Dynamics of gene expression associated with anabolism
Biomass as an important process parameter oscillated periodically in CVEF, indicating that the anabolism of yeast cells may also experience the changing cycle. Transcriptome analysis showed that a large amount of genes related to ribosome synthesis were also expressed in a periodic pattern. As shown in Figure 6, most DEGs of yeast cells at P2 were up-regulated in comparison with P1, and also in the comparison of gene expression of yeast cells at P5 to P4, while the DEGs of yeast cells at P4 were down-regulated compared with P3. However, there was no significant difference between the gene expression of yeast cells at P2 and P3. Further, the overview of changes in expression of the ribosome synthesis genes were presented as the non-standard 0π phase pattern that only decreased in π/2 period, not in the π period. It was indicated that ribosome synthesis was robust in the 3π/2 period of the oscillation (the phase from P4, P1, P2 to P3), while much lower in the remaining 1/4 oscillation period (the phase from P3 to P4).
The up-regulated expression of genes related to ribosome synthesis symbolized the start of anabolism. Thus, it can be speculated that cell anabolism was initiated at P4, and continued to P3 (P4→P5(P1)→P2→P3, 3/4 oscillation period), while the biomass presented as the π phase pattern that exist about π phase later than the ribosome synthesis. The increased expression of ribosomal genes prior to biomass accumulation indicated that ribosome synthesis was a material preparation process during the interval of cell division and that the genes related to ribosome synthesis were prioritized and expressed. In addition, the periodic change of ribosomal synthesis gene were opposite to the ethanol concentration, and there was a π phase difference between them, which may suggest that the regulation of ribosomal synthesis during VHG oscillation is also related to the ethanol stress.