Integrating metabolomics and whole genome sequencing to elucidate the metabolic pathways in Methylosinus trichosporium OB3b

Samanta, Dipayan; Singh, Ram N.; Goh, Kian Mau; Sani, Rajesh K.

doi:10.1007/s43393-023-00214-y

Cited by 2 publications

(2 citation statements)

References 73 publications

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“…At this stage, Samanta et al showed the bifurcation of the pathway in M. trichosporium OB3b, which is consistent for a few other type II methylotrophs (especially Methylocystis sp.) ( 94 – 96 ). A portion of the 2-phospho-D-glycerate is converted by phosphoglycerate mutase (2,3-diphosphoglycerate dependent) (EC 5.4.2.11) into 3-phospho-D-glycerate.…”

Section: Discussionmentioning

confidence: 99%

From genome to evolution: investigating type II methylotrophs using a pangenomic analysis

Samanta,

Rauniyar,

Saxena

et al. 2024

mSystems

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A comprehensive pangenomic approach was employed to analyze the genomes of 75 type II methylotrophs spanning various genera. Our investigation revealed 256 exact core gene families shared by all 75 organisms, emphasizing their crucial role in the survival and adaptability of these organisms. Additionally, we predicted the functionality of 12 hypothetical proteins. The analysis unveiled a diverse array of genes associated with key metabolic pathways, including methane, serine, glyoxylate, and ethylmalonyl-CoA (EMC) metabolic pathways. While all selected organisms possessed essential genes for the serine pathway, Methylooceanibacter marginalis lacked serine hydroxymethyltransferase (SHMT), and Methylobacterium variabile exhibited both isozymes of SHMT, suggesting its potential to utilize a broader range of carbon sources. Notably, Methylobrevis sp. displayed a unique serine-glyoxylate transaminase isozyme not found in other organisms. Only nine organisms featured anaplerotic enzymes (isocitrate lyase and malate synthase) for the glyoxylate pathway, with the rest following the EMC pathway. Methylovirgula sp. 4MZ18 stood out by acquiring genes from both glyoxylate and EMC pathways, and Methylocapsa sp. S129 featured an A-form malate synthase, unlike the G-form found in the remaining organisms. Our findings also revealed distinct phylogenetic relationships and clustering patterns among type II methylotrophs, leading to the proposal of a separate genus for Methylovirgula sp. 4M-Z18 and Methylocapsa sp. S129. This pangenomic study unveils remarkable metabolic diversity, unique gene characteristics, and distinct clustering patterns of type II methylotrophs, providing valuable insights for future carbon sequestration and biotechnological applications. IMPORTANCE Methylotrophs have played a significant role in methane-based product production for many years. However, a comprehensive investigation into the diverse genetic architectures across different genera of methylotrophs has been lacking. This study fills this knowledge gap by enhancing our understanding of core hypothetical proteins and unique enzymes involved in methane oxidation, serine, glyoxylate, and ethylmalonyl-CoA pathways. These findings provide a valuable reference for researchers working with other methylotrophic species. Furthermore, this study not only unveils distinctive gene characteristics and phylogenetic relationships but also suggests a reclassification for Methylovirgula sp. 4M-Z18 and Methylocapsa sp. S129 into separate genera due to their unique attributes within their respective genus. Leveraging the synergies among various methylotrophic organisms, the scientific community can potentially optimize metabolite production, increasing the yield of desired end products and overall productivity.

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Section: Discussionmentioning

confidence: 99%

From genome to evolution: investigating type II methylotrophs using a pangenomic analysis

Samanta,

Rauniyar,

Saxena

et al. 2024

mSystems

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“…trichosporium OB3b was batch-cultured in serum bottles (media-to-gas ratio was maintained at 1:1 in a total volume of 500 mL) sealed with rubber septa and aluminum caps. The medium used for growth was NMS medium that contained (for 1 L media) NaNO 3 at 11 mM, K 2 SO 4 at 0.98 mM, MgSO 4 •7H 2 O at 0.30 mM, CaCl 2 •2H 2 O at 68 µM, 1 mL of phosphate buffer solution (0.2 mM, pH 7.2), and 2 mL of trace elements solution [60]. The phosphate buffer solution consisted of Na 2 HPO 4 •12H 2 O at 200 mM and KH 2 PO A serum bottle without supplemental Cu was used as a control.…”

Section: Growth Conditionsmentioning

confidence: 99%

Genetical and Biochemical Basis of Methane Monooxygenases of Methylosinus trichosporium OB3b in Response to Copper

Samanta,

Govil,

Saxena

et al. 2024

Methane

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Over the past decade, copper (Cu) has been recognized as a crucial metal in the differential expression of soluble (sMMO) and particulate (pMMO) forms of methane monooxygenase (MMO) through a mechanism referred to as the “Cu switch”. In this study, we used Methylosinus trichosporium OB3b as a model bacterium to investigate the range of Cu concentrations that trigger the expression of sMMO to pMMO and its effect on growth and methane oxidation. The Cu switch was found to be regulated within Cu concentrations from 3 to 5 µM, with a strict increase in the methane consumption rates from 3.09 to 3.85 µM occurring on the 6th day. Our findings indicate that there was a decrease in the fold changes in the expression of methanobactin (Mbn) synthesis gene (mbnA) with a higher Cu concentration, whereas the Ton-B siderophore receptor gene (mbnT) showed upregulation at all Cu concentrations. Furthermore, the upregulation of the di-heme enzyme at concentrations above 5 µM Cu may play a crucial role in the copper switch by increasing oxygen consumption; however, the role has yet not been elucidated. We developed a quantitative assay based on the naphthalene–Molisch principle to distinguish between the sMMO- and pMMO-expressing cells, which coincided with the regulation profile of the sMMO and pMMO genes. At 0 and 3 µM Cu, the naphthol concentration was higher (8.1 and 4.2 µM, respectively) and gradually decreased to 0 µM naphthol when pMMO was expressed and acted as the sole methane oxidizer at concentrations above 5 µM Cu. Using physical protein–protein interaction, we identified seven transporters, three cell wall biosynthesis or degradation proteins, Cu resistance operon proteins, and 18 hypothetical proteins that may be involved in Cu toxicity and homeostasis. These findings shed light on the key regulatory genes of the Cu switch that will have potential implications for bioremediation and biotechnology applications.

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Integrating metabolomics and whole genome sequencing to elucidate the metabolic pathways in Methylosinus trichosporium OB3b

Cited by 2 publications

References 73 publications

From genome to evolution: investigating type II methylotrophs using a pangenomic analysis

From genome to evolution: investigating type II methylotrophs using a pangenomic analysis

Genetical and Biochemical Basis of Methane Monooxygenases of Methylosinus trichosporium OB3b in Response to Copper

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