Comparison of Repressor and Transcriptional Attenuator Systems for Control of Amino Acid Biosynthetic Operons Johan Elf 1 , Otto G. Berg 2 and Ma Ê ns Ehrenberg 1 * 1 Department of Cell and Molecular Biology, BMC Box 596, SE-751 24 Uppsala Sweden 2 Department of Molecular Evolution, Evolutionary Biology Centre, SE-753 26 Uppsala Sweden In bacteria, expression from amino acid biosynthetic operons is transcrip- tionally controlled by two main mechanisms with principally different modes of action. When the supply of an amino acid is in excess over demand, its concentration will be high and when the supply is de®cient the amino acid concentration will be low. In repressor control, such con- centration variations in amino acid pools are used to regulate expression from the corresponding amino acid synthetic operon; a high concen- tration activates and a low concentration inactivates repressor binding to the operator site on DNA so that initiation of transcription is down or up-regulated, respectively. Excess or de®cient supply of an amino acid also speeds or slows, respectively, the rate by which the ribosome trans- lates mRNA base triplets encoding this amino acid. In attenuation of transcription, it is the rate by which the ribosome translates such ``own'' codons in the leader of an amino acid biosynthetic operon that decides whether the RNA polymerase will continue into the operon, or whether transcription will be aborted (attenuated). If the ribosome rate is fast (excess synthesis of amino acid), transcription will be terminated and if the rate is slow (de®cient amino acid supply) transcription will continue and produce more messenger RNAs. Repressor and attenuation control systems have been modelled math- ematically so that their behaviour in living cells can be predicted and their system properties compared. It is found that both types of control systems are unexpectedly sensitive when they operate in the cytoplasm of bacteria. In the repressor case, this is because amino acid concen- trations are hypersensitive to imbalances between supply and demand. In the attenuation case, the reason is that the rate by which ribosomes translate own codons is hypersensitive to the rate by which the con- trolled amino acid is synthesised. Both repressor and attenuation mechanisms attain close to Boolean properties in vivo: gene expression is either fully on or fully off except in a small interval around the point where supply and demand of an amino acid are perfectly balanced. Our results suggest that repressors have signi®cantly better intracellu- lar performance than attenuator mechanisms. The reason for this is that repressor, but not attenuator, mechanisms can regulate expression from biosynthetic operons also when transfer RNAs are fully charged with amino acids so that the ribosomes work with maximal speed. # 2001 Academic Press Keywords: attenuation; aminoacylation; control of gene expression; repressor control; Boolean control *Corresponding author Introduction The two major principles for transcriptional regulation of amino acid biosynthetic operons in Escherichia coli and Salmonella typhimurium are clas- E-mail address of the corresponding author: ehrenberg@xray.bmc.uu.se doi:10.1006/jmbi.2001.5096 available online at http://www.idealibrary.com on J. Mol. Biol. (2001) 313, 941±954 0022-2836/01/050941±14 $35.00/0 # 2001 Academic Press