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Capela J, Lagoa D, Rodrigues R, Cunha E, Cruz F, Barbosa A, Bastos J, Lima D, Ferreira EC, Rocha M, Dias O. merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models. Nucleic Acids Res 2022; 50:6052-6066. [PMID: 35694833 PMCID: PMC9226533 DOI: 10.1093/nar/gkac459] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/10/2022] [Indexed: 01/18/2023] Open
Abstract
Genome-scale metabolic models have been recognised as useful tools for better understanding living organisms' metabolism. merlin (https://www.merlin-sysbio.org/) is an open-source and user-friendly resource that hastens the models' reconstruction process, conjugating manual and automatic procedures, while leveraging the user's expertise with a curation-oriented graphical interface. An updated and redesigned version of merlin is herein presented. Since 2015, several features have been implemented in merlin, along with deep changes in the software architecture, operational flow, and graphical interface. The current version (4.0) includes the implementation of novel algorithms and third-party tools for genome functional annotation, draft assembly, model refinement, and curation. Such updates increased the user base, resulting in multiple published works, including genome metabolic (re-)annotations and model reconstructions of multiple (lower and higher) eukaryotes and prokaryotes. merlin version 4.0 is the only tool able to perform template based and de novo draft reconstructions, while achieving competitive performance compared to state-of-the art tools both for well and less-studied organisms.
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Affiliation(s)
- João Capela
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Davide Lagoa
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Ruben Rodrigues
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Emanuel Cunha
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Fernando Cruz
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Ana Barbosa
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - José Bastos
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Diogo Lima
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Eugénio C Ferreira
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Miguel Rocha
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Oscar Dias
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
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2
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Fedoryshchak RO, Ocasio CA, Strutton B, Mattocks J, Corran AJ, Tate EW. Wheat pathogen Zymoseptoria tritici N-myristoyltransferase inhibitors: on-target antifungal activity and an unusual metabolic defense mechanism. RSC Chem Biol 2020; 1:68-78. [PMID: 34458749 PMCID: PMC8341946 DOI: 10.1039/d0cb00020e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 04/27/2020] [Indexed: 12/15/2022] Open
Abstract
Zymoseptoria tritici is the causative agent of Septoria tritici blotch (STB), which costs billions of dollars annually to major wheat-producing countries in terms of both fungicide use and crop loss. Agricultural pathogenic fungi have acquired resistance to most commercially available fungicide classes, and the rate of discovery and development of new fungicides has stalled, demanding new approaches and insights. Here we investigate a potential mechanism of targeting an important wheat pathogen Z. tritici via inhibition of N-myristoyltransferase (NMT). We characterize Z. tritici NMT biochemically for the first time, profile the in vivo Z. tritici myristoylated proteome and identify and validate the first Z. tritici NMT inhibitors. Proteomic investigation of the downstream effects of NMT inhibition identified an unusual and novel mechanism of defense against chemical toxicity in Z. tritici through the application of comparative bioinformatics to deconvolute function from the previously largely unannotated Z. tritici proteome. Research into novel fungicidal modes-of-action is essential to satisfy an urgent unmet need for novel fungicide targets, and we anticipate that this study will serve as a useful proteomics and bioinformatics resource for researchers studying Z. tritici.
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Affiliation(s)
- Roman O Fedoryshchak
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub Wood Lane London W12 0BZ UK
- The Francis Crick Institute 1 Midland Rd London NW1 1AT UK
| | - Cory A Ocasio
- The Francis Crick Institute 1 Midland Rd London NW1 1AT UK
| | | | - Jo Mattocks
- Syngenta AG, Jealott's Hill Research Centre Bracknell UK
| | | | - Edward W Tate
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub Wood Lane London W12 0BZ UK
- The Francis Crick Institute 1 Midland Rd London NW1 1AT UK
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Díaz-Fernández D, Aguiar TQ, Martín VI, Romaní A, Silva R, Domingues L, Revuelta JL, Jiménez A. Microbial lipids from industrial wastes using xylose-utilizing Ashbya gossypii strains. BIORESOURCE TECHNOLOGY 2019; 293:122054. [PMID: 31487616 DOI: 10.1016/j.biortech.2019.122054] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 05/08/2023]
Abstract
This work presents the exploitation of waste industrial by-products as raw materials for the production of microbial lipids in engineered strains of the filamentous fungus Ashbya gossypii. A lipogenic xylose-utilizing strain was used to apply a metabolic engineering approach aiming at relieving regulatory mechanisms to further increase the biosynthesis of lipids. Three genomic manipulations were applied: the overexpression of a feedback resistant form of the acetyl-CoA carboxylase enzyme; the expression of a truncated form of Mga2, a regulator of the main Δ9 desaturase gene; and the overexpression of an additional copy of DGA1 that codes for diacylglycerol acyltransferase. The performance of the engineered strain was evaluated in culture media containing mixed formulations of corn-cob hydrolysates, sugarcane molasses or crude glycerol. Our results demonstrate the efficiency of the engineered strains, which were able to accumulate about 40% of cell dry weight (CDW) in lipid content using organic industrial wastes as feedstocks.
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Affiliation(s)
- David Díaz-Fernández
- Metabolic Engineering Group, Department of Microbiology and Genetics, University of Salamanca, Campus Miguel de Unamuno, E-37007 Salamanca, Spain
| | - Tatiana Q Aguiar
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Victoria Isabel Martín
- Metabolic Engineering Group, Department of Microbiology and Genetics, University of Salamanca, Campus Miguel de Unamuno, E-37007 Salamanca, Spain
| | - Aloia Romaní
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Rui Silva
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - José Luis Revuelta
- Metabolic Engineering Group, Department of Microbiology and Genetics, University of Salamanca, Campus Miguel de Unamuno, E-37007 Salamanca, Spain.
| | - Alberto Jiménez
- Metabolic Engineering Group, Department of Microbiology and Genetics, University of Salamanca, Campus Miguel de Unamuno, E-37007 Salamanca, Spain.
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Silva R, Aguiar TQ, Oliveira C, Domingues L. Physiological characterization of a pyrimidine auxotroph exposes link between uracil phosphoribosyltransferase regulation and riboflavin production in Ashbya gossypii. N Biotechnol 2018; 50:1-8. [PMID: 30590201 DOI: 10.1016/j.nbt.2018.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 12/21/2018] [Accepted: 12/23/2018] [Indexed: 01/13/2023]
Abstract
The blockage of the de novo pyrimidine biosynthetic pathway at the orotidine-5'-phosphate decarboxylase level was previously demonstrated to affect riboflavin production in the industrial producer fungus Ashbya gossypii. However, the molecular basis for the unusual sensitivity to uracil displayed by the pyrimidine auxotroph A. gossypii Agura3 was unknown. Here, uridine was shown to be the only intermediate of the pyrimidine salvage pathway able to fully restore this mutant's growth. Conversely, uracil, which is routinely used to rescue pyrimidine auxotrophs, had a dose-dependent growth-inhibitory effect. Uracil phosphoribosyltransferase (UPRT) is the pyrimidine salvage pathway enzyme responsible for converting uracil to uridine monophosphate in the presence of phosphoribosyl pyrophosphate (PRPP). Characterization of the A. gossypii UPRT, as produced and purified from Escherichia coli, revealed that uracil concentrations above 1 mM negatively affected its activity, thus explaining the hypersensitivity of the Agura3 mutant to uracil. Accordingly, overexpression of the AgUPRT encoding-gene in A. gossypii Agura3 led to similar growth on rich medium containing 5 mM uracil or uridine. Decreased UPRT activity ultimately favors the preservation of PRPP, which otherwise may be directed to other pathways. In A. gossypii, increased PRPP availability promotes overproduction of riboflavin. Thus, this UPRT modulation mechanism reveals a putative means of saving precursors essential for riboflavin overproduction by this fungus. A similar uracil-mediated regulation mechanism of the UPRT activity is reported only in two protozoan parasites, whose survival depends on the availability of PRPP. Physiological evidence here discussed indicate that it may be extended to other distantly related flavinogenic fungi.
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Affiliation(s)
- Rui Silva
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Tatiana Q Aguiar
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Carla Oliveira
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal.
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Cypriano DZ, da Silva LL, Tasic L. High value-added products from the orange juice industry waste. WASTE MANAGEMENT (NEW YORK, N.Y.) 2018; 79:71-78. [PMID: 30343803 DOI: 10.1016/j.wasman.2018.07.028] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 07/12/2018] [Accepted: 07/13/2018] [Indexed: 05/26/2023]
Abstract
An underutilized residue called Citrus Pulp of Floater (CPF), which causes problems during the industrial process of manufacturing of orange juice, was explored for the production of high value-added products. Mixed, first (1G) and second generation (2G) ethanol, a clean and renewable biofuel, was obtained after an enzyme cocktail isolated from the Xanthomonas axonopodis pv. citri (Xac) was applied in hydrolysis of this biomass. Then, mono- and co-culture fermentations were performed using the yeast Saccharomyces cerevisiae and two Candida strains (Candida parapsilosis IFM 48375 and NRRL Y-12969), where the last two were isolated from the orange bagasse in natura. After the enzymatic hydrolysis step, sugars obtained were converted to ethanol achieving a yield of almost 100% after co-fermentation. Hesperidin, a flavonoid widely used for its antimicrobial and/or antioxidant activities, was also extracted from CPF by liquid-solid extraction and precipitation, with the yield of 1.2% and 92.6% pure. Finally, nanocellulose was produced through processes such as extraction, bleaching and nanonization with the yield of 1.4% and over 98% of purity. These products - ethanol, hesperidin and nanocellulose were obtained from three independent processes: (1) after an enzyme-based hydrolysis of CPF, liquid part was used for ethanol production, and solid was preserved; (2) hesperidin was isolated from a dry CPF, and solid residue was preserved; and (3) nanocellulose was obtained from the solid residues after processes cited in 1 and 2.
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Affiliation(s)
- Daniela Z Cypriano
- Chemical Biology Laboratory, Institute of Chemistry, Organic Chemistry Department, State University of Campinas, P.O. Box 6154, Campinas, SP 13083-970, Brazil
| | - Lucimara Lopes da Silva
- Chemical Biology Laboratory, Institute of Chemistry, Organic Chemistry Department, State University of Campinas, P.O. Box 6154, Campinas, SP 13083-970, Brazil; Bioprocess Engineering and Biotechnology Course, Federal Technological University of Paraná - UTFPR, Estrada para Boa Esperança, Km 04, Dois Vizinhos, PR 85660-000, Brazil.
| | - Ljubica Tasic
- Chemical Biology Laboratory, Institute of Chemistry, Organic Chemistry Department, State University of Campinas, P.O. Box 6154, Campinas, SP 13083-970, Brazil.
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Methods for automated genome-scale metabolic model reconstruction. Biochem Soc Trans 2018; 46:931-936. [PMID: 30065105 DOI: 10.1042/bst20170246] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 06/04/2018] [Accepted: 06/06/2018] [Indexed: 11/17/2022]
Abstract
In the era of next-generation sequencing and ubiquitous assembly and binning of metagenomes, new putative genome sequences are being produced from isolate and microbiome samples at ever-increasing rates. Genome-scale metabolic models have enormous utility for supporting the analysis and predictive characterization of these genomes based on sequence data. As a result, tools for rapid automated reconstruction of metabolic models are becoming critically important for supporting the analysis of new genome sequences. Many tools and algorithms have now emerged to support rapid model reconstruction and analysis. Here, we are comparing and contrasting the capabilities and output of a variety of these tools, including ModelSEED, Raven Toolbox, PathwayTools, SuBliMinal Toolbox and merlin.
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Aguiar TQ, Silva R, Domingues L. New biotechnological applications for Ashbya gossypii: Challenges and perspectives. Bioengineered 2016; 8:309-315. [PMID: 27791453 DOI: 10.1080/21655979.2016.1234543] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The filamentous fungus Ashbya gossypii has long been considered a paradigm of the White Biotechnology in what concerns riboflavin production. Its industrial relevance led to the development of a significant molecular and in silico modeling toolbox for its manipulation. This, together with the increasing knowledge of its genome and metabolism has helped designing effective metabolic engineering strategies for optimizing riboflavin production, but also for developing new A. gossypii strains for novel biotechnological applications, such as production of recombinant proteins, single cell oils (SCOs), and flavour compounds. With the recent availability of its genome-scale metabolic model, the exploration of the full biotechnological potential of A. gossypii is now in the spotlight. Here, we will discuss some of the challenges that these emerging A. gossypii applications still need to overcome to become economically attractive and will present future perspectives for these and other possible biotechnological applications for A. gossypii.
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Affiliation(s)
- Tatiana Q Aguiar
- a CEB - Centre of Biological Engineering , University of Minho , Braga , Portugal
| | - Rui Silva
- a CEB - Centre of Biological Engineering , University of Minho , Braga , Portugal
| | - Lucília Domingues
- a CEB - Centre of Biological Engineering , University of Minho , Braga , Portugal
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Aguiar TQ, Silva R, Domingues L. Ashbya gossypii beyond industrial riboflavin production: A historical perspective and emerging biotechnological applications. Biotechnol Adv 2015; 33:1774-86. [DOI: 10.1016/j.biotechadv.2015.10.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 09/28/2015] [Accepted: 10/04/2015] [Indexed: 10/22/2022]
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Dias O, Rocha M, Ferreira EC, Rocha I. Reconstructing genome-scale metabolic models with merlin. Nucleic Acids Res 2015; 43:3899-910. [PMID: 25845595 PMCID: PMC4417185 DOI: 10.1093/nar/gkv294] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 03/18/2015] [Indexed: 01/13/2023] Open
Abstract
The Metabolic Models Reconstruction Using Genome-Scale Information (merlin) tool is a user-friendly Java application that aids the reconstruction of genome-scale metabolic models for any organism that has its genome sequenced. It performs the major steps of the reconstruction process, including the functional genomic annotation of the whole genome and subsequent construction of the portfolio of reactions. Moreover, merlin includes tools for the identification and annotation of genes encoding transport proteins, generating the transport reactions for those carriers. It also performs the compartmentalisation of the model, predicting the organelle localisation of the proteins encoded in the genome and thus the localisation of the metabolites involved in the reactions promoted by such enzymes. The gene-proteins-reactions (GPR) associations are automatically generated and included in the model. Finally, merlin expedites the transition from genomic data to draft metabolic models reconstructions exported in the SBML standard format, allowing the user to have a preliminary view of the biochemical network, which can be manually curated within the environment provided by merlin.
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Affiliation(s)
- Oscar Dias
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Miguel Rocha
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Eugénio C Ferreira
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Isabel Rocha
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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