11th week:

Chapter 8.
Regulation of Gene Expression
(유전자 발현의 조절)
 Chapter 8

Chapter 9
(12th Edition)
Regulation of Gene Expression
(유전자 발현의 조절)
 Overview of Regulation (조절의 개요)
• Gene expression: transcription of gene into mRNA followed by
translation of mRNA into a protein
• Most proteins are enzymes that carry out biochemical reactions
essential for cell growth
• Constitutive proteins are needed at the same level all the time
• Microbial genomes encode many more proteins than are present at any
one time
• Regulation is important in all cells and helps conserve energy and
resources
 Overview of Regulation (조절의 개요)
• Two major levels of regulation in the cell
– One controls the activity of preexisting enzymes
• Posttranslational regulation
• Very rapid process (seconds)
– One controls the amount of an enzyme
• Regulate level of transcription
• Regulate translation
• Slower process (minutes)

Source: Brock Biology of Microorganisms 12th edition.

Figure 9.1
 DNA-Binding Proteins (DNA-결합 단백질)
• mRNA transcripts generally have a short half-life
– Prevents the production of unneeded proteins
• Regulation of transcription typically requires proteins that can bind to
DNA
• Small molecules influence the binding of regulatory proteins to DNA
– Proteins actually regulate transcription
• Most DNA-binding proteins interact with DNA in a sequence-specific
manner
– Specificity provided by interactions between amino acid side chains and
chemical groups on the bases and sugar-phosphate backbone of DNA
– Major groove of DNA is the main site of protein binding
– Inverted repeats frequently are binding site for regulatory proteins
 DNA-Binding Proteins (DNA-결합 단백질)
• Homodimeric proteins: proteins composed of two identical polypeptides
• Protein dimers interact with inverted repeats on DNA
– Each of the polypeptides binds to one inverted repeat
• Several classes of protein domains are critical for proper binding of
proteins to DNA
– Helix-turn-helix
• Classes of Protein Domains
– Zinc finger
• Protein structure that binds a zinc ion
• Typically two or three zinc fingers on proteins that use them for DNA
binding
– Leucine zipper
• Leucine residues are spaced every seven amino acids
• Does not interact directly with DNA
 DNA-Binding Proteins (DNA-결합 단백질)
• Multiple outcomes after DNA binding are possible
1) DNA-binding protein may catalyze a specific reaction on the DNA molecule
(i.e., transcription by RNA polymerase)

2) The binding event can block transcription (negative regulation)

3) The binding event can activate transcription (positive regulation)

DNA-Binding Proteins (DNA-결합 단백질)

Source: Brock Biology of Microorganisms 12th edition.

Figures 9.2, 9.3 & 9.4
 Regulation of Transcription (전사의 조절)
• Several mechanisms for controlling gene expression in bacteria
– These systems are greatly influenced by environment in which the organism
is growing
– Presence or absence of specific small molecules
– Interaction between small molecules and DNA-binding proteins result in
control of transcription or translation
• Negative control: a regulatory mechanism that stops transcription
– Repression: preventing the synthesis of an enzyme in response to a signal
• Enzymes affected by any repression make up a small fraction of total
proteins in the cell
• Typically affects anabolic enzymes (i.e., arginine biosynthesis)
– Induction: production of an enzyme in response to a signal
• Typically affects catabolic enzymes (i.e., lac operon)
• Enzymes are synthesized only when they are needed
– no wasted energy
Regulation of Transcription (전사의 조절)

Source: Brock Biology of Microorganisms 12th edition.

Figures 9.5 & 9.6
 Regulation of Transcription (전사의 조절)
• Inducer: substance that induces enzyme synthesis
• Corepressor: substance that represses enzyme synthesis
• Effectors: collective term for inducers and repressors
• Effectors affect transcription indirectly by binding to specific DNA-binding
proteins
– Repressor molecules bind to an allosteric repressor protein
– Allosteric repressor becomes active and binds to region of DNA near
promoter called the operator
• Operon: cluster of genes arranged in a linear fashion whose expression is
under control of a single operator
– Operator is located downstream of the promoter
– Transcription is physically blocked when repressor binds to operator
• Enzyme induction can also be controlled by a repressor
– Addition of inducer inactivates repressor and transcription can proceed
• Repressor’s role is inhibitory so it is called negative control
Regulation of Transcription (전사의 조절)

Source: Brock Biology of Microorganisms 12th edition.

Figures 9.7 & 9.8
 Regulation of Transcription (전사의 조절)
• Positive control: regulator protein activates the binding of RNA
polymerase to DNA
• Maltose catabolism in E. coli
– Maltose activator protein cannot bind to DNA unless it first binds maltose
• Activator proteins bind specifically to certain DNA sequence
– Called activator binding site, not operator
• Promoters of positively controlled operons only weakly bind RNA
polymerase
• Activator protein helps RNA polymerase recognize promoter
– May cause a change in DNA structure
– May interact directly with RNA polymerase
• Activator-binding site may be close to the promoter or several hundred
base pairs away
 Regulation of Transcription (전사의 조절)
• Genes for maltose are spread out over the chromosome in several
operons
– Each operon has an activator-binding site
– Multiple operons controlled by the same regulatory protein are called a regulon
• Regulons also exist for negatively controlled systems

Source: Brock Biology of Microorganisms 12th edition.

Figure 9.11
 Global Control and the lac Operon
• Global control systems: regulate expression of many different genes
simultaneously
• Catabolite repression is an example of global control
– Synthesis of unrelated catabolic enzymes is repressed if glucose is present in
growth medium
– lac operon is under control of catabolite repression
– Ensures the “best” carbon and energy source is used first
• Diauxic growth: two exponential growth phases
• Dozens of catabolic operons affected by catabolite repression
– Enzymes for degrading lactose, maltose, and other common carbon sources
• Flagellar genes are also controlled by catabolite repression
– No need to swim in search of nutrients
 Signal Transduction (신호전달)
• Prokaryotes regulate cellular metabolism in response to environmental
fluctuations
• External signal is not always transmitted directly to the target to be
regulated
• Signal transduction: External signal can be detected by a sensor and
transmitted to regulatory machinery
• Most signal transduction systems are two-component regulatory
systems
• Two-component regulatory systems
– Made up of two different proteins
• Sensor kinase: (cytoplasmic membrane) detects environmental signal and
autophosphorylates
• Response regulator: (cytoplasm) DNA-binding protein that regulates
transcription
– Absent in bacteria that live as parasites of higher organisms
 Quorum Sensing (균체밀도감지)
• Prokaryotes can respond to the presence of other cells of the same
species
• Quorum sensing: mechanism by which bacteria assess their population
density
– Ensures sufficient number of cells are present before initiating a response that requires a certain
cell density to have an effect (i.e., toxin production in pathogenic bacterium)
• Each species of bacterium produces a specific autoinducer molecule
– Diffuses freely across the cell envelope
– Reaches high concentrations inside cell only if many cells are near
– Binds to specific activator protein and triggers transcription of specific genes
• Several different classes of autoinducers
– Acyl homoserine lactone was the first autoinducer to be identified
• Quorum sensing first discovered as mechanism regulating light
production in bacteria including V. fischeri
– Lux operon encodes bioluminescence
 RNA-Based Regulation
• Regulatory RNA molecules exert their effects by base pairing with
mRNA
– Double-stranded region prevents translation of mRNA
– These small RNAs (~100 nucleotides) are called antisense RNAs
– Each antisense RNA can regulate multiple mRNAs
– Transcription of antisense RNA is enhanced when its target genes need to be
turned off
– Some antisense RNA actually enhance translation
• Riboswitches: RNA domains in an mRNA molecule that can bind small
molecules to control translation of mRNA
– Located at 5′ end of mRNA
– Binding results from folding of RNA into a 3-D structure
– Similar to a protein recognizing a substrate
– Riboswitch control is analogous to negative control
– Found in some bacteria, fungi, and plants
 RNA-Based Regulation
• Attenuation
• Transcriptional control that functions by premature termination of mRNA
synthesis
– Control exerted after the initiation of transcription, but before its completion
– First example was the tryptophan operon in E. coli
– mRNA stem-loop structure and synthesis of leader peptide are determining
factors in attenuation
• Genomic evidence suggests attenuation exists in Archaea
RNA-Based Regulation
Mechanism of Attenuation

Source: Brock Biology of Microorganisms 12th edition.

Figure 9.27