SILEX and ECO Powder Media

Silantes SILEX and ECO media are powder media obtained from the Silantes OD2 medium.

The SILEX Powder Medium is a lyophilisate of the Silantes OD2 medium. It combines the performance of the OD2 medium with a good shelf life.

The ECO Powder Medium is also a lyophilisate of the OD2 medium, but with a higher variation in the occurrence of low molecular weight oligopeptides. This makes the performance of the ECO medium less reliable compared to the SILEX medium. The ECO powder medium is particularly suitable for validating new systems for isotope-labeled growth at low cost.

The Silantes Powder Media are available in standard pack sizes or in bulk sizes and can be provided in all ²H, ¹³C and ¹⁵N combinations.

Our webshop shows a selection of key products. Please contact customer service for the complete product list or for special requests.

Boost the performance of Minimal Media with Silantes Rich Media

Stable isotope-labeled proteins are often expressed in minimal media (or “M9” media). As minimal media contains only essential nutrients required for growth, this can result in slower growth rates and lower biomass compared to rich media, ultimately leading to lower protein yields. This problem can be solved by supplementing the M9 medium with Silantes Rich Media.

Figure 1 demonstrates that 1 % w/v SILEX Powder Medium (or corresponding 1.7 % v/v OD10 Concentrate Medium) added as a supplement to M9 medium increases the initial cell growth rate and the final optical density.

Every delivery includes a manual that provides instructions for use as both “stand-alone” and “supplement to M9”.

No Addition of ¹³C-Glucose Needed

As the raw material ¹³C-Glucose becomes more and more scarce and thus expensive, it is important to explore alternative options to these chemicals, especially for academic applications. One such alternative is the use of stable isotope-labeled complex media from Silantes: All Silantes cell growth media are prepared from uniformly labeled Cupriavidus necator bacterial cell hydrolysate. This isotopically labeled biomass is a perfect nutrient medium for bacteria and yeasts, eliminating the need for expensive ¹³C glucose if used as a stand-alone medium.

Find out more about the ¹³C-glucose price dynamics in the blog article “Why has the stable isotope price skyrocketed?”

Maximum cost efficiency

The high performance of Silantes complex media combined with the economic benefits of powder media offer you maximum cost efficiency. This excellent property also extends to cell growth under deuterated conditions:

Figure 2 shows the growth curve of E.coli in ²H-labeled Silantes OD2 Solution Medium for E.coli and in 1 % (=10g/L) Silantes SILEX Powder Medium for E.coli in D₂O. Both media have the same excellent performance in D₂O and exceed OD₆₀₀ 2.5 in less than 24 hours.

In order to evaluate the cost-effectiveness of Silantes Rich media for your project, the respective costs of a corresponding minimal medium in relation to the protein yield can be used for comparison. For the Silantes SILEX and ECO media the following applies:

• Price Silantes SILEX Medium = Price minimal medium + 15%
  > If you achieve a 15% increase in your protein yield by using the Silantes SILEX medium, you save money by using the SILEX medium.
• Price Silantes ECO Medium = Price minimum medium
  > If you achieve the same protein yield by using the Silantes ECO medium, you save money by using the ECO medium.

We have validated that expression can be increased by over 200% for a number of proteins using Silantes Rich Medium compared to Minimal Medium.

To validate Silantes Rich Media for your system, contact us for a free sample

High Standards in Quality Control

Silantes media are tested for reproducibility of the fermentation results. Moreover, each batch is adjusted to yield the same cell density. The isotopic enrichment of > 98 % is validated by mass spectrometry and the biological competence by growth tests. All test results are documented in a quality certificate, which is provided with every delivery.

Medium composition

The medium is based on a Cupriavidus necator bacterial hydrolysate. Below are the literature values for a number of components.

Component	Composition (g/g DCW) *	Source
Protein	0.680	Srinivasan et al. (2002)
Phospholipid	0.050	Gmeiner et al. (1980)
Cofactors and vitamins	0.030**	Ingraham et al., 1983
Cell wall	0.150
Cell wall (Lipopolysaccharide)	0.034	Neidhardt et al. (1996)
Cell wall (Carbohydrate)	0.055	Determined in own study
Cell wall (Peptidoglycan)	0.060 ***	Determined in own study

* DCW = Dry Cell Weight. The values are calculated for an average macromolecular composition of Cupriavidus necator H16 in MR minimal medium with D-fructose. The biomass composition was experimentally measured during the exponential growth phase of aerobic batch cultivation (specific growth rate: 0.2 h-1 average of three samples). The molecular weight of one water molecule was subtracted from the molecular weight of each molecule to account for esterification or peptide bonding.

** The assumption is based on the fact that small molecules make up less than 3 % of the dry cell weight.

*** In this study, carbohydrates made up about 5.5 % of the cell wall. The rest was assumed to be peptidoglycan.

The amino acid composition determined for OD2 medium (equivalent to 10g SILEX powder):

Amino Acid	AA [µmol / l OD2]	%
As	131.8	21.5
Thr	17.5	2.9
Ser	24.9	4.1
Glu	75.7	12.4
Gly	68.0	11.1
Ala	77.7	12.7
Val	19.2	3.1
Met	9.1	1.5
Ileu	15.5	2.5
Leu	32.9	5.4
Tyr	10.5	1.7
Phe	17.7	2.9
His	58.2	9.5
Lys	21.0	3.4
Arg	14.4	2.4
Pro	17.5	2.9
	611.7	100

Related products

Silantes also offers stable isotope labeled reagents for M9 media such as ¹³C-glucose, D₂O and ¹⁵NH₄Cl.

References

Relevant manuals:

• Expression of Stable Isotope Labeled Protein with Silantes Cell Growth Media for E.coli
• Expression of Stable Isotope Labeled Protein with Silantes Cell Growth Media for yeast

Use cases of the Silantes OD2 Medium in scientific publications:

• Mallagaray, A., Creutznacher, R., Dülfer, J., Mayer, P. H. O., Grimm, L. L., Orduña, J. M., … Peters, T. (2019). A post-translational modification of human Norovirus capsid protein attenuates glycan binding. Nature Communications, 10(1). https://doi.org/10.1038/s41467-019-09251-5
• Niesteruk, A., Jonker, H. R. A., Richter, C., Linhard, V., Sreeramulu, S., & Schwalbe, H. (2018). The domain architecture of PtkA, the first tyrosine kinase from Mycobacterium tuberculosis, differs from the conventional kinase architecture. Journal of Biological Chemistry, 293(30), 11823–11836. https://doi.org/10.1074/jbc.ra117.000120
• Pimienta, G. (2004). Structural characterization of a protein/RNA complex : human TAP/NXF1 protein/retroviral CTE RNA. Heidelberg University Library. https://doi.org/10.11588/HEIDOK.00005077
• Borland, K., Diesend, J., Ito-Kureha, T., Heissmeyer, V., Hammann, C., Buck, A. H., … Kellner, S. (2019). Production and Application of Stable Isotope-Labeled Internal Standards for RNA Modification Analysis. Genes, 10(1), 26. https://doi.org/10.3390/genes10010026

Use cases of the Silantes SILEX Powder Medium in scientific publications:

• 2H 13C 15N SILEX Medium for E.coli as substitute to M9: Movellan, K. T., Najbauer, E. E., Pratihar, S., Salvi, M., Giller, K., Becker, S., & Andreas, L. B. (2019). Alpha protons as NMR probes in deuterated proteins. Journal of Biomolecular NMR, 73(1–2), 81–91. https://doi.org/10.1007/s10858-019-00230-y
• 2H 13C 15N OD2 Medium for E.coli as substitute to M9: Botuyan, M. V. E., Nominé, Y., Yu, X., Juranic, N., Macura, S., Chen, J., & Mer, G. (2004). Structural basis of BACH1 phosphopeptide recognition by BRCA1 tandem BRCT domains. Structure, 12(7), 1137–1146. https://doi.org/10.1016/j.str.2004.06.002
• 2H 13C 15N OD2 Medium for E.coli as substitute to M9: Lingel, A., Simon, B., Izaurralde, E., & Sattler, M. (2005). The structure of the flock house virus B2 protein, a viral suppressor of RNA interference, shows a novel mode of double‐stranded RNA recognition. EMBO Reports, 6(12), 1149–1155. https://doi.org/10.1038/sj.embor.7400583

Relevant blog articles:

• Why has the stable isotope price skyrocketed?
• Stable isotope labeled rich growth media
• Applying Silantes Cell Growth Media to study Human RNA Modification Dynamics