Systems Biology and Metabolic Modeling of C1-Metabolism

Akberdin, Ilya R.; Thompson, Merlin; Kalyuzhnaya, Marina G.

doi:10.1007/978-3-319-74866-5_7

Cited by 2 publications

(2 citation statements)

References 79 publications

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“…Besides reaching the overarching aim of genome reconstruction and inspecting carbon fluxes under different conditions, many of the GEM studies explored long-standing questions about methanotrophic metabolism, the production of various metabolites by methanotrophs, and some started to disentangle the interactions of methanotrophs with other organisms ( Table 1 ). In the forthcoming sections, we focus on these selected topics due to their relevance in the field of microbial ecology, while other reviews highlighting the usage of GEMs for methanotrophs in the field of microbial engineering have been provided elsewhere [ 43–48 ].…”

Section: Better Understanding Of Aerobic Methanotrophs Through Gemsmentioning

confidence: 99%

Leveraging genome-scale metabolic models to understand aerobic methanotrophs

Wutkowska,

Tláskal,

Bordel

et al. 2024

The ISME Journal

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Genome-scale metabolic models (GEMs) are valuable tools serving systems biology and metabolic engineering. However, GEMs are still an underestimated tool in informing microbial ecology. Since their first application for aerobic gammaproteobacterial methane oxidizers less than a decade ago, GEMs have substantially increased our understanding of the metabolism of methanotrophs, a microbial guild of high relevance for the natural and biotechnological mitigation of methane efflux to the atmosphere. Particularly, GEMs helped to elucidate critical metabolic and regulatory pathways of several methanotrophic strains, predicted microbial responses to environmental perturbations, and were used to model metabolic interactions in cocultures. Here, we conducted a systematic review of GEMs exploring aerobic methanotrophy, summarizing recent advances, pointing out weaknesses, and drawing out probable future uses of GEMs to improve our understanding of the ecology of methane oxidizers. We also focus on their potential to unravel causes and consequences when studying interactions of methane-oxidizing bacteria with other methanotrophs or members of microbial communities in general. This review aims to bridge the gap between applied sciences and microbial ecology research on methane oxidizers as model organisms and to provide an outlook for future studies.

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Section: Better Understanding Of Aerobic Methanotrophs Through Gemsmentioning

confidence: 99%

Leveraging genome-scale metabolic models to understand aerobic methanotrophs

Wutkowska,

Tláskal,

Bordel

et al. 2024

The ISME Journal

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“…This has always been considered a very unique microbial function. Over the past decade, knowledge of methane metabolism has been broadened by the help of systems biology approaches [16]. However, it also highlighted a…”

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confidence: 99%

Bioproduction of Isoprenoids and Other Secondary Metabolites Using Methanotrophic Bacteria as an Alternative Microbial Cell Factory Option: Current Stage and Future Aspects

2019

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Methane is a promising carbon feedstock for industrial biomanufacturing because of its low price and high abundance. Recent advances in metabolic engineering and systems biology in methanotrophs have made it possible to produce a variety of value-added compounds from methane, including secondary metabolites. Isoprenoids are one of the largest family of secondary metabolites and have many useful industrial applications. In this review, we highlight the current efforts invested to methanotrophs for the production of isoprenoids and other secondary metabolites, including riboflavin and ectoine. The future outlook for improving secondary metabolites production (especially of isoprenoids) using metabolic engineering of methanotrophs is also discussed. gas-to-liquid bioconversion using methanotrophs, such as limited mass transfer rates of methane, low volumetric productivity, and instability of recombinant strains [11].Secondary metabolites produced by plants and microorganisms have many useful biological activities. Among the many secondary metabolites, isoprenoids are the largest family of natural products, with more than 50,000 members identified [12][13][14]. Many isoprenoids have been used in many applications such as pharmaceuticals, nutraceuticals, fragrances, as well as the chemical industry. Additionally, due to the methyl-branched and cyclized hydrocarbon alkene structure, some isoprenoids have attracted more attention for their potential use as advanced biofuels. Plants are the major sources of isoprenoids. However, there are still many limitations for the production of high quantities of natural isoprenoids, including slow growth and tissue-specific biosynthesis, and difficulties in harvesting and extraction [12][13][14]. In contrast, a promising alternative method for isoprenoid production is the reconstruction of isoprenoid biosynthesis pathways from plants into microbes. The application of this approach has been extensively studied on model organisms like Escherichia coli or Saccharomyces cerevisiae for a variety of isoprenoids [12,14]. E. coli and S. cerevisiae are promising hosts since they possess simple genetic backgrounds, high growth rates as well as well-developed genetic tools. For example, high production of isoprenoid-based biofuels has been achieved in the metabolic engineering of microbes via endogenous or heterologous biosynthetic pathways in these hosts. However, the vast majority of these microbe-based isoprenoid production cases rely on sugar-based metabolism, which is likely to increase in the price of isoprenoids produced in large quantity.The use of alternative carbon sources is attractive in industrial biotechnology for isoprenoid production. Furthermore, different type of pathway regulation in different microbes utilizing unusual carbon substrate like methane can play a vital role in metabolic engineering of various microbes including model organisms. Thus, metabolic engineering of methane-utilizing methanotrophs has recently attracted much attention, due to not only cheaper price of...

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Systems Biology and Metabolic Modeling of C1-Metabolism

Cited by 2 publications

References 79 publications

Leveraging genome-scale metabolic models to understand aerobic methanotrophs

Leveraging genome-scale metabolic models to understand aerobic methanotrophs

Bioproduction of Isoprenoids and Other Secondary Metabolites Using Methanotrophic Bacteria as an Alternative Microbial Cell Factory Option: Current Stage and Future Aspects

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