Summary of Study ST003707

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002301. The data can be accessed directly via it's Project DOI: 10.21228/M86G1Z This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study ID	ST003707
Study Title	Reprogramming the metabolome of Centella asiatica (L.) Urban callus: Profiling of newly synthesized cryptic anthocyanins triggered by LED light exposure
Study Type	Plant metabolomics
Study Summary	In addition to the pentacyclic triterpenoid centelloids, Centella asiatica also synthesizes hydroxycinnamic acid conjugates as well as flavonoids. The latter is the major class of secondary plant metabolites and comprises of various subclasses, including anthocyanidins. Anthocyanins are rarely reported in extracts from C. asiatica and differ structurally due to a flavylium (2-phenylchromenylium) ion that carries a positive charge at the oxygen atom of the C-ring of the basic flavonoid structure. Callus of C. asiatica was initiated and propagated on synthetic media and subjected to different light regimes. White callus resulted from white fluorescent illumination, while purple callus developed in response to white light emitting diode (LED) illumination. In order to profile the metabolites responsible for the intense purple colouration, methanolic extracts were prepared from the two cell lines. Total phenolic, flavonoid and anthocyanin content were determined and indicated (i) very low levels of flavonoids and anthocyanins in white callus and (ii) that anthocyanins dominate the flavonoid content of the purple callus. Extracts were subjected to untargeted ultra high-performance liquid chromatography coupled to high-definition mass spectrometry to profile newly synthesised anthocyanins. Metabolite annotation was based on accurate mass determination and characteristic fragmentation patterns. We report on the reprogramming of the metabolome of white C. asiatica callus due to LED illumination and profile the cryptic anthocyanins as well as putative flavonoid and caffeoylquinic acid co-pigments in purple callus. This study will provide contribute to the knowledge this understudied class of metabolites and will bring light into the role of LED in the activation their production in vitro.
Institute	University of Johannesburg
Department	Biochemistry
Laboratory	Prof Dubery Lab
Last Name	Hamany Djande
First Name	Claude Yasmine
Address	81A Fourth Avenue Westdene
Email	claudehamany@gmail.com
Phone	0814415123
Submit Date	2025-01-22
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2025-02-24
Release Version	1

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Project:

Project ID:	PR002301
Project DOI:	doi: 10.21228/M86G1Z
Project Title:	Reprogramming the metabolome of Centella asiatica (L.) Urban callus: Profiling of newly synthesized cryptic anthocyanins triggered by LED light exposure
Project Type:	Plant metabolomics
Project Summary:	In addition to the pentacyclic triterpenoid centelloids, Centella asiatica also synthesizes hydroxycinnamic acid conjugates as well as flavonoids. The latter is the major class of secondary plant metabolites and comprises of various subclasses, including anthocyanidins. Anthocyanins are rarely reported in extracts from C. asiatica and differ structurally due to a flavylium (2-phenylchromenylium) ion that carries a positive charge at the oxygen atom of the C-ring of the basic flavonoid structure. Callus of C. asiatica was initiated and propagated on synthetic media and subjected to different light regimes. White callus resulted from white fluorescent illumination, while purple callus developed in response to white light emitting diode (LED) illumination. In order to profile the metabolites responsible for the intense purple colouration, methanolic extracts were prepared from the two cell lines. Total phenolic, flavonoid and anthocyanin content were determined and indicated (i) very low levels of flavonoids and anthocyanins in white callus and (ii) that anthocyanins dominate the flavonoid content of the purple callus. Extracts were subjected to untargeted ultra high-performance liquid chromatography coupled to high-definition mass spectrometry to profile newly synthesised anthocyanins. Metabolite annotation was based on accurate mass determination and characteristic fragmentation patterns. We report on the reprogramming of the metabolome of white C. asiatica callus due to LED illumination and profile the cryptic anthocyanins as well as putative flavonoid and caffeoylquinic acid co-pigments in purple callus.
Institute:	University of Johannesburg
Department:	Biochemistry
Laboratory:	Prof Dubery Lab
Last Name:	Hamany Djande
First Name:	Claude Yasmine
Address:	81A Fourth Avenue Westdene
Email:	claudeh@uj.ac.za
Phone:	0814415123

Subject:

Subject ID:	SU003839
Subject Type:	Cultured cells
Subject Species:	Centella asiatica
Taxonomy ID:	48106

Factors:

Subject type: Cultured cells; Subject species: Centella asiatica (Factor headings shown in green)

mb_sample_id	local_sample_id	Sample source	Callus type
SA405940	SKW Continuum #1a	Centella callus	Centella purple callus
SA405941	SKW Continuum #2a	Centella callus	Centella purple callus
SA405942	SKW Continuum #3a	Centella callus	Centella purple callus
SA405943	SKW Continuum #4a	Centella callus	Centella purple callus
SA405944	SKW Continuum #5a	Centella callus	Centella purple callus
SA405945	SKW Continuum #6a	Centella callus	Centella purple callus
SA405946	SKR Continuum #1a	Centella callus	Centella white callus
SA405947	SKR Continuum #2a	Centella callus	Centella white callus
SA405948	SKR Continuum #3a	Centella callus	Centella white callus
SA405949	SKR Continuum #4a	Centella callus	Centella white callus
SA405950	SKR Continuum #5a	Centella callus	Centella white callus
SA405951	SKR Continuum #6a	Centella callus	Centella white callus

Showing results 1 to 12 of 12

Showing results 1 to 12 of 12

Collection:

Collection ID:	CO003832
Collection Summary:	Commercially cultivated C. asiatica was obtained from a local nursery (Gauteng province, South Africa). A voucher specimen (J. James 1-JRAU) was deposited in the herbarium of the Botany Department, University of Johannesburg, South Africa. Callus from stem segments of C. asiatica plants was initiated on Murashige and Skoog (MS) medium solidified with phytoagar with Murashige and Skoog (MS) vitamins and hormones (Ducheva, Haarlem, Netherlands). The vitamins and organics were: 50 mg nicotinic acid, 50 mg thiamine HCl, 10 mg pyridoxine HCl, 10 mg myo-inositol, 0.1 g casein hydrolysate and 3 g sucrose per 100 mL). The phytohormones were 2 µM dichloro-phenoxyacetic acid (2,4-D) and 0.5 µM 6-benylaminopurine (BAP). To obtain callus proliferation, 1 g of callus was dissected from the ends of the stem segments and aseptically transferred to Petri-dishes with the medium as described above for further cultivation.
Sample Type:	Cultured cells

Treatment:

Treatment ID:	TR003848
Treatment Summary:	The cultures were kept in an incubator cabinet with white fluorescent lights (~ 20 μmol/m2/s) with a 18/6 h light/dark cycle and regulated temperature at 23°C. Callus was sub-cultured every two weeks and eventually achieved a pure white appearance. When transferred to a plant growth room with cool white LED illumination above cultivation shelves (~60 μmol/ m2/s), the edges of the calli turned a light red colour. Further selection under the LED lights of calli displaying the red colour eventually resulted in calli with a uniform, purple appearance (Fig. 1). All calli were sub-cultured on fresh media at two-week intervals.

Treatment ID:

TR003848

Treatment Summary:

The cultures were kept in an incubator cabinet with white fluorescent lights (~ 20 μmol/m2/s) with a 18/6 h light/dark cycle and regulated temperature at 23°C. Callus was sub-cultured every two weeks and eventually achieved a pure white appearance. When transferred to a plant growth room with cool white LED illumination above cultivation shelves (~60 μmol/ m2/s), the edges of the calli turned a light red colour. Further selection under the LED lights of calli displaying the red colour eventually resulted in calli with a uniform, purple appearance (Fig. 1). All calli were sub-cultured on fresh media at two-week intervals.

Sample Preparation:

Sampleprep ID:	SP003845
Sampleprep Summary:	Unless otherwise specified, all chemicals used in the research were obtained from Merck-Sigma-Aldrich, (Modderfontein, South Africa) and all solvents were analytical grade and obtained from SpS, Romil (Cambridge, UK). For phytochemical screening, metabolites were extracted based on the metabolites of interest and as described in each section. Irrespective of the purpose of the extraction, a 1:2 (w/v) ratio was used, either with analytical grade methanol or ethanol as stipulated. White and purple callus were used, two weeks following sub-culture. 1.5 g of the calli were taken and extracted into 3.0 mL (1:2 m/v) analytical grade solvent. The tissue was homogenised using an Ultra-turrax type shaft homogeniser (CAT, Berlin, Germany) for 2 min, followed by sonication in an ultrasonic bath for 15 min. The homogenates were centrifuged at 13,000 g and the supernatants transferred to 2 mL microcentrifuge tubes. Extractions were repeatedly performed as described above over a period of one year with consistent results.

Sampleprep ID:

SP003845

Sampleprep Summary:

Unless otherwise specified, all chemicals used in the research were obtained from Merck-Sigma-Aldrich, (Modderfontein, South Africa) and all solvents were analytical grade and obtained from SpS, Romil (Cambridge, UK). For phytochemical screening, metabolites were extracted based on the metabolites of interest and as described in each section. Irrespective of the purpose of the extraction, a 1:2 (w/v) ratio was used, either with analytical grade methanol or ethanol as stipulated. White and purple callus were used, two weeks following sub-culture. 1.5 g of the calli were taken and extracted into 3.0 mL (1:2 m/v) analytical grade solvent. The tissue was homogenised using an Ultra-turrax type shaft homogeniser (CAT, Berlin, Germany) for 2 min, followed by sonication in an ultrasonic bath for 15 min. The homogenates were centrifuged at 13,000 g and the supernatants transferred to 2 mL microcentrifuge tubes. Extractions were repeatedly performed as described above over a period of one year with consistent results.

Combined analysis:

Analysis ID	AN006082
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Waters Acquity
Column	Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)
MS Type	ESI
MS instrument type	QTOF
MS instrument name	Waters Synapt-XS
Ion Mode	POSITIVE
Units	Peak area

Chromatography:

Chromatography ID:	CH004618
Chromatography Summary:	For UHPLC-MS analysis, extracted samples were concentrated to half of the original volumes at 50 °C in a dry bath in a fume hood and centrifuged again at 13, 000 g for 10 min before transfer to chromatography vials, capped and stored for analysis. Samples were analysed using a Waters Acquity Premier UPLC system (Waters Corporation, Milford, MA, USA) and separation was obtained with a Waters HSS T3 C18 UPLC column (150 mm x 2.1 mm, 1.8 µm). A solvent mixture was used consisting of ultra-pure water (solvent A) and UPLC-grade acetonitrile (solvent B). Both solvents contained 10 mM formic acid. The initial conditions were 95% A for 1 min, followed by a gradient to 1% A at 16 min. These chromatographic conditions were maintained for 1 min whereafter the initial conditions were re-instated. The flow rate was kept constant at 0.4 mL/min and the column temperature maintained at 60 °C. The runtime was 20 min with injection volumes varying between 1 and 5 μL. The Waters Sample Manager temperature was maintained at 6 °C. The Flow rate was 0.4 mL/min. Gradient information: Initial %A95 %B5 1min %A95 %B5 16min %A10 %B90 16.10min %A1 %B99 17min %A1 %B99 18min %A1 %B99 18.30min %A95 %B5 20min %A95 %B5
Instrument Name:	Waters Acquity
Column Name:	Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)
Column Temperature:	60
Flow Gradient:	Initial %A95 %B5; 1min %A95 %B5; 16min %A10 %B90; 16.10min %A1 %B99; 17min %A1 %B99; 18min %A1 %B99; 18.30min %A95 %B5; 20min %A95 %B5
Flow Rate:	0.4 mL/min
Solvent A:	100% Water; 0.1% formic acid
Solvent B:	100% Acetonitrile; 0.1% formic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS005789
Analysis ID:	AN006082
Instrument Name:	Waters Synapt-XS
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	For high-definition quadrupole time-of-flight mass spectrometry (HD-qTOF) MS analysis, a Waters Synapt XS system, equipped with a 4 kDalton (Da) quadrupole, was used in sensitivity mode. Accurate mass measurements were obtained using leucine encephalin (554.2615 Da) as the ‘lockmass’ calibrant at a fixed concentration of 200 pg/mL and a constant flow rate of 5 μL/min. The instrument was used in sensitivity mode with an electrospray ionisation (ESI) interface. Analysis was done in positive ionisation mode using a capillary voltage of 0.6 kV, a sample cone voltage of 30 V and source offset of 4 V. Data was collected from 100 to 1500 Da at a scan speed of 0.1 sec. The source temperature was set at 120 °C and a desolvation temperature of 450 °C was used for all the analysis. High purity nitrogen gas was used as the nebulisation gas at a flow rate of 700 L/h and the cone gas flow rate was 50 L/h. MassLynxTM software, V4.2 SCN1028 (Waters corporation, Milford, MA, USA) was used to control the instrumentation and to collect and process all the data.
Ion Mode:	POSITIVE