Supporting information
Supplemental Table 1: List of oligonucleotides
RND3-fw
5’-TGCAGGAATTCCTAAGGAGAGAAGAGCCAGCCAG
RND3-rev
5’-CCAGAATTCTCACATCACAGTGCAGCTCTTCG
DDX56-fw1
5’-CGGCAATTGAGCGCCATGGAGGACTCTGAAGCACTG
DD56-rev1
5’-CCGCCTGCAGGTCAGGAGGGCTTGGCTGTGGGTCTG
DDX56-fw2
5’-TGGGATCCAGCGCCATGGAGGACTCTGAAGCACTG
DDX56-rev2
5’-CCAGATATCCGAGCCTGCAGGCTTGTCATC
FAA-QC1
5’-ATCTTCTGGGTCAGCAAGTTCGCGGACTATTCGGACAAG
FAA-QC2
5’-CTTGTCCGAATAGTCCGCGAACTTGCTGACCCAGAAGAT
FAA-QC3
5’-TATGGCCTTGGGTATCAGGCGTGTGACAACAGTGTGGG
FAA-QC4
5’-CCCACACTGTTGTCACACGCCTGATACCCAAGGCCATA
Supplemental Table 2: Excel table with protein groups identified during the SILAC time
course. Contaminants, proteins identified with the concatenated reversed database, proteins that
were only identified by site and proteins that were identified with <2 peptides were removed.
Protein groups that were used for further analysis (variance <0.25) were placed in different
sheets for each time point. Identified CHIKV proteins were placed in a separate sheet.
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Supplemental Table 3: Relative protein intensity in percentages originating from CHIKV
proteins. To estimate what percentage of the total protein in infected cells was of viral origin,
the sum of the intensities of all protein groups that originated from the CHIKV nonstructural
polyprotein, structural polyprotein and total CHIKV protein was divided by the sum of all
intensities for a given biological replicate. The average of the total amount of CHIKV protein in
the 2 biological replicates at each time point is also shown. The amount of structural proteins
was about 2 to 4-fold higher than that of the of the nsPs at the various time points post infection.
8 h p.i.
10 h p.i.
12 h p.i.
replicate
1
replicate
2
replicate
1
replicate
2
replicate
1
replicate
2
Nonstructural
polyprotein
(%)
0.10
0.24
0.34
0.23
0.16
0.19
Structural
polyprotein
(%)
0.32
0.55
0.92
0.73
0.74
0.54
Total CHIKV
protein (%)
0.43
0.79
1.26
0.95
0.90
0.72
Average total
CHIKV
protein (%)
0.61
1.11
0.81
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Supplemental Table 4: Excel table with the proteins that showed significantly different
abundance during CHIKV infection. Each time point is placed in a different sheet.
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Supplemental Figure 1: Schematic overview of CHIKV genome organization and protein
expression. A) Schematic representations of CHIKV constructs used in this paper. CHIKV has a
single-stranded positive polarity RNA genome that encodes for two polyproteins. The genome is
5’capped and has a 3’poly-A tail. The CHIKV-LS3-GFP genome contains a second subgenomic
promotor from which GFP is expressed. B) Schematic overview of viral protein expression.
Upon entering the cell the CHIKV genome is directly translated by cellular ribosomes into the
nonstructural polyprotein. The RNA dependent RNA polymerase nsP4 is only expressed upon
translational readthrough of the stop codon between nsP3 and nsP4. The protease domain in nsP2
processes the polyprotein into the different subunits. The viral replication complex transcribes
minus (-) strands from the +RNA genome. These are used as templates to transcribe new CHIKV
genomes. A subgenomic promotor on the –strand is used to transcribe a subgenomic RNA that is
translated into the structural polyprotein, which is proteolytically processed into individual
subunits by the protease domain in C and host proteases. C) Schematic overview of the
accumulation of negative strand, genomic RNA, subgenomic RNA, nonstructural and structural
proteins and the release of infectious virions, during the replication of CHIKV in 293/ACE2
cells. In addition the progression of the transcriptional and translational host shut-off are shown.
Plots are based on data from Scholte et al. (RNA, viral titers, host shut-off) [1], and this paper
(protein; see panel D and Supplemental Table 3). Arrows indicate the time points that were
analyzed in our proteomics experiment. D) Western blot analysis of samples from CHIKV-LS3
infected 293/ACE2 cells showing the expression of nsP1, nsP2, nsP3, C, E1, E3-E2 and E2 from
2-12 h p.i. Mock-infected cells were included as controls to demonstrate the specificity of the
antibodies used.
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Supplemental Figure 2: Comparison of observed and predicted log2 ratios over time of 6
proteins that were hardly affected at 8 h p.i. but were significantly downregulated later
during CHIKV infection. The predicted change in relative abundance was calculated using
published half-lives (indicated in each graph) [2] and assuming virus-induced host translational
shut-off starts 8 h p.i. A) Proteins of which the observed decay was very similar to the predicted
curve. B) Proteins that were degraded faster than predicted during CHIKV infection.
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Supplemental Figure 3: (Over)expression of different FLAG-tagged host factors, followed
by infection with a GFP-expressing AdenoV at 10 h p.t. and an MOI of 5. At 10 h p.i., the
cells were fixed, permeabilized and stained with anti-FLAG-APC. APC staining and GFP
expression were quantified by FACS. A) The first scatter plot shows side- and forward scatter
and the gate that was used to select cells to display in contour plots. The contour plots show aFLAG-APC staining and GFP expression. For each host factor a mock- and adenovirus-infected
plot is shown. pCDNA3.0 was used as an empty vector control and FLAG-Ub as a negative
control. Each plot contains approximately 10,000 events. The x-axis shows the level of GFP
expression, the y-axis shows the intensity of APC staining. The numbers in the upper right of
each panel indicate the percentage of cells in each quadrant. B) Summary of FACS data. The
number of events that was recorded in each quadrant during FACS analysis is shown. The
percentage of adenovirus-infected cells was calculated using the total number of transfected cells
and the total number of non-transfected cells. The fold reduction in number of infected cells is
shown in the last column. TF= Transfected, NTF= non-transfected, Inf= infected.
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Supplemental Figure 4: FACS contour plots of transfected uninfected control cells.
293/ACE2 cells were transfected with FLAG-tagged host factors and at 10 h p.t. mockinfected. Cells were fixed 10 h later, permeabilized and stained with anti-FLAG-APC. APC
staining and GFP expression were measured by FACS. The first plot shows side- and forward
scatter and the gate that was used to select cells to display in the contour plots. Each plot
contains approximately 10,000 events. X-axis shows GFP expression, y-axis shows APC
staining. Numbers in upper right of each panel indicate the percentage of cells in each quadrant.
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Supplemental Figure 5: Sequence alignments of the proteins that were used in the followup experiments of our proteomics study. Alignments were made for each of the four proteins
that were selected for follow-up (overexpression) studies, using sequences from Homo sapiens,
Macaca mulatta, Papio anubis, Pan troglodytes, Gorilla gorilla and Pongo abelii. Alignments
were made with Geneious 7.1.5 [3]. The uniprot identifier for each sequence that was used for
the alignment is shown after the species name. The level of sequence identity is shown in the
green bar above the sequence. The peptides identified in the LC-MS/MS analysis are indicated
with grey bars underneath the sequence. A) Rnd3, B) DDX56, C) UbcH10, D) Plk1.
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Supplemental Figure 6: Schematic overview of possible functions of significantly
downregulated proteins during CHIKV infection. The POLR2 complex is required for host
transcription and degradation of its subunits results in a decrease in host transcription. The
POLR1 and POLR3 complexes are involved in tRNA synthesis and rRNA synthesis,
respectively, and degradation of their subunits affects host translation. Rnd3 is an antagonist of
RhoA induced stress fibers and the protein might affect CHIKV entry or the replication and
transcription complex (RTC). Rnd3 also inhibits translation of mRNAs with highly structured
5’UTRs and could affect translation of CHIKV genomes through this function. Overexpression
of DDX56 inhibits CHIKV infection but how it affects replication is still unclear. The effect of
overexpression of UbcH10 on CHIKV infection was minimal and it is still unknown how
inhibition would take place. Plk1 has several functions in regulation of the cell cycle and
interferon-β production. Since mutations in the kinase- and polobox-domain of this protein had
no effect on the inhibitory effect that overexpression of Plk1 had on CHIKV infection it might
inhibit CHIKV through yet another function.
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References
[1] Scholte, F. E., Tas, A., Martina, B. E., Cordioli, P., et al., Characterization of synthetic
Chikungunya viruses based on the consensus sequence of recent E1-226V isolates. PloS one
2013, 8, e71047.
[2] Schwanhausser, B., Busse, D., Li, N., Dittmar, G., et al., Global quantification of mammalian
gene expression control. Nature 2011, 473, 337-342.
[3] Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., et al., Geneious Basic: an integrated and
extendable desktop software platform for the organization and analysis of sequence data.
Bioinformatics (Oxford, England) 2012, 28, 1647-1649.
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