Modulation of Chemical Composition and Other Parameters of the Cell at Different Exponential Growth Rates

Abstract

This review begins by briefly presenting the history of research on the chemical composition and other parameters of cells of E. coli and S. enterica at different exponential growth rates. Studies have allowed us to determine the in vivo strength of promoters and have allowed us to distinguish between factor-dependent transcriptional control of the promoter and changes in promoter activity due to changes in the concentration of free functional RNA polymerase associated with different growth conditions. The total, or bulk, amounts of RNA and protein are linked to the growth rate, because most bacterial RNA is ribosomal RNA (rRNA). Since ribosomes are required for protein synthesis, their number and their rate of function determine the rate of protein synthesis and cytoplasmic mass accumulation. Many mRNAs made in the presence of amino acids have strong ribosome binding sites whose presence reduces the expression of all other active genes. This implies that there can be profound differences in the spectrum of gene activities in cultures grown in different media that produce the same growth rate. Five classes of growth-related parameters that are generally useful in describing or establishing the macromolecular composition of bacterial cultures are described in detail in this review. A number of equations have been reported that describe the macromolecular composition of an average cell in an exponential culture as a function of the culture doubling time and five additional parameters: the C- and D-periods, protein per origin (PO), ribosome activity, and peptide chain elongation rate.

Micron-scale holes terminate the phage infection cycle

“…Hence, a cell with a width of ∼1 μm results in images of very poor signal because of the multiple inelastic scattering events despite the use of an energy filter. In an attempt to reduce the size of the cells, we took advantage of the coupling between cell mass and growth rate (17) and tested several minimal medium conditions (18) for the ability to support the slowest possible growth rate but still allow the precisely scheduled lysis characteristic of cells grown in rich medium. Among several carbon sources tested, succinate was found to support a doubling time of 80 min and preserved rod-shaped morphology; induction of the fully functional lysis cassette led to sharply defined lysis at 30 min after induction (Fig.…”

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

“…As an integral structural component of ribosomes, rRNA is a fundamental constituent of all known microorganisms and most rRNA found in a cell is ribosome associated (Lindahl, 1975;Nomura et al, 1984). Total RNA concentration is generally proportional to rRNA concentration and to the number of ribosomes in the cell, and has often been employed as a proxy for both (Kerkhof and Ward, 1993;Poulsen et al, 1993;Bremer and Dennis, 1996). In pure-culture experiments, cell counts can be done to determine RNA or ribosome concentration per cell.…”

“…Two principal lines of evidence used to support rRNA as an indicator of current activity originate from earlier studies testing how rRNA scales with growth rate. First, total RNA and rRNA content correlate well with growth rate for a handful of microbes in pure culture, over a wide range of growth rates under balanced growth conditions (that is, growing in an unchanging environment) (Schaechter et al, 1958;Neidhardt and Magasanik, 1960;Rosset et al, 1966;Koch, 1970;Kemp et al, 1993;Kerkhof and Ward, 1993;Poulsen et al, 1993;Wagner, 1994;Bremer and Dennis, 1996;Ramos et al, 2000). Second, decreased rRNA content is associated with decreased growth rate for some organisms growing under specific nutrient-limiting conditions (Mandelstam and Halvorson, 1960;Davis et al, 1986;Kramer and Singleton, 1992;Tolker-Nielsen et al, 1997).…”

Evolutionary optimization of speed and accuracy of decoding on the ribosome

“…Following the recognition of the codon by the anticodon of aa-tRNA and GTP hydrolysis by EF-Tu, aa-tRNA is accommodated in the A site of the 50S subunit and takes part in peptide bond formation. The rate of protein elongation in bacteria is between 4 and 22 amino acids per second at 378C [1][2][3][4][5]; thus, a protein of an average length of 330 amino acids [6] is completed in about 10-80 s. The times required for initiation, termination and ribosome recycling (around 1 s each [3]) are short enough to make elongation rate-limiting for protein synthesis [7]. Translation of a particular codon depends on both the nature and abundance of the respective tRNAs, particularly on the non-random use of synonymous codons and the availability of the respective isoacceptor tRNAs [8].…”