Supporting Information (Baig et al., 2014)
200
rplA
rplC
rplE
rplJ
rplL
rplN
rplQ
rplR
rpmD
rpmI
rpmJ
rpsA
rpsF
rpsG
rpsH
rpsL
rpsM
rpsN
rpsP
rpsU
A) Induced VP1GFP
150
100
50
Normalized Gene Expression
0
200
0
10
20
30
40
50
60
C) Ribosomal Subunits
150
100
50
0
0
10 20 30 40 50 60
Time Post-Induction (min)
Figure S.1: Gene expression profiles for the ribosomal subunit genes with differential gene
expression. The individual gene expression profiles are shown to demonstrate that the average
gene expression profile for these 20 genes (rplACEJLNQR, rpmDIJ, rpsAFGHLMNPU)
accurately represents the behavior of all genes in this group for a particular culture condition: A)
VP1GFP and B) GFPCAT cultures; ANOVA analysis (p ≤ 0.10) and regression analysis (p ≤
0.05) and/or by Tukey’s W comparisons (p ≤ 0.05). C) The average gene expression profiles for
all 20 differentially expressed ribosomal subunit genes. VP1GFP (, ), GFPCAT (▲, );
Uninduced (, ) and Induced (, ▲). Gene expression levels were normalized to 100, which
represents the “average” gene expression intensity on the DNA microarray. Standard error bars
are shown.
Supplement Page 1
Supporting Information (Baig et al., 2014)
Figure S.2: Gene expression profiles for the ribosomal subunit genes that did not meet
statistical significance. The average of the non-significant ribosomal subunit gene expression
profiles (rplBDFIKMOPSTUVWXY, rpmABCEFGH, rpsBCDEIJKOQRST, and sra) indicate
similar behavior between the 35 non-significant and the 20 significant ribosomal subunit genes
(rplACEJLNQR, rpmDIJ, and rpsAFGHLMNPU); ANOVA(p > 0.10), regression analysis (p >
0.05) and/or Tukey’s W comparisons (p > 0.05). VP1GFP (, ), GFPCAT (▲, ), and
ethanol-treated VP1GFP (, ). Uninduced (, , ) and Induced (, ▲, ). Gene
expression levels were normalized to 100, which represents the “average” gene expression
intensity on the DNA microarray. Standard error bars are shown.
Figure S.3: Gene expression profiles for the cofactor synthesis genes with differential gene
expression. Gene expression profiles are shown for the cofactor synthesis genes (dxs, folC,
hemL, ispEFG, and thiCMS) that were identified for increased expression due to VP1GFP
accumulation; ANOVA analysis (p ≤ 0.10) and regression analysis (p ≤ 0.05) and/or Tukey’s W
comparisons (p ≤ 0.05). VP1GFP (, ), GFPCAT (▲, ), and ethanol-treated VP1GFP (,
). Uninduced (, , ) and Induced (, ▲, ). Gene expression levels were normalized
to 100, which represents the “average” gene expression intensity on the DNA microarray.
Standard error bars are shown.
Supplement Page 2
Normalized Gene Expression
Supporting Information (Baig et al., 2014)
150
tktA
125
100
75
50
0 10 20 30 40 50 60
Time Post-Induction (min)
Figure S.4: Gene expression profiles for the pyruvate dehydrogenase complex and
transketolase genes that were not differentially expressed. Gene expression profiles are
shown for the pyruvate dehydrogenase complex (aceEF and lpd) and transketolase (tktA) genes;
ANOVA (p ≤ 0.10) and subsequent regression analysis (p ≤ 0.05) and/or Tukey’s W
comparisons (p ≤ 0.05). VP1GFP (, ), GFPCAT (▲, ), and ethanol-treated VP1GFP (,
). Uninduced (, , ) and Induced (, ▲, ). Gene expression levels were normalized
to 100, which represents the “average” gene expression intensity on the DNA microarray.
Standard error bars are shown.
Supplement Page 3
Supporting Information (Baig et al., 2014)
Figure S.5: Gene expression profiles for the TCA cycle genes that were not differentially
expressed. Gene expression profiles are shown for nine TCA cycle genes (acnA, fumA, icd, lpd,
mdh, sdhCD, and sucAD) that were not differentially expressed, but had similar profiles to the
TCA genes that were significant effected; ANOVA (p > 0.10), regression analysis (p > 0.05),
and/or Tukey’s W comparisons (p > 0.05). VP1GFP (, ), GFPCAT (▲, ), and ethanoltreated VP1GFP (, ). Uninduced (, , ) and Induced (, ▲, ). Gene expression
levels were normalized to 100, which represents the “average” gene expression intensity on the
DNA microarray. Standard error bars are shown.
Figure S.6: Gene expression profiles for the ATP synthase genes. The atpF gene was
identified by ANOVA analysis (p ≤ 0.10) and regression analysis (p ≤ 0.05). The remaining ATP
synthase genes did not meet statistical significance (atpABCDEGH); ANOVA (p > 0.10),
regression analysis (p > 0.05), and/or Tukey’s W comparisons (p > 0.05). VP1GFP (, ),
GFPCAT (▲, ), and ethanol-treated VP1GFP (, ). Uninduced (, , ) and Induced
(, ▲, ). Gene expression levels were normalized to 100, which represents the “average”
gene expression intensity on the DNA microarray. Standard error bars are shown.
Supplement Page 4
Normalized Gene Expression
Supporting Information (Baig et al., 2014)
150
Electron Transport Chain
125
100
75
50
0 10 20 30 40 50 60
Time Post-Induction (min)
Figure S.7: Gene expression profiles for the electron transport chain genes with
differential gene expression. Gene expression profiles are shown for the eight differentially
expressed electron transport chain genes (appC, dld, hyaDE, napD, narW, nuoCG); ANOVA
analysis (p ≤ 0.10) and by regression analysis (p ≤ 0.05) and/or Tukey’s W comparisons (p ≤
0.05). VP1GFP (, ), GFPCAT (▲, ), and ethanol-treated VP1GFP (, ). Uninduced
(, , ) and Induced (, ▲, ). Gene expression levels were normalized to 100, which
represents the “average” gene expression intensity on the DNA microarray. Standard error bars
are shown.
Figure S.8: Gene expression profiles for the transcription regulation genes with differential
gene expression. Gene expression profiles are shown for the ten differentially expressed
transcription regulation genes (atoS, dcuR, hcaR, lexA, lysR, nadR, rcnR, rfaH, rhaR, and sdiA)
with decreased expression in response to VP1GFP production; ANOVA analysis (p ≤ 0.10) and
by regression analysis (p ≤ 0.05) and/or Tukey’s W comparisons (p ≤ 0.05). VP1GFP (, ),
GFPCAT (▲, ), and ethanol-treated VP1GFP (, ). Uninduced (, , ) and Induced
(, ▲, ). Gene expression levels were normalized to 100, which represents the “average”
gene expression intensity on the DNA microarray. Standard error bars are shown.
Supplement Page 5
Supporting Information (Baig et al., 2014)
Figure S.9: Gene expression profiles for the transcription regulation genes with differential
gene expression. Gene expression profiles are shown for the transcription regulation genes
(kdgR, nusA, phoQ) that were observed to have increased expression due to VP1GFP production;
ANOVA analysis (p ≤ 0.10) and by regression analysis (p ≤ 0.05) and/or Tukey’s W
comparisons (p ≤ 0.05). VP1GFP (, ), GFPCAT (▲, ), and ethanol-treated VP1GFP (,
). Uninduced (, , ) and Induced (, ▲, ). Gene expression levels were normalized
to 100, which represents the “average” gene expression intensity on the DNA microarray.
Standard error bars are shown.
Supplement Page 6