Nuclear Structure and Function Research Group

This page provides supporting information to Bon, M., McGowan, S., and Cook, P.R. (2006). Many expressed genes in bacteria and yeast are transcribed only once per cell cycle. FASEB J. 20, 1721-1723. [PubMed] [pdf]

Overview/Abstract
The steady-state levels of all mature transcripts expressed in bacteria and yeast have been catalogued, but we do not yet know the numbers of nascent transcripts and so RNA polymerases engaged on all genes. Such catalogs are presented here. As mRNA levels depend on the balance between synthesis and degradation, we use published data to calculate the numbers of engaged polymerases required to maintain these levels in the face of the known rate of degradation. Most genes – including essential ones – prove not to be transcribed most of the time, and many produce only one message per cell cycle. Some cells even fail to produce an essential message during a cycle, and so must depend on their mother’s messages and/or proteins for survival. We speculate that evolution sets the rate of message production so low to conserve energy, minimize transcription-induced mutation, and permit regulation over the widest range.

• E. coli
Relative numbers of all mRNAs and their half lives in Luria broth (LB) or M9 + glucose have been catalogued using microarrays (Bernstein et al., 2002). We first convert relative numbers of each mRNA to absolute numbers knowing the total number of all mRNAs in the cell. We then calculate the numbers of engaged polymerases required to maintain these levels using the known rates of transcript elongation and degradation (Bremer and Dennis, 1996). As microarray data for structural RNA genes (e.g., rRNA, tRNA) are not available, polymerase densities on these genes are calculated using the known rates of initiation.  Values are corrected for gene length and copy number, which depend on genome position and growth rate.

• S. cerevisiae
Holstege et al. (1998) catalogued relative numbers of mRNAs and their half lives, and calculated the rate of mRNA production required to maintain those numbers. We calculate polymerase densities (after correcting for copy number) using the known rate of elongation (Edwards et al., 1991; Shermoen and O'Farrell, 1991).  Data for structural RNAs are not included (as they are unavailable).

Search
        ► Search for a gene of interest.

Downloads [Catalogs in 'Excel' spreadsheets (Microsoft Office Professional Edition 2003).]
• E. coli
    Ordered from high to low expression level
        ► polymerases / transcription unit (in LB)
        ► polymerases / transcription unit (in M9 + glucose)
        ► number of transcripts produced per cell cycle (in LB)
        ► number of transcripts produced per cycle (in M9 + glucose)
    Ordered by nucleotide position in genome
        ► The master spreadsheet
    Assumptions, calculations, validation
        ► Assumptions, calculations, validation
• S. cerevisiae in YPD
    Ordered from high to low expression level
        ► polymerases / ORF
        ► number of transcripts produced per cell cycle
    Ordered by nucleotide position in genome
        ► The master spreadsheet
    Assumptions, calculations, validation
        ► Assumptions, calculations, validation

References
Bernstein, J.A. et al.. Proc. Natl. Acad. Sci. USA 99, 9697-9702 (2002).
Bremer, H. & Dennis, P.P. In Escherichia coli and Salmonella typhimurium: cellular and molecular biology, F. C. Neidhardt et al., Eds. (ASM Press, Washington) pp 1553-1569 (1996).
Holstege, F.C. et al.. Cell 95, 717-728 (1998).
Edwards, A.M. et al.. J. Biol. Chem. 266, 71-75 (1991).
Shermoen, A.W. & O'Farrell, P.H. Cell 67, 303-310 (1991).

Top | Home | Maintained by Peter Cook |