1
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Zhang L, Vaccari F, Bandini F, Puglisi E, Trevisan M, Lucini L. The short-term effect of microplastics in lettuce involves size- and dose-dependent coordinate shaping of root metabolome, exudation profile and rhizomicrobiome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 945:174001. [PMID: 38879040 DOI: 10.1016/j.scitotenv.2024.174001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 06/02/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024]
Abstract
Micro- and nano-plastics (MNPs) in the soil can impact the microbial diversity within rhizospheres and induce modifications in plants' morphological, physiological, and biochemical parameters. However, a significant knowledge gap still needs to be addressed regarding the specific effects of varying particle sizes and concentrations on the comprehensive interplay among soil dynamics, root exudation, and the overall plant system. In this sense, different omics techniques were employed to clarify the mechanisms of the action exerted by four different particle sizes of polyethylene plastics considering four different concentrations on the soil-roots exudates-plant system was studied using lettuce (Lactuca sativa L. var. capitata) as a model plant. The impact of MNPs was investigated using a multi-omics integrated approach, focusing on the tripartite interaction between the root metabolic process, exudation pattern, and rhizosphere microbial modulation. Our results showed that particle size and their concentrations significantly modulated the soil-roots exudates-plant system. Untargeted metabolomics highlighted that fatty acids, amino acids, and hormone biosynthesis pathways were significantly affected by MNPs. Additionally, they were associated with the reduction of rhizosphere bacterial α-diversity, following a size-dependent trend for specific taxa. The omics data integration highlighted a correlation between Pseudomonadata and Actinomycetota phyla and Bacillaceae family (Peribacillus simplex) and the exudation of flavonoids, phenolic acids, and lignans in lettuce exposed to increasing sizes of MNPs. This study provides a novel insight into the potential effects of different particle sizes and concentrations of MNPs on the soil-plant continuum, providing evidence about size- and concentration-dependent effects, suggesting the need for further investigation focused on medium- to long-term exposure.
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Affiliation(s)
- Leilei Zhang
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Filippo Vaccari
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Francesca Bandini
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Edoardo Puglisi
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Marco Trevisan
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Luigi Lucini
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy.
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Shrestha P, Karmacharya J, Han SR, Lee JH, Oh TJ. Elucidation of bacterial trehalose-degrading trehalase and trehalose phosphorylase: physiological significance and its potential applications. Glycobiology 2024; 34:cwad084. [PMID: 37847605 PMCID: PMC10969515 DOI: 10.1093/glycob/cwad084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 10/19/2023] Open
Abstract
Bacteria possess diverse metabolic and genetic processes, resulting in the inability of certain bacteria to degrade trehalose. However, some bacteria do have the capability to degrade trehalose, utilizing it as a carbon source, and for defense against environmental stress. Trehalose, a disaccharide, serves as a carbon source for many bacteria, including some that are vital for pathogens. The degradation of trehalose is carried out by enzymes like trehalase (EC 3.2.1.28) and trehalose phosphorylase (EC 2.4.1.64/2.4.1.231), which are classified under the glycoside hydrolase families GH37, GH15, and GH65. Numerous studies and reports have explored the physiological functions, recombinant expression, enzymatic characteristics, and potential applications of these enzymes. However, further research is still being conducted to understand their roles in bacteria. This review aims to provide a comprehensive summary of the current understanding of trehalose degradation pathways in various bacteria, focusing on three key areas: (i) identifying different trehalose-degrading enzymes in Gram-positive and Gram-negative bacteria, (ii) elucidating the mechanisms employed by trehalose-degrading enzymes belonging to the glycoside hydrolases GH37, GH15, and GH65, and (iii) discussing the potential applications of these enzymes in different sectors. Notably, this review emphasizes the bacterial trehalose-degrading enzymes, specifically trehalases (GH37, GH15, and GH65) and trehalose phosphorylases (GH65), in both Gram-positive and Gram-negative bacteria, an aspect that has not been highlighted before.
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Affiliation(s)
- Prasansah Shrestha
- Department of Life Sciences and Biochemical Engineering, Graduate School, Sun Moon University, 70 Sunmoon-ro 221beon-gil, Tangjeong-myeon, Asan-si, Chungcheongnam-do, 31460, South Korea
| | - Jayram Karmacharya
- Department of Life Sciences and Biochemical Engineering, Graduate School, Sun Moon University, 70 Sunmoon-ro 221beon-gil, Tangjeong-myeon, Asan-si, Chungcheongnam-do, 31460, South Korea
| | - So-Ra Han
- Department of Life Sciences and Biochemical Engineering, Graduate School, Sun Moon University, 70 Sunmoon-ro 221beon-gil, Tangjeong-myeon, Asan-si, Chungcheongnam-do, 31460, South Korea
- Genome-based Bio-IT Convergence Institute, 70 Sunmoon-ro 221beon-gil, Tangjeong-myeon Asan-si, Chungcheongnam-do, 31460, South Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Materials, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, South Korea
| | - Tae-Jin Oh
- Department of Life Sciences and Biochemical Engineering, Graduate School, Sun Moon University, 70 Sunmoon-ro 221beon-gil, Tangjeong-myeon, Asan-si, Chungcheongnam-do, 31460, South Korea
- Genome-based Bio-IT Convergence Institute, 70 Sunmoon-ro 221beon-gil, Tangjeong-myeon Asan-si, Chungcheongnam-do, 31460, South Korea
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, 70 Sunmoon-ro 221beon-gil, Tangjeong-myeon, Asan-si, Chungcheongnam-do 31460, South Korea
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Li X, Xu L, Demaree B, Noecker C, Bisanz JE, Weisgerber DW, Modavi C, Turnbaugh PJ, Abate AR. Microbiome single cell atlases generated with a commercial instrument. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.08.551713. [PMID: 37609281 PMCID: PMC10441329 DOI: 10.1101/2023.08.08.551713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Single cell sequencing is useful for resolving complex systems into their composite cell types and computationally mining them for unique features that are masked in pooled sequencing. However, while commercial instruments have made single cell analysis widespread for mammalian cells, analogous tools for microbes are limited. Here, we present EASi-seq (Easily Accessible Single microbe sequencing). By adapting the single cell workflow of the commercial Mission Bio Tapestri instrument, this method allows for efficient sequencing of individual microbes' genomes. EASi-seq allows thousands of microbes to be sequenced per run and, as we show, can generate detailed atlases of human and environmental microbiomes. The ability to capture large shotgun genome datasets from thousands of single microbes provides new opportunities in discovering and analyzing species subpopulations. To facilitate this, we develop a companion bioinformatic pipeline that clusters microbes by similarity, improving whole genome assembly, strain identification, taxonomic classification, and gene annotation. In addition, we demonstrate integration of metagenomic contigs with the EASi-seq datasets to reduce capture bias and increase coverage. Overall, EASi-seq enables high quality single cell genomic data for microbiome samples using an accessible workflow that can be run on a commercially available platform.
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Colosimo R, Harris HC, Ahn-Jarvis J, Troncoso-Rey P, Finnigan TJA, Wilde PJ, Warren FJ. Colonic in vitro fermentation of mycoprotein promotes shifts in gut microbiota, with enrichment of Bacteroides species. Commun Biol 2024; 7:272. [PMID: 38443511 PMCID: PMC10915147 DOI: 10.1038/s42003-024-05893-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 02/07/2024] [Indexed: 03/07/2024] Open
Abstract
Mycoprotein is a fungal-derived ingredient used for meat alternative products whose fungal cell walls are rich in dietary fibre (β-glucans and chitin) and defines its structure. Several health benefits have been reported after mycoprotein consumption, however, little is known about the impact of mycoprotein fermentation on the gut microbiota. This study aims to identify changes in microbiome composition and microbial metabolites during colonic fermentation of mycoprotein following simulated upper gastrointestinal digestion. Changes in microbial populations and metabolites produced by the fermentation of mycoprotein fibre were investigated and compared to a plant (oat bran) and an animal (chicken) comparator. In this model fermentation system, mycoprotein and oat showed different but marked changes in the microbial population compared to chicken, which showed minimal differentiation. In particular, Bacteroides species known for degrading β-glucans were found in abundance following fermentation of mycoprotein fibre. Mycoprotein fermentation resulted in short-chain fatty acid production comparable with oat and chicken at 72 h. Significantly higher branched-chain amino acids were observed following chicken fermentation. This study suggests that the colonic fermentation of mycoprotein can promote changes in the colonic microbial profile. These results highlight the impact that the unique structure of mycoprotein can have on digestive processes and the gut microbiota.
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Affiliation(s)
- Raffaele Colosimo
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- Elsevier B.V, Radarweg 29a, 1043, NX, Amsterdam, Netherlands
| | - Hannah C Harris
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Jennifer Ahn-Jarvis
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Perla Troncoso-Rey
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Tim J A Finnigan
- Marlow Foods Ltd, Station Road, Stokesley, North Yorkshire, TS9 7AB, UK
| | - Pete J Wilde
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Frederick J Warren
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK.
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Zhang L, Vaccari F, Ardenti F, Fiorini A, Tabaglio V, Puglisi E, Trevisan M, Lucini L. The dosage- and size-dependent effects of micro- and nanoplastics in lettuce roots and leaves at the growth, photosynthetic, and metabolomics levels. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108531. [PMID: 38513516 DOI: 10.1016/j.plaphy.2024.108531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/16/2024] [Accepted: 02/25/2024] [Indexed: 03/23/2024]
Abstract
The occurrence of microplastics (MPs) and nanoplastics (NPs) in soils potentially induce morphological, physiological, and biochemical alterations in plants. The present study investigated the effects of MPs/NPs on lettuce (Lactuca sativa L. var. capitata) plants by focusing on (i) four different particle sizes of polyethylene micro- and nanoplastics, at (ii) four concentrations. Photosynthetic activity, morphological changes in plants, and metabolomic shifts in roots and leaves were investigated. Our findings revealed that particle size plays a pivotal role in influencing various growth traits of lettuce (biomass, color segmentation, greening index, leaf area, and photosynthetic activity), physiological parameters (including maximum quantum yield - Fv/Fmmax, or quantum yield in the steady-state Fv/FmLss, NPQLss, RfdLss, FtLss, FqLss), and metabolomic signatures. Smaller plastic sizes demonstrated a dose-dependent impact on aboveground plant structures, resulting in an overall elicitation of biosynthetic processes. Conversely, larger plastic size had a major impact on root metabolomics, leading to a negative modulation of biosynthetic processes. Specifically, the biosynthesis of secondary metabolites, phytohormone crosstalk, and the metabolism of lipids and fatty acids were among the most affected processes. In addition, nitrogen-containing compounds accumulated following plastic treatments. Our results highlighted a tight correlation between the qPCR analysis of genes associated with the soil nitrogen cycle (such as NifH, NirK, and NosZ), available nitrogen pools in soil (including NO3- and NH4), N-containing metabolites and morpho-physiological parameters of lettuce plants subjected to MPs/NPs. These findings underscore the intricate relationship between specific plastic contaminations, nitrogen dynamics, and plant performance.
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Affiliation(s)
- Leilei Zhang
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Filippo Vaccari
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Federico Ardenti
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Andrea Fiorini
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Vincenzo Tabaglio
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Edoardo Puglisi
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Marco Trevisan
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Luigi Lucini
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy.
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6
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Abate A, Li X, Xu L, Demaree B, Noecker C, Bisanz J, Weisgerber D, Modavi C, Turnbaugh P. Microbiome single cell atlases generated with a commercial instrument. RESEARCH SQUARE 2023:rs.3.rs-3253785. [PMID: 37790580 PMCID: PMC10543498 DOI: 10.21203/rs.3.rs-3253785/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Single cell sequencing is useful for resolving complex systems into their composite cell types and computationally mining them for unique features that are masked in pooled sequencing. However, while commercial instruments have made single cell analysis widespread for mammalian cells, analogous tools for microbes are limited. Here, we present EASi-seq (Easily Accessible Single microbe sequencing). By adapting the single cell workflow of the commercial Mission Bio Tapestri instrument, this method allows for efficient sequencing of individual microbes' genomes. EASi-seq allows thousands of microbes to be sequenced per run and, as we show, can generate detailed atlases of human and environmental microbiomes. The ability to capture large shotgun genome datasets from thousands of single microbes provides new opportunities in discovering and analyzing species subpopulations. To facilitate this, we develop a companion bioinformatic pipeline that clusters microbes by similarity, improving whole genome assembly, strain identification, taxonomic classification, and gene annotation. In addition, we demonstrate integration of metagenomic contigs with the EASi-seq datasets to reduce capture bias and increase coverage. Overall, EASi-seq enables high quality single cell genomic data for microbiome samples using an accessible workflow that can be run on a commercially available platform.
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7
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Vasconcelos L, Aburjaile F, Andrade L, Cancio AF, Seyffert N, Aguiar ERGR, Ristow P. Genomic insights into the c-di-GMP signaling and biofilm development in the saprophytic spirochete Leptospira biflexa. Arch Microbiol 2023; 205:180. [PMID: 37031284 DOI: 10.1007/s00203-023-03519-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 03/20/2023] [Accepted: 03/26/2023] [Indexed: 04/10/2023]
Abstract
C-di-GMP is a bacterial second messenger with central role in biofilm formation. Spirochete bacteria from Leptospira genus present a wide diversity, with species of medical importance and environmental species, named as saprophytic. Leptospira form biofilms in the rat's reservoir kidneys and in the environment. Here, we performed genomic analyses to identify enzymatic and effector c-di-GMP proteins in the saprophytic biofilm-forming species Leptospira biflexa serovar Patoc. We identified 40 proteins through local alignments. Amongst them, 16 proteins are potentially functional diguanylate cyclases, phosphodiesterases, or hybrid proteins. We also identified nine effectors, including PilZ proteins. Enrichment analyses suggested that c-di-GMP interacts with cAMP signaling system, CsrA system, and flagella assembly regulation during biofilm development of L. biflexa. Finally, we identified eight proteins in the pathogen Leptospira interrogans serovar Copenhageni that share high similarity with L. biflexa c-di-GMP-related proteins. This work revealed proteins related to c-di-GMP turnover and cellular response in Leptospira and their potential roles during biofilm development.
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Affiliation(s)
- Larissa Vasconcelos
- Institute of Biology, Federal University of Bahia, Salvador, Bahia, Brazil
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Flávia Aburjaile
- Preventive Veterinary Medicine Department, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Lara Andrade
- Institute of Biology, Federal University of Bahia, Salvador, Bahia, Brazil
| | | | - Núbia Seyffert
- Institute of Biology, Federal University of Bahia, Salvador, Bahia, Brazil
- Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, Brazil
| | - Eric R G R Aguiar
- Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, Brazil
- Department of Biological Science, Center of Biotechnology and Genetics, State University of Santa Cruz, Ilhéus, Bahia, Brazil
| | - Paula Ristow
- Institute of Biology, Federal University of Bahia, Salvador, Bahia, Brazil.
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Federal University of Bahia, Salvador, Bahia, Brazil.
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Gendoo DMA. Overview of Bioinformatics Software and Databases for Metabolic Engineering. Methods Mol Biol 2023; 2553:265-274. [PMID: 36227548 DOI: 10.1007/978-1-0716-2617-7_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The explosion of the "omics" era has introduced a growing number of sets and tools that facilitate molecular interrogation of the metabolome. These include various bioinformatics and pharmacogenomics resources that can be utilized independently or collectively to facilitate metabolic engineering across disease, clinical oncology, and understanding of molecular changes across larger systems. This review provides starting points for accessing publicly available data and computational tools that support assessment of metabolic profiles and metabolic regulation, providing both a depth-and-breadth approach toward understanding the metabolome. We focus in particular on pathway databases and tools, which provide in-depth analysis of metabolic pathways, which is at the heart of metabolic engineering.
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Affiliation(s)
- Deena M A Gendoo
- Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom.
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom.
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Deutsch L, Debevec T, Millet GP, Osredkar D, Opara S, Šket R, Murovec B, Mramor M, Plavec J, Stres B. Urine and Fecal 1H-NMR Metabolomes Differ Significantly between Pre-Term and Full-Term Born Physically Fit Healthy Adult Males. Metabolites 2022; 12:metabo12060536. [PMID: 35736470 PMCID: PMC9228004 DOI: 10.3390/metabo12060536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/30/2022] [Accepted: 06/02/2022] [Indexed: 12/04/2022] Open
Abstract
Preterm birth (before 37 weeks gestation) accounts for ~10% of births worldwide and remains one of the leading causes of death in children under 5 years of age. Preterm born adults have been consistently shown to be at an increased risk for chronic disorders including cardiovascular, endocrine/metabolic, respiratory, renal, neurologic, and psychiatric disorders that result in increased death risk. Oxidative stress was shown to be an important risk factor for hypertension, metabolic syndrome and lung disease (reduced pulmonary function, long-term obstructive pulmonary disease, respiratory infections, and sleep disturbances). The aim of this study was to explore the differences between preterm and full-term male participants' levels of urine and fecal proton nuclear magnetic resonance (1H-NMR) metabolomes, during rest and exercise in normoxia and hypoxia and to assess general differences in human gut-microbiomes through metagenomics at the level of taxonomy, diversity, functional genes, enzymatic reactions, metabolic pathways and predicted gut metabolites. Significant differences existed between the two groups based on the analysis of 1H-NMR urine and fecal metabolomes and their respective metabolic pathways, enabling the elucidation of a complex set of microbiome related metabolic biomarkers, supporting the idea of distinct host-microbiome interactions between the two groups and enabling the efficient classification of samples; however, this could not be directed to specific taxonomic characteristics.
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Affiliation(s)
- Leon Deutsch
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (L.D.); (S.O.)
| | - Tadej Debevec
- Faculty of Sports, University of Ljubljana, SI-1000 Ljubljana, Slovenia;
- Department of Automation, Biocybernetics and Robotics, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
| | - Gregoire P. Millet
- Institute of Sport Sciences, University of Lausanne, CH-1015 Lausanne, Switzerland;
| | - Damjan Osredkar
- Department of Pediatric Neurology, University Children’s Hospital, University Medical Centre Ljubljana, SI-1000 Ljubljana, Slovenia;
- Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Simona Opara
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (L.D.); (S.O.)
| | - Robert Šket
- Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, SI-1000 Ljubljana, Slovenia;
| | - Boštjan Murovec
- Faculty of Electrical Engineering, University of Ljubljana, Jamova 2, SI-1000 Ljubljana, Slovenia;
| | - Minca Mramor
- Department of Infectious Diseases, University Medical Centre Ljubljana, SI-1000 Ljubljana, Slovenia;
| | - Janez Plavec
- National Institute of Chemistry, NMR Center, SI-1000 Ljubljana, Slovenia;
| | - Blaz Stres
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (L.D.); (S.O.)
- Department of Automation, Biocybernetics and Robotics, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
- Institute of Sanitary Engineering, Faculty of Civil and Geodetic Engineering, University of Ljubljana, SI-1000 Ljubljana, Slovenia
- Correspondence: ; Tel.: +386-4156-7633
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Shrestha P, Kim MS, Elbasani E, Kim JD, Oh TJ. Prediction of trehalose-metabolic pathway and comparative analysis of KEGG, MetaCyc, and RAST databases based on complete genome of Variovorax sp. PAMC28711. BMC Genom Data 2022; 23:4. [PMID: 34991451 PMCID: PMC8734048 DOI: 10.1186/s12863-021-01020-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 12/17/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Metabolism including anabolism and catabolism is a prerequisite phenomenon for all living organisms. Anabolism refers to the synthesis of the entire compound needed by a species. Catabolism refers to the breakdown of molecules to obtain energy. Many metabolic pathways are undisclosed and many organism-specific enzymes involved in metabolism are misplaced. When predicting a specific metabolic pathway of a microorganism, the first and foremost steps is to explore available online databases. Among many online databases, KEGG and MetaCyc pathway databases were used to deduce trehalose metabolic network for bacteria Variovorax sp. PAMC28711. Trehalose, a disaccharide, is used by the microorganism as an alternative carbon source. RESULTS While using KEGG and MetaCyc databases, we found that the KEGG pathway database had one missing enzyme (maltooligosyl-trehalose synthase, EC 5.4.99.15). The MetaCyc pathway database also had some enzymes. However, when we used RAST to annotate the entire genome of Variovorax sp. PAMC28711, we found that all enzymes that were missing in KEGG and MetaCyc databases were involved in the trehalose metabolic pathway. CONCLUSIONS Findings of this study shed light on bioinformatics tools and raise awareness among researchers about the importance of conducting detailed investigation before proceeding with any further work. While such comparison for databases such as KEGG and MetaCyc has been done before, it has never been done with a specific microbial pathway. Such studies are useful for future improvement of bioinformatics tools to reduce limitations.
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Affiliation(s)
- Prasansah Shrestha
- Department of Life Science and Biochemical Engineering, Graduate School, Sun Moon University, Asan, 31460 Korea
| | - Min-Su Kim
- Department of Life Science and Biochemical Engineering, Graduate School, Sun Moon University, Asan, 31460 Korea
| | - Ermal Elbasani
- Department of Computer Science and Engineering, Sun Moon University, Asan, 31460 Korea
| | - Jeong-Dong Kim
- Department of Computer Science and Engineering, Sun Moon University, Asan, 31460 Korea
- Genome-based BioIT Convergence Institute, Asan, 31460 Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, Sun Moon University, Asan, 31460 Korea
- Genome-based BioIT Convergence Institute, Asan, 31460 Korea
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460 Korea
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Fu J, Zhang Y, Liu J, Lian X, Tang J, Zhu F. Pharmacometabonomics: data processing and statistical analysis. Brief Bioinform 2021; 22:6236068. [PMID: 33866355 DOI: 10.1093/bib/bbab138] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/09/2021] [Accepted: 03/23/2021] [Indexed: 12/14/2022] Open
Abstract
Individual variations in drug efficacy, side effects and adverse drug reactions are still challenging that cannot be ignored in drug research and development. The aim of pharmacometabonomics is to better understand the pharmacokinetic properties of drugs and monitor the drug effects on specific metabolic pathways. Here, we systematically reviewed the recent technological advances in pharmacometabonomics for better understanding the pathophysiological mechanisms of diseases as well as the metabolic effects of drugs on bodies. First, the advantages and disadvantages of all mainstream analytical techniques were compared. Second, many data processing strategies including filtering, missing value imputation, quality control-based correction, transformation, normalization together with the methods implemented in each step were discussed. Third, various feature selection and feature extraction algorithms commonly applied in pharmacometabonomics were described. Finally, the databases that facilitate current pharmacometabonomics were collected and discussed. All in all, this review provided guidance for researchers engaged in pharmacometabonomics and metabolomics, and it would promote the wide application of metabolomics in drug research and personalized medicine.
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Affiliation(s)
- Jianbo Fu
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Ying Zhang
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Jin Liu
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Xichen Lian
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Jing Tang
- Department of Bioinformatics in Chongqing Medical University, China
| | - Feng Zhu
- College of Pharmaceutical Sciences in Zhejiang University, China
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Hanspers K, Riutta A, Summer-Kutmon M, Pico AR. Pathway information extracted from 25 years of pathway figures. Genome Biol 2020; 21:273. [PMID: 33168034 PMCID: PMC7649569 DOI: 10.1186/s13059-020-02181-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/16/2020] [Indexed: 12/16/2022] Open
Abstract
Thousands of pathway diagrams are published each year as static figures inaccessible to computational queries and analyses. Using a combination of machine learning, optical character recognition, and manual curation, we identified 64,643 pathway figures published between 1995 and 2019 and extracted 1,112,551 instances of human genes, comprising 13,464 unique NCBI genes, participating in a wide variety of biological processes. This collection represents an order of magnitude more genes than found in the text of the same papers, and thousands of genes missing from other pathway databases, thus presenting new opportunities for discovery and research.
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Affiliation(s)
- Kristina Hanspers
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA USA
| | - Anders Riutta
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA USA
| | - Martina Summer-Kutmon
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Alexander R. Pico
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA USA
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13
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Schultz A, Akbani R. SAMMI: a semi-automated tool for the visualization of metabolic networks. Bioinformatics 2020; 36:2616-2617. [PMID: 31851289 DOI: 10.1093/bioinformatics/btz927] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/14/2019] [Accepted: 12/16/2019] [Indexed: 01/26/2023] Open
Abstract
SUMMARY Here we present a browser-based Semi-Automated Metabolic Map Illustrator (SAMMI) for the visualization of metabolic networks. While automated features allow for easy network partitioning, navigation, and node positioning, SAMMI also offers a wide array of manual map editing features. This combination allows for fast, context-specific visualization of metabolic networks as well as the development of standardized, large-scale, visually appealing maps. The implementation of SAMMI with popular constraint-based modeling toolboxes also allows for effortless visualization of simulation results of genome-scale metabolic models. AVAILABILITY AND IMPLEMENTATION SAMMI has been implemented as a standalone web-based tool and as plug-ins for the COBRA and COBRApy toolboxes. SAMMI and its COBRA plugins are available under the GPL 3.0 license and are available along with documentation, tutorials, and source code at www.SammiTool.com. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Andre Schultz
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rehan Akbani
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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14
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Lane AN, Higashi RM, Fan TWM. NMR and MS-based Stable Isotope-Resolved Metabolomics and Applications in Cancer Metabolism. Trends Analyt Chem 2018; 120. [PMID: 32523238 DOI: 10.1016/j.trac.2018.11.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
There is considerable interest in defining metabolic reprogramming in human diseases, which is recognized as a hallmark of human cancer. Although radiotracers have a long history in specific metabolic studies, stable isotope-enriched precursors coupled with modern high resolution mass spectrometry and NMR spectroscopy have enabled systematic mapping of metabolic networks and fluxes in cells, tissues and living organisms including humans. These analytical platforms are high in information content, are complementary and cross-validating in terms of compound identification, quantification, and isotope labeling pattern analysis of a large number of metabolites simultaneously. Furthermore, new developments in chemoselective derivatization and in vivo spectroscopy enable tracking of labile/low abundance metabolites and metabolic kinetics in real-time. Here we review developments in Stable Isotope Resolved Metabolomics (SIRM) and recent applications in cancer metabolism using a wide variety of stable isotope tracers that probe both broad and specific aspects of cancer metabolism required for proliferation and survival.
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Affiliation(s)
- Andrew N Lane
- Center for Environmental and Systems Biochemistry, Dept. Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536 USA
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry, Dept. Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536 USA
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, Dept. Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536 USA
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15
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Foerster H, Bombarely A, Battey JND, Sierro N, Ivanov NV, Mueller LA. SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases. Database (Oxford) 2018; 2018:4995113. [PMID: 29762652 PMCID: PMC5946812 DOI: 10.1093/database/bay035] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 03/13/2018] [Accepted: 03/15/2018] [Indexed: 01/20/2023]
Abstract
Database URL https://solgenomics.net/tools/solcyc/.
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Affiliation(s)
- Hartmut Foerster
- Boyce Thompson Institute, 533 Tower Road, Ithaca, New York, 14853-1801, USA
| | - Aureliano Bombarely
- Department of Horticulture, Virginia Polytechnic Institute and State University, 220 Ag Quad Lane, Blacksburg, VA 24061, USA
| | - James N D Battey
- PMI R&D, Philip Morris Products S.A (Part of Philip Morris International group of companies), Quai Jeanrenaud 6, Neuchâtel CH-2000, Switzerland
| | - Nicolas Sierro
- PMI R&D, Philip Morris Products S.A (Part of Philip Morris International group of companies), Quai Jeanrenaud 6, Neuchâtel CH-2000, Switzerland
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A (Part of Philip Morris International group of companies), Quai Jeanrenaud 6, Neuchâtel CH-2000, Switzerland
| | - Lukas A Mueller
- Boyce Thompson Institute, 533 Tower Road, Ithaca, New York, 14853-1801, USA
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16
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Abd Algfoor Z, Shahrizal Sunar M, Abdullah A, Kolivand H. Identification of metabolic pathways using pathfinding approaches: a systematic review. Brief Funct Genomics 2017; 16:87-98. [PMID: 26969656 DOI: 10.1093/bfgp/elw002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Metabolic pathways have become increasingly available for various microorganisms. Such pathways have spurred the development of a wide array of computational tools, in particular, mathematical pathfinding approaches. This article can facilitate the understanding of computational analysis of metabolic pathways in genomics. Moreover, stoichiometric and pathfinding approaches in metabolic pathway analysis are discussed. Three major types of studies are elaborated: stoichiometric identification models, pathway-based graph analysis and pathfinding approaches in cellular metabolism. Furthermore, evaluation of the outcomes of the pathways with mathematical benchmarking metrics is provided. This review would lead to better comprehension of metabolism behaviors in living cells, in terms of computed pathfinding approaches.
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Affiliation(s)
- Zeyad Abd Algfoor
- MaGIC-X (Media and Games Innovation Centre of Excellence), UTM-IRDA Digital Media Centre, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | - Mohd Shahrizal Sunar
- MaGIC-X (Media and Games Innovation Centre of Excellence), UTM-IRDA Digital Media Centre, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | - Afnizanfaizal Abdullah
- Boston University School of Medicine, Boston Medical Center, Boston, MA, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA.,Global Health Program, Duke Kunshan University, Jiangsu, China
| | - Hoshang Kolivand
- Department of Computer Science, Liverpool John Moores University, Liverpool, UK
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17
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Guasch-Ferré M, Bhupathiraju SN, Hu FB. Use of Metabolomics in Improving Assessment of Dietary Intake. Clin Chem 2017; 64:82-98. [PMID: 29038146 DOI: 10.1373/clinchem.2017.272344] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 09/07/2017] [Indexed: 01/23/2023]
Abstract
BACKGROUND Nutritional metabolomics is rapidly evolving to integrate nutrition with complex metabolomics data to discover new biomarkers of nutritional exposure and status. CONTENT The purpose of this review is to provide a broad overview of the measurement techniques, study designs, and statistical approaches used in nutrition metabolomics, as well as to describe the current knowledge from epidemiologic studies identifying metabolite profiles associated with the intake of individual nutrients, foods, and dietary patterns. SUMMARY A wide range of technologies, databases, and computational tools are available to integrate nutritional metabolomics with dietary and phenotypic information. Biomarkers identified with the use of high-throughput metabolomics techniques include amino acids, acylcarnitines, carbohydrates, bile acids, purine and pyrimidine metabolites, and lipid classes. The most extensively studied food groups include fruits, vegetables, meat, fish, bread, whole grain cereals, nuts, wine, coffee, tea, cocoa, and chocolate. We identified 16 studies that evaluated metabolite signatures associated with dietary patterns. Dietary patterns examined included vegetarian and lactovegetarian diets, omnivorous diet, Western dietary patterns, prudent dietary patterns, Nordic diet, and Mediterranean diet. Although many metabolite biomarkers of individual foods and dietary patterns have been identified, those biomarkers may not be sensitive or specific to dietary intakes. Some biomarkers represent short-term intakes rather than long-term dietary habits. Nonetheless, nutritional metabolomics holds promise for the development of a robust and unbiased strategy for measuring diet. Still, this technology is intended to be complementary, rather than a replacement, to traditional well-validated dietary assessment methods such as food frequency questionnaires that can measure usual diet, the most relevant exposure in nutritional epidemiologic studies.
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Affiliation(s)
- Marta Guasch-Ferré
- Department of Nutrition, Harvard TH Chan School of Public Health, Boston, MA
| | - Shilpa N Bhupathiraju
- Department of Nutrition, Harvard TH Chan School of Public Health, Boston, MA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Frank B Hu
- Department of Nutrition, Harvard TH Chan School of Public Health, Boston, MA; .,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA.,Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA
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18
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Metabolomics: Definitions and Significance in Systems Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 965:3-17. [DOI: 10.1007/978-3-319-47656-8_1] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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19
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Baa-Puyoulet P, Parisot N, Febvay G, Huerta-Cepas J, Vellozo AF, Gabaldón T, Calevro F, Charles H, Colella S. ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw081. [PMID: 27242037 PMCID: PMC5630938 DOI: 10.1093/database/baw081] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 04/25/2016] [Indexed: 01/25/2023]
Abstract
Arthropods interact with humans at different levels with highly beneficial roles (e.g. as pollinators), as well as with a negative impact for example as vectors of human or animal diseases, or as agricultural pests. Several arthropod genomes are available at present and many others will be sequenced in the near future in the context of the i5K initiative, offering opportunities for reconstructing, modelling and comparing their metabolic networks. In-depth analysis of these genomic data through metabolism reconstruction is expected to contribute to a better understanding of the biology of arthropods, thereby allowing the development of new strategies to control harmful species. In this context, we present here ArthropodaCyc, a dedicated BioCyc collection of databases using the Cyc annotation database system (CycADS), allowing researchers to perform reliable metabolism comparisons of fully sequenced arthropods genomes. Since the annotation quality is a key factor when performing such global genome comparisons, all proteins from the genomes included in the ArthropodaCyc database were re-annotated using several annotation tools and orthology information. All functional/domain annotation results and their sources were integrated in the databases for user access. Currently, ArthropodaCyc offers a centralized repository of metabolic pathways, protein sequence domains, Gene Ontology annotations as well as evolutionary information for 28 arthropod species. Such database collection allows metabolism analysis both with integrated tools and through extraction of data in formats suitable for systems biology studies. Database URL:http://arthropodacyc.cycadsys.org/
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Affiliation(s)
| | - Nicolas Parisot
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Gérard Febvay
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Jaime Huerta-Cepas
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Augusto F Vellozo
- Univ Lyon, Univ Lyon1, CNRS, LBBE, UMR5558, F-69622, Villeurbanne, France
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Federica Calevro
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Hubert Charles
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Stefano Colella
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
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20
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Kim W, Park H, Seo S. Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome. PLoS One 2016; 11:e0150974. [PMID: 26992093 PMCID: PMC4798299 DOI: 10.1371/journal.pone.0150974] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/22/2016] [Indexed: 11/23/2022] Open
Abstract
The sequence of cattle genome provided a valuable opportunity to systematically link genetic and metabolic traits of cattle. The objectives of this study were 1) to reconstruct genome-scale cattle-specific metabolic pathways based on the most recent and updated cattle genome build and 2) to identify duplicated metabolic genes in the cattle genome for better understanding of metabolic adaptations in cattle. A bioinformatic pipeline of an organism for amalgamating genomic annotations from multiple sources was updated. Using this, an amalgamated cattle genome database based on UMD_3.1, was created. The amalgamated cattle genome database is composed of a total of 33,292 genes: 19,123 consensus genes between NCBI and Ensembl databases, 8,410 and 5,493 genes only found in NCBI or Ensembl, respectively, and 266 genes from NCBI scaffolds. A metabolic reconstruction of the cattle genome and cattle pathway genome database (PGDB) was also developed using Pathway Tools, followed by an intensive manual curation. The manual curation filled or revised 68 pathway holes, deleted 36 metabolic pathways, and added 23 metabolic pathways. Consequently, the curated cattle PGDB contains 304 metabolic pathways, 2,460 reactions including 2,371 enzymatic reactions, and 4,012 enzymes. Furthermore, this study identified eight duplicated genes in 12 metabolic pathways in the cattle genome compared to human and mouse. Some of these duplicated genes are related with specific hormone biosynthesis and detoxifications. The updated genome-scale metabolic reconstruction is a useful tool for understanding biology and metabolic characteristics in cattle. There has been significant improvements in the quality of cattle genome annotations and the MetaCyc database. The duplicated metabolic genes in the cattle genome compared to human and mouse implies evolutionary changes in the cattle genome and provides a useful information for further research on understanding metabolic adaptations of cattle.
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Affiliation(s)
- Woonsu Kim
- Department of Animal Biosystem Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Hyesun Park
- Department of Animal Biosystem Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Seongwon Seo
- Department of Animal Biosystem Sciences, Chungnam National University, Daejeon, Republic of Korea
- * E-mail:
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21
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Hényková E, Vránová HP, Amakorová P, Pospíšil T, Žukauskaitė A, Vlčková M, Urbánek L, Novák O, Mareš J, Kaňovský P, Strnad M. Stable isotope dilution ultra-high performance liquid chromatography-tandem mass spectrometry quantitative profiling of tryptophan-related neuroactive substances in human serum and cerebrospinal fluid. J Chromatogr A 2016; 1437:145-157. [PMID: 26879452 DOI: 10.1016/j.chroma.2016.02.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 01/29/2016] [Accepted: 02/02/2016] [Indexed: 10/22/2022]
Abstract
Many compounds related to L-tryptophan (L-TRP) have interesting biological or pharmacological activity, and their abnormal neurotransmission seems to be linked to a wide range of neurodegenerative and psychiatric diseases. A high-throughput method based on ultra-high performance liquid chromatography connected to electrospray tandem mass spectrometry (UHPLC-ESI-MS/MS) was developed for the quantitative analysis of L-TRP and 16 of its metabolites in human serum and cerebrospinal fluid (CSF), representing both major and minor routes of L-TRP catabolism. The combination of a fast LC gradient with selective tandem mass spectrometry enabled accurate analysis of almost 100 samples in 24h. The standard isotope dilution method was used for quantitative determination. The method's lower limits of quantification for serum and cerebrospinal fluid ranged from 0.05 to 15nmol/L and 0.3 to 45nmol/L, respectively. Analytical recoveries ranged from 10.4 to 218.1% for serum and 22.1 to 370.0% for CSF. The method's accuracy ranged from 82.4 to 128.5% for serum matrix and 90.7 to 127.7% for CSF matrix. All intra- and inter-day coefficients of variation were below 15%. These results demonstrate that the new method is capable of quantifying endogenous serum and CSF levels of a heterogeneous group of compounds spanning a wide range of concentrations. The method was used to determine the physiological levels of target analytes in serum and CSF samples from 18 individuals, demonstrating its reliability and potential usefulness in large-scale epidemiological studies.
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Affiliation(s)
- Eva Hényková
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science of Palacký University & Institute of Experimental Botany CAS, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic
| | - Hana Přikrylová Vránová
- Department of Neurology, University Hospital in Olomouc, I. P. Pavlova 6, CZ-775 20 Olomouc, Czech Republic
| | - Petra Amakorová
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science of Palacký University & Institute of Experimental Botany CAS, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic
| | - Tomáš Pospíšil
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science of Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic
| | - Asta Žukauskaitė
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science of Palacký University & Institute of Experimental Botany CAS, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic; Department of Biology, Faculty of Medicine and Dentistry, Palacký University, Hněvotínská 3, CZ-775 15 Olomouc, Czech Republic
| | - Magdaléna Vlčková
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science of Palacký University & Institute of Experimental Botany CAS, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic
| | - Lubor Urbánek
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science of Palacký University & Institute of Experimental Botany CAS, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science of Palacký University & Institute of Experimental Botany CAS, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic.
| | - Jan Mareš
- Department of Neurology, University Hospital in Olomouc, I. P. Pavlova 6, CZ-775 20 Olomouc, Czech Republic
| | - Petr Kaňovský
- Department of Neurology, University Hospital in Olomouc, I. P. Pavlova 6, CZ-775 20 Olomouc, Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science of Palacký University & Institute of Experimental Botany CAS, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic.
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22
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Comparative genome analysis of Oceanimonas sp. GK1, a halotolerant bacterium with considerable xenobiotics degradation potentials. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1156-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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23
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Gerard MF, Stegmayer G, Milone DH. EvoMS: An evolutionary tool to find de novo metabolic pathways. Biosystems 2015; 134:43-7. [PMID: 26092635 DOI: 10.1016/j.biosystems.2015.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 11/19/2022]
Abstract
The evolutionary metabolic synthesizer (EvoMS) is an evolutionary tool capable of finding novel metabolic pathways linking several compounds through feasible reactions. It allows system biologists to explore different alternatives for relating specific metabolites, offering the possibility of indicating the initial compound or allowing the algorithm to automatically select it. Searching process can be followed graphically through several plots of the evolutionary process. Metabolic pathways found are displayed in a web browser as directed graphs. In all cases, solutions are networks of reactions that produce linear or branched metabolic pathways which are feasible from the specified set of available compounds. Source code of EvoMS is available at http://sourceforge.net/projects/sourcesinc/files/evoms/. Subsets of reactions are provided, as well as four examples for searching metabolic pathways among several compounds. Available as a web service at http://fich.unl.edu.ar/sinc/web-demo/evoms/.
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Affiliation(s)
- Matias F Gerard
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL/CONICET, Argentina.
| | - Georgina Stegmayer
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL/CONICET, Argentina.
| | - Diego H Milone
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL/CONICET, Argentina.
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24
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Karp PD, Billington R, Holland TA, Kothari A, Krummenacker M, Weaver D, Latendresse M, Paley S. Computational Metabolomics Operations at BioCyc.org. Metabolites 2015; 5:291-310. [PMID: 26011592 PMCID: PMC4495374 DOI: 10.3390/metabo5020291] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 02/28/2015] [Accepted: 03/30/2015] [Indexed: 01/29/2023] Open
Abstract
BioCyc.org is a genome and metabolic pathway web portal covering 5500 organisms, including Homo sapiens, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli. These organism-specific databases have undergone variable degrees of curation. The EcoCyc (Escherichia coli Encyclopedia) database is the most highly curated; its contents have been derived from 27,000 publications. The MetaCyc (Metabolic Encyclopedia) database within BioCyc is a "universal" metabolic database that describes pathways, reactions, enzymes and metabolites from all domains of life. Metabolic pathways provide an organizing framework for analyzing metabolomics data, and the BioCyc website provides computational operations for metabolomics data that include metabolite search and translation of metabolite identifiers across multiple metabolite databases. The site allows researchers to store and manipulate metabolite lists using a facility called SmartTables, which supports metabolite enrichment analysis. That analysis operation identifies metabolite sets that are statistically over-represented for the substrates of specific metabolic pathways. BioCyc also enables visualization of metabolomics data on individual pathway diagrams and on the organism-specific metabolic map diagrams that are available for every BioCyc organism. Most of these operations are available both interactively and as programmatic web services.
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Affiliation(s)
- Peter D Karp
- Bioinformatics Research Group, SRI International, 333 Ravenswood Ave AE206, Menlo Park, CA 94025, USA.
| | - Richard Billington
- Bioinformatics Research Group, SRI International, 333 Ravenswood Ave AE206, Menlo Park, CA 94025, USA.
| | - Timothy A Holland
- Bioinformatics Research Group, SRI International, 333 Ravenswood Ave AE206, Menlo Park, CA 94025, USA.
| | - Anamika Kothari
- Bioinformatics Research Group, SRI International, 333 Ravenswood Ave AE206, Menlo Park, CA 94025, USA.
| | - Markus Krummenacker
- Bioinformatics Research Group, SRI International, 333 Ravenswood Ave AE206, Menlo Park, CA 94025, USA.
| | - Daniel Weaver
- Bioinformatics Research Group, SRI International, 333 Ravenswood Ave AE206, Menlo Park, CA 94025, USA.
| | - Mario Latendresse
- Bioinformatics Research Group, SRI International, 333 Ravenswood Ave AE206, Menlo Park, CA 94025, USA.
| | - Suzanne Paley
- Bioinformatics Research Group, SRI International, 333 Ravenswood Ave AE206, Menlo Park, CA 94025, USA.
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25
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Chai J, Kora G, Ahn TH, Hyatt D, Pan C. Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam. BMC Evol Biol 2014; 14:207. [PMID: 25293379 PMCID: PMC4194380 DOI: 10.1186/s12862-014-0207-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Accepted: 09/22/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Phylogenetic studies have provided detailed knowledge on the evolutionary mechanisms of genes and species in Bacteria and Archaea. However, the evolution of cellular functions, represented by metabolic pathways and biological processes, has not been systematically characterized. Many clades in the prokaryotic tree of life have now been covered by sequenced genomes in GenBank. This enables a large-scale functional phylogenomics study of many computationally inferred cellular functions across all sequenced prokaryotes. RESULTS A total of 14,727 GenBank prokaryotic genomes were re-annotated using a new protein family database, UniFam, to obtain consistent functional annotations for accurate comparison. The functional profile of a genome was represented by the biological process Gene Ontology (GO) terms in its annotation. The GO term enrichment analysis differentiated the functional profiles between selected archaeal taxa. 706 prokaryotic metabolic pathways were inferred from these genomes using Pathway Tools and MetaCyc. The consistency between the distribution of metabolic pathways in the genomes and the phylogenetic tree of the genomes was measured using parsimony scores and retention indices. The ancestral functional profiles at the internal nodes of the phylogenetic tree were reconstructed to track the gains and losses of metabolic pathways in evolutionary history. CONCLUSIONS Our functional phylogenomics analysis shows divergent functional profiles of taxa and clades. Such function-phylogeny correlation stems from a set of clade-specific cellular functions with low parsimony scores. On the other hand, many cellular functions are sparsely dispersed across many clades with high parsimony scores. These different types of cellular functions have distinct evolutionary patterns reconstructed from the prokaryotic tree.
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Affiliation(s)
- Juanjuan Chai
- />Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Guruprasad Kora
- />Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Tae-Hyuk Ahn
- />Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Doug Hyatt
- />BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- />Joint Institute for Biological Sciences, University of Tennessee, Knoxville TN, USA
| | - Chongle Pan
- />Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- />BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
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Simons M, Saha R, Guillard L, Clément G, Armengaud P, Cañas R, Maranas CD, Lea PJ, Hirel B. Nitrogen-use efficiency in maize (Zea mays L.): from 'omics' studies to metabolic modelling. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5657-71. [PMID: 24863438 DOI: 10.1093/jxb/eru227] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In this review, we will present the latest developments in systems biology with particular emphasis on improving nitrogen-use efficiency (NUE) in crops such as maize and demonstrating the application of metabolic models. The review highlights the importance of improving NUE in crops and provides an overview of the transcriptome, proteome, and metabolome datasets available, focusing on a comprehensive understanding of nitrogen regulation. 'Omics' data are hard to interpret in the absence of metabolic flux information within genome-scale models. These models, when integrated with 'omics' data, can serve as a basis for generating predictions that focus and guide further experimental studies. By simulating different nitrogen (N) conditions at a pseudo-steady state, the reactions affecting NUE and additional gene regulations can be determined. Such models thus provide a framework for improving our understanding of the metabolic processes underlying the more efficient use of N-based fertilizers.
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Affiliation(s)
- Margaret Simons
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Rajib Saha
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lenaïg Guillard
- Adaptation des Plantes à leur Environnement, Unité Mixte de Recherche 1318, INRA-Agro-ParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, RD 10, 78026 Versailles cedex, France
| | - Gilles Clément
- Plateau Technique Spécifique de Chimie du Végétal, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, Unité Mixte de Recherche 1318, INRA-Agro-ParisTech, Route de St Cyr, F-78026 Versailles Cedex, France
| | - Patrick Armengaud
- Adaptation des Plantes à leur Environnement, Unité Mixte de Recherche 1318, INRA-Agro-ParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, RD 10, 78026 Versailles cedex, France
| | - Rafael Cañas
- Adaptation des Plantes à leur Environnement, Unité Mixte de Recherche 1318, INRA-Agro-ParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, RD 10, 78026 Versailles cedex, France
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Peter J Lea
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Bertrand Hirel
- Adaptation des Plantes à leur Environnement, Unité Mixte de Recherche 1318, INRA-Agro-ParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, RD 10, 78026 Versailles cedex, France
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O′Hagan S, Swainston N, Handl J, Kell DB. A 'rule of 0.5' for the metabolite-likeness of approved pharmaceutical drugs. Metabolomics 2014; 11:323-339. [PMID: 25750602 PMCID: PMC4342520 DOI: 10.1007/s11306-014-0733-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 09/08/2014] [Indexed: 12/20/2022]
Abstract
We exploit the recent availability of a community reconstruction of the human metabolic network ('Recon2') to study how close in structural terms are marketed drugs to the nearest known metabolite(s) that Recon2 contains. While other encodings using different kinds of chemical fingerprints give greater differences, we find using the 166 Public MDL Molecular Access (MACCS) keys that 90 % of marketed drugs have a Tanimoto similarity of more than 0.5 to the (structurally) 'nearest' human metabolite. This suggests a 'rule of 0.5' mnemonic for assessing the metabolite-like properties that characterise successful, marketed drugs. Multiobjective clustering leads to a similar conclusion, while artificial (synthetic) structures are seen to be less human-metabolite-like. This 'rule of 0.5' may have considerable predictive value in chemical biology and drug discovery, and may represent a powerful filter for decision making processes.
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Affiliation(s)
- Steve O′Hagan
- School of Chemistry, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
- The Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
| | - Neil Swainston
- The Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
- School of Computer Science, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
| | - Julia Handl
- Manchester Business School, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
| | - Douglas B. Kell
- School of Chemistry, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
- The Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
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Naithani S, Raja R, Waddell EN, Elser J, Gouthu S, Deluc LG, Jaiswal P. VitisCyc: a metabolic pathway knowledgebase for grapevine (Vitis vinifera). FRONTIERS IN PLANT SCIENCE 2014; 5:644. [PMID: 25538713 PMCID: PMC4260676 DOI: 10.3389/fpls.2014.00644] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Accepted: 11/01/2014] [Indexed: 05/23/2023]
Abstract
We have developed VitisCyc, a grapevine-specific metabolic pathway database that allows researchers to (i) search and browse the database for its various components such as metabolic pathways, reactions, compounds, genes and proteins, (ii) compare grapevine metabolic networks with other publicly available plant metabolic networks, and (iii) upload, visualize and analyze high-throughput data such as transcriptomes, proteomes, metabolomes etc. using OMICs-Viewer tool. VitisCyc is based on the genome sequence of the nearly homozygous genotype PN40024 of Vitis vinifera "Pinot Noir" cultivar with 12X v1 annotations and was built on BioCyc platform using Pathway Tools software and MetaCyc reference database. Furthermore, VitisCyc was enriched for plant-specific pathways and grape-specific metabolites, reactions and pathways. Currently VitisCyc harbors 68 super pathways, 362 biosynthesis pathways, 118 catabolic pathways, 5 detoxification pathways, 36 energy related pathways and 6 transport pathways, 10,908 enzymes, 2912 enzymatic reactions, 31 transport reactions and 2024 compounds. VitisCyc, as a community resource, can aid in the discovery of candidate genes and pathways that are regulated during plant growth and development, and in response to biotic and abiotic stress signals generated from a plant's immediate environment. VitisCyc version 3.18 is available online at http://pathways.cgrb.oregonstate.edu.
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Affiliation(s)
- Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
- *Correspondence: Sushma Naithani, Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR-97331, USA e-mail:
| | - Rajani Raja
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
| | - Elijah N. Waddell
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
| | | | - Laurent G. Deluc
- Department of Horticulture, Oregon State UniversityCorvallis, OR, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
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Optimal design of isotope labeling experiments. Methods Mol Biol 2013. [PMID: 24218214 DOI: 10.1007/978-1-62703-661-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Stable isotope labeling experiments (ILE) constitute a powerful methodology for estimating metabolic fluxes. An optimal label design for such an experiment is necessary to maximize the precision with which fluxes can be determined. But often, precision gained in the determination of one flux comes at the expense of the precision of other fluxes, and an appropriate label design therefore foremost depends on the question the investigator wants to address. One could liken ILE to shadows that metabolism casts on products. Optimal label design is the placement of the lamp; creating clear shadows for some parts of metabolism and obscuring others.An optimal isotope label design is influenced by: (1) the network structure; (2) the true flux values; (3) the available label measurements; and, (4) commercially available substrates. The first two aspects are dictated by nature and constrain any optimal design. The second two aspects are suitable design parameters. To create an optimal label design, an explicit optimization criterion needs to be formulated. This usually is a property of the flux covariance matrix, which can be augmented by weighting label substrate cost. An optimal design is found by using such a criterion as an objective function for an optimizer. This chapter uses a simple elementary metabolite units (EMU) representation of the TCA cycle to illustrate the process of experimental design of isotope labeled substrates.
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Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res 2013; 42:D459-71. [PMID: 24225315 PMCID: PMC3964957 DOI: 10.1093/nar/gkt1103] [Citation(s) in RCA: 792] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible database describing metabolic pathways and enzymes from all domains of life. MetaCyc pathways are experimentally determined, mostly small-molecule metabolic pathways and are curated from the primary scientific literature. MetaCyc contains >2100 pathways derived from >37 000 publications, and is the largest curated collection of metabolic pathways currently available. BioCyc (BioCyc.org) is a collection of >3000 organism-specific Pathway/Genome Databases (PGDBs), each containing the full genome and predicted metabolic network of one organism, including metabolites, enzymes, reactions, metabolic pathways, predicted operons, transport systems and pathway-hole fillers. Additions to BioCyc over the past 2 years include YeastCyc, a PGDB for Saccharomyces cerevisiae, and 891 new genomes from the Human Microbiome Project. The BioCyc Web site offers a variety of tools for querying and analysis of PGDBs, including Omics Viewers and tools for comparative analysis. New developments include atom mappings in reactions, a new representation of glycan degradation pathways, improved compound structure display, better coverage of enzyme kinetic data, enhancements of the Web Groups functionality, improvements to the Omics viewers, a new representation of the Enzyme Commission system and, for the desktop version of the software, the ability to save display states.
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Affiliation(s)
- Ron Caspi
- SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA, Carnegie Institution, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA and Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, New York 14853 USA
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Stobbe MD, Swertz MA, Thiele I, Rengaw T, van Kampen AHC, Moerland PD. Consensus and conflict cards for metabolic pathway databases. BMC SYSTEMS BIOLOGY 2013; 7:50. [PMID: 23803311 PMCID: PMC3703255 DOI: 10.1186/1752-0509-7-50] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 06/20/2013] [Indexed: 01/04/2023]
Abstract
Background The metabolic network of H. sapiens and many other organisms is described in multiple pathway databases. The level of agreement between these descriptions, however, has proven to be low. We can use these different descriptions to our advantage by identifying conflicting information and combining their knowledge into a single, more accurate, and more complete description. This task is, however, far from trivial. Results We introduce the concept of Consensus and Conflict Cards (C2Cards) to provide concise overviews of what the databases do or do not agree on. Each card is centered at a single gene, EC number or reaction. These three complementary perspectives make it possible to distinguish disagreements on the underlying biology of a metabolic process from differences that can be explained by different decisions on how and in what detail to represent knowledge. As a proof-of-concept, we implemented C2CardsHuman, as a web application http://www.molgenis.org/c2cards, covering five human pathway databases. Conclusions C2Cards can contribute to ongoing reconciliation efforts by simplifying the identification of consensus and conflicts between pathway databases and lowering the threshold for experts to contribute. Several case studies illustrate the potential of the C2Cards in identifying disagreements on the underlying biology of a metabolic process. The overviews may also point out controversial biological knowledge that should be subject of further research. Finally, the examples provided emphasize the importance of manual curation and the need for a broad community involvement.
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Affiliation(s)
- Miranda D Stobbe
- Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, PO Box 22700, Amsterdam 1100 DE, the Netherlands
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Altman T, Travers M, Kothari A, Caspi R, Karp PD. A systematic comparison of the MetaCyc and KEGG pathway databases. BMC Bioinformatics 2013; 14:112. [PMID: 23530693 PMCID: PMC3665663 DOI: 10.1186/1471-2105-14-112] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 03/04/2013] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The MetaCyc and KEGG projects have developed large metabolic pathway databases that are used for a variety of applications including genome analysis and metabolic engineering. We present a comparison of the compound, reaction, and pathway content of MetaCyc version 16.0 and a KEGG version downloaded on Feb-27-2012 to increase understanding of their relative sizes, their degree of overlap, and their scope. To assess their overlap, we must know the correspondences between compounds, reactions, and pathways in MetaCyc, and those in KEGG. We devoted significant effort to computational and manual matching of these entities, and we evaluated the accuracy of the correspondences. RESULTS KEGG contains 179 module pathways versus 1,846 base pathways in MetaCyc; KEGG contains 237 map pathways versus 296 super pathways in MetaCyc. KEGG pathways contain 3.3 times as many reactions on average as do MetaCyc pathways, and the databases employ different conceptualizations of metabolic pathways. KEGG contains 8,692 reactions versus 10,262 for MetaCyc. 6,174 KEGG reactions are components of KEGG pathways versus 6,348 for MetaCyc. KEGG contains 16,586 compounds versus 11,991 for MetaCyc. 6,912 KEGG compounds act as substrates in KEGG reactions versus 8,891 for MetaCyc. MetaCyc contains a broader set of database attributes than does KEGG, such as relationships from a compound to enzymes that it regulates, identification of spontaneous reactions, and the expected taxonomic range of metabolic pathways. MetaCyc contains many pathways not found in KEGG, from plants, fungi, metazoa, and actinobacteria; KEGG contains pathways not found in MetaCyc, for xenobiotic degradation, glycan metabolism, and metabolism of terpenoids and polyketides. MetaCyc contains fewer unbalanced reactions, which facilitates metabolic modeling such as using flux-balance analysis. MetaCyc includes generic reactions that may be instantiated computationally. CONCLUSIONS KEGG contains significantly more compounds than does MetaCyc, whereas MetaCyc contains significantly more reactions and pathways than does KEGG, in particular KEGG modules are quite incomplete. The number of reactions occurring in pathways in the two DBs are quite similar.
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Affiliation(s)
- Tomer Altman
- Bioinformatics Research Group, SRI International, Menlo Park, USA
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35
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Booth SC, Weljie AM, Turner RJ. Computational tools for the secondary analysis of metabolomics experiments. Comput Struct Biotechnol J 2013; 4:e201301003. [PMID: 24688685 PMCID: PMC3962093 DOI: 10.5936/csbj.201301003] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Revised: 12/17/2012] [Accepted: 12/24/2012] [Indexed: 01/30/2023] Open
Abstract
Metabolomics experiments have become commonplace in a wide variety of disciplines. By identifying and quantifying metabolites researchers can achieve a systems level understanding of metabolism. These studies produce vast swaths of data which are often only lightly interpreted due to the overwhelmingly large amount of variables that are measured. Recently, a number of computational tools have been developed which enable much deeper analysis of metabolomics data. These data have been difficult to interpret as understanding the connections between dozens of altered metabolites has often relied on the biochemical knowledge of researchers and their speculations. Modern biochemical databases provide information about the interconnectivity of metabolism which can be automatically polled using metabolomics secondary analysis tools. Starting with lists of altered metabolites, there are two main types of analysis: enrichment analysis computes which metabolic pathways have been significantly altered whereas metabolite mapping contextualizes the abundances and significances of measured metabolites into network visualizations. Many different tools have been developed for one or both of these applications. In this review the functionality and use of these software is discussed. Together these novel secondary analysis tools will enable metabolomics researchers to plumb the depths of their data and produce farther reaching biological conclusions than ever before.
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Affiliation(s)
- Sean C Booth
- Department of Biological Sciences, University of Calgary, Calgary, AB. 2500 University Dr. NW, Calgary, Alberta, T2N 1N4, Canada
| | - Aalim M Weljie
- Department of Pharmacology, University of Pennsylvania, Philadelphia, United States
| | - Raymond J Turner
- Department of Biological Sciences, University of Calgary, Calgary, AB. 2500 University Dr. NW, Calgary, Alberta, T2N 1N4, Canada
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Blais EM, Chavali AK, Papin JA. Linking genome-scale metabolic modeling and genome annotation. Methods Mol Biol 2013; 985:61-83. [PMID: 23417799 DOI: 10.1007/978-1-62703-299-5_4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genome-scale metabolic network reconstructions, assembled from annotated genomes, serve as a platform for integrating data from heterogeneous sources and generating hypotheses for further experimental validation. Implementing constraint-based modeling techniques such as flux balance analysis (FBA) on network reconstructions allows for interrogating metabolism at a systems level, which aids in identifying and rectifying gaps in knowledge. With genome sequences for various organisms from prokaryotes to eukaryotes becoming increasingly available, a significant bottleneck lies in the structural and functional annotation of these sequences. Using topologically based and biologically inspired metabolic network refinement, we can better characterize enzymatic functions present in an organism and link annotation of these functions to candidate transcripts; both steps can be experimentally validated.
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Affiliation(s)
- Edik M Blais
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
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37
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Stobbe MD, Jansen GA, Moerland PD, van Kampen AHC. Knowledge representation in metabolic pathway databases. Brief Bioinform 2012. [PMID: 23202525 DOI: 10.1093/bib/bbs060] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The accurate representation of all aspects of a metabolic network in a structured format, such that it can be used for a wide variety of computational analyses, is a challenge faced by a growing number of researchers. Analysis of five major metabolic pathway databases reveals that each database has made widely different choices to address this challenge, including how to deal with knowledge that is uncertain or missing. In concise overviews, we show how concepts such as compartments, enzymatic complexes and the direction of reactions are represented in each database. Importantly, also concepts which a database does not represent are described. Which aspects of the metabolic network need to be available in a structured format and to what detail differs per application. For example, for in silico phenotype prediction, a detailed representation of gene-protein-reaction relations and the compartmentalization of the network is essential. Our analysis also shows that current databases are still limited in capturing all details of the biology of the metabolic network, further illustrated with a detailed analysis of three metabolic processes. Finally, we conclude that the conceptual differences between the databases, which make knowledge exchange and integration a challenge, have not been resolved, so far, by the exchange formats in which knowledge representation is standardized.
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Affiliation(s)
- Miranda D Stobbe
- Bioinformatics Laboratory, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam, the Netherlands. Tel.: ++31 20 5667096;
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Cadenas C, Marchan R, Godoy P, Reif R, von Recklinghausen I, Schöbel N. Key messages of recent publications in the field of toxicology. EXCLI JOURNAL 2012; 11:715-42. [PMID: 27350775 PMCID: PMC4920042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 11/08/2012] [Indexed: 10/26/2022]
Affiliation(s)
- C. Cadenas
- Leibniz Institut für Arbeitsforschung an der TU Dortmund, Leibniz Research Centre for Working Environment and Human Factors (IfADo), Ardeystrasse 67, 44139 Dortmund, Germany
| | - R. Marchan
- Leibniz Institut für Arbeitsforschung an der TU Dortmund, Leibniz Research Centre for Working Environment and Human Factors (IfADo), Ardeystrasse 67, 44139 Dortmund, Germany
| | - P. Godoy
- Leibniz Institut für Arbeitsforschung an der TU Dortmund, Leibniz Research Centre for Working Environment and Human Factors (IfADo), Ardeystrasse 67, 44139 Dortmund, Germany,*To whom correspondence should be addressed: P. Godoy, Leibniz Institut für Arbeitsforschung an der TU Dortmund, Leibniz Research Centre for Working Environment and Human Factors (IfADo), Ardeystrasse 67, 44139 Dortmund, Germany, E-mail:
| | - R. Reif
- Leibniz Institut für Arbeitsforschung an der TU Dortmund, Leibniz Research Centre for Working Environment and Human Factors (IfADo), Ardeystrasse 67, 44139 Dortmund, Germany
| | - I. von Recklinghausen
- Leibniz Institut für Arbeitsforschung an der TU Dortmund, Leibniz Research Centre for Working Environment and Human Factors (IfADo), Ardeystrasse 67, 44139 Dortmund, Germany
| | - N. Schöbel
- Leibniz Institut für Arbeitsforschung an der TU Dortmund, Leibniz Research Centre for Working Environment and Human Factors (IfADo), Ardeystrasse 67, 44139 Dortmund, Germany
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Stewart JD, Marchan R. Current developments in toxicology. EXCLI JOURNAL 2012; 11:692-702. [PMID: 27231472 PMCID: PMC4876666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 10/30/2012] [Indexed: 11/23/2022]
Affiliation(s)
- J. D. Stewart
- Leibniz-Institut für Arbeitsforschung an der TU Dortmund, Leibniz Research Centre for Working Environment and Human Factors (IfADo), Ardeystrasse 67, 44139 Dortmund, Germany
| | - R. Marchan
- Leibniz-Institut für Arbeitsforschung an der TU Dortmund, Leibniz Research Centre for Working Environment and Human Factors (IfADo), Ardeystrasse 67, 44139 Dortmund, Germany,*To whom correspondence should be addressed: R. Marchan, Leibniz-Institut für Arbeitsforschung an der TU Dortmund, Leibniz Research Centre for Working Environment and Human Factors (IfADo), Ardeystrasse 67, 44139 Dortmund, Germany, E-mail:
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Bolt HM, Marchan R, Hengstler JG. Nanotoxicology and oxidative stress control: cutting-edge topics in toxicology. Arch Toxicol 2012; 86:1629-35. [DOI: 10.1007/s00204-012-0953-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Abstract
Nutritional metabolomics is rapidly maturing to use small-molecule chemical profiling to support integration of diet and nutrition in complex biosystems research. These developments are critical to facilitate transition of nutritional sciences from population-based to individual-based criteria for nutritional research, assessment, and management. This review addresses progress in making these approaches manageable for nutrition research. Important concept developments concerning the exposome, predictive health, and complex pathobiology serve to emphasize the central role of diet and nutrition in integrated biosystems models of health and disease. Improved analytic tools and databases for targeted and nontargeted metabolic profiling, along with bioinformatics, pathway mapping, and computational modeling, are now used for nutrition research on diet, metabolism, microbiome, and health associations. These new developments enable metabolome-wide association studies (MWAS) and provide a foundation for nutritional metabolomics, along with genomics, epigenomics, and health phenotyping, to support the integrated models required for personalized diet and nutrition forecasting.
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Affiliation(s)
- Dean P. Jones
- Department of Medicine, Emory University, Atlanta, GA 30322 USA
| | - Youngja Park
- Department of Medicine, Emory University, Atlanta, GA 30322 USA
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Stobbe MD, Houten SM, Kampen AHC, Wanders RJA, Moerland PD. Improving the description of metabolic networks: the TCA cycle as example. FASEB J 2012; 26:3625-36. [DOI: 10.1096/fj.11-203091] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Miranda D. Stobbe
- Bioinformatics LaboratoryUniversity of AmsterdamAmsterdamThe Netherlands
- Netherlands Bioinformatics CentreNijmegenThe Netherlands
| | - Sander M. Houten
- Laboratory Genetic Metabolic DiseasesAcademic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Antoine H. C. Kampen
- Bioinformatics LaboratoryUniversity of AmsterdamAmsterdamThe Netherlands
- Biosystems Data AnalysisSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamThe Netherlands
- Netherlands Consortium for Systems BiologyUniversity of AmsterdamAmsterdamThe Netherlands
- Netherlands Bioinformatics CentreNijmegenThe Netherlands
| | - Ronald J. A. Wanders
- Laboratory Genetic Metabolic DiseasesAcademic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Perry D. Moerland
- Bioinformatics LaboratoryUniversity of AmsterdamAmsterdamThe Netherlands
- Netherlands Bioinformatics CentreNijmegenThe Netherlands
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Copeland WB, Bartley BA, Chandran D, Galdzicki M, Kim KH, Sleight SC, Maranas CD, Sauro HM. Computational tools for metabolic engineering. Metab Eng 2012; 14:270-80. [PMID: 22629572 PMCID: PMC3361690 DOI: 10.1016/j.ymben.2012.03.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A great variety of software applications are now employed in the metabolic engineering field. These applications have been created to support a wide range of experimental and analysis techniques. Computational tools are utilized throughout the metabolic engineering workflow to extract and interpret relevant information from large data sets, to present complex models in a more manageable form, and to propose efficient network design strategies. In this review, we present a number of tools that can assist in modifying and understanding cellular metabolic networks. The review covers seven areas of relevance to metabolic engineers. These include metabolic reconstruction efforts, network visualization, nucleic acid and protein engineering, metabolic flux analysis, pathway prospecting, post-structural network analysis and culture optimization. The list of available tools is extensive and we can only highlight a small, representative portion of the tools from each area.
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Affiliation(s)
- Wilbert B Copeland
- Department of Bioengineering, University of Washington, Seattle, WA 98195-5061, USA.
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Latendresse M, Krummenacker M, Trupp M, Karp PD. Construction and completion of flux balance models from pathway databases. ACTA ACUST UNITED AC 2012; 28:388-96. [PMID: 22262672 PMCID: PMC3268246 DOI: 10.1093/bioinformatics/btr681] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION Flux balance analysis (FBA) is a well-known technique for genome-scale modeling of metabolic flux. Typically, an FBA formulation requires the accurate specification of four sets: biochemical reactions, biomass metabolites, nutrients and secreted metabolites. The development of FBA models can be time consuming and tedious because of the difficulty in assembling completely accurate descriptions of these sets, and in identifying errors in the composition of these sets. For example, the presence of a single non-producible metabolite in the biomass will make the entire model infeasible. Other difficulties in FBA modeling are that model distributions, and predicted fluxes, can be cryptic and difficult to understand. RESULTS We present a multiple gap-filling method to accelerate the development of FBA models using a new tool, called MetaFlux, based on mixed integer linear programming (MILP). The method suggests corrections to the sets of reactions, biomass metabolites, nutrients and secretions. The method generates FBA models directly from Pathway/Genome Databases. Thus, FBA models developed in this framework are easily queried and visualized using the Pathway Tools software. Predicted fluxes are more easily comprehended by visualizing them on diagrams of individual metabolic pathways or of metabolic maps. MetaFlux can also remove redundant high-flux loops, solve FBA models once they are generated and model the effects of gene knockouts. MetaFlux has been validated through construction of FBA models for Escherichia coli and Homo sapiens. AVAILABILITY Pathway Tools with MetaFlux is freely available to academic users, and for a fee to commercial users. Download from: biocyc.org/download.shtml. CONTACT mario.latendresse@sri.com SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mario Latendresse
- Bioinformatics Research Group/Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA.
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Cadenas C, Marchan R. A user-friendly guide on how to obtain and accurately interpret information from metabolic databases. Arch Toxicol 2012; 85:1013-4. [PMID: 21850519 DOI: 10.1007/s00204-011-0744-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Tonon T, Eveillard D, Prigent S, Bourdon J, Potin P, Boyen C, Siegel A. Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:883-92. [PMID: 22136637 DOI: 10.1089/omi.2011.0089] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Brown algae belong to a phylogenetic lineage distantly related to land plants and animals. They are almost exclusively found in the intertidal zone, a harsh and frequently changing environment where organisms are submitted to marine and terrestrial constraints. In relation with their unique evolutionary history and their habitat, they feature several peculiarities, including at the level of their primary and secondary metabolism. The establishment of Ectocarpus siliculosus as a model organism for brown algae has represented a framework in which several omics techniques have been developed, in particular, to study the response of these organisms to abiotic stresses. With the recent publication of medium to high throughput profiling data, it is now possible to envision integrating observations at the cellular scale to apply systems biology approaches. As a first step, we propose a protocol focusing on integrating heterogeneous knowledge gained on brown algal metabolism. The resulting abstraction of the system will then help understanding how brown algae cope with changes in abiotic parameters within their unique habitat, and to decipher some of the mechanisms underlying their (1) acclimation and (2) adaptation, respectively consequences of (1) the behavior or (2) the topology of the system resulting from the integrative approach.
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Affiliation(s)
- Thierry Tonon
- UPMC Univ Paris 6 , UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680 Roscoff, France.
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Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Pujar A, Shearer AG, Travers M, Weerasinghe D, Zhang P, Karp PD. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 2011; 40:D742-53. [PMID: 22102576 PMCID: PMC3245006 DOI: 10.1093/nar/gkr1014] [Citation(s) in RCA: 430] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The MetaCyc database (http://metacyc.org/) provides a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. MetaCyc contains more than 1800 pathways derived from more than 30 000 publications, and is the largest curated collection of metabolic pathways currently available. Most reactions in MetaCyc pathways are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes and literature citations. BioCyc (http://biocyc.org/) is a collection of more than 1700 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism. The network, which is predicted by the Pathway Tools software using MetaCyc as a reference database, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs contain additional features, including predicted operons, transport systems and pathway-hole fillers. The BioCyc website and Pathway Tools software offer many tools for querying and analysis of PGDBs, including Omics Viewers and comparative analysis. New developments include a zoomable web interface for diagrams; flux-balance analysis model generation from PGDBs; web services; and a new tool called Web Groups.
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Affiliation(s)
- Ron Caspi
- SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA, USA
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