Figure S1: Fatty acid composition in milk fat from transgenic and control cows.

Transcription

1 FA% Increased gene dosage for β- and κ-casein in transgenic cattle improves milk composition through complex effects Götz Laible, Grant Smolenski, Thomas Wheeler, Brigid Brophy C: C: C8: C1: C1: C1: 3 1 C1: C18: Stage of Lactation Figure S1: Fatty acid composition in milk fat from transgenic and control cows.

2 induced natural WT TG3 Figure S: Full size gels used for the two-dimensional milk protein analysis documented in Fig. 1. Cy5, Transgenic Cy3, Wild type Cy5/Cy3, Merged Figure S3: Full size gels used for the DIGE analysis of milk proteins shown in Fig. 5.

3 Table S3: First lactation milk yields of transgenic and wild type cows. Cow Sum of Milk, am Sum of Milk, pm Sum of Milk Total Days in milk Avg. daily milk TG TG TG TG TG TG TG WT WT WT WT WT WT TG, avg WT, avg P value, (TG vs. WT)

4 Table S: Summary of MS identification of individual protein spots generated by D separation of milk proteins. DIGE code Protein identification Avg. mass (Da) # peptides # unique peptides Coverage Phosphorylation αs-1 α-s-casein 19 9 Ser, Ser 158 αs- α-s-casein αs-3 α-s-casein Ser, Ser 1, Thr 155, Ser 158 Ser, Ser 1, Thr 155, Ser 158 αs- α-s-casein Ser 158 αs-5 α-s-casein Ser, Ser 158 αs- α-s-casein Ser, Ser 158 βcn-a1 β-casein (variant A1) Ser 5 βcn-a β-casein (variant A) Ser 5 β-casein (variant A3) Ser 5 βcn-a3 β-casein (variant A3) Ser 5 β-casein (variant A) Ser 5 βlg β-lactoglobulin αlac α -lactalbumin κcn-a1 κ-casein (variant A) Thr 138 κcn-a3 κ-casein (variant A) Thr 138 κcn-a κ-casein (variant A) κ-casein (variant B) κcn-b1 κ-casein (variant B) κ-casein (variant A) κcn-b κ-casein (variant B) κ-casein (variant A) κcn-b3 κ-casein (variant B) κ-casein (variant A) κcn-b κ-casein (variant B) κ-casein (variant A) κcn-b5 κ-casein (variant B) κ-casein (variant A)

5 DIGE code Protein identification Avg. mass (Da) # peptides # unique peptides Coverage (%) κcn-bx1 κ-casein (variant B) Phosphorylation site κ-casein (variant A) κcn-bx κ-casein (variant B) κ-casein (variant A) κcn-bx3 κ-casein (variant B) κ-casein (variant A) κcn-bx? κ-casein (variant B) κ-casein (variant A) 19 11

6 Table S5: Quantification of selected DIGE spots for separated isoforms of the main milk proteins and their variants in TG3 and WT milk. Protein Cy3 (WT) Cy5 (Tg) Fold change Significance Spot Abund. SE Abund. SE Cy5/Cy3 T-test* β-casein A β-casein A β-casein A3 73 de novo β-casein total κ-casein A <.1 κ-casein A κ-casein A κ-casein A κ-casein A κ-casein B de novo κ-casein B 8.9 de novo κ-casein B de novo κ-casein B 5. de novo κ-casein B5 5.3 de novo κ-casein BX? 1 3. de novo κ-casein BX de novo κ-casein BX de novo κ-casein BX3 18. de novo κ-casein, total <.1 α-s 1 casein <.1 α-s casein <.1 α-s casein α-s casein <.1 α-s casein <.1 α-s casein α-s casein <.1 α-s casein, total <.1 α-lactalbumin <.1 β-lactoglobulin * P values below.5 were considered a significant difference and are shown in bold italics. P- values were determined by paired t-test using log transformed spot abundance.

7 SUPPLEMENTARY MATERIALS AND METHODS In-gel tryptic digestion: Protein spots of interest were excised from the -DE gel with a disposable scalpel blade and destained as previously described 1. Following destaining, in-gel tryptic digestion was performed as described below: The gel pieces were dehydrated by the addition of 5 µl 1% acetonitrile and then dried under vacuum. The gel pieces were rehydrated with 1 µl.1 mg/ml modified trypsin (Promega, cat #V5111) in 5 mm ammonium bicarbonate, ph 7.8/5% acetonitrile. After min, a further 3 µl of 5 mm ammonium bicarbonate, ph 7.8/5% acetonitrile was added to cover the gel pieces and incubated at 37 C for 1 h (overnight) at 37 C. The mixtures were sonicated for 1 min, after which the supernatant was removed and kept. Peptides were then extracted with two µl washes of extraction buffer (% acetonitrile/.% formic acid) in a sonicating water bath, and then finally with µl 1% acetonitrile. The pooled peptide extracts were lyophilised with a vacuum concentrator (SpeedVac), and resuspended in 5 µl.% formic acid/% acetonitrile for mass spectrometric analysis. Reduction of disulphide bonds with dithiothreitol and alkylation with iodoacetamide was not required for -DE spots, as this process had been performed during IPG-strip equilibration. UHPLC-separation: An Ultimate 3 UHPLC system (Thermo Fisher Scientific, Waltham MA, USA) was used for the separation of the protein digests. Buffer A (.% formic acid in water) and buffer B (.% formic acid in acetonitrile) were used as mobile phases for gradient separation. For each run, 5 µl of protein digest was automatically loaded onto a Thermo Scientific Hypersil Gold C18 column (1 mm.1 mm, 1.9 μm particle size) at 3% buffer B with a flow rate of. ml/min. The column temperature was maintained at 55 C. Bound peptides were eluted by linear gradient separation as follows: 3-5% B from 1.5 to min, 5-9% B from to. min, 9% B from. to 1. min, 9-3% B from 1. to 1.5 min, and 3% B from 1.5 to 5 min. Mass spectrometry: Peptides eluted from the column were analysed in data-dependent MS/MS mode on a qexactive OrbiTrap mass spectrometer (Thermo Fisher Scientific, Dan Jose, USA) using a heated electrospray ionization (HESI-II) source for ionization in positive ion mode. The instrument parameters were as follows: the capillary temperature was set to 35 C, and the electrospray voltage was. kv. The MS instrument was operated in a top 5 data-dependent acquisition (DDA) mode to automatically switch between full-scan MS and MS/MS acquisition. Fullscan MS spectra (m/z ) were acquired in the Orbitrap with resolution 7, (at m/z ). Automatic gain control (AGC) target value was 1e counts, and the maximum injection time was 1 ms. For tandem MS spectra, the five most abundant precursor ions with charge state were fragmented in the HCD collision cell, using an isolation width of. m/z, a normalized collision energy of 3%, and a mass resolution of 17,5 (at m/z ). The ion selection threshold was 1e5 counts, and the maximum allowed ion accumulation time was 5 ms. For all analyses, the dynamic exclusion time was set to 15 s. Database searching:

8 Raw data files were imported in PEAKS Studio v7.5 (Waterloo, ON, Canada) and searched against an in-house bovine milk protein database that contained separate entries for the three β-casein and two κ-casein isoforms. Database searching parameters included up to two missed cleavages for semi-tryptic digestion, precursor ion mass tolerance 1 ppm, product ion mass tolerance.1 Da, cysteine carbamidomethylation as a fixed modification, and oxidised methionine, phosphorylated (STY) and deamidated (NQ) as variable modifications. The peptide false discovery rate was estimated by the decoy fusion method and was set at a maximum of 1%. REFERENCES: 1 Smolenski G, Haines S, Kwan FY, Bond J, Farr V, Davis SR, Stelwagen K, Wheeler TT. Characterisation of host defence proteins in milk using a proteomic approach. J. Proteome Res, 7-15, doi:1.11/pr35 (7). Zhang J, Xin L, Shan B, Chen W, Xie M, Yuen D, Zhang W, Zhang Z, Lajoie GA, Ma B. PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identification. Mol Cell Proteomics. 11, M , doi:1.17/mcp.m (1).