Metabolic characterisation of<i>Magnetospirillum gryphiswaldense</i>MSR-1 using LC-MS-based metabolite profiling

Abdelrazig, Salah; Safo, Laudina; Rance, Graham A.; Fay, Michael W.; Theodosiou, Eirini; Topham, Paul D.; Kim, Dong-Hyun; Fernández-Castañé, Alfred

doi:10.1039/d0ra05326k

Cited by 52 publications

(28 citation statements)

References 46 publications

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“…Extraction was then performed by four freeze/thaw cycles (flash frozen in liquid nitrogen for 1 min, thawed on ice and vortexed for 30 s). Samples were then centrifuged at 17,000 rpm at 4°C for 10 min, transferred to pre-cooled tubes and stored at -80°C until LC-MS analysis [14].…”

Section: Metabolite Extractionmentioning

confidence: 99%

“…Global metabolite profiling offers a comprehensive measurement of small biomolecules produced in living cells, excreted metabolites from the cells into their microenvironment and taken up by the cells from a culture medium [13,14]. Especially, liquid chromatographymass spectrometry (LC-MS)-based metabolomics is a powerful analytical tool allowing the monitoring of alterations in cell metabolism and producing a rapid snapshot of the comprehensive physiological status of the cells.…”

Section: Introductionmentioning

confidence: 99%

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Osteogenic Response of Human Mesenchymal Stem Cells Analysed Using Combined Intracellular and Extracellular Metabolomic Monitoring

2021

Cell Physiol Biochem

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Background/Aims: The skeleton is a metabolically active organ undergoing continuous remodelling initiated by mesenchymal progenitors present in bone and bone marrow. Under certain pathological conditions this remodelling balance shifts towards increased resorption resulting in weaker bone microarchitecture, and there is consequently a therapeutic need to identify pathways that could inversely enhance bone formation from stem cells. Metabolomics approaches recently applied to stem cell characterisation could help identify new biochemical markers involved in osteogenic differentiation. Methods: Combined intra- and extracellular metabolite profiling was performed by liquid chromatography-mass spectrometry (LC-MS) on human mesenchymal stem cells (MSCs) undergoing osteogenic differentiation in vitro. Using a combination of univariate and multivariate analyses, changes in metabolite and nutrient concentration were monitored in cultures under osteogenic treatment over 10 days. Results: A subset of differentially detected compounds was identified in differentiating cells, suggesting a direct link to metabolic processes involved in osteogenic response. Conclusion: These results highlight new metabolite candidates as potential biomarkers to monitor stem cell differentiation towards the bone lineage.

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Section: Metabolite Extractionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Osteogenic Response of Human Mesenchymal Stem Cells Analysed Using Combined Intracellular and Extracellular Metabolomic Monitoring

2021

Cell Physiol Biochem

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“…Metabolite quantification and identification were performed by PANOMIX (Chengdu, China). Metabolites were identified using the public HMDB [ 42 ], massbank [ 43 ], LipidMaps [ 44 ], mzcloud [ 45 ], and KEGG [ 46 ] databases and the self-built database of BioNovoGene (Chengdu, Sichuan, China) ( , v1.0.0.2, accessed on 25 August 2022), with the following parameters: retention time, ppm (<30 ppm), and fragmentation model. Differentially accumulated metabolites (DAMs) were screened under the following filtering conditions: variable importance in projection (VIP) ≥ 1 and absolute log2 (fold change (FC)) ≥ 1 ( p ≤ 0.05).…”

Section: Methodsmentioning

confidence: 99%

Integrative Metabolomic and Transcriptomic Analysis Reveals the Mechanism of Specific Color Formation in Phoebe zhennan Heartwood

Yang

et al. 2022

IJMS

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Nanmu (Phoebe zhennan) is an extremely valuable tree plant that is the main source of famous “golden-thread nanmu” wood. The potential metabolites and gene regulation mechanisms involved in golden thread formation are poorly understood, even though the color change from sapwood to heartwood has been investigated in several tree plants. Here, five radial tissues from sapwood to heartwood were compared via integrative metabolomic and transcriptomic analysis to reveal the secondary metabolites and molecular mechanisms involved in golden thread formation. During heartwood formation, gradual starch grain loss is accompanied by the cell lumen deposition of lipids and color-related extractives. Extractives of 20 phenylpropanoids accumulated in heartwood, including cinnamic acids and derivatives, coumarin acid derivatives, and flavonoids, which were identified as being closely related to the golden thread. Phenylpropanoids co-occurring with abundant accumulated metabolites of prenol lipids, fatty acyls, steroids, and steroid derivatives may greatly contribute to the characteristics of golden thread formation. Additionally, the expression of nine genes whose products catalyze phenylpropanoid and flavonoids biosynthesis was upregulated in the transition zone, then accumulated and used to color the heartwood. The expression levels of transcription factors (e.g., MYB, bHLH, and WRKY) that act as the major regulatory factors in the synthesis and deposition of phenylpropanoid and flavonoids responsible for golden thread formation were also higher than in sapwood. Our results not only explain golden thread formation in nanmu, but also broaden current knowledge of special wood color formation mechanisms. This work provides a framework for future research focused on improving wood color.

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“…The metabolites were identified by accuracy mass (< 30 ppm) and MS/MS data which were matched with HMDB (Wishart et al, 2007) (http://www.hmdb. ca), massbank (Horai et al, 2010) (http://www.massbank.jp/), LipidMaps (Sud et al, 2007) (http://www.lipidmaps.org), mzclound (Abdelrazig et al, 2020) (https://www.mzcloud.org) and KEGG (Ogata et al, 1999) (http://www.genome.jp/kegg/). The robust LOESS signal correction (QC-RLSC) (Gagnebin et al, 2017) was applied for data normalization to correct for any systematic bias.…”

Section: Metabolomic Analysismentioning

confidence: 99%

Combined metabolomic and transcriptomic analysis reveals key components of OsCIPK17 overexpression improves drought tolerance in rice

Lü

Chen²,

Wang³

et al. 2023

Front. Plant Sci.

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Oryza Sativa is one of the most important food crops in China, which is easily affected by drought during its growth and development. As a member of the calcium signaling pathway, CBL-interacting protein kinase (CIPK) plays an important role in plant growth and development as well as environmental stress. However, there is no report on the function and mechanism of OsCIPK17 in rice drought resistance. We combined transcriptional and metabonomic analysis to clarify the specific mechanism of OsCIPK17 in response to rice drought tolerance. The results showed that OsCIPK17 improved drought resistance of rice by regulating deep roots under drought stress; Response to drought by regulating the energy metabolism pathway and controlling the accumulation of citric acid in the tricarboxylic acid (TCA) cycle; Our exogenous experiments also proved that OsCIPK17 responds to citric acid, and this process involves the auxin metabolism pathway; Exogenous citric acid can improve the drought resistance of overexpression plants. Our research reveals that OsCIPK17 positively regulates rice drought resistance and participates in the accumulation of citric acid in the TCA cycle, providing new insights for rice drought resistance.

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Metabolic characterisation ofMagnetospirillum gryphiswaldenseMSR-1 using LC-MS-based metabolite profiling

Abstract: Metabolic pathways in Magnetospirillum gryphiswaldense MSR-1 are significantly altered under microaerobic (O2-limited) growth conditions enabling magnetosome formation.

Cited by 52 publications

References 46 publications

Osteogenic Response of Human Mesenchymal Stem Cells Analysed Using Combined Intracellular and Extracellular Metabolomic Monitoring

Osteogenic Response of Human Mesenchymal Stem Cells Analysed Using Combined Intracellular and Extracellular Metabolomic Monitoring

Integrative Metabolomic and Transcriptomic Analysis Reveals the Mechanism of Specific Color Formation in Phoebe zhennan Heartwood

Combined metabolomic and transcriptomic analysis reveals key components of OsCIPK17 overexpression improves drought tolerance in rice

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