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Prescott’s Microbiology, 9th Edition
14
Regulation of Bacterial 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.
LEARNING OUTCOMES
After reading this chapter you should be able to:
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list when, during the flow of genetic information, bacterial cells can regulate gene expression
speculate why microbial geneticists for many years focused almost exclusively on the regulation of
transcription initiation
compare and contrast housekeeping, constitutive, inducible, and repressible genes
describe two common motifs n DNA-binding proteins
summarize how negative transcriptional control and positive transcriptional control can be used to regulate both
inducible and repressible genes
outline the regulatory “decisions” made by cells
describe in general terms how the trp operon of E. coli is regulated by attenuation
compare and contrast regulation of transcription elongation by attenuation and riboswitches
explain why the coupling of transcription and translation in bacterial cells is important to the regulatory
mechanisms they use
distinguish translational riboswitches from transcriptional riboswitches
discuss regulation of translation by antisense RNAs
compare and contrast two-component signal transduction systems with phosphorelay signal transduction
systems
list the nucleotides that are used by bacteria as second messengers
explain how alternate sigma factors can be used to initiate transcription of distinct sets of operons
summarize how CAP, cAMP, and the lac repressor work together to cause diauxic growth as well as other
outcomes related to regulation of the lactose operon
hypothesize how other operons encoding catabolic enzymes might be regulated by catabolite repression
outline how the proteins of the E. coli chemotaxis system function to control flagellar rotation in the presence
of a chemoattractant
predict the events that would occur if E. coli were in a gradient of a chemorepellent
differentiate quorum sensing observed in Vibrio fischeri from that in Vibrio harveyi
describe the stringent response
outline the regulatory mechanisms used by Bacillus subtilis to control endospore formation
CHAPTER OUTLINE
I.
Levels of Regulation
A. Regulation of gene expression (controlling enzyme synthesis) occurs at different levels, including control
of transcription, translation, and posttranslation
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manner. This document may not be copied, scanned, duplicated, forwarded, distributed, or posted on a website, in whole or part.
Prescott’s Microbiology, 9th Edition
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
II. 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
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
III. Regulation of Transcription Elongation
A. Attenuation:ribosome behavior influences transcription
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
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© 2014 by McGraw-Hill Education. This is proprietary material solely for authorized instructor use. Not authorized for sale or distribution in any
manner. This document may not be copied, scanned, duplicated, forwarded, distributed, or posted on a website, in whole or part.
Prescott’s Microbiology, 9th Edition
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:effector molecule-mRNA interaction regulates transcription
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. Regulating Complex Cellular Processes
A. 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
B. Catabolite repression in E. coli
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
C. Chemotaxis in E. coli
3. 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
4. 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
D
Quorum sensing
5. Intercellular communication (quorum sensing) in prokaryotes is important in gene regulation; even
microbes of different species can affect each other's gene expression
6. Quorum sensing is typically mediated by the release to homoserine lactones as autoinducers; in some
cases a two-component regulatory system is involved
E
Stringent response in E. coli
7. In addition to cAMP, guanosine tetraphosphate (ppGpp) and cyclic dimeric GMP (c-di-GMP)
regulate gene expression
8. 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
F
Sporulation in B. subtilis
9. Sporulation is a complex process that is controlled at several levels through phosphorelay,
transcription factors, posttranslational modifications, and alternate sigma factors
10. 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
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© 2014 by McGraw-Hill Education. This is proprietary material solely for authorized instructor use. Not authorized for sale or distribution in any
manner. This document may not be copied, scanned, duplicated, forwarded, distributed, or posted on a website, in whole or part.
Prescott’s Microbiology, 9th Edition
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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© 2014 by McGraw-Hill Education. This is proprietary material solely for authorized instructor use. Not authorized for sale or distribution in any
manner. This document may not be copied, scanned, duplicated, forwarded, distributed, or posted on a website, in whole or part.
Prescott’s Microbiology, 9th Edition
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:
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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.
3. The paradigm of the lac operon is a classic example of an inducible catabolic operon. Suppose you wished to
design a bacterial operon to degrade the disaccharide cellobiose in the absence of the preferred monosaccharide
glucose. What promoter elements would you adopt or manipulate from the lac operon to help you design the
promoter for cellobiose degrading genes?
CONCEPT MAPPING CHALLENGE
Construct a concept map that describes the regulation of the lactose operon. Use the concepts that follow, and any
other concepts or terms you need, and your own linking words between each pair of concepts in your map.
Operator, Promoter, Inducer, lac repressor, CAP, cAMP, positive activator, Catabolite repression
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© 2014 by McGraw-Hill Education. This is proprietary material solely for authorized instructor use. Not authorized for sale or distribution in any
manner. This document may not be copied, scanned, duplicated, forwarded, distributed, or posted on a website, in whole or part.