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Lecture #13:
Regulation of Gene
Expression (Part 2)
Lecture #13 Reading Assignment
Physiology & Biochemistry of Prokaryotes 3rd Ed.:
Ch. 10, pp. 291; Ch. 18, pp. 496-503, 554-561, 509-518
Brock Biology of Microorganisms 11th Ed:
Ch.8, pp. 221-227
Brock Biology of Microorganisms 12th ed.:
Ch.9, pp. 231-234, 244-248
Article(s) to be discussed  Majdalani Review (Bacterial
Small RNA regulators)
Small Things Considered
Essay for Lecture #13
Topics:
 Transcriptional control by attenuation
 Two-component regulatory systems
 Quorum sensing
 Bacterial small RNA regulators
Transcriptional Regulation: Attenuation
 A system for regulating gene expression by control of
transcriptional termination
 Does not involve DNA-binding proteins
Leader Peptide Sequence of the Trp Operon
Attenuation Control of the Trp Operon
Overall Trp Operon Control
TrpR
Signal Transduction and Two-component
Regulatory Systems
 Sensor kinase has
Histidine kinase activity
 Response regulator
has aspartate residue
that becomes
phosphorylated
 In some systems, the
de-phosphorylated
regulator may be the
active DNA-binding
species.
Two-component Regulation: Phosphate Uptake System
phoA: alkaline phosphatase
pstSCAB: phosphate-specific transporter
phoE: outermembrane porin
UgpBAEC: hexose-6-P and G-3-P uptake
From: Tetsch and Jung. Molecular Microbiology (2009) 73(6), 982–991
Quorum Sensing: Control of the lux Operon
LuxR
Bobtail squid colonized
with luminescent Vibrio
harveyi (1011 cells/ml)
Vibrio
Autoinducer (VAI)
ArcA/ArcB and LuxR-LuxI-mediated regulation of
bioluminescence in V. fischeri
5 redundant small RNAs
(qrr1…qrr5) function to
destabilize luxR transcript
when there’s low VAI levels
From: Septer et al. 2012. Volume 7, Issue 11, e49590
Effect of Small RNA Regulators on Gene Expression
Mechanisms:
1) Base pair
with other
nucleic acids
2)
Bind to and
modify
proteins
Bacterial and plasmid
small RNAs are indicated
in red and
Eukaryotic sRNAs are
shown in blue
Positive interactions are
indicated by arrows
Negative regulation is
indicated by the bars
cis acting: coded on the
opposite strand of targeted
mRNA
trans acting: encoded at a
location distant from the
target
From: Storz G., Altuvia, S., Wassarman K. 2005. An Abundance of RNA Regulators. Annu. Rev. Biochem.
74:199-217
Advantages of small RNAs
over protein Regulators
1) Small RNAs require fewer
resources to make than a
(Cheaper)
regulatory protein. Many small
RNAs are expressed when carbon
and energy are limiting.
2) Small RNAs act at the posttranscriptional level allowing a fast
regulatory response.
(Faster)
3) cis-encoded RNA regulators
evolve with the target
(Adapting)
General Mechanisms by which RNA
Regulators Modulate Transcription
Ex.: 6S RNA
Ex.: SRA
Ex.: RepE and
RNAI
From: Storz G., Opdyke, JA., Wassarman KM. 2006. Regulating Bacterial Transcription with Small
RNAs. Cold Spring Harbor Symposia on Quantitative Biology vol LXXI. Pp 269-273.
Regulation of Transcription by the 6S sRNA
6S sRNA sequesters the polymerase complex during nutrient
limitation, requiring the expression of genes controlled by an alternate
sigma factor (sigma S)
From: Pichon C., Felden, B. 2007. Proteins That Interact with Bacterial Small RNA Regulators.
FEMS Microbiol. Rev. 31:614-625.
The Structure of the Small RNA Regulator DsrA
DsrA functions to stimulate the translation of the rpoS mRNA
DsrA functions to inhibit translation of hns mRNA
Stimulation of RpoS translation by DsrA
DsrA requires RNA chaperone Hfq
Role of Hfq in Small Regulatory RNA Function
Possible Outcomes:
1)
Promote base pairing
between the small RNA
and the target mRNA
2)
Change the target
mRNA’s accessibility to
RNases.
3)
Protect RNA from
RNAase E digestion.
Hfq mutants are viable but are slow growers.
From: Gottesman, S. et al. 2006. Small RNA Regulators and the Bacterial Response to
Stress. Cold Spring Harbor Symposia on Quantitative Biology vol LXXI. Pp. 1-10.
From: Gottesman, S. et al. 2006. Small RNA Regulators and the Bacterial Response to
Stress. Cold Spring Harbor Symposia on Quantitative Biology vol LXXI. Pp. 1-10.
Global Regulation by the Small RNAbinding Protein CsrA
CsrA
CsrB
Transmission electron microscopy of negatively
stained CsrA-CsrB complexes. A, native complex
(micrograph); B, EDTA-treated preparation (digital image).
Liu, M. Y. et al. J. Biol. Chem. 1997;272:17502-17510
CsrA (carbon storage regulator) is a 61 amino acid protein
that binds RNA
CsrB is a 250 nucleotide RNA that does not code for protein
Expression of genes affected by CsrA (E.coli)
Pathways Neg. Regulated by CsrA:
 Glycogen biosynthesis
 Glycogen catabolism
 Gluconeogenesis
Pathways Pos. Regulated by CsrA:
 Glycolysis
 Glyoxylate shunt
 Acetate metabolism
 Flagella biosynthesis
CsrA regulates CCM
CsrB and CsrC RNA: Titrators of CsrA
CsrB and CsrC levels
increase 3-fold when E. coli
cells enter stationary phase
CsrB
CsrC
The BarA/UvrY 2component regulatory
system has been shown
to regulate CsrB and
CsrC expression
Regulation of CsrA
Proposed Model for Post-transcriptional Regulation of
Gene Expression by CsrA and CsrB/CsrC RNA
CsrA-CsrC
complex
Encodes glycogen
biosynthesis enzymes
From: Romeo, T. 1998. Global Regulation by the Small RNA-binding Protein CsrA and the Noncoding RNA molecule CsrB. Mol. Microbiol. 29:1321-1330.
Proposed Model for Post-transcriptional Regulation of
Gene Expression by CsrA and CsrB/CsrC RNA
Benefits of this Regulatory Strategy
(1)There is a low energy investment and short
synthesis time to produce an RNA regulator.
(2) A single RNA can bind 18 regulator proteins,
thereby amplifying its control
(3) Post-transcriptional control results in almost
immediate changes in gene expression.
CRISPR: adaptive RNA regulation
This system is found
in bacteria and
archaea. The spacers
regions can be an
indication of evolution.
From: Bhaya et al. 2011. CRISPR-Cas Systems in Bacteria and Archaea: versatile small RNSs
for adaptive immunity. Annu. Rev Genet. 45:273-297.
CRISPR: self vs non-self
From: Marraffini LA and Sontheimer EJ. CRISPR Interference: RNA-directed adaptive immunity
in bacteria and archaea.
Pairing with the repeat prevents cleavage of self-DNA.
CRISPR: a tool for genome editing
Genes are targeted by creating a
spacer with homology to the gene
of interest.
From: NEB.com