13
Regulation of Cellular Processes
CHAPTER OVERVIEW
This chapter considers a variety of mechanisms by which gene expression is regulated. The discussion begins
by giving the levels of regulation of gene expression. The regulation of transcription initiation includes
induction and repression using the lac, trp, and ara operons as examples, and includes two-component
regulatory systems. Regulation at the level of transcription continues with attenuation and riboswitches.
Translational and posttranslational regulation are discussed. Global regulatory systems include discussions of
sigma factors, catabolite repression, chemotaxis, quorum sensing, and sporulation. The chapter concludes with
information about gene regulation in eukaryotes and archaea.
CHAPTER OBJECTIVES
After reading this chapter you should be able to:
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discuss levels of regulation of gene expression
describe induction and repression using example operons
discuss regulation of enzyme synthesis by negative and positive regulatory proteins
describe two-component regulatory systems
describe attenuation and riboswitches
discuss translational and posttranslational regulation
discuss global regulation of gene expression
describe quorum sensing and catabolite repression
contrast regulation in eukaryotes, bacteria, and archaea
CHAPTER OUTLINE
I.
II.
Levels of Regulation
A. Regulation of gene expression (controlling enzyme synthesis) occurs at different levels, including
control of transcription, translation, and posttranslation
B. Although there are similarities in the regulation of gene expression in organisms from different
domains, there are many differences in chromosome organization, mRNA transcripts, signaling, and
cell structure
Regulation of Transcription Initiation
A. Induction and repression of enzyme synthesis
1. Enzymes central to metabolic processes, routinely needed by cells, are encoded by
housekeeping genes; these are constitutive genes that are continuously expressed
2. Synthesis of enzymes involved in catabolic pathways are often inducible and are only
expressed when needed; the initial substrate of the pathway (or some derivative of it) is usually
the inducer; induction increases the amount of mRNA encoding the enzymes
3. Synthesis of enzymes involved in anabolic pathways is often repressible and expressed when
biosynthesis of the end product is needed; the end product of the pathway usually acts as a
corepressor; repression decreases the amount of mRNA encoding the enzymes
B. Control of transcription initiation by regulatory proteins
1. Regulatory proteins in bacteria contain recognizable DNA-binding domains such as zinc
fingers and helix-turn-helix domains
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2.
Negative transcriptional control occurs when a repressor protein inhibits initiation of
transcription; positive transcriptional control occurs when activator protein promotes initiation
of transcription
3. Even in operons where expression is repressed, a low basal level of transcription occurs; genes
are only expressed when needed (substrate present; product absent)
4. Repressor proteins bind to the operator, a region of DNA overlapping or downstream of the
promoter, and block RNA polymerase binding; activator proteins bind activator-binding sites,
often upstream of the promoter
5. In inducible systems, the repressor protein is active until bound to the inducer (binding of
inducer inactivates the repressor) whereas in repressible systems, the repressor is inactive until
bound to the corepressor (binding of corepressor activates the repressor)
6. In bacteria, a set of related structural genes controlled by a single operator and promoter is
called an operon
C. Lactose operon: negative transcriptional control of inducible genes
1. The lactose (lac) operon, which encodes genes for the catabolism of lactose, is an excellent
example of negative regulation of an inducible gene; binding of the lac repressor to the lac
operators bends the DNA and inhibits RNA polymerase binding or blocks the movement of
RNA polymerase
2. The lac repressor is inactivated by binding the inducer, allolactose, a derivative of lactose; the
presence of lactose induces expression of the lac operon by inhibiting repressor binding
3. The lac operon also is regulated by catabolite activator protein (CAP), part of a global
regulatory system
D. Tryptophan operon: negative transcriptional control of repressible genes
1. The tryptophan (trp) operon, which encodes genes for the synthesis of tryptophan, is an
excellent example of a repressible operon; the trp operon is expressed unless the trp repressor
binds its corepressor, tryptophan, the end product of the pathway
2. The trp operon also is controlled at the level of transcription elongation through attenuation
E. Arabinose operon: transcriptional control by a protein that acts both positively and negatively
1. The arabinose (ara) operon encodes genes for the catabolism of arabinose
a. When arabinose is absent the ara operon is repressed by the interaction of two AraC
molecules at the operators
b. When arabinose is present, this interaction is prevented and the AraC molecules stimulate
expression
F. Two-component regulatory systems and phosphorelay systems
1. Signal transduction systems regulate gene expression in response to environmental conditions,
rather than metabolite levels
2. In two-component regulatory systems, a sensor kinase protein in the plasma membrane senses
changes in the environment and can phosphorylate a response-regulator protein, a DNAbinding protein that regulates gene expression
3. Phosphorelay systems are longer pathways that use transfer of phosphoryl groups to control
gene transcription and protein activity
III. Regulation of Transcription Elongation
A. Attenuation
1. There are two decision points for regulating transcription of anabolic pathways: initiation of
transcription and continuation of transcription; attenuation regulates continuation of
transcription
2. In systems where transcription and translation are tightly coupled, ribosome behavior in the
leader region of the mRNA can control continuation of transcription
a. If ribosomes actively translate the leader region (attenuator), which contains several
codons for the amino acid product of the operon, a transcription terminator forms and
transcription will not continue
b. If ribosomes stall during translation of the leader region because the appropriate charged
aminoacyl-tRNA is absent, the terminator does not form and transcription will continue
B. Riboswitches
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1.
Riboswitches (sensory RNAs) are a form of attenuation that does not involve the ribosome;
regulation is based on differential folding of the mRNA leader sequence
2. Alternative folding, creating antitermination and termination loops, is controlled by the
binding of an effector molecule
IV. Regulation of Translation
A. Regulation of translation by riboswitches is similar to the regulation of transcription by
riboswitches, except here the binding of effector molecules changes the folding of the mRNA in
such a way as to inhibit ribosomal binding and initiation of translation
B. Regulation of translation by small RNA molecules
1. Small RNAs (sRNAs), also called noncoding RNAs (ncRNAs), are involved in regulating
cellular processes by directly pairing with mRNAs
2. One kind of sRNA is antisense RNA, which is complementary to the leader sequence of an
mRNA molecule, and specifically binds to it, thereby blocking translation
V. Posttranslational Regulation
A. Regulation of enzyme pathways through allosteric control or covalent modification are forms of
posttranslational regulation; covalent modification can be reversible (phosphorylation) or
irreversible (proteolysis)
B. Chemotaxis
1. A phosphorelay system is used to regulate the chemotactic response of bacteria and determine
directional motion of flagellum; the system includes a sensor kinase and a response regulator
2. Attractants (or repellants) are detected by chemoreceptors, leading to transfer of phosphoryl
groups to proteins by sensor kinases that interact with response regulators which control the
flagellar motor
VI. Global Regulatory Systems
A. Overview
1. Global regulatory systems affect many genes and pathways simultaneously, allowing for both
independent regulation of operons as well as cooperation of operons
2. A regulon is a group of genes or operons controlled by a common regulatory protein; a
modulon is more complex and has a common regulatory protein that controls an operon
network, but individual operons are controlled separately as well; a stimulon is a regulatory
system in which all operons respond together to an environmental stimulus
B. Mechanisms used for global regulation
1. Bacteria produce a number of different sigma factors; each enables RNA polymerase to
recognize and bind to specific promoters
2. Alternate sigma factors available to RNA polymerase change gene expression
C. Catabolite repression
1. Diauxic growth—a biphasic growth pattern observed when a bacterium is grown on two
different sugars (e.g., glucose and lactose)
2. For E. coli, availability of glucose (the preferred carbon and energy source) causes a drop in
cAMP levels, resulting in the deactivation of CAP (a positive regulator of several catabolic
pathways, including the lac operon); deactivation of CAP allows the bacterium to use glucose
preferentially over another sugar when both are present in the environment
D. Regulation by other nucleotides
1. In addition to cAMP, guanosine tetraphosphate (ppGpp) and cyclic dimeric GMP (c-di-GMP)
regulate gene expression
2. The stringent response involving ppGpp occurs in cells starved for amino acids
a. When protein synthesis stops due to a lack of charged tRNAs, ppGpp is produced
b. ppGpp downregulates tRNA and rRNA synthesis, while upregulating amino acid
biosynthesis
E. Quorum sensing
1. Intercellular communication (quorum sensing) in prokaryotes is important in gene regulation;
even microbes of different species can affect each other's gene expression
2. Quorum sensing is typically mediated by the release to homoserine lactones as autoinducers; in
some cases a two-component regulatory system is involved
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F.
Sporulation in Bacillus subtilis
1. Sporulation is a complex process that is controlled at several levels through phosphorelay,
transcription factors, posttranslational modifications, and alternate sigma factors
2. Under certain environmental stimuli, a response-regulator protein, Spo0A, alters the expression
over 500 genes, including alternate sigma factors that differentially control gene expression in
the forespore and mother cell
VII. Regulation of Gene Expression in Eukarya and Archaea
A. In eukaryotes, numerous general transcription factors are required; there are regulatory transcription
factors that are specific to one or more genes and alter the rate of transcription; activators bind
regulatory sites called enhancers, while repressors bind sites called silencers
B. sRNAs act in eukaryotes as antisense RNAs and function at the level of translation; the smallest
types are called microRNAs (miRNAs); some sRNAs work with the spliceosome
C. Gene regulation in archaea is not understood; in most cases archaeal regulatory proteins function
like bacterial activators and repressors, while in others they function like eukaryotic regulatory
transcription factors
TERMS AND DEFINITIONS
Place the letter of each term in the space next to the definition or description that best matches it.
____ 1.
____ 2.
____ 3.
____ 4.
____ 5.
____ 6.
____ 7.
____ 8.
____ 9.
____ 10.
____ 11.
____ 12.
____ 13.
Small molecules that inactivate
repressor proteins and thereby increase
the synthesis of certain enzymes
Small molecules that activate repressor
proteins and thereby decrease the
synthesis of certain enzymes
The site on the DNA to which a
repressor binds
A promoter, an operator, and the
structural genes that they control
A transcription termination site found in
the leader region of certain operons that
controls continuation of transcription of
that operon
An RNA molecule that specifically
binds to a target RNA, thereby
preventing the utilization of that target
RNA
Regulate gene expression in response
to environmental conditions
Plasma membrane protein that senses
changes in the environment.
DNA-binding protein that regulates
gene expression after phosphorylation
by a sensor kinase
Affect many genes and pathways
simultaneously
Common regulatory protein controls
operon network, but individual operons
also controlled separately
Regulatory system where operons
respond together to environmental
stimulus
Proteins that enable RNA polymerase
____ 14.
____ 15.
____ 16.
____ 17.
____ 18.
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to recognize and bind to specific
promoters
Intercellular communication important
in gene regulation
In eukaryotes, these bind regulatory
sites called enhancers
The smallest sRNAs in eukaryotes that
act at the level of translation
Sensory RNAs that participate in a
form of attenuation that does not
involve the ribosome.
A collection of genes or operons that is
controlled by a common regulatory
protein
a.
b.
c.
d.
e.
f.
g.
h.
i.
j.
activators
antisense RNA
attenuator
corepressors
global regulatory systems
inducers
microRNAs (miRNAs)
modulon
operator
operon
k.
l.
m.
n.
o.
p.
q.
r.
quorum sensing
regulon
response-regulation protein
riboswitches
sensor kinase
sigma factors
signal transduction systems
stimulon
FILL IN THE BLANK
1.
If E. coli is grown in a medium that contains both glucose and lactose, it uses ____________
preferentially until this sugar is exhausted. Then after a short lag, growth resumes using ____________ as
a carbon source. This biphasic growth pattern is called ____________ growth.
2. For negatively regulated operons containing genes for a catabolic pathway, the initial substrates of the
pathways often act as ____________, while for negatively regulated operons containing genes for
anabolic pathways, the end products of the pathways usually act as ____________.
3. The regulatory mechanism,
, is observed for numerous amino acid biosynthetic pathways.
In this mechanism, the behavior of ribosomes impacts the continuation of transcription. Between the
operator and the structural genes of the operon is the
region. This region encodes a leader
peptide that has two or more codons for the amino acid end product of the pathway, and it has an
,
a rho-independent transcription termination site that can form a terminator hairpin. If the ribosome
successfully translates the leader peptide sequence of the mRNA, then the terminator hairpin forms and
stops continuation of transcription of the operon. This can only happen if the amino acid is readily
available and activated by the appropriate
. If the amino acid is not readily
available, the ribosome will briefly stall during translation of the leader peptide sequence. If this occurs
while the leader region is still being transcribed, it prevents formation of the terminator hairpin.
Therefore, transcription continues, the mRNA is translated, the enzymes of the pathway are synthesized,
and the needed amino acid is synthesized. Such a regulatory process is only possible when the processes
of transcription and translation are
. Therefore, it is only seen in ____________
organisms and not in ____________ organisms.
4. Some operons are regulated by
proteins, which bind the operator and prevent transcription.
This type of regulation of gene expression is called
control. Other operons are regulated by
activator proteins (e.g.,
activator protein, which regulates the lactose operon and other
operons in E. coli), which promote transcription. This type of regulation is called
operon
control.
5. Many biosynthetic enzymes are
enzymes whose levels are reduced in the presence of end
products called
. In this type of regulatory system, the newly synthesized repressor protein is
inactive and referred to as the
. It is activated by the
.
6. When arabinose is absent the ara operon is ___________ by AraC; however, when _________ is
present, this interaction is prevented and AraC _________ expression.
7. In response to environmental conditions, a membrane-bound
protein
acts on a ______________ protein by phosphorylating it. This
system can
regulate gene expression. Longer pathways that use transfer of phosphoryl groups to control gene
expression are called _________ systems.
8. Intercellular communication important in gene expression, known as
, is
mediated in prokaryotes by the release of
that act as ___________, in
some cases through two-component regulatory systems.
9. In eukaryotes, many ___________ transcription factors are required, that includes stimulation by
__________ that bind _________ and repressors that bind __________.
10. During amino acid starvation, cells exhibit the ____________ ____________ when protein synthesis
stops, generating the regulatory nucleotide _______. Genes for __________ and _________ are
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downregulated, while those for _________ __________ ____________ are upregulated.
11. The sporulation and chemotaxis regulatory systems of bacteria are examples of
systems, which have two major components: a sensor kinase and a response regulator. In the chemotaxis
regulatory system,
proteins (MCPs) contribute to the regulation of flagellar
rotation.
MULTIPLE CHOICE
For each of the questions below select the one best answer.
1. Which of the following is NOT a regulatory mechanism used to control the lactose operon in E. coli?
a. induction
b. catabolite repression
c. attenuation
d. All of the above are used to regulate the lactose operon.
2. Which of the following is NOT a regulatory mechanism used to control the tryptophan operon in E. coli?
a. repression
b. catabolite repression
c. attenuation
d. All of the above are used to regulate the tryptophan operon in E. coli.
3. Which of the following is least likely to mediate rapid responses to changes in environmental conditions?
a. metabolic channeling
b. adjustment of enzyme activity
c. regulation of gene expression
d. All of the above are equally likely to respond to rapid environmental changes.
4. Which of the following will most likely conserve the greatest amount of energy for the cell?
a. metabolic channeling
b. adjustment of enzyme activity
c. regulation of gene expression
d. All of the above conserve nearly equal amounts of energy.
5. Which of the following is the inducer for the lactose operon of E. coli?
a. catabolite activator protein (CAP)
b. 3′, 5′ cyclic adenosine monophosphate (cAMP)
c. lactose (allolactose)
d. cyclic AMP receptor protein (CRP)
6. Which of the following is NOT a level at which gene expression can be controlled?
a.
transcription
b.
translation
c.
posttranslation
d.
All can be points of control.
7. Which of the following is a role for riboswitches?
a.
stalling ribosomes during translation
b.
inducing expression of ribosomal proteins
c.
differential folding of mRNA leader sequences
d.
transmitting signals from environmental sensor proteins
8. Riboswitches lead to alternative folding of mRNAs during transcription and lead to the formation of:
a.
termination loops
b.
antitermination loops
c.
both (a) and (b)
d.
neither (a) nor (b)
9. When alternate sigma factors are available to RNA polymerase?
a.
gene expression changes
b.
binding to enhancers is blocked
c.
operator sequences are not used
d.
rho factors are needed for expression
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10.
Which of the following is NOT an example of a global regulatory system?
a.
stimulon
b.
regulon
c.
modulon
d.
alteron
11. Which of the following is control of metabolic pathways by modulation of the activity of certain
regulatory enzymes?
a. transcriptional regulation
b. translational regulation
c. posttranscriptional regulation
d. global regulation
TRUE/FALSE
____ 1.
____ 2.
____ 3.
____ 4.
____ 5.
____ 6.
____ 7.
____ 8.
____ 9.
____ 10.
____ 11.
____ 12.
____ 13.
If a particular energy source is unavailable, the enzymes required for its utilization are needed and
energy is expended to produce them.
In the presence of both glucose and lactose, the lactose repressor is not bound to the operator;
however, the genes of the lactose operon are still not expressed: catabolite repression affects the
binding of RNA polymerase to the promoter, but does not involve the operator.
Although DNA replication and cell division are separate processes, they are tightly coordinated.
Therefore, if a drug or a gene mutation inhibits DNA synthesis, cell division is also blocked.
Even at high rates of cell division (doubling time less than 60 minutes), DNA replication for the
next doubling is not initiated until the previous round of cell division has been completed.
β-galactosidase is a repressible enzyme.
One example of the regulation of gene expression by small RNA molecules (sRNAs) is the binding
of heterogeneous nuclear RNA molecules (hnRNAs) to target mRNA, thus blocking their
translation.
Riboswitches act at both the level of transcription and translation.
The corepressor for the trp operon is tryptophan.
In most cases, archaeal regulatory proteins function like those of eukaryotes.
One prokaryotic cell cannot affect the gene expression of another cell.
Sporulation in Bacillus subtilis is controlled in part by a phosphorelay system.
The arabinose operon is both positively and negatively controlled at the level of transcription.
Sensor kinases are important intracellular proteins found in the nucleoid region.
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CRITICAL THINKING
1.
Look at the following two diagrams. Compare and contrast the regulatory mechanisms depicted in (A)
with those in (B). Which is more likely to regulate the enzymes of a catabolic pathway and which is more
likely to regulate an anabolic pathway? Explain.
A
B
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2. After inoculating a flask of minimal broth containing glucose and lactose with E. coli and following
the growth kinetics, you obtain the following growth curve:
V
IV
III
II
I
a.
Describe each stage of the growth curve (I–V) in terms of growth rates, growth substrates, and
general metabolic activity.
b.
Diagram the lactose operon. What differences are there in the state of the operon during phase
I, phase II, phase III, and phase IV of the given growth curve? Be sure to discuss the promoter
and operator regions as well as the roles of the lac repressor and CAP in each of the first four
phases.
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ANSWER KEY
Terms and Definitions
1. f, 2. d, 3. i, 4. j, 5. c, 6. b, 7. q, 8. o, 9. m, 10. e, 11. h, 12. r, 13. p, 14. k, 15. a, 16. g, 17. n, 18. l
Fill in the Blank
1. glucose; lactose; diauxic 2. inducers; corepressors 3. attenuation; leader; attenuator; aminoacyl-tRNA
synthetases; tightly coupled; prokaryotic; eukaryotic 4. repressor; negative; catabolite; positive 5. repressible;
corepressors; aporepressor; corepressor 6. repressed; arabinose; stimulates 7. sensor kinase; responseregulator; signal transduction; phosophorelay 8. quorum sensing; homoserine lactones; autoinducers 9. general;
activators; enhancers; silencers 10. stringent response; ppGpp; tRNAs; rRNAs; amino acid biosynthesis 11.
two-component phosphorelay; methyl-accepting chemotaxis
Multiple Choice
1. c, 2. b, 3. c, 4. c, 5. c, 6. d, 7. c, 8. c, 9. a, 10. d, 11. c
True/False
1. F, 2. T, 3. T, 4. F, 5. F, 6. F, 7. T, 8. T, 9. F, 10. F, 11. T, 12. T, 13. F
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