Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z

Pereira, Bruno; Miguel, Joana; Vilaça, Paulo; Soares, Simão; Rocha, Isabel; Carneiro, Sônia Maria Marchiorato

doi:10.1186/s12918-018-0585-7

Cited by 26 publications

(23 citation statements)

References 72 publications

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“…Since 2015, tenths of high-quality GSMM were reconstructed using merlin and at least 11 were published (30)(31)(32)(33)(34)(35)(36). A list of models completely developed in merlin is provided in Table S2.3 (Supplementary material).…”

Section: Validationmentioning

confidence: 99%

merlinv4.0: an updated platform for the reconstruction of high-quality genome-scale metabolic models

Capela

Lagoa

Rodrigues

et al. 2021

Preprint

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Genome-scale metabolic models have been recognized as useful tools for better understanding living organism's metabolism. Merlin (https://merlin-sysbio.org/) is an open-source and user-friendly resource that hastens these models' reconstruction process, conjugating manual, and automatic procedures, while leveraging user's expertise with a curation-oriented graphical interface. An updated and redesigned version of merlin is herein presented. Since 2015, several features were implemented in merlin, along with profound changes in the software architecture, operating 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 led to an increase in the user-base, resulting in multiple published works including genome metabolic (re-)annotation and model reconstruction of multiple (lower and higher) eukaryotes and prokaryotes.

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Section: Validationmentioning

confidence: 99%

merlinv4.0: an updated platform for the reconstruction of high-quality genome-scale metabolic models

Capela

Lagoa

Rodrigues

et al. 2021

Preprint

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“…As far as A. succinogenes is concerned, a patent for the production of SA using this strain was registered in 1996 [19], and the first strain isolated from bovine rumen was published in 1999 [20]. [15,16], 2 [21], 3 [22], 4 [23], 5 [24], 6 [19], 7 [25], 8 [20], 9 [2], 10 [26], 11 [27], 12 [27], 13 [8], 14 [18], 15 [3], 16 [28], 17 [29], 18 [30].…”

Section: Major Randd Advancements On Sa and A Succinogenesmentioning

confidence: 99%

Insights on the Advancements of In Silico Metabolic Studies of Succinic Acid Producing Microorganisms: A Review with Emphasis on Actinobacillus succinogenes

et al. 2021

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Succinic acid (SA) is one of the top candidate value-added chemicals that can be produced from biomass via microbial fermentation. A considerable number of cell factories have been proposed in the past two decades as native as well as non-native SA producers. Actinobacillus succinogenes is among the best and earliest known natural SA producers. However, its industrial application has not yet been realized due to various underlying challenges. Previous studies revealed that the optimization of environmental conditions alone could not entirely resolve these critical problems. On the other hand, microbial in silico metabolic modeling approaches have lately been the center of attention and have been applied for the efficient production of valuable commodities including SA. Then again, literature survey results indicated the absence of up-to-date reviews assessing this issue, specifically concerning SA production. Hence, this review was designed to discuss accomplishments and future perspectives of in silico studies on the metabolic capabilities of SA producers. Herein, research progress on SA and A. succinogenes, pathways involved in SA production, metabolic models of SA-producing microorganisms, and status, limitations and prospects on in silico studies of A. succinogenes were elaborated. All in all, this review is believed to provide insights to understand the current scenario and to develop efficient mathematical models for designing robust SA-producing microbial strains.

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“…To elaborate the metabolic machinery of A. succinogenes clearly, 13 C metabolic flux analyses, flow calculation, several central carbon metabolism models, and the major biomass components models were used recently . Subsequently, several efficient expression methods like pLGZ920 plasmid and electroporation markerless knockout methods were proposed .…”

Section: Succinic Acid Production By Metabolically Engineered Strainsmentioning

confidence: 99%

Bio‐based succinic acid: an overview of strain development, substrate utilization, and downstream purification

Dai

Guo

Zhang

et al. 2019

Biofuels Bioprod Bioref

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Succinic acid is an industrially important platform chemical that could be used as precursor for the establishment of a sustainable chemical industry. Due to the depletion of crude oil and the need for sustainable development, the biological production of succinic acid from renewable resources has attracted wide attention. To establish an economical bio‐based succinic acid production process, various metabolic engineering strategies have been developed and applied to improve the strain performance, including efficient CO2 fixation, by‐product elimination, use of metabolic modeling approaches, engineering of transcriptional regulations and optimization of reducing power balance. The utilization of renewable waste resources and the optimization of purification process have also been investigated to decrease the cost. This review will provide insights for current advances in succinic acid production and perspectives on further research to make bio‐based succinic acid production more efficient and economical. © 2019 Society of Chemical Industry and John Wiley & Sons, Ltd

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Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z

Cited by 26 publications

References 72 publications

merlinv4.0: an updated platform for the reconstruction of high-quality genome-scale metabolic models

merlinv4.0: an updated platform for the reconstruction of high-quality genome-scale metabolic models

Insights on the Advancements of In Silico Metabolic Studies of Succinic Acid Producing Microorganisms: A Review with Emphasis on Actinobacillus succinogenes

Bio‐based succinic acid: an overview of strain development, substrate utilization, and downstream purification

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