Structure and Function of the Bacterial Genome. Charles J. Dorman

Structure and Function of the Bacterial Genome - Charles J. Dorman


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from a shortage of amino acids to charge the tRNAs and is an indication that the translational capacity of the cell exceeds demand. Hence the feedback loop that shuts down the transcription of genes involved in the production of ribosomes and other parts of the translational apparatus. The stringent response also affects DNA synthesis and mRNA translation both negatively and directly, while stimulating the transcription of genes outside the stringently regulated group (Ferullo and Lovett 2008; Haugen et al. 2006; Paul et al. 2005). What distinguishes the members of the two groups? One important factor is the possession by stringently regulated promoters of a discriminator sequence consisting of a G+C‐rich DNA between its −10 and +1 elements (Figure 1.19) (Lamond and Travers 1985; Mizushima‐Sugano and Kaziro 1985; Travers 1980; Travers et al. 1986; Zacharias et al. 1989). The discriminator is an effective barrier to open complex formation, possibly due to the extra hydrogen bonding between DNA strands consisting of G+C‐rich sequences. Negative supercoiling of the DNA has a stimulatory effect on the promoters of stable RNA genes and this may assist with the melting of the recalcitrant discriminators when negative supercoiling is available (Schneider et al. 2000). However, in bacteria experiencing low metabolic flux (e.g. those in lag phase or stationary phase) this stimulatory influence is absent and the resulting relaxation of the DNA template, combined with the negative influences of the (p)ppGpp alarmone and the DksA protein, cooperate to repress transcription of stable RNA genes (Potrykus and Cashel 2008; Schneider et al. 2000). Genes subject to stimulation by (p)ppGpp and DksA also possess a discriminator, but in these cases this element is an A+T‐rich DNA sequence (Figure 1.19) (Gummesson et al. 2013).

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      In order to exert its influence on DNA topology, FIS must be present in the cell. This restricts its influence to the early stages of exponential growth when it is most abundant (Schneider et al. 1997). An exception has been discovered in bacteria growing under micro‐aerobic conditions: here FIS levels are sustained into the stationary phase of growth (Cameron et al. 2013; O Cróinín and Dorman 2007). This may be of special significance in environments such as the mammalian gut epithelial surface where FIS‐dependent gene expression is required for colonisation and invasion (Falconi et al. 2001; Kelly et al. 2004; Prosseda et al. 2004; Rossiter et al. 2015).

      

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