Chapter Summary


  • Regulatory proteins help a cell sense changes in its internal environment and alter gene expression to match.
  • Repressor and activator proteins bind to operator and activator DNA sequences, respectively, in front of target genes. Repressors prevent transcription, whereas activator proteins stimulate transcription.
  • Two-component signal transduction systems also help the cell sense and respond to its environment, both inside and outside.
  • Gene expression can be controlled at several levels: DNA sequence, transcription, translation, or by modifying the protein posttranslationally.
  • Integrated control circuits connect many individual regulatory systems to coordinate regulation throughout the cell.


  • The lactose utilization lacZYA operon of E. coli was the first gene regulatory system described.
  • LacI binds as a tetramer to the operator region and represses the lac operon by preventing open complex formation by RNA polymerase.
  • Beta-galactosidase (LacZ), when at low concentration, cleaves and rearranges lactose to make the inducer allolactose.
  • Allolactose complexes to LacI, reducing repressor affinity for the operator and allowing induction of the operon.
  • The cAMP-CRP complex binds to the lac operator region and stimulates RNA polymerase through CRP interaction with the C-terminal domain of the RNA polymerase alpha subunit. cAMP-CRP regulates many types of operons.
  • In catabolite repression, a preferred carbon source prevents the induction of an operon that enables catabolism of a different carbon source. One example is catabolite repression of the lac operon by glucose. Glucose transport through the PTS system causes catabolite repression by inhibiting LacY permease activity (inducer exclusion) and lowers cAMP levels.


  • DNA-binding proteins often recognize symmetrical DNA sequences.
  • Many anabolic pathway genes (for example, for amino acid biosynthesis) are repressed by the end product of the pathway (for example, the amino acid), which binds to a corepressor that inhibits transcription.
  • AraC-like proteins are a large family of regulators, present in many bacterial species, that can activate or repress operons by assuming different conformations.
  • Attenuation is a transcriptional regulatory mechanism in which translation of a leader peptide affects transcription of a downstream structural gene.
  • Idling ribosomes synthesize the signal molecule ppGpp, which interacts with the beta subunit of RNA polymerase and decreases the affinity of RNA polymerase for ribosomal RNA and a variety of other genes needed for rapid growth. The result, called the stringent response, is lower transcription of these genes, reduced levels of rRNA, and a decrease in the number of ribosomes.


  • Changing the synthesis or activity of alternative sigma factors is used to coordinately regulate sets of related genes.
  • Sigma factors can be controlled by altered transcription, translation, proteolysis, and anti-sigma factors.
  • Secondary structures at the 5′ end of mRNA can obscure access to ribosome-binding sites. Conditions that melt the secondary structures will increase translation of the sigma factor.
  • Chaperones can direct certain sigma factors toward degradation by proteases. Conditions that draw those chaperones away from the sigma factor will allow the sigma factor to accumulate.
  • Sporulation relies on the hierarchical activation of a series of different sigma factors.
  • Temporary asymmetrical distribution of the chromosome between the forespore and the mother cell results in differential activation of compartmentspecific alternative sigma factors.
  • Sigma F is a forespore-specific sigma factor regulated by anti-sigma and anti-anti-sigma factors. Sigma F is preferentially activated by temporary asymmetrical distribution of the chromosome during the early stages of sporulation.


  • Small regulatory RNAs found within bacterial intergenic regions regulate the transcription or stability of specific mRNA molecules.
  • The antisense nature of sRNA allows these molecules to bind target mRNA. Binding can either stabilize the target mRNA or make it susceptible to degradation.
  • Identifying sRNAs is more complex than identifying ORFs.
  • Eukaryotic microbes use small interfering RNA to silence genes.


  • Small regulatory RNAs found within bacterial intergenic regions regulate the transcription or stability of specific mRNA molecules.
  • In phase variation, the structure of a bacterial protein reversibly changes from one form to another via a genetic mechanism.
  • An invertible promoter switch regulates two genes of Salmonella enterica encoding two alternative structural types of flagellin.
  • Slippage while replicating through repetitive DNA sequences, a process called slipped-strand mispairing, can reversibly activate or inactivate a series of outer membrane proteins in Neisseria gonorrhoeae.


  • Bacterial genes are regulated by a hierarchy of regulators that form integrated gene circuits.
  • Gene switches can regulate “decision-making” processes in microbes.
  • Chemotaxis is a behavior in which motile microbes swim toward favorable environments (chemoattractants) or away from unfavorable environments (chemorepellents).
  • The direction of flagellar motor rotation determines the type of movement. Counterclockwise rotation results in smooth swimming; clockwise rotation, in tumbling.
  • Random movement toward an attractant causes a drop in CheY-P levels, which allows counterclockwise rotation and smooth swimming.
  • Methyl-accepting chemotaxis proteins (MCPs) clustered at cell poles bind chemoattractants and initiate a series of events lowering CheY-P levels. Reversible methylation or demethylation of MCPs desensitizes or sensitizes MCPs, respectively.
  • The NtrB-NtrC two-component signal transduction system regulates nitrogen assimilation by altering transcription of the gene encoding glutamine synthetase (glnA).
  • The protein GlnB links the biochemical control and genetic regulation of nitrogen assimilation.


  • The transcriptome and proteome constitute all of a cell’s mRNA molecules and proteins, respectively. Transcriptomes and proteomes change as environmental conditions change.
  • A DNA microarray chip is used to monitor the levels of thousands of individual mRNA molecules made during growth.
  • Two-dimensional gels separate proteins by isoelectric point and molecular weight. They offer a snapshot of the proteome at any given point of growth or under any given growth condition.
  • Mass spectrometry can determine the exact molecular weight of a protein (or the sequence of a component peptide) taken from an otherwise anonymous spot on a two-dimensional gel. The exact molecular weight or peptide sequence is compared against the database of ORFs deduced from the genomic sequence of the organism. A successful match, therefore, determines the protein’s identity.