A comparative transcriptome analysis of the novel obligate methanotroph Methylomonas sp. DH-1 reveals key differences in transcriptional responses in C1 and secondary metabolite pathways during growth on methane and methanol

Abstract

BackgroundMethanotrophs play an important role in biotechnological applications, with their ability to utilize single carbon (C1) feedstock such as methane and methanol to produce a range of high-value compounds. A newly isolated obligate methanotroph strain, Methylomonas sp. DH-1, became a platform strain for biotechnological applications because it has proven capable of producing chemicals, fuels, and secondary metabolites from methane and methanol. In this study, transcriptome analysis with RNA-seq was used to investigate the transcriptional change of Methylomonas sp. DH-1 on methane and methanol. This was done to improve knowledge about C1 assimilation and secondary metabolite pathways in this promising, but under-characterized, methane-bioconversion strain.ResultsWe integrated genomic and transcriptomic analysis of the newly isolated Methylomonas sp. DH-1 grown on methane and methanol. Detailed transcriptomic analysis indicated that (i) Methylomonas sp. DH-1 possesses the ribulose monophosphate (RuMP) cycle and the Embden–Meyerhof–Parnas (EMP) pathway, which can serve as main pathways for C1 assimilation, (ii) the existence and the expression of a complete serine cycle and a complete tricarboxylic acid (TCA) cycle might contribute to methane conversion and energy production, and (iii) the highly active endogenous plasmid pDH1 may code for essential metabolic processes. Comparative transcriptomic analysis on methane and methanol as a sole carbon source revealed different transcriptional responses of Methylomonas sp. DH-1, especially in C1 assimilation, secondary metabolite pathways, and oxidative stress. Especially, these results suggest a shift of central metabolism when substrate changed from methane to methanol in which formaldehyde oxidation pathway and serine cycle carried more flux to produce acetyl-coA and NADH. Meanwhile, downregulation of TCA cycle when grown on methanol may suggest a shift of its main function is to provide de novo biosynthesis, but not produce NADH.ConclusionsThis study provides insights into the transcriptomic profile of Methylomonas sp. DH-1 grown on major carbon sources for C1 assimilation, providing in-depth knowledge on the metabolic pathways of this strain. These observations and analyses can contribute to future metabolic engineering with the newly isolated, yet under-characterized, Methylomonas sp. DH-1 to enhance its biochemical application in relevant industries.Electronic supplementary materialThe online version of this article (10.1186/s12864-019-5487-6) contains supplementary material, which is available to authorized users.

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

“…It has been found that the expression of the serine cycle was more activated on methanol and deletion of PPi-PFK showed more defects on this pathway, suggesting the operation of a functional serine cycle. In agreement with this observation, when shifting the substrate from methane to methanol, our current studies showed the activation of serine cycle on methanol-grown for energy regulation [10,16,18], while the serine cycle only carries negligible flux for growth on methane [8]. In summary, those results demonstrated the impact of pfk knockouts on the metabolic phenotype is more expressive and also showed to have a different influence on the metabolism of grown on methane and methanol.…”

“…On methane, the expression level of pmo along with xoxF showed a similar expression pattern when pfk was removed. Our previous study suggested that xoxF could contribute to the methane oxidation process in type I methanotrophs [18] by formation of an alternative structure of MDH-pMMO association with the binding of XoxF monomer to pMMO [25]. So that, pfk likely serve as regulatory effects to control this structure.…”

“…2b). When substrate shifts from methane to methanol, pmo was extremely down-regulated in wild-type because methane is one of key enhancer factors for pmo expression [18]. Not similar to that of wild-type, this effect did not occur in Δpfk whereas similar expression of pmo was observed on methane and methanol (Additional file 1: Figure S3A, B).…”

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

“…In agreement with this suggestion, our comparative transcriptome analysis of Methylomonas sp. DH-1 showed the extreme upregulation of MEP pathway encoding genes when shifting substrates from methane to methanol [38]. In addition, the pools of pyruvate and G3P, precursors for the MEP pathway, were approximately 150 and 30-fold higher than that of the acetyl-CoA pool, suggesting that the MEP pathway in methanotrophs is a suitable route to produce isoprenoid-related products [39].…”

Molecular Mechanism Associated With the Impact of Methane/Oxygen Gas Supply Ratios on Cell Growth of Methylomicrobium buryatense 5GB1 Through RNA-Seq

“…Similarly, a comparative transcriptome analysis was utilized in Methylomonas sp. DH-1 to explore the roles of secondary metabolite pathways during growth on CH 4 and methanol (Nguyen et al, 2019). However, there is no systematical research on M. buryatense 5GB1 under different CH 4 /O 2 ratios.…”