Table 1.
Model Parameters
Table 2.
Protein Composition of VSV Particle and Lengths of Its Encoded Products
Figure 1.
Estimated Production of Viral mRNAs and Proteins from Infected BHK Cells
All the viral proteins that are in the cytoplasm, plasma membrane, or assembled virion particles are counted.
(A) Viral mRNAs.
(B) Viral proteins.
(C) Estimated levels of free viral proteins in infected BHK cells. Free viral proteins include all the proteins in the cytoplasm or plasma membrane, but exclude the proteins that are incorporated into nucleocapsids and virion particles. Vex(0) = 3.
Figure 2.
Estimated Distribution of Genome-Size Viral RNAs That Are Produced in Infected BHK and DBT Cells
Virion and (-)NC indicate viral genomes that are incorporated into virion particles and intracellular nucleocapsids, respectively. (+)NC indicates anti-genomes that are incorporated into intracellular nucleocapsids. Vex(0) = 3.
Figure 3.
Hijacking of Host Translation Resources by Virus
(A) The estimated distributions between active (equipped with the required accessory factors) and inactive (not equipped) ribosomes, and between ribosomes available for viral and host mRNAs are shown.
“- Time window -” indicates the time period during which viral translation is actively supported by host ribosomes.
(B) The estimated numbers of ribosomes available for viral translation and actually occupied by viral mRNAs are shown for the cases of infected BHK and DBT cells. Non-occupied ribosomes are considered as free ribosomes. When two lines coincide, no free ribosomes exist (all the available ribosomes are occupied by viral mRNAs). Vex(0) = 3.
Figure 4.
Relative Expression Rates of Viral Proteins in BHK Cells Infected by Individual VSV Strain
The expression rate of each protein was normalized by that of N protein. Therefore, the relative expression rate of N protein is defined as one. X and Y coordinates of datapoints indicate the results of experiments and simulations, respectively. All the experimental datapoints were obtained from the literature [18]. The four datapoints in the circle denote the relative protein expression rates for the genes located at the second genome position in the cases of MGP, MPG, GPM, and GMP strains having gene orders 3′-N-M-G-P-L-5′, 3′-N-M-P-G-L-5′, 3′-N-G-P-M-L-5′, and 3′-N-G-M-P-L-5′, respectively. PMG and PGM strains have the gene orders 3′-N-P-M-G-L-5′ and 3′-N-P-G-M-L-5′, respectively. The two rectangular boxes include four datapoints where there are the largest discrepancies between simulation and experimental results. Vex(0) = 5.
Figure 5.
The Growth of Gene-Rearranged VSV Strains in BHK Cells
(A) Experimental data.
(B) Simulation results. The growth of the N1 VSV strain is the fitting result, but the growth of the other three strains is the model prediction result. Vex(0) = 3.
Figure 6.
The Effects of Relative Promoter Strength and N Gene Rearrangement on the Growth Phenotype of VSV
(A) The balance of the production between genome and anti-genome is determined by the promoter strength of the anti-genome relative to that of the genome (Sprom). The changes of virion production in BHK and DBT cells by the variation of the parameter are observed. The black circles indicate the virion productions of wild-type (Sprom = 5.4) in BHK and DBT cells.
(B) The extension of phenotypic variations by double genomic manipulations was predicted. As an important phenotype of virus for vaccine use, the changes of virion production by the relocation of N gene along with the variation in the promoter strength of the anti-genome relative to that of the genome (Sprom) are shown. The black circle indicates the virion production of wild-type in BHK cells. Vex(0) = 3.
Figure 7.
Estimated Levels of G Protein in BHK Cells Infected with Six Gene-Shuffled VSV Strains
The intracellular level of G protein is highly dependent upon the location of G gene on the viral genome. In the late infection stage, a large fraction of G proteins are incorporated into progeny particles, which significantly decreases the intracellular protein level. Vex(0) = 3.
Figure 8.
Predicted Levels of Virion Production and G Protein Expression in BHK Cells Infected with VSV Strains (Total 20 Strains)
(A) Virion production.
(B) G protein expression.
The size of each circle shows the relative level for each VSV strain, and the coordinate of each circle indicates the gene order in each strain's genome. The gray and white circles denote the cases of wild-type (N1G4) and non–wild-type strains, respectively. Under the line there is no VSV strain case (e.g., N1G1, N2G2, etc.). Vex(0) = 3.
Table 3.
Burst Size of VSV Strains
Figure 9.
(A) Infection cycle of VSV.
(B) Segmentation of genome-size viral templates to simulate the spatial–temporal changes of polymerase concentration on the templates.
(C) VSV partial transcription termination (or attenuation) mechanism.
Table 4.
Nomenclature