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1 Normalized 95% gray value interval h Supplemental Figure 1: Symptom score of root samples used in the proteomics study. For each time point, the normalized 95% gray value interval is an averaged value of three biological replicates consisting of two root slices each. Mean ± SD of 6 replicates are shown. Photographs of root slices at, 6, 12 and after harvest and slicing.
2 response to wounding phenylpropanoid biosynthetic process intracellular signaling cascade systemic acquired resistance small molecule biosynthetic process cellular aromatic compound metabolic process cell death monocarboxylic acid metabolic process lipid metabolic process response to salicylic acid stimulus response to chemical stimulus nucleoside metabolic process response to cadmium ion response to fungus sulfur metabolic process response to salt stress response to stress cellular aldehyde metabolic process toxin catabolic process flavonoid metabolic process cellular response to organic substance phenylpropanoid metabolic process defense response to fungus LG1(1/p-value) Supplemental Figure 2: Biological process categories over-represented in the proteins regulated during post-harvest physiological deterioration Category over-representation was performed with Arabidopsis identifiers and determined relative to the background set of all identified proteins for which an Arabidopsis identifier was available to take into account the bias introduced by extraction and detection methods.
3 APX activity (U mg-1 total protein) h PPD time points Supplemental Figure 3: Ascorbate peroxidase (APX) enzymatic activities in protein fractions from collected time points (3 biological replicates). Error bars represent standard deviation.
4 MDA content ( nmol g-1 FW) h PPD time points Supplemental Figure 4: Malondialdehyde (MDA) content of cassava root slices from collected time points (3 biological replicates). Error bars represent standard deviation.
5 A Ladder PAT-GPX-1 PAT-GPX-3 PAT-GPX-4 PAT-GPX-11 PAT-GPX PAT-GPX-3 Wild-type B GPX activity (Units/mg protein) Wild-Type PAT-GPX-3 PAT-GPX- 11 PAT-GPX-13 7 PAT-GPX-3 Supplemental Figure 5: Characterization of transgenic PAT-GPX cassava lines. A. Southern blot, B. GPX activity in cassava storage roots (3 biological replicates, error bars represent standard deviation)
6 A h 48 h MDA content (nmol g-1 FW) B H22 content (nmol g-1 FW) CNTRL PAT-GPX-11 CNTRL PAT-GPX-11 CNTRL PAT-GPX-11 CNTRL PAT-GPX-11 CNTRL PAT-GPX-11 CNTRL PAT-GPX-11 Supplemental Figure 6: Characterization of control and transgenic cassava storage roots during PPD. A. Malondialdehyde (MDA) content in control and transgenic PAT-GPX lines at h,,, and 48 h after harvest, B. 2 content in control and transgenic PAT-GPX lines at h,,, and 48 h after harvest. Mean ± SD of 3 biological replicates are shown.
7 Ethene biosynthesis L-methionine ATP diphosphate phosphate methionine adenosyltransferase (cassava4.1_9245m) h (p<,1; max fold change 6,8) S-adenosyl-L-methionine 5 -methylthioadenosine 1-aminocyclopropane-1-carboxylate synthase (not detected) 1-aminocyclopropane-1-carboxylate 2 L-ascorbate aminocyclopropanecarboxylate oxidase (cassava4.1_1252m) 5 2 L-dehydroascorbate hydrogen cyanide C 2 ethene h (p<,1; max fold change 41,81) Supplemental Figure 7: Detection and regulation of proteins involved in ethene biosynthesis. Means of normalized protein ± SD of 3 biological replicates are shown.
8 Scopoletin biosynthesis 4-coumarate phenylpropanoid biosynthesis ATP diphosphate AMP 4-coumarate-CoA Ligase 1 (cassava4.1_514m)* h (p<,1; max fold change 14,3) coumaroyl-coa caffeoyl-coa S-adenosyl-L-methionine S-adenosyl-L-homocysteine caffeoyl-coa -methyltransferase (cassava4.1_11832m)** h (p<,1; max fold change 5,9) feruoyl-coa 2-oxoglutarate-dependent dioxygenase (cassava4.1_3324m) h (p<,1; max fold change 8,16 6 -hydroxyferuoyl-coa scopoletin phenylpropanoid glucosyltransferase (not detected) Beta-glucosidase (detected, no significant regulation, p>.5) scopolin * 4-coumarate-CoA Ligase 2 (4CL2, cassava4.1_56m) displayed significant regulation ** 3 cassava homologs (cassava4.1_ 11832m; cassava4.1_14783m; cassava4.1_24269m) displayed signficant regulation Supplemental Figure 8: Detection and regulation of proteins involved in scopoletin biosynthesis. Means of normalized protein ± SD of 3 biological replicates are shown.
9 Phenylpropanoid biosynthesis ATP diphosphate AMP 4-coumarate coumaroyl-coa 4-coumarate-CoA Ligase 1 (cassava4.1_514m)* h (p<,1; max fold change 14,3) H+ NADPH quinate shikimate cinnamoyl-coa reductase (detected, no significant regulation, p=.13) NADP + 4-coumaroyl-CoA:quinate -(hydroxycinnamoyl) transferase (detected, no significant regulation, p=.12) 4-coumaroyl-CoA:quinate -(hydroxycinnamoyl) transferase (detected, no significant regulation, p=.12) cinnamyl-alcohol dehydrogenase (cassava4.1_1153m)** h (p<,5; max fold change 1,69) coumaraldehyde NADPH NADP + coumaryl-alcohol 4-coumaroylquinate p-coumaroyl shikimate/quinate NADPH 2 NADP + caffeoylquinate 3'-hydroxylase (cassava4.1_591m) h (p<,1; max fold change 5,45) 4-coumaroylshikimate p-coumaroyl shikimate/quinate 2 NADPH NADP + caffeoylshikimate 3'-hydroxylase (cassava4.1_591m) h (p<,1; max fold change 5,45) 4-coumaroyl-CoA:quinate -(hydroxycinnamoyl) transferase (detected, no significant regulation, p=.12) 4-coumaroyl-CoA:quinate -(hydroxycinnamoyl) transferase (detected, no significant regulation, p=.12) quinate shikimate Monolignol glucoside biosynthesis UDP-glycosyltransferase (cassava4.1_6353m) S-adenosyl-Lmethionine S-adenosyl-Lmethionine NADPH caffeoyl-coa feruloyl-coa caffeoyl-coa -methyltransferase (cassava4.1_11832m)*** h cinnamoyl-coa reductase (detected, no significant regulation, p=.13) (p<,1; max fold change 5,9) h (p<,5; max fold change 22,76) NADP + coniferaldehyde glucoside coniferin UDP UDP-D-glucose coniferyl aldehyde 2 NADPH NADP + coniferyl aldehyde 5-hydroxylase (not detected) 5-hydroxy-coniferaldehyde NADPH NADP + coniferyl alcohol cinnamyl-alcohol dehydrogenase (cassava4.1_1153m)** h (p<,5; max fold change 1,69) UDP UDP-D-glucose S-adenosyl-Lmethionine caffeate -methyltransferase (not detected) S-adenosyl-Lhomocysteine sinapaldehyde glucoside UDP UDP-D-glucose synapaldehyde NADPH NADP + cinnamyl-alcohol dehydrogenase (cassava4.1_1153m)** h syringin UDP UDP-D-glucose synapyl-alcohol (p<,5; max fold change 1,69) * 4-coumarate-CoA Ligase 2 (4CL2, cassava4.1_56m) displayed significant regulation ** 5 cassava homologs (cassava4.1_1316m, cassava4.1_1332m, cassava4.1_1333m, cassava4.1_1153m, cassava4.1_114m) displayed significant regulation *** 3 cassava homologs (cassava4.1_11832m, cassava4.1_24269m, cassava4.1_14783m) displayed significant regulation Supplemental Figure 9: Detection and regulation of proteins involved in phenylpropanoid biosynthesis Means of normalized protein ± SD of 3 biological replicates are shown.
10 PAL activity (U mg-1 total protein) 1..8 * * h 6h 12h 24h PPD time points Supplemental Figure 1: Enzymatic activities of Phenylalanine ammonia lyase (PAL) in protein fractions from collected time points. Means ± SD of 3 biological replicates are shown. (Student s t test, * p <.5)
11 Fatty acid α-oxidation fatty acid α-dioxygenase (DX1) (cassava4.1_3891m) a 2,3,4- saturated fatty acid h (p<,1; max fold change 15,9) a fatty acid a 2(R)-hydroperoxy fatty acid a 2(R)-hydroxy fatty acid NADH spontaneous aldehyde dehydrogenase (NAD+) (cassava4.1_592m) NAD + a fatty aldehyde C 2 h (p<,1; max fold change 2,46) Supplemental Figure 11: Detection and regulation of proteins involved the fatty acid α-oxidation pathway. Means of normalized protein ± SD of 3 biological replicates are shown.
12 Folate transformations II dihydrofolate reductase / thymidylate synthase (not detected) dump dtmp 7,8- dihydrofolate glycine hydroxymethyltransferase (cassava4.1_6924m) NADPH dihydrofolate reductase / thymidylate synthase (not detected) NADP + h (p<,1; max fold change 2,54) 5,1 methylene-thf tetrahydrofolate (THF) glycine L-serine NADH 5,1-methylenetetrahydrofolate reductase (cassava4.1_387m) h (p<,1; max fold change 3,1) NAD + NADH C 2 ammonia glycine NAD + glycine decarboxylase (detected, no significant regulation, p=.17) 5-methyl- THF N1-formyl- THF L-homocysteine ADP phosphate L-methionine methionine synthase (cassava4.1_2156m)* h (p<,1; max fold change 2,67) formate ATP methylenetetrahydrofolate cyclohydrolase (cassava4.1_12783m) 2 formate tetrahydrofolate ligase (detected, no significant regulation, p=.33) h (p<,5; max fold change 1,52) NADP + NADPH 5,1-methyl- THF methylenetetrahydrofolate cyclohydrolase (cassava4.1_12783m) serine hydroxymethyltransferase (not detected) ADP phosphate 5-formyltetrahydrofolate cyclo-ligase (detected, no significant regulation, p=.22) h (p<,5; max fold change 1,52) ATP N5-formyl- THF * 2 cassava homologs (cassava4.1_2156m, cassava4.1_1712m) displayed significant regulation Supplemental Figure 12: Detection and regulation of proteins involved in folate transformation II Means of normalized protein ± SD of 3 biological replicates are shown.
13 S-adenosyl-L-methionine cycle II methionine synthase (cassava4.1_2156m)** h (p<,1; max fold change 2,67) tetrahydropteroyltri- L-glutamate homomethionine biosynthesis L-methionine ATP methionine adenosyltransferase (cassava4.1_9245m)* h (p<,1; max fold change 6,8) 5-methyltetra- hydropteroyltri- L-glutamate diphosphate phosphate L-homocysteine S-adenosyl- L-methionine adenosyl homocysteinase (cassava4.1_658m)*** adenosine a fatty aldehyde a demethylated methyl acceptor a methylated methyl acceptor h (p<,1; max fold change 1,97) * 3 cassava homologs (cassava4.1_9356m, cassava4.1_9247m, cassava4.1_9245m) displayed significant regulation ** 2 cassava homologs (cassava4.1_2156m, cassava4.1_1712m) displayed significant regulation *** 2 cassava homologs (cassava4.1_658m, cassava4.1_6498m) displayed significant regulation Supplemental Figure 13: Detection and regulation of proteins involved in S-adenosyl-L-methionine (SAM) cycle II Means of normalized protein ± SD of 3 biological replicates are shown.
14 Sulfate reduction II sulfate ATP diphosphate sulfate adenylyltransferase (APS2) (cassava4.1_6467m)* h (p<,5; max fold change 76,5) adenosine 5 -phosphosulfate 2 glutathione glutathione disulfide AMP 2 adenylyl-sulfate reductase APR3 (cassava4.1_7228m) detected no significant regulation, p= a reduced ferredoxin 3 an oxidized ferredoxin 3 sulfite sulfite reductase (cassava4.1_6467m)* h (p<,1; max fold change 4,23) hydrogen sulfide * APS1 (cassava4.1_716m) was detected but not significantly regulated Supplemental Figure 14: Detection and regulation of proteins involved in sulfate reduction II. Means of normalized protein ± SD of 3 biological replicates are shown.
15 Suberin biosynthesis L-phenylalanine ammonia phenylalanine ammonia lyase 1 (cassava4.1_279m)* h (p<,1; max fold change 17,51) trans-cinnamate NADPH 2 NADP+ cinnamate 4-hydroxylase (cassava4.1_5978m) h (p<,1; max fold change 5,42) 4-coumarate 2 NADPH NADP + coumarate 3-hydroxylase (cassava4.1_591m) h (p<,1; max fold change 5,45) trans-caffeate caffeate o-methyltransferase (detected, no significant regulation, p=.8) S-adenosyl-Lmethionine S-adenosyl-Lmethionine ATP diphosphate AMP 4-coumarate-CoA Ligase 1 (cassava4.1_514m)** h (p<,1; max fold change 14,3) ferulate caffeoyl-coa 4-coumarate-CoA Ligase 1 (cassava4.1_514m)** h (p<,1; max fold change 14,3) ATP diphosphate AMP S-adenosyl-Lmethionine S-adenosyl-Lmethionine caffeoyl-coa -methyltransferase (cassava4.1_11832m)*** h (p<,1; max fold change 5,9) feruloyl-coa tyramine tyramine N-feruloyltransferase (detected, no significant regulation, p=.7) N-feruloyltyramine * 4 cassava homologs (cassava4.1_28434m, cassava4.1_279m, cassava4.1_34377m, cassava4.1_2628m) displayed significant regulation ** 4-coumarate-CoA Ligase 2 (4CL2, cassava4.1_56m) displayed significant regulation *** 3 cassava homologs (cassava4.1_11832m, cassava4.1_24269m, cassava4.1_14783m) displayed significant regulation Supplemental Figure 15: Detection and regulation of proteins involved in suberin biosynthesis. Means of normalized protein ± SD of 3 biological replicates are shown.
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