts biologically relevant metabolic pathways from biochemical networks, and how the proposed network structure enables the application of efficient graph search algorithms that improve navigation and pathway identification in big metabolic networks. The weighted reactant–product pairs of an example network and the corresponding graph search algorithm are available online. The proposed method extracts metabolic pathways fast and reliably from big biochemical networks, which is inherently important for all applications involving the engineering of metabolic networks.

Availability and implementation

https://github.com/EPFL-LCSB/nicepath.

Supplementary information

Supplementary data are available at Bioinformatics online.

Stepping on the Gas to a Circular Economy: Accelerating Development of Carbon-Negative Chemical Production from Gas Fermentation

Owing to rising levels of greenhouse gases in our atmosphere and oceans, climate change poses significant environmental, economic, and social challenges globally. Technologies that enable carbon capture and conversion of greenhouse gases into useful products will help mitigate climate change by enabling a new circular carbon economy. Gas fermentation usingcarbon-fixing microorganisms offers an economically viable and scalable solution with unique feedstock and product flexibility that has been commercialized recently. We review the state of the art of gas fermentation and discuss opportunities to accelerate future development and rollout. We discuss the current commercial process for conversion of waste gases to ethanol, including the underlying biology, challenges in process scale-up, and progress on genetic tool development and metabolic engineering to expand the product spectrum. We emphasize key enabling technologies to accelerate strain development for acetogens and other nonmodel organisms.

Curating a comprehensive set of enzymatic reaction rules for efficient novel biosynthetic pathway design

Enzyme substrate promiscuity has significant implications for metabolic engineering. The ability to predict the space of possible enzymatic side reactions is crucial for elucidating underground metabolic networks in microorganisms, as well as harnessing novel biosynthetic capabilities of enzymes to produce desired chemicals. Reaction rule-based cheminformatics platforms have been implemented to computationally enumerate possible promiscuous reactions, relying on existing knowledge of enzymatic transformations to inform novel reactions. However, past versions of curated reaction rules have been limited by a lack of comprehensiveness in representing all possible transformations, as well as the need to prune rules to enhance computational efficiency in pathway expansion. To this end, we curated a set of 1224 most generalized reaction rules, automatically abstracted from atom-mapped MetaCyc reactions and verified to uniquely cover all common enzymatic transformations. We developed a framework to systematically identify and correct redundancies and errors in the curation process, resulting in a minimal, yet comprehensive, rule set. These reaction rules were capable of reproducing more than 85% of all reactions in the KEGG and BRENDA databases, for which a large fraction of reactions is not present in MetaCyc. Our rules exceed all previously published rule sets for which reproduction was possible in this coverage analysis, which allows for the exploration of a larger space of known enzymatic transformations. By leveraging the entire knowledge of possible metabolic reactions through generalized enzymatic reaction rules, we are able to better utilize underground metabolic pathways and accelerate novel biosynthetic pathway design to enable bioproduction towards a wider range of new molecules.

Enzyme Promiscuity Prediction Using Hierarchy-Informed Multi-Label Classification

MOTIVATION

As experimental efforts are costly and time consuming, computational characterization of enzyme capabilities is an attractive alternative. We present and evaluate several machine-learning models to predict which of 983 distinct enzymes, as defined via the Enzyme Commission (EC) numbers, are likely to interact with a given query molecule. Our data consists of enzyme-substrate interactions from the BRENDA database. Some interactions are attributed to natural selection and involve the enzyme's natural substrates. The majority of the interactions however involve non-natural substrates, thus reflecting promiscuous enzymatic activities.

RESULTS

We frame this "enzyme promiscuity prediction" problem as a multi-label classification task. We maximally utilize inhibitor and unlabelled data to train prediction models that can take advantage of known hierarchical relationships between enzyme classes. We report that a hierarchical multi-label neural network, EPP-HMCNF, is the best model for solving this problem, outperforming k-nearest neighbours similarity-based and other machine learning models. We show that inhibitor information during training consistently improves predictive power, particularly for EPP-HMCNF. We also show that all promiscuity prediction models perform worse under a realistic data split when compared to a random data split, and when evaluating performance on non-natural substrates compared to natural substrates.

AVAILABILITY AND IMPLEMENTATION

We provide Python code for EPP-HMCNF and other models in a repository termed EPP (Enzyme Promiscuity Prediction) at https://github.com/hassounlab/EPP.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Automated engineering of synthetic metabolic pathways for efficient biomanufacturing

Metabolic engineering involves the engineering and optimization of processes from single-cell to fermentation in order to increase production of valuable chemicals for health, food, energy, materials and others. A systems approach to metabolic engineering has gained traction in recent years thanks to advances in strain engineering, leading to an accelerated scaling from rapid prototyping to industrial production. Metabolic engineering is nowadays on track towards a truly manufacturing technology, with reduced times from conception to production enabled by automated protocols for DNA assembly of metabolic pathways in engineered producer strains. In this review, we discuss how the success of the metabolic engineering pipeline often relies on retrobiosynthetic protocols able to identify promising production routes and dynamic regulation strategies through automated biodesign algorithms, which are subsequently assembled as embedded integrated genetic circuits in the host strain. Those approaches are orchestrated by an experimental design strategy that provides optimal scheduling planning of the DNA assembly, rapid prototyping and, ultimately, brings forward an accelerated Design-Build-Test-Learn cycle and the overall optimization of the biomanufacturing process. Achieving such a vision will address the increasingly compelling demand in our society for delivering valuable biomolecules in an affordable, inclusive and sustainable bioeconomy.

Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks

Over the last decade, a giant leap forward has been made in resolving the main bottleneck in metabolomics, i.e., the structural characterization of the many unknowns. This has led to the next challenge in this research field: retrieving biochemical pathway information from the various types of networks that can be constructed from metabolome data. Searching putative biochemical pathways, referred to as biotransformation paths, is complicated because several flaws occur during the construction of metabolome networks. Multiple network analysis tools have been developed to deal with these flaws, while in silico retrosynthesis is appearing as an alternative approach. In this review, the different types of metabolome networks, their flaws, and the various tools to trace these biotransformation paths are discussed.

Network-based strategies in metabolomics data analysis and interpretation: from molecular networking to biological interpretation

INTRODUCTION

Metabolomics has become a crucial part of systems biology; however, data analysis is still often undertaken in a reductionist way focusing on changes in individual metabolites. Whilst such approaches indeed provide relevant insights into the metabolic phenotype of an organism, the intricate nature of metabolic relationships may be better explored when considering the whole system.

AREAS COVERED

This review highlights multiple network strategies that can be applied for metabolomics data analysis from different perspectives including: association networks based on quantitative information, mass spectra similarity networks to assist metabolite annotation and biochemical networks for systematic data interpretation. We also highlight some relevant insights into metabolic organization obtained through the exploration of such approaches.

EXPERT OPINION

Network based analysis is an established method that allows the identification of non-intuitive metabolic relationships as well as the identification of unknown compounds in mass spectrometry. Additionally, the representation of data from metabolomics within the context of metabolic networks is intuitive and allows for the use of statistical analysis that can better summarize relevant metabolic changes from a systematic perspective.

Prediction of Adverse Drug Reactions by Combining Biomedical Tripartite Network and Graph Representation Model

As one of the primary contributors to high clinical attrition rates of drugs, toxicity evaluation is of critical significance to new drug discovery. Unsurprisingly, a vast number of computational methods have been developed at various stages of development pipeline to evaluate potential adverse drug reactions (ADRs). Despite previous success of these methods on individual ADR or certain drug family, there are great challenges to toxicity evaluation. In this study, a novel strategy was developed to predict the drug-ADR associations by combining deep learning and the biomedical tripartite network. This heterogeneous network contains biomedical linked data of three entities, for example, drugs, targets, and ADRs. For the first time, GraRep, a deep learning method for distributed representations, is introduced to learn graph representations and identify hidden features from the tripartite network which are further used for ADR prediction. Through this approach, drug-ADR associations could possibly be discovered from a systemic perspective. The accuracy of our method is 0.95 based on internal resource validation and 0.88 based on external resource validation. Moreover, our results show the prediction accuracy using the tripartite network is better than the one with bipartite network, suggesting the model performance can be improved with further enrichment on information. According to the result of 10-fold cross validation, the deep learning model outperforms two traditional methods (topology-based measures and chemical structure-based measures). Additionally, predictive models are also constructed using other deep learning methods, and comparable results are achieved. In summary, the biomedical tripartite network-based deep learning model proposed here proves to offer a promising solution for prediction of ADRs.

Metabolic engineering of Escherichia coli for the production of isoprenoids

Metabolic engineering is the practice of using directed genetic manipulations to rewire cellular metabolism primarily with the aim to transform the organism into a single-celled chemical factory. Using biological processes, we can produce more complex chemicals in a more sustainable way. This is particularly important for chemicals which are hard to synthesize using traditional chemistry. However, cells have evolved for growth and must be engineered to produce a single chemical at commercially viable levels. This review focuses on the strategies used to rewire cellular metabolism to produce chemicals using isoprenoid production in Escherichia coli as an example that illustrates many of the challenges faced in metabolic engineering.

A Robust Strategy for Sustainable Organic Chemicals Utilizing Bioprivileged Molecules

Biobased chemicals will inevitably be an important part of a sustainable organic chemical industry. Current efforts in biobased chemicals are largely driven by opportunistic chemical product targets requiring complete technology development from feedstock to final product for a specific molecule. To enhance the development of biobased chemicals, it is important to create strategies that can be more systematic and can leverage advancements across multiple final products. Discussed here is the concept of bioprivileged molecules, which are chemical intermediates that have the potential to be efficiently converted into a range of product molecules that can both directly replace existing petrochemicals and are novel molecules that impart enhanced performance properties in end-use applications.

Cheminformatics approach to exploring and modeling trait-associated metabolite profiles

Developing predictive and transparent approaches to the analysis of metabolite profiles across patient cohorts is of critical importance for understanding the events that trigger or modulate traits of interest (e.g., disease progression, drug metabolism, chemical risk assessment). However, metabolites’ chemical structures are still rarely used in the statistical modeling workflows that establish these trait-metabolite relationships. Herein, we present a novel cheminformatics-based approach capable of identifying predictive, interpretable, and reproducible trait-metabolite relationships. As a proof-of-concept, we utilize a previously published case study consisting of metabolite profiles from non-small-cell lung cancer (NSCLC) adenocarcinoma patients and healthy controls. By characterizing each structurally annotated metabolite using both computed molecular descriptors and patient metabolite concentration profiles, we show that these complementary features enhance the identification and understanding of key metabolites associated with cancer. Ultimately, we built multi-metabolite classification models for assessing patients’ cancer status using specific groups of metabolites identified based on high structural similarity through chemical clustering. We subsequently performed a metabolic pathway enrichment analysis to identify potential mechanistic relationships between metabolites and NSCLC adenocarcinoma. This cheminformatics-inspired approach relies on the metabolites’ structural features and chemical properties to provide critical information about metabolite-trait associations. This method could ultimately facilitate biological understanding and advance research based on metabolomics data, especially with respect to the identification of novel biomarkers.

Integrating bioinformatics approaches for a comprehensive interpretation of metabolomics datasets

Access to high quality metabolomics data has become a routine component for biological studies. However, interpreting those datasets in biological contexts remains a challenge, especially because many identified metabolites are not found in biochemical pathway databases. Starting from statistical analyses, a range of new tools are available, including metabolite set enrichment analysis, pathway and network visualization, pathway prediction, biochemical databases and text mining. Integrating these approaches into comprehensive and unbiased interpretations must carefully consider both caveats of the metabolomics dataset itself as well as the structure and properties of the biological study design. Special considerations need to be taken when adopting approaches from genomics for use in metabolomics. R and Python programming language are enabling an easier exchange of diverse tools to deploy integrated workflows. This review summarizes the key ideas and latest developments in regards to these approaches.

A pathway for every product? Tools to discover and design plant metabolism

The vast diversity of plant natural products is a powerful indication of the biosynthetic capacity of plant metabolism. Synthetic biology seeks to capitalize on this ability by understanding and reconfiguring the biosynthetic pathways that generate this diversity to produce novel products with improved efficiency. Here we review the algorithms and databases that presently support the design and manipulation of metabolic pathways in plants, starting from metabolic models of native biosynthetic pathways, progressing to novel combinations of known reactions, and finally proposing new reactions that may be carried out by existing enzymes. We show how these tools are useful for proposing new pathways as well as identifying side reactions that may affect engineering goals.

PathEmb: Random Walk Based Document Embedding for Global Pathway Similarity Search

Pathway analysis is a cornerstone of system biology. In particular, pathway similarity search plays a key role in establishing structural, functional, and evolutionary relationships between different biological entities. Given a query pathway as well as a database, a pathway similarity search aims to identify novel pathways that are homologous to the query pathway. Unfortunately, the pathway similarity search is computationally inefficient due to the NP-complete graph isomorphism problem. In this study, we introduce a novel algorithmic framework for pathway similarity search, named PathEmb (Pathway Embedding), which is analogous to the Skip-gram model where each pathway is represented as a "document." PathEmb exploits a second order random walk strategy to explore diverse pathway patterns. All signaling paths traversed from random walks are regarded as "sentences," which are constituted as a "document" afterwards. Then, the "document" pattern for the individual pathway is mapped into a low-dimensional feature space for downstream tasks. Furthermore, PathEmb is a topology-free pathway similarity search algorithm, which is feasible to handle any pathway with arbitrary structure. We have extensively evaluated PathEmb and other cutting-edge methods on three pathway datasets. The experimental results demonstrate that PathEmb outperforms the existing methods in terms of computational efficiency and search accuracy. The source code of PathEmb are freely available online https://github.com/zhangjiaobxy/PathEmb.

SimCAL: a flexible tool to compute biochemical reaction similarity

Background

Computation of reaction similarity is a pre-requisite for several bioinformatics applications including enzyme identification for specific biochemical reactions, enzyme classification and mining for specific inhibitors. Reaction similarity is often assessed at either two levels: (i) comparison across all the constituent substrates and products of a reaction, reaction level similarity, (ii) comparison at the transformation center with various degrees of neighborhood, transformation level similarity. Existing reaction similarity computation tools are designed for specific applications and use different features and similarity measures. A single system integrating these diverse features enables comparison of the impact of different molecular properties on similarity score computation.

Results

To address these requirements, we present SimCAL, an integrated system to calculate reaction similarity with novel features and capability to perform comparative assessment. SimCAL provides reaction similarity computation at both whole reaction level and transformation level. Novel physicochemical features such as stereochemistry, mass, volume and charge are included in computing reaction fingerprint. Users can choose from four different fingerprint types and nine molecular similarity measures. Further, a comparative assessment of these features is also enabled. The performance of SimCAL is assessed on 3,688,122 reaction pairs with Enzyme Commission (EC) number from MetaCyc and achieved an area under the curve (AUC) of > 0.9. In addition, SimCAL results showed strong correlation with state-of-the-art EC-BLAST and molecular signature based reaction similarity methods.

Conclusions

SimCAL is developed in java and is available as a standalone tool, with intuitive, user-friendly graphical interface and also as a console application. With its customizable feature selection and similarity calculations, it is expected to cater a wide audience interested in studying and analyzing biochemical reactions and metabolic networks.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2248-5) contains supplementary material, which is available to authorized users.

Biochemical control systems for small molecule damage in plants

As a system, plant metabolism is far from perfect: small molecules (metabolites, cofactors, coenzymes, and inorganic molecules) are frequently damaged by unwanted enzymatic or spontaneous reactions. Here, we discuss the emerging principles in small molecule damage biology. We propose that plants evolved at least three distinct systems to control small molecule damage: (i) repair, which returns a damaged molecule to its original state; (ii) scavenging, which converts reactive molecules to harmless products; and (iii) steering, in which the possible formation of a damaged molecule is suppressed. We illustrate the concept of small molecule damage control in plants by describing specific examples for each of these three categories. We highlight interesting insights that we expect future research will provide on those systems, and we discuss promising strategies to discover new small molecule damage-control systems in plants.

Thermodynamic analysis of computed pathways integrated into the metabolic networks of E. coli and Synechocystis reveals contrasting expansion potential

Introducing biosynthetic pathways into an organism is both reliant on and challenged by endogenous biochemistry. Here we compared the expansion potential of the metabolic network in the photoautotroph Synechocystis with that of the heterotroph E. coli using the novel workflow POPPY (Prospecting Optimal Pathways with PYthon). First, E. coli and Synechocystis metabolomic and fluxomic data were combined with metabolic models to identify thermodynamic constraints on metabolite concentrations (NET analysis). Then, thousands of automatically constructed pathways were placed within each network and subjected to a network-embedded variant of the max-min driving force analysis (NEM). We found that the networks had different capabilities for imparting thermodynamic driving forces toward certain compounds. Key metabolites were constrained differently in Synechocystis due to opposing flux directions in glycolysis and carbon fixation, the forked tri-carboxylic acid cycle, and photorespiration. Furthermore, the lysine biosynthesis pathway in Synechocystis was identified as thermodynamically constrained, impacting both endogenous and heterologous reactions through low 2-oxoglutarate levels. Our study also identified important yet poorly covered areas in existing metabolomics data and provides a reference for future thermodynamics-based engineering in Synechocystis and beyond. The POPPY methodology represents a step in making optimal pathway-host matches, which is likely to become important as the practical range of host organisms is diversified.

A review of computational tools for design and reconstruction of metabolic pathways

Metabolic pathways reflect an organism's chemical repertoire and hence their elucidation and design have been a primary goal in metabolic engineering. Various computational methods have been developed to design novel metabolic pathways while taking into account several prerequisites such as pathway stoichiometry, thermodynamics, host compatibility, and enzyme availability. The choice of the method is often determined by the nature of the metabolites of interest and preferred host organism, along with computational complexity and availability of software tools. In this paper, we review different computational approaches used to design metabolic pathways based on the reaction network representation of the database (i.e., graph or stoichiometric matrix) and the search algorithm (i.e., graph search, flux balance analysis, or retrosynthetic search). We also put forth a systematic workflow that can be implemented in projects requiring pathway design and highlight current limitations and obstacles in computational pathway design.

Predicting novel substrates for enzymes with minimal experimental effort with active learning

Enzymatic substrate promiscuity is more ubiquitous than previously thought, with significant consequences for understanding metabolism and its application to biocatalysis. This realization has given rise to the need for efficient characterization of enzyme promiscuity. Enzyme promiscuity is currently characterized with a limited number of human-selected compounds that may not be representative of the enzyme's versatility. While testing large numbers of compounds may be impractical, computational approaches can exploit existing data to determine the most informative substrates to test next, thereby more thoroughly exploring an enzyme's versatility. To demonstrate this, we used existing studies and tested compounds for four different enzymes, developed support vector machine (SVM) models using these datasets, and selected additional compounds for experiments using an active learning approach. SVMs trained on a chemically diverse set of compounds were discovered to achieve maximum accuracies of ~80% using ~33% fewer compounds than datasets based on all compounds tested in existing studies. Active learning-selected compounds for testing resolved apparent conflicts in the existing training data, while adding diversity to the dataset. The application of these algorithms to wide arrays of metabolic enzymes would result in a library of SVMs that can predict high-probability promiscuous enzymatic reactions and could prove a valuable resource for the design of novel metabolic pathways.

A Method for Finding Metabolic Pathways Using Atomic Group Tracking

A fundamental computational problem in metabolic engineering is to find pathways between compounds. Pathfinding methods using atom tracking have been widely used to find biochemically relevant pathways. However, these methods require the user to define the atoms to be tracked. This may lead to failing to predict the pathways that do not conserve the user-defined atoms. In this work, we propose a pathfinding method called AGPathFinder to find biochemically relevant metabolic pathways between two given compounds. In AGPathFinder, we find alternative pathways by tracking the movement of atomic groups through metabolic networks and use combined information of reaction thermodynamics and compound similarity to guide the search towards more feasible pathways and better performance. The experimental results show that atomic group tracking enables our method to find pathways without the need of defining the atoms to be tracked, avoid hub metabolites, and obtain biochemically meaningful pathways. Our results also demonstrate that atomic group tracking, when incorporated with combined information of reaction thermodynamics and compound similarity, improves the quality of the found pathways. In most cases, the average compound inclusion accuracy and reaction inclusion accuracy for the top resulting pathways of our method are around 0.90 and 0.70, respectively, which are better than those of the existing methods. Additionally, AGPathFinder provides the information of thermodynamic feasibility and compound similarity for the resulting pathways.

Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function

Decades of biochemical, bioinformatic, and sequencing data are currently being systematically compiled into genome-scale metabolic reconstructions (GEMs). Such reconstructions are knowledge-bases useful for engineering, modeling, and comparative analysis. Here we review the fifteen GEMs of archaeal species that have been constructed to date. They represent primarily members of the Euryarchaeota with three-quarters comprising representative of methanogens. Unlike other reviews on GEMs, we specially focus on archaea. We briefly review the GEM construction process and the genealogy of the archaeal models. The major insights gained during the construction of these models are then reviewed with specific focus on novel metabolic pathway predictions and growth characteristics. Metabolic pathway usage is discussed in the context of the composition of each organism's biomass and their specific energy and growth requirements. We show how the metabolic models can be used to study the evolution of metabolism in archaea. Conservation of particular metabolic pathways can be studied by comparing reactions using the genes associated with their enzymes. This demonstrates the utility of GEMs to evolutionary studies, far beyond their original purpose of metabolic modeling; however, much needs to be done before archaeal models are as extensively complete as those for bacteria.

Computational methods to identify metabolic sub-networks based on metabolomic profiles

Untargeted metabolomics makes it possible to identify compounds that undergo significant changes in concentration in different experimental conditions. The resulting metabolomic profile characterizes the perturbation concerned, but does not explain the underlying biochemical mechanisms. Bioinformatics methods make it possible to interpret results in light of the whole metabolism. This knowledge is modelled into a network, which can be mined using algorithms that originate in graph theory. These algorithms can extract sub-networks related to the compounds identified. Several attempts have been made to adapt them to obtain more biologically meaningful results. However, there is still no consensus on this kind of analysis of metabolic networks. This review presents the main graph approaches used to interpret metabolomic data using metabolic networks. Their advantages and drawbacks are discussed, and the impacts of their parameters are emphasized. We also provide some guidelines for relevant sub-network extraction and also suggest a range of applications for most methods.

Designing overall stoichiometric conversions and intervening metabolic reactions

Existing computational tools for de novo metabolic pathway assembly, either based on mixed integer linear programming techniques or graph-search applications, generally only find linear pathways connecting the source to the target metabolite. The overall stoichiometry of conversion along with alternate co-reactant (or co-product) combinations is not part of the pathway design. Therefore, global carbon and energy efficiency is in essence fixed with no opportunities to identify more efficient routes for recycling carbon flux closer to the thermodynamic limit. Here, we introduce a two-stage computational procedure that both identifies the optimum overall stoichiometry (i.e., optStoic) and selects for (non-)native reactions (i.e., minRxn/minFlux) that maximize carbon, energy or price efficiency while satisfying thermodynamic feasibility requirements. Implementation for recent pathway design studies identified non-intuitive designs with improved efficiencies. Specifically, multiple alternatives for non-oxidative glycolysis are generated and non-intuitive ways of co-utilizing carbon dioxide with methanol are revealed for the production of C₂₊ metabolites with higher carbon efficiency.

Heading in the right direction: thermodynamics-based network analysis and pathway engineering

Thermodynamics-based network analysis through the introduction of thermodynamic constraints in metabolic models allows a deeper analysis of metabolism and guides pathway engineering. The number and the areas of applications of thermodynamics-based network analysis methods have been increasing in the last ten years. We review recent applications of these methods and we identify the areas that such analysis can contribute significantly, and the needs for future developments. We find that organisms with multiple compartments and extremophiles present challenges for modeling and thermodynamics-based flux analysis. The evolution of current and new methods must also address the issues of the multiple alternatives in flux directionalities and the uncertainties and partial information from analytical methods.