Genome-scale evaluation of core one-carbon metabolism in gammaproteobacterial methanotrophs grown on methane and methanol

Nguyen, Anh Duc; Park, Joon‐Young; Hwang, In Yeub; Hamilton, Richard; Kalyuzhnaya, Marina G.; Kim, Donghyuk; Lee, Eun Yeol

doi:10.1016/j.ymben.2019.10.004

Cited by 43 publications

(41 citation statements)

References 42 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A pattern of reversed transcriptional regulation of the alternative MDH enzymes in response to hypoxia has been noted previously (19). As for other methylotrophy functions, the transcription of genes for MMO (genes 2846 to 2848) was slightly upregulated, while the transcription of most of the genes for the assimilatory ribulose monophosphate and the (partial) serine cycles (27,28) as well as of genes for formaldehyde and formate oxidation was downregulated (up to 45-fold) ( Fig. 1; Tables S1 and S2).…”

mentioning

confidence: 56%

A Complex Interplay between Nitric Oxide, Quorum Sensing, and the Unique Secondary Metabolite Tundrenone Constitutes the Hypoxia Response in Methylobacter

et al. 2020

View full text Add to dashboard Cite

Methylobacter species, members of the Methylococcales, have recently emerged as some of the globally widespread, cosmopolitan species that play a key role in the environmental consumption of methane across gradients of dioxygen tensions. In this work, we approached the question of how Methylobacter copes with hypoxia, via laboratory manipulation. Through comparative transcriptomics of cultures grown under high dioxygen partial pressure versus cultures exposed to hypoxia, we identified a gene cluster encoding a hybrid cluster protein along with sensing and regulatory functions. Through mutant analysis, we demonstrated that this gene cluster is involved in the hypoxia stress response. Through additional transcriptomic analyses, we uncovered a complex interconnection between the NO-mediated stress response, quorum sensing, the secondary metabolite tundrenone, and methanol dehydrogenase functions. This novel and complex hypoxia stress response system is so far unique to Methylobacter species, and it may play a role in the environmental fitness of these organisms and in their cosmopolitan environmental distribution. IMPORTANCE Here, we describe a novel and complex hypoxia response system in a methanotrophic bacterium that involves modules of central carbon metabolism, denitrification, quorum sensing, and a secondary metabolite, tundrenone. This intricate stress response system, so far unique to Methylobacter species, may be responsible for the persistence and activity of these species across gradients of dioxygen tensions and for the cosmopolitan distribution of these organisms in freshwater and soil environments in the Northern Hemisphere, including the fast-melting permafrosts.

show abstract

mentioning

confidence: 56%

A Complex Interplay between Nitric Oxide, Quorum Sensing, and the Unique Secondary Metabolite Tundrenone Constitutes the Hypoxia Response in Methylobacter

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Compared to methane, the growth rate of M. alcaliphilum 20Z on methanol is much higher [16]. Moreover, it was reported that Methylotuvimicrobium species could accumulate a large amount of glycogen up to 30% dry cell weight and formate when cells are grown on methanol [10,17]. Interestingly, our current study revealed that C1 assimilation pathways and energy regulatory mechanisms were regulated in a different manner for different carbon sources including methane and methanol in M. alcaliphilum 20Z [10].…”

Section: Different Transcriptional Response Of Ppi-pfk Knockout On Mementioning

confidence: 60%

“…In order to assess the metabolic role and its impact of PPi-PFK on methane and energy metabolism of M. alcaliphilum 20Z under different culture conditions, a pfk mutant strain was constructed using marker-exchange protocol [7,10]. After isolation of the pfk mutant on the selective plate, it was confirmed with Sanger sequencing and PCR [7,10]. To evaluate the physiological effect of PPi-PFK, the pfk mutant was then cultured in liquid culture using NMS medium and the growth rate of Δpfk was monitored on 2 different carbon sources, methane and methanol.…”

Section: Ppi-pfk Is Required For Efficient Methanotrophic Growth Of Mmentioning

confidence: 99%

“…Methylotuvimicrobium alcaliphilum 20Z, formerly known as Methylomicrobium alcaliphilum 20Z, is a model obligate methanotroph and it has been studied and developed to serve as an advantageous industrial biocatalyst for methane bioconversion [7][8][9]. Systems biology oriented knowledge-bases in accompany with the repositories of conventional genetic toolboxes in this model provide opportunities for a better understanding of central metabolism on different nutritional conditions for methanotrophs and further to guiding metabolic engineering strategy to produce relevant biochemical products [10].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Metabolic role of pyrophosphate-linked phosphofructokinase pfk for C1 assimilation in Methylotuvimicrobium alcaliphilum 20Z

et al. 2020

Self Cite

View full text Add to dashboard Cite

Background: Methanotrophs is a promising biocatalyst in biotechnological applications with their ability to utilize single carbon (C1) feedstock to produce high-value compounds. Understanding the behavior of biological networks of methanotrophic bacteria in different parameters is vital to systems biology and metabolic engineering. Interestingly, methanotrophic bacteria possess the pyrophosphate-dependent 6-phosphofructokinase (PPi-PFK) instead of the ATP-dependent 6-phosphofructokinase, indicating their potentials to serve as promising model for investigation the role of inorganic pyrophosphate (PPi) and PPi-dependent glycolysis in bacteria. Gene knockout experiments along with global-omics approaches can be used for studying gene functions as well as unraveling regulatory networks that rely on the gene product. Results: In this study, we performed gene knockout and RNA-seq experiments in Methylotuvimicrobium alcaliphilum 20Z to investigate the functional roles of PPi-PFK in C1 metabolism when cells were grown on methane and methanol, highlighting its metabolic importance in C1 assimilation in M. alcaliphilum 20Z. We further conducted adaptive laboratory evolution (ALE) to investigate regulatory architecture in pfk knockout strain. Whole-genome resequencing and RNA-seq approaches were performed to characterize the genetic and metabolic responses of adaptation to pfk knockout. A number of mutations, as well as gene expression profiles, were identified in pfk ALE strain to overcome insufficient C1 assimilation pathway which limits the growth in the unevolved strain. Conclusions: This study first revealed the regulatory roles of PPi-PFK on C1 metabolism and then provided novel insights into mechanism of adaptation to the loss of this major metabolic enzyme as well as an improved basis for future strain design in type I methanotrophs.

show abstract

“…Others demonstrated that the Embden Meyerhof pathway (EMP) is the main route for C1 assimilation in Methylomicrobium alcaliphilum 20Z and Methylomonas sp. LW13 [26,27].…”

Section: Introductionmentioning

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

Self Cite

View full text Add to dashboard Cite

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...

show abstract

Genome-scale evaluation of core one-carbon metabolism in gammaproteobacterial methanotrophs grown on methane and methanol

Cited by 43 publications

References 42 publications

A Complex Interplay between Nitric Oxide, Quorum Sensing, and the Unique Secondary Metabolite Tundrenone Constitutes the Hypoxia Response in Methylobacter

A Complex Interplay between Nitric Oxide, Quorum Sensing, and the Unique Secondary Metabolite Tundrenone Constitutes the Hypoxia Response in Methylobacter

Metabolic role of pyrophosphate-linked phosphofructokinase pfk for C1 assimilation in Methylotuvimicrobium alcaliphilum 20Z

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

Contact Info

Product

Resources

About