S70: Dynamics of Cellular Physiology: a View Through Comparative Transcriptome and Proteome

Cellular physiology is in a dynamic state, with cells constantly responding to cues and changes in their environment. Such dynamic state is facilitated by as well as reflected in the dynamics of transcriptome and proteome. We have been investigating the transcriptomic and proteomic dynamics in a variety of organisms of industrial and medical significance, ranging from recombinant protein producing mammalian cell, antibiotic producing Streptomycete, solvent producing Clostridium and antibiotic resistance transmitting Enterococcus. The collected transcriptome data from DNA microarrays and RNA-seq, as well as SILAC and iTRAQ proteomics afford us to gain a comparative view of the cellular dynamics.

Comparative analysis of transcriptome and proteome data using arrays and iTRAQ over a longer time scale, revealed a similar trend in their dynamics in Streptomyces and Clostridium. However, in one case more than 10% of genes surveyed exhibited opposite trends of expression at transcript and protein levels with varying degrees. In a multi-tagging study coupling SILAC and iTRAQ labeling we quantified protein turnover rates. The data suggested that those more dynamic proteins with faster turnover rates may contribute significantly to the divergent trends between protein and transcript. However, in a short time scale of the induction of conjugational machinery in Enterococcus, a fast turnover of transcripts is not followed by dynamic response at protein levels. The dynamism of transcriptome and proteome profoundly affects the physiology of the organism. The importance of a system-level assessment of the dynamics of transcriptome and proteome, and the uncertainty in quantifying their dynamics will be discussed.